nebius/SWE-bench-extra · Datasets at Hugging Face

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ValvePython__steam-359	diff --git a/requirements.txt b/requirements.txt index 92661a9..14293fb 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,7 +3,8 @@ pycryptodomex>=3.7.0 requests>=2.9.1 vdf>=3.3 gevent>=1.3.0 -protobuf>=3.0.0 +protobuf>~3.0; python_version >= '3' +protobuf<3.18.0; python_version < '3' gevent-eventemitter~=2.1 cachetools>=3.0.0 enum34==1.1.2; python_version < '3.4' diff --git a/setup.py b/setup.py index 16b8870..382f8f2 100644 --- a/setup.py +++ b/setup.py @@ -26,7 +26,8 @@ install_requires = [ install_extras = { 'client': [ 'gevent>=1.3.0', - 'protobuf>=3.0.0', + 'protobuf>~3.0; python_version >= "3"', + 'protobuf<3.18.0; python_version < "3"', 'gevent-eventemitter~=2.1', ], } diff --git a/steam/game_servers.py b/steam/game_servers.py index 07b09f1..80bf108 100644 --- a/steam/game_servers.py +++ b/steam/game_servers.py @@ -142,8 +142,11 @@ def _u(data): class StructReader(_StructReader): - def read_cstring(self): - return _u(super(StructReader, self).read_cstring()) + def read_cstring(self, binary=False): + raw = super(StructReader, self).read_cstring() + if binary: + return raw + return _u(raw) class MSRegion(IntEnum): @@ -526,7 +529,7 @@ def a2s_players(server_addr, timeout=2, challenge=0): return players -def a2s_rules(server_addr, timeout=2, challenge=0): +def a2s_rules(server_addr, timeout=2, challenge=0, binary=False): """Get rules from server :param server_addr: (ip, port) for the server @@ -535,9 +538,11 @@ def a2s_rules(server_addr, timeout=2, challenge=0): :type timeout: float :param challenge: (optional) challenge number :type challenge: int + :param binary: (optional) return rules as raw bytes + :type binary: bool :raises: :class:`RuntimeError`, :class:`socket.timeout` :returns: a list of rules - :rtype: :class:`list` + :rtype: :class:`dict` """ ss = socket.socket(socket.AF_INET, socket.SOCK_DGRAM) ss.connect(server_addr) @@ -571,13 +576,14 @@ def a2s_rules(server_addr, timeout=2, challenge=0): rules = {} while len(rules) != num_rules: - name = data.read_cstring() - value = data.read_cstring() - - if _re_match(r'^\-?[0-9]+$', value): - value = int(value) - elif _re_match(r'^\-?[0-9]+\.[0-9]+$', value): - value = float(value) + name = data.read_cstring(binary=binary) + value = data.read_cstring(binary=binary) + + if not binary: + if _re_match(r'^\-?[0-9]+$', value): + value = int(value) + elif _re_match(r'^\-?[0-9]+\.[0-9]+$', value): + value = float(value) rules[name] = value	ValvePython/steam	061ca33842c9ec5aa7c0866d20cbeed0759d5ea5	diff --git a/tests/test_game_servers.py b/tests/test_game_servers.py new file mode 100644 index 0000000..47fc89e --- /dev/null +++ b/tests/test_game_servers.py @@ -0,0 +1,64 @@ +import mock +import socket +import unittest + +from steam.game_servers import a2s_rules + + +class TestA2SRules(unittest.TestCase): + @mock.patch("socket.socket") + def test_returns_rules_with_default_arguments(self, mock_socket_class): + mock_socket = mock_socket_class.return_value + mock_socket.recv.side_effect = [ + b"\xff\xff\xff\xffA\x01\x02\x03\x04", + b"\xff\xff\xff\xffE\x03\0text\0b\x99r\0int\x0042\0float\x0021.12\0" + ] + + rules = a2s_rules(("addr", 1234)) + + self.assertEqual( + { + "text": u"b\ufffdr", + "int": 42, + "float": 21.12 + }, + rules) + + mock_socket_class.assert_called_once_with( + socket.AF_INET, socket.SOCK_DGRAM) + + mock_socket.connect.assert_called_once_with(("addr", 1234)) + mock_socket.settimeout.assert_called_once_with(2) + + self.assertEqual(2, mock_socket.send.call_count) + mock_socket.send.assert_has_calls([ + mock.call(b"\xff\xff\xff\xffV\0\0\0\0"), + mock.call(b"\xff\xff\xff\xffV\x01\x02\x03\x04") + ]) + + self.assertEqual(2, mock_socket.recv.call_count) + mock_socket.recv.assert_has_calls([ + mock.call(512), + mock.call(2048) + ]) + + mock_socket.close.assert_called_once_with() + + @mock.patch("socket.socket") + def test_returns_rules_as_bytes_when_binary_is_true( + self, mock_socket_class): + mock_socket = mock_socket_class.return_value + mock_socket.recv.side_effect = [ + b"\xff\xff\xff\xffA\x01\x02\x03\x04", + b"\xff\xff\xff\xffE\x03\0text\0b\x99r\0int\x0042\0float\x0021.12\0" + ] + + rules = a2s_rules(("addr", 1234), binary=True) + + self.assertEqual( + { + b"text": b"b\x99r", + b"int": b"42", + b"float": b"21.12" + }, + rules)	Option to return a2s_rules as bytes instead of strings The `steam.game_servers.a2s_rules` function currently returns the server rules as a dictionary of strings to strings (`Dict[str, str]`), which is suitable for plain text rules. However, some game servers use the Steam `A2S_RULES` API to return binary data. For example, Bohemia Interactive's Arma and DayZ servers use the rules API to return required DLC and Mod information (see https://community.bistudio.com/wiki/Arma_3:_ServerBrowserProtocol3 for details). Unfortunately, because `steam.game_servers.a2s_rules` decodes the A2S_RULES server response data as UTF-8 with `"replace"` as the `errors` option, important binary data is lost when querying an Arma or DayZ server's rules. For example: ```python >>> pprint(a2s_rules(("192.169.82.235",2303))) {'\x01\x01': '\x01\x01\x01\x02\x01\x02\x01\x02\x02��_\x04ITv�\x0eNamalsk ' 'Island#�:\x13Ԓ\x11\x0b' 'Livonia DLC\x03\x0eCrimsonZamboni\x04dayz\x06sumrak', 'allowedBuild': 0, 'dedicated': 1, 'island': 'namalsk', 'language': 65545, 'platform': 'win', 'requiredBuild': 0, 'requiredVersion': 113, 'timeLeft': 15} ``` It would be very helpful if we could get a server's `A2S_RULES` information as raw `bytes`, instead of `str` objects. Perhaps an optional keyword argument could be added to the `steam.game_servers.a2s_rules` function? For example: ```python a2s_rules(("192.169.82.235",2303), binary=True) ``` The default should be `binary=False` to maintain backwards compatibility but when `binary=True`, the resulting rule names and values would be returned as `bytes` objects (i.e. `Dict[bytes, bytes]`), allowing the caller to further decode the binary data, as needed.	061ca33842c9ec5aa7c0866d20cbeed0759d5ea5	[ "tests/test_game_servers.py::TestA2SRules::test_returns_rules_as_bytes_when_binary_is_true" ]	[ "tests/test_game_servers.py::TestA2SRules::test_returns_rules_with_default_arguments" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-09-25 17:38:38+00:00	mit	817
Viatorus__quom-34	diff --git a/README.md b/README.md index db84fbb..4486b8c 100644 --- a/README.md +++ b/README.md @@ -44,6 +44,10 @@ optional arguments: --trim, -t Reduce continuous line breaks to one. Default: True --include_directory INCLUDE_DIRECTORY, -I INCLUDE_DIRECTORY Add include directories for header files. + --source_directory SOURCE_DIRECTORY, -S SOURCE_DIRECTORY + Set the source directories for source files. + Use ./ in front of a path to mark as relative to the header file. + ``` ## Simple example diff --git a/quom/__main__.py b/quom/__main__.py index d717853..ed25d0b 100644 --- a/quom/__main__.py +++ b/quom/__main__.py @@ -1,12 +1,12 @@ import argparse import sys -import traceback from pathlib import Path +from typing import List from .quom import Quom -def main(): +def main(args: List[str]): parser = argparse.ArgumentParser(prog='quom', description='Single header generator for C/C++ libraries.') parser.add_argument('input_path', metavar='input', type=Path, help='Input file path of the main file.') parser.add_argument('output_path', metavar='output', type=Path, @@ -20,12 +20,33 @@ def main(): help='Reduce continuous line breaks to one. Default: %(default)s') parser.add_argument('--include_directory', '-I', type=Path, action='append', default=[], help='Add include directories for header files.') + parser.add_argument('--source_directory', '-S', type=str, action='append', default=['.'], + help='Set the source directories for source files. ' + 'Use ./ in front of a path to mark as relative to the header file.') - args = parser.parse_args() + args = parser.parse_args(args) + + # Transform source directories to distingue between: + # - relative from header file (starting with dot) + # - relative from workdir + # - absolute path + relative_source_directories = [] + source_directories = [] + for src in args.source_directory: + path = Path(src) + if src == '.' or src.startswith('./'): + relative_source_directories.append(path) + else: + source_directories.append(path.resolve()) with args.output_path.open('w+') as file: - Quom(args.input_path, file, args.stitch, args.include_guard, args.trim, args.include_directory) + Quom(args.input_path, file, args.stitch, args.include_guard, args.trim, args.include_directory, + relative_source_directories, source_directories) + + +def run(): + main(sys.argv[1:]) if __name__ == '__main__': - sys.exit(main()) + run() diff --git a/quom/quom.py b/quom/quom.py index 20bc83e..d366219 100644 --- a/quom/quom.py +++ b/quom/quom.py @@ -1,3 +1,4 @@ +import os import re from pathlib import Path from queue import Queue @@ -29,12 +30,17 @@ def contains_only_whitespace_and_comment_tokens(tokens: List[Token]): class Quom: def __init__(self, src_file_path: Union[Path, str], dst: TextIO, stitch_format: str = None, include_guard_format: str = None, trim: bool = True, - include_directories: List[Union[Path, str]] = None): + include_directories: List[Union[Path, str]] = None, + relative_source_directories: List[Union[Path]] = None, + source_directories: List[Union[Path]] = None): self.__dst = dst self.__stitch_format = stitch_format self.__include_guard_format = re.compile('^{}$'.format(include_guard_format)) if include_guard_format else None self.__trim = trim self.__include_directories = [Path(x) for x in include_directories] if include_directories else [] + self.__relative_source_directories = relative_source_directories if relative_source_directories else [] \ + if source_directories else [Path('.')] + self.__source_directories = source_directories if source_directories else [Path('.')] self.__processed_files = set() self.__source_files = Queue() @@ -87,7 +93,9 @@ class Quom: self.__write_token(token, is_main_header) - self.__find_possible_source_file(file_path) + file_path = self.__find_possible_source_file(file_path) + if file_path: + self.__source_files.put(file_path) def __write_token(self, token: Token, is_main_header: bool): if isinstance(token, StartToken) or isinstance(token, EndToken): @@ -129,16 +137,21 @@ class Quom: contains_only_whitespace_and_comment_tokens(token.preprocessor_arguments[i + 1:]): return True - def __find_possible_source_file(self, header_file_path: Path): + def __find_possible_source_file(self, header_file_path: Path) -> Union[Path, None]: if header_file_path.suffix in ['.c', '.cpp', '.cxx', '.cc', '.c++', '.cp', '.C']: return # Checks if a equivalent compilation unit exits. for extension in ['.c', '.cpp', '.cxx', '.cc', '.c++', '.cp', '.C']: - file_path = header_file_path.with_suffix(extension) - if file_path.exists(): - self.__source_files.put(file_path) - break + for src_dir in self.__relative_source_directories: + file_path = (header_file_path.parent / src_dir / header_file_path.name).with_suffix(extension) + if file_path.exists(): + return file_path + for src_dir in self.__source_directories: + file_path = (src_dir / header_file_path.name).with_suffix(extension).resolve() + if file_path.exists(): + return file_path + return None def __scan_for_include(self, file_path: Path, token: Token, is_source_file: bool) -> Union[Token, None]: if not isinstance(token, PreprocessorIncludeToken) or not token.is_local_include:	Viatorus/quom	b4bb7665357892411081b86b7c33c0ffc18d2f1b	diff --git a/tests/test_quom/test_normal.py b/tests/test_quom/test_normal.py index f0928dd..38d53f0 100644 --- a/tests/test_quom/test_normal.py +++ b/tests/test_quom/test_normal.py @@ -4,6 +4,7 @@ from pathlib import Path import pytest from quom import Quom, QuomError +from quom.__main__ import main FILE_MAIN_HPP = """\ #pragma once @@ -247,3 +248,13 @@ def test_with_missing_source_file(fs): Quom(Path('main.hpp'), dst) assert dst.getvalue() == RESULT_NORMAL_WITHOUT_SOURCES + + +def test_main(fs): + init() + + main(['main.hpp', 'result.hpp']) + assert Path('result.hpp').read_text() == RESULT_NORMAL + + main(['main.hpp', 'result.hpp', '-S', '.']) + assert Path('result.hpp').read_text() == RESULT_NORMAL diff --git a/tests/test_quom/test_source_directory.py b/tests/test_quom/test_source_directory.py new file mode 100644 index 0000000..790d417 --- /dev/null +++ b/tests/test_quom/test_source_directory.py @@ -0,0 +1,62 @@ +import os +from io import StringIO +from pathlib import Path + +from quom import Quom +from quom.__main__ import main + +FILE_MAIN_HPP = """ +int foo = 3; + +int foo(); +""" + +FILE_MAIN_CPP = """ +int foo() { return 42; } +""" + +RESULT = """ +int foo = 3; + +int foo(); + +int foo() { return 42; } +""" + + +def test_source_directory(fs): + os.makedirs('project/') + os.chdir('project/') + os.makedirs('include/') + os.makedirs('src/') + + with open('include/main.hpp', 'w+') as file: + file.write(FILE_MAIN_HPP) + + with open('src/main.cpp', 'w+') as file: + file.write(FILE_MAIN_CPP) + + dst = StringIO() + Quom(Path('include/main.hpp'), dst) + assert dst.getvalue() != RESULT + + dst = StringIO() + Quom(Path('include/main.hpp'), dst, relative_source_directories=[Path('../src')]) + assert dst.getvalue() == RESULT + + dst = StringIO() + Quom(Path('include/main.hpp'), dst, source_directories=[Path('src').resolve()]) + assert dst.getvalue() == RESULT + + dst = StringIO() + Quom(Path('include/main.hpp'), dst, source_directories=[Path('/project/src')]) + assert dst.getvalue() == RESULT + + main(['include/main.hpp', 'result.hpp', '-S', './../src']) + assert Path('result.hpp').read_text() == RESULT + + main(['include/main.hpp', 'result.hpp', '-S', 'src']) + assert Path('result.hpp').read_text() == RESULT + + main(['include/main.hpp', 'result.hpp', '-S', '/project/src']) + assert Path('result.hpp').read_text() == RESULT	Feature request - Additional directories to search for sources Hi, I found this package very useful, but when trying to use it - encounter with a small problem. The case when sources are located in different directory then their headers - are not supported. The common folder structure of any project can be as follows: _project/_    _public/_    _include/_    _src/_ So it would be nice if it will be possible to specify source directories relative to include directories. For instance via `--relative_source_dir` or `-SI` argument. The most common use can be: `-SI "./" -SI "../" -SI "../src"` By default the directory suffixes array is ["./'] but if at least one -SI argument provided it should be overwritten.	b4bb7665357892411081b86b7c33c0ffc18d2f1b	[ "tests/test_quom/test_normal.py::test_main", "tests/test_quom/test_source_directory.py::test_source_directory" ]	[ "tests/test_quom/test_normal.py::test_with_missing_source_file", "tests/test_quom/test_normal.py::test_with_include_guard_format", "tests/test_quom/test_normal.py::test_with_mismatching_include_guard_format", "tests/test_quom/test_normal.py::test_normal", "tests/test_quom/test_normal.py::test_normal_without_trim", "tests/test_quom/test_normal.py::test_with_mismatching_stitch", "tests/test_quom/test_normal.py::test_with_stitch_location", "tests/test_quom/test_normal.py::test_with_missing_header_file" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-04-22 19:15:57+00:00	mit	818
Viatorus__quom-43	diff --git a/src/quom/quom.py b/src/quom/quom.py index 5dbaad9..5f7d51c 100644 --- a/src/quom/quom.py +++ b/src/quom/quom.py @@ -80,6 +80,7 @@ class Quom: raise QuomError('Include not found: "{}"'.format(include_path)) # Skip already processed files. + file_path = file_path.resolve() if file_path in self.__processed_files: return self.__processed_files.add(file_path)	Viatorus/quom	8d13a41baea1a930d27a869ff468aa72fe25b100	diff --git a/tests/test_quom/same_file_different_include.py b/tests/test_quom/same_file_different_include.py new file mode 100644 index 0000000..8ef3b9d --- /dev/null +++ b/tests/test_quom/same_file_different_include.py @@ -0,0 +1,41 @@ +import os +from io import StringIO + +from quom import Quom + +FILE_FOO_HPP = """ +#include "../b/bar.hpp" +""" + +FILE_BAR_HPP = """ +int foo(); +""" + +FILE_MAIN_CPP = """ +#include "a/foo.hpp" +#include "b/bar.hpp" +""" + +RESULT = """ + +int foo(); +""" + + +def test_same_file_different_include(fs): + os.makedirs('a') + os.makedirs('b') + + with open('main.cpp', 'w+') as file: + file.write(FILE_MAIN_CPP) + + with open('a/foo.hpp', 'w+') as file: + file.write(FILE_FOO_HPP) + + with open('b/bar.hpp', 'w+') as file: + file.write(FILE_BAR_HPP) + + dst = StringIO() + Quom('main.cpp', dst) + + assert dst.getvalue() == RESULT	option to skip already included files Hello and thanks for creating such awesome utility! I'm using it in my [CTRE](https://github.com/hanickadot/compile-time-regular-expressions) project. I noticed sometimes quom include same file multiple times. Would be possible to add an option to ignore already included files? Based on normalised URL preferably. Thanks! ❤️	8d13a41baea1a930d27a869ff468aa72fe25b100	[ "tests/test_quom/same_file_different_include.py::test_same_file_different_include" ]	[]	{ "failed_lite_validators": [ "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }	2021-06-15 18:54:32+00:00	mit	819
Viatorus__quom-44	diff --git a/src/quom/__main__.py b/src/quom/__main__.py index 77d99b3..bb62485 100644 --- a/src/quom/__main__.py +++ b/src/quom/__main__.py @@ -29,6 +29,8 @@ def main(args: List[str]): parser.add_argument('--source_directory', '-S', type=str, action='append', default=['.'], help='Set the source directories for source files. ' 'Use ./ or .\\ in front of a path to mark as relative to the header file.') + parser.add_argument('--encoding', '-e', type=str, default='utf-8', + help='The encoding used to read and write all files.') args = parser.parse_args(args) @@ -45,9 +47,9 @@ def main(args: List[str]): else: source_directories.append(path.resolve()) - with args.output_path.open('w+') as file: + with args.output_path.open('w+', encoding=args.encoding) as file: Quom(args.input_path, file, args.stitch, args.include_guard, args.trim, args.include_directory, - relative_source_directories, source_directories) + relative_source_directories, source_directories, args.encoding) def run(): diff --git a/src/quom/quom.py b/src/quom/quom.py index 5f7d51c..3cf4e13 100644 --- a/src/quom/quom.py +++ b/src/quom/quom.py @@ -31,7 +31,8 @@ class Quom: include_guard_format: str = None, trim: bool = True, include_directories: List[Union[Path, str]] = None, relative_source_directories: List[Union[Path]] = None, - source_directories: List[Union[Path]] = None): + source_directories: List[Union[Path]] = None, + encoding: str = 'utf-8'): self.__dst = dst self.__stitch_format = stitch_format self.__include_guard_format = re.compile('^{}$'.format(include_guard_format)) if include_guard_format else None @@ -40,6 +41,7 @@ class Quom: self.__relative_source_directories = relative_source_directories if relative_source_directories else [] \ if source_directories else [Path('.')] self.__source_directories = source_directories if source_directories else [Path('.')] + self.__encoding = encoding self.__processed_files = set() self.__source_files = Queue() @@ -65,16 +67,11 @@ class Quom: is_main_header=False): # First check if file exists relative. file_path = relative_path / include_path - if file_path.exists(): - with file_path.open() as file: - tokens = tokenize(file.read()) - else: + if not file_path.exists(): # Otherwise search in include directories. for include_directory in self.__include_directories: file_path = include_directory / include_path if file_path.exists(): - with file_path.open() as file: - tokens = tokenize(file.read()) break else: raise QuomError('Include not found: "{}"'.format(include_path)) @@ -85,6 +82,9 @@ class Quom: return self.__processed_files.add(file_path) + # Tokenize the file. + tokens = tokenize(file_path.read_text(encoding=self.__encoding)) + for token in tokens: # Find local includes. token = self.__scan_for_include(file_path, token, is_source_file)	Viatorus/quom	1c180ae75c91edf5c174053332aa96007fe13caa	diff --git a/tests/test_quom/same_file_different_include.py b/tests/test_quom/same_file_different_include.py index 8ef3b9d..a913dbc 100644 --- a/tests/test_quom/same_file_different_include.py +++ b/tests/test_quom/same_file_different_include.py @@ -26,13 +26,13 @@ def test_same_file_different_include(fs): os.makedirs('a') os.makedirs('b') - with open('main.cpp', 'w+') as file: + with open('main.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_MAIN_CPP) - with open('a/foo.hpp', 'w+') as file: + with open('a/foo.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_FOO_HPP) - with open('b/bar.hpp', 'w+') as file: + with open('b/bar.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_BAR_HPP) dst = StringIO() diff --git a/tests/test_quom/test_file_encoding.py b/tests/test_quom/test_file_encoding.py new file mode 100644 index 0000000..416a993 --- /dev/null +++ b/tests/test_quom/test_file_encoding.py @@ -0,0 +1,40 @@ +from pathlib import Path + +import pytest + +from quom.__main__ import main + +FILE_MAIN_HPP = """ +int foo(); // qθομ""" + + +def test_file_encoding_default_encoding(fs): + with open('main.hpp', 'w+', encoding='utf-8') as file: + file.write(FILE_MAIN_HPP) + + main(['main.hpp', 'result.hpp']) + assert Path('result.hpp').read_text('utf-8') == FILE_MAIN_HPP + + with pytest.raises(UnicodeDecodeError): + Path('result.hpp').read_text('ascii') + + with pytest.raises(UnicodeDecodeError): + Path('result.hpp').read_text('utf-32') + + +def test_file_encoding_custom_encoding(fs): + with open('main.hpp', 'w+', encoding='utf-32') as file: + file.write(FILE_MAIN_HPP) + + main(['main.hpp', 'result.hpp', '--encoding=utf-32']) + + assert Path('result.hpp').read_text('utf-32') == FILE_MAIN_HPP + + with pytest.raises(UnicodeDecodeError): + Path('result.hpp').read_text('utf-8') + + with pytest.raises(UnicodeDecodeError): + main(['main.hpp', 'result.hpp']) + + with pytest.raises(UnicodeDecodeError): + main(['main.hpp', 'result.hpp', '--encoding=utf-8']) diff --git a/tests/test_quom/test_include_directory.py b/tests/test_quom/test_include_directory.py index 1d8e572..1666ecf 100644 --- a/tests/test_quom/test_include_directory.py +++ b/tests/test_quom/test_include_directory.py @@ -79,28 +79,28 @@ def test_include_directory(fs): os.makedirs('include/my_lib/util') os.makedirs('include/my_other_lib/') - with open('include/my_lib/main.hpp', 'w+') as file: + with open('include/my_lib/main.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_MAIN_HPP) - with open('include/my_lib/core/core.hpp', 'w+') as file: + with open('include/my_lib/core/core.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_CORE_HPP) - with open('include/my_lib/core/core.cpp', 'w+') as file: + with open('include/my_lib/core/core.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_CORE_CPP) - with open('include/my_lib/util/foo.hpp', 'w+') as file: + with open('include/my_lib/util/foo.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_FOO_HPP) - with open('include/my_lib/util/foo.cpp', 'w+') as file: + with open('include/my_lib/util/foo.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_FOO_CPP) - with open('include/my_other_lib/bar.hpp', 'w+') as file: + with open('include/my_other_lib/bar.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_BAR_HPP) - with open('include/my_other_lib/bar.cpp', 'w+') as file: + with open('include/my_other_lib/bar.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_BAR_CPP) - with open('include/my_other_lib/info.hpp', 'w+') as file: + with open('include/my_other_lib/info.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_INFO_HPP) dst = StringIO() diff --git a/tests/test_quom/test_last_source_file.py b/tests/test_quom/test_last_source_file.py index 96e2c98..c227c21 100644 --- a/tests/test_quom/test_last_source_file.py +++ b/tests/test_quom/test_last_source_file.py @@ -82,13 +82,13 @@ int foo = 42;""" def init(): - with open('main.hpp', 'w+') as file: + with open('main.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_MAIN_HPP) - with open('foo.hpp', 'w+') as file: + with open('foo.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_FOO_HPP) - with open('foo.cpp', 'w+') as file: + with open('foo.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_FOO_CPP) @@ -111,7 +111,7 @@ def test_normal_without_trim(fs): def test_without_newline_at_end(fs): - with open('main.hpp', 'w+') as file: + with open('main.hpp', 'w+', encoding='utf-8') as file: file.write('int a;') dst = StringIO() diff --git a/tests/test_quom/test_normal.py b/tests/test_quom/test_normal.py index a718b87..48dd016 100644 --- a/tests/test_quom/test_normal.py +++ b/tests/test_quom/test_normal.py @@ -166,13 +166,13 @@ int foo = 42; def init(): - with open('main.hpp', 'w+') as file: + with open('main.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_MAIN_HPP) - with open('foo.hpp', 'w+') as file: + with open('foo.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_FOO_HPP) - with open('foo.cpp', 'w+') as file: + with open('foo.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_FOO_CPP) diff --git a/tests/test_quom/test_source_directory.py b/tests/test_quom/test_source_directory.py index 790d417..9bd63bc 100644 --- a/tests/test_quom/test_source_directory.py +++ b/tests/test_quom/test_source_directory.py @@ -30,10 +30,10 @@ def test_source_directory(fs): os.makedirs('include/') os.makedirs('src/') - with open('include/main.hpp', 'w+') as file: + with open('include/main.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_MAIN_HPP) - with open('src/main.cpp', 'w+') as file: + with open('src/main.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_MAIN_CPP) dst = StringIO()	Open files with UTF-8 encoding On Windows, Python uses ANSI encoding as its default text encoding when opening files. This is fine if you only use ASCII characters since ANSI is compatible with ASCII. But otherwise you will get errors like the following: ```py File "C:\Users\Username\AppData\Roaming\Python\Python39\site-packages\quom\__main__.py", line 54, in run main(sys.argv[1:]) File "C:\Users\Username\AppData\Roaming\Python\Python39\site-packages\quom\__main__.py", line 49, in main Quom(args.input_path, file, args.stitch, args.include_guard, args.trim, args.include_directory, File "C:\Users\Username\AppData\Roaming\Python\Python39\site-packages\quom\quom.py", line 49, in __init__ self.__process_file(Path(), src_file_path, False, True) File "C:\Users\Username\AppData\Roaming\Python\Python39\site-packages\quom\quom.py", line 70, in __process_file tokens = tokenize(file.read()) UnicodeDecodeError: 'gbk' codec can't decode byte 0xbf in position 2: illegal multibyte sequence ``` (GBK, or CP936, is the ANSI encoding under Simplified Chinese) My suggestion is to change to using UTF-8 encoding to open files, which is more appropriate for most programmers: ```py file_path.open(encoding='utf-8') ```	1c180ae75c91edf5c174053332aa96007fe13caa	[ "tests/test_quom/test_file_encoding.py::test_file_encoding_custom_encoding" ]	[ "tests/test_quom/same_file_different_include.py::test_same_file_different_include", "tests/test_quom/test_file_encoding.py::test_file_encoding_default_encoding", "tests/test_quom/test_include_directory.py::test_include_directory", "tests/test_quom/test_last_source_file.py::test_normal", "tests/test_quom/test_last_source_file.py::test_normal_without_trim", "tests/test_quom/test_last_source_file.py::test_without_newline_at_end", "tests/test_quom/test_normal.py::test_normal", "tests/test_quom/test_normal.py::test_normal_without_trim", "tests/test_quom/test_normal.py::test_with_include_guard_format", "tests/test_quom/test_normal.py::test_with_mismatching_include_guard_format", "tests/test_quom/test_normal.py::test_with_stitch_location", "tests/test_quom/test_normal.py::test_with_mismatching_stitch", "tests/test_quom/test_normal.py::test_with_missing_header_file", "tests/test_quom/test_normal.py::test_with_missing_source_file", "tests/test_quom/test_normal.py::test_main", "tests/test_quom/test_source_directory.py::test_source_directory" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-06-15 19:31:50+00:00	mit	820
Viatorus__quom-46	diff --git a/src/quom/quom.py b/src/quom/quom.py index 3cf4e13..0f6f7cd 100644 --- a/src/quom/quom.py +++ b/src/quom/quom.py @@ -1,3 +1,4 @@ +import os import re from pathlib import Path from queue import Queue @@ -46,6 +47,7 @@ class Quom: self.__processed_files = set() self.__source_files = Queue() self.__cont_lb = CONTINUOUS_LINE_BREAK_START + self.__used_linesep = None self.__prev_token = EmptyToken() self.__process_file(Path(), src_file_path, False, True) @@ -56,12 +58,7 @@ class Quom: .format(stitch_format)) while not self.__source_files.empty(): self.__process_file(Path(), self.__source_files.get(), True) - # Write last token. - self.__write_token(self.__prev_token, True) - elif self.__cont_lb == CONTINUOUS_LINE_BREAK_START or not isinstance(self.__prev_token, - LinebreakWhitespaceToken): - # Write last token, if not a continuous line break. - self.__write_token(self.__prev_token, True) + self.__write_line_break_if_missing() def __process_file(self, relative_path: Path, include_path: Path, is_source_file: bool, is_main_header=False): @@ -109,9 +106,8 @@ class Quom: if self.__is_cont_line_break(token): return - # Write previous token, store current. - if self.__prev_token: - self.__dst.write(str(self.__prev_token.raw)) + # Write token and store. + self.__dst.write(str(token.raw)) self.__prev_token = token @staticmethod @@ -171,10 +167,15 @@ class Quom: while not self.__source_files.empty(): self.__process_file(Path(), self.__source_files.get(), True) + self.__write_line_break_if_missing() return True def __is_cont_line_break(self, token: Token) -> bool: + # Save a used line break for later. + if self.__used_linesep is None and isinstance(token, LinebreakWhitespaceToken): + self.__used_linesep = token.raw + if not self.__trim: return False @@ -187,3 +188,9 @@ class Quom: self.__cont_lb = CONTINUOUS_LINE_BREAK_START return self.__cont_lb >= CONTINUOUS_BREAK_REACHED + + def __write_line_break_if_missing(self): + if not isinstance(self.__prev_token, LinebreakWhitespaceToken): + if self.__used_linesep is None: + self.__used_linesep = os.linesep # fallback + self.__dst.write(self.__used_linesep)	Viatorus/quom	4633b5aaba35454c425227ec498ea1e19caade39	diff --git a/tests/test_quom/test_last_source_file.py b/tests/test_quom/test_last_source_file.py index c227c21..7f148d2 100644 --- a/tests/test_quom/test_last_source_file.py +++ b/tests/test_quom/test_last_source_file.py @@ -53,7 +53,8 @@ extern int foo; #include <algorithm> -int foo = 42;""" +int foo = 42; +""" RESULT_NORMAL_WITHOUT_TRIM = """\ #pragma once @@ -78,7 +79,8 @@ extern int foo; #include <algorithm> -int foo = 42;""" +int foo = 42; +""" def init(): diff --git a/tests/test_quom/test_line_breaks_when_stitching.py b/tests/test_quom/test_line_breaks_when_stitching.py new file mode 100644 index 0000000..0bb6c37 --- /dev/null +++ b/tests/test_quom/test_line_breaks_when_stitching.py @@ -0,0 +1,98 @@ +from io import StringIO +from pathlib import Path + +from quom import Quom + +FILE_MAIN_CPP = """\ +#include "a.hpp" +int main() { + return 0; +} +// Stitch Begin +// End +""" + +FILE_A_HPP = 'int a;' + +FILE_A_CPP = """\ +#include "b.hpp" +#include "c.hpp" +void mid() {}""" + +FILE_B_HPP = 'int b;' +FILE_C_HPP = 'int c;' + +FILE_B_CPP = """\ +#include <b>""" + +FILE_C_CPP = """\ +#include <c>""" + +RESULT = """\ +int a; +int main() { + return 0; +} +// Stitch Begin +// End +int b; +int c; +void mid() {} +#include <b> +#include <c> +""" + +RESULT_STITCH = """\ +int a; +int main() { + return 0; +} +int b; +int c; +void mid() {} +#include <b> +#include <c> + +// End +""" + + +def init(): + with open('main.hpp', 'w+', encoding='utf-8') as file: + file.write(FILE_MAIN_CPP) + + with open('a.hpp', 'w+', encoding='utf-8') as file: + file.write(FILE_A_HPP) + + with open('a.cpp', 'w+', encoding='utf-8') as file: + file.write(FILE_A_CPP) + + with open('b.hpp', 'w+', encoding='utf-8') as file: + file.write(FILE_B_HPP) + + with open('b.cpp', 'w+', encoding='utf-8') as file: + file.write(FILE_B_CPP) + + with open('c.hpp', 'w+', encoding='utf-8') as file: + file.write(FILE_C_HPP) + + with open('c.cpp', 'w+', encoding='utf-8') as file: + file.write(FILE_C_CPP) + + +def test_add_line_break_in_stitched_files_if_missing(fs): + init() + + dst = StringIO() + Quom(Path('main.hpp'), dst) + + assert dst.getvalue() == RESULT + + +def test_add_line_break_in_stitched_files_if_missing_at_stitch_location(fs): + init() + + dst = StringIO() + Quom(Path('main.hpp'), dst, stitch_format='Stitch Begin') + + assert dst.getvalue() == RESULT_STITCH	when source files have no newline at EOF, content of next file is concatenated right after last closing curly bracket When one of source files has no newline at EOF, the "#include ..."s of the next file appears right after the last closing curly bracket and that causes a compilation error. I know it's a trivial problem to resolve when compiling fails but it would be nice to ensure the content of all source files are separated by newline. ```c++ // bad.cpp void foo(){ // there is no newline at EOF, file ends right after this closing curly bracket. } // b.cpp #include <iostream> // this include is at first line and located outside current build directory // main.cpp include "bad.hpp" include "b.hpp" ... ``` And the source file quom produces has something like: ```c++ void foo(){ }#include <iostream> // this include comes from b.cpp ``` I wrote a test to demonstrate this problem. The following test will fail at current commit which is ```4633b5aa```. ---- ```python from io import StringIO from pathlib import Path from quom import Quom FILE_MAIN_CPP = """\ #include "a.hpp" #include "b.hpp" int main() { return 0; } """ FILE_A_HPP = """\ #ifndef A_HPP_ #define A_HPP_ #endif //A_HPP_ """ FILE_A_CPP = """\ #include "a.hpp" #include "b.hpp" int mid() { }""" FILE_B_HPP = """\ #ifndef B_HPP_ #define B_HPP_ #endif //B_HPP_ """ FILE_B_CPP = """\ #include <memory> """ RESULT = """\ #ifndef A_HPP_ #define A_HPP_ #endif //A_HPP_ #ifndef B_HPP_ #define B_HPP_ #endif //B_HPP_ int main() { return 0; } void mid() { } #include <memory> """ def init(): with open('main.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_MAIN_CPP) with open('a.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_A_HPP) with open('a.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_A_CPP) with open('b.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_B_HPP) with open('b.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_B_CPP) def test_issue_one(fs): init() dst = StringIO() Quom(Path('main.hpp'), dst) assert dst.getvalue() == RESULT ```	4633b5aaba35454c425227ec498ea1e19caade39	[ "tests/test_quom/test_last_source_file.py::test_normal", "tests/test_quom/test_last_source_file.py::test_normal_without_trim", "tests/test_quom/test_line_breaks_when_stitching.py::test_add_line_break_in_stitched_files_if_missing", "tests/test_quom/test_line_breaks_when_stitching.py::test_add_line_break_in_stitched_files_if_missing_at_stitch_location" ]	[ "tests/test_quom/test_last_source_file.py::test_without_newline_at_end" ]	{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-07-27 20:35:58+00:00	mit	821
VictorPelaez__coral-reef-optimization-algorithm-43	diff --git a/cro/cro.py b/cro/cro.py index 44c17ae..ebc560b 100644 --- a/cro/cro.py +++ b/cro/cro.py @@ -20,6 +20,7 @@ class CRO(object): self.Pd = Pd self.fitness_coral = fitness_coral self.opt = opt + self.opt_multiplier = -1 if opt == "max" else 1 self.L = L self.ke = ke self.seed = seed @@ -83,7 +84,7 @@ class CRO(object): coral_fitness = self.fitness_coral(coral) REEF_fitness.append(coral_fitness) - return np.array(REEF_fitness) + return self.opt_multipliernp.array(REEF_fitness) def broadcastspawning(self, REEF, REEFpob): """ @@ -197,7 +198,6 @@ class CRO(object): - REEFfitness: new reef fitness """ k = self.k - opt = self.opt np.random.seed(seed=self.seed) Nlarvae = larvae.shape[0] @@ -222,10 +222,7 @@ class CRO(object): REEFfitness[reef_index] = larva_fitness REEF[reef_index] = 1 else: # occupied coral - if opt == "max": - fitness_comparison = larva_fitness > REEFfitness[reef_indices] - else: - fitness_comparison = larva_fitness < REEFfitness[reef_indices] + fitness_comparison = larva_fitness < REEFfitness[reef_indices] if np.any(fitness_comparison): reef_index = reef_indices[np.where(fitness_comparison)[0][0]] @@ -243,7 +240,6 @@ class CRO(object): - pob: reef population - fitness: reef fitness - Fa: fraction of corals to be duplicated - - opt: type of optimization ('max' or 'min') Output: - Alarvae: created larvae, - Afitness: larvae's fitness @@ -255,8 +251,7 @@ class CRO(object): N = pob.shape[0] NA = int(np.round(FaN)) - if self.opt=='max': ind = np.argsort(-fitness); - else: ind = np.argsort(fitness) + ind = np.argsort(fitness) fitness = fitness[ind] Alarvae = pob[ind[0:NA], :] @@ -284,10 +279,8 @@ class CRO(object): Pd = self.Pd np.random.seed(seed = self.seed) - if (self.opt=='max'): - ind = np.argsort(REEFfitness) - else: - ind = np.argsort(-REEFfitness) + # Sort by worse fitness (hence the minus sign) + ind = np.argsort(-REEFfitness) sortind = ind[:int(np.round(FdREEFpob.shape[0]))] p = np.random.rand(len(sortind)) @@ -390,13 +383,10 @@ class CRO(object): Bestfitness = [] Meanfitness = [] - if opt=='max': - if verbose: print('Reef initialization:', np.max(REEFfitness)) - Bestfitness.append(np.max(REEFfitness)) - else: - if verbose: print('Reef initialization:', np.min(REEFfitness)) - Bestfitness.append(np.min(REEFfitness)) - Meanfitness.append(np.mean(REEFfitness)) + Bestfitness.append(self.opt_multipliernp.min(REEFfitness)) + Meanfitness.append(self.opt_multipliernp.mean(REEFfitness)) + if verbose: + print('Reef initialization:', self.opt_multipliernp.min(REEFfitness)) for n in range(Ngen): @@ -420,23 +410,18 @@ class CRO(object): (REEF, REEFpob, REEFfitness) = self.depredation(REEF, REEFpob, REEFfitness) (REEF, REEFpob, REEFfitness) = self.extremedepredation(REEF, REEFpob, REEFfitness, int(np.round(self.keNM))) - if opt=='max': Bestfitness.append(np.max(REEFfitness)) - else: Bestfitness.append(np.min(REEFfitness)) - Meanfitness.append(np.mean(REEFfitness)) + Bestfitness.append(self.opt_multipliernp.min(REEFfitness)) + Meanfitness.append(self.opt_multipliernp.mean(REEFfitness)) - if (n%10==0) & (n!=Ngen): - if (opt=='max') & (verbose): print('Best-fitness:', np.max(REEFfitness), '\n', str(n/Ngen100) + '% completado \n' ); - if (opt=='min') & (verbose): print('Best-fitness:', np.min(REEFfitness), '\n', str(n/Ngen100) + '% completado \n' ); + if all([n%10 == 0, n != Ngen, verbose]): + print('Best-fitness:', self.opt_multipliernp.min(REEFfitness), '\n', str(n/Ngen100) + '% completado \n' ); - if opt=='max': - if verbose: print('Best-fitness:', np.max(REEFfitness), '\n', str(100) + '% completado \n' ) - ind_best = np.where(REEFfitness == np.max(REEFfitness))[0][0] - else: - if verbose: print('Best-fitness:', np.min(REEFfitness), '\n', str(100) + '% completado \n' ) - ind_best = np.where(REEFfitness == np.min(REEFfitness))[0][0] + if verbose: + print('Best-fitness:', self.opt_multipliernp.min(REEFfitness), '\n', str(100) + '% completado \n' ) + ind_best = np.where(REEFfitness == np.min(REEFfitness))[0][0] self.plot_results(Bestfitness, Meanfitness) print('Best coral: ', REEFpob[ind_best, :]) - print('Best solution:', REEFfitness[ind_best]) + print('Best solution:', self.opt_multiplierREEFfitness[ind_best]) return (REEF, REEFpob, REEFfitness, ind_best, Bestfitness, Meanfitness)	VictorPelaez/coral-reef-optimization-algorithm	9939a280c87090b7ae575a23670f49a265ad017a	diff --git a/cro/tests.py b/cro/tests.py index abd19cf..9bde3df 100644 --- a/cro/tests.py +++ b/cro/tests.py @@ -91,14 +91,14 @@ def test_larvaesettling_nonemptyreef(): [1,0,1,1]]) REEF = np.array([0,1,1,1]) - REEFfitness = np.array([0,1,2,11]) + REEFfitness = -np.array([0,1,2,11]) larvae = np.array([[1,0,0,0], [0,1,1,0], [0,1,0,0], [1,0,0,1]]) - larvaefitness = np.array([8,6,4,9]) + larvaefitness = -np.array([8,6,4,9]) N, L = REEFpob.shape M = 1 @@ -126,7 +126,7 @@ def test_larvaesettling_nonemptyreef(): [1,0,0,1], [0,0,1,0], [1,0,1,1]]) - REEFfitness_exp = np.array([8,9,2,11]) + REEFfitness_exp = -np.array([8,9,2,11]) np.testing.assert_almost_equal(REEF_res, np.array([1,1,1,1])) np.testing.assert_almost_equal(REEFpob_res, REEFpob_exp)	create a opt_multiplier (-1 or 1) with opt argument One of the main point suggested in Issue #22. Using opt argument, create a self.opt_multiplier (1, -1) It looks an improvement in 2 functions: - budding() ``` if self.opt=='max': ind = np.argsort(-fitness); else: ind = np.argsort(fitness) ``` - depredation() ``` if (self.opt=='max'): ind = np.argsort(REEFfitness) else: ind = np.argsort(-REEFfitness) ``` @apastors Did your proposal cover anything else? regards	9939a280c87090b7ae575a23670f49a265ad017a	[ "cro/tests.py::test_larvaesettling_nonemptyreef" ]	[ "cro/tests.py::test_croCreation", "cro/tests.py::test_croInit", "cro/tests.py::test_reefinitializationDisc", "cro/tests.py::test_larvaesettling_emptyreef" ]	{ "failed_lite_validators": [ "has_issue_reference", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2017-10-29 08:56:15+00:00	mit	822
VictorPelaez__coral-reef-optimization-algorithm-45	diff --git a/.travis.yml b/.travis.yml index 8bc2fee..15ab2f9 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,7 +9,6 @@ install: - pip install -r requirements.txt script: - pytest tests/ - deploy: provider: pypi user: victorpelaez diff --git a/cro/cro.py b/cro/cro.py index b7231dd..7c24105 100644 --- a/cro/cro.py +++ b/cro/cro.py @@ -1,15 +1,24 @@ #!/usr/bin/env python # coding=utf-8 ############################################################################### - -from __future__ import division +from __future__ import division, print_function +import sys +import logging import numpy as np + +from .reef_initialization import get_reefinit_function from .larvaemutation import get_larvaemutation_function class CRO(object): def __init__(self, Ngen, N, M, Fb, Fa, Fd, r0, k, Pd, fitness_coral, opt, L=None, ke=0.2, npolyps=1, seed=None, mode='bin', param_grid={}, verbose=False): + # Set logging configuration + logging_level = logging.INFO if verbose else logging.WARNING + logging.basicConfig(stream=sys.stdout, + format="%(message)s") + logging.getLogger().setLevel(logging_level) + self.Ngen = Ngen self.N = N self.M = M @@ -29,9 +38,11 @@ class CRO(object): self.mode = mode self.param_grid = param_grid self.verbose = verbose - - print("[Running] Initialization: ", self.opt) + self.reefinit_function = get_reefinit_function(mode) + self.larvaemutation_function = get_larvaemutation_function(mode) + logging.info("Running Initialization: %s", self.opt) + def reefinitialization (self): """ function [REEF,REEFpob]=reefinitialization(M,N,r0,L) @@ -45,37 +56,9 @@ class CRO(object): - REEF: reef matrix - REEFpob: population matrix """ - - # print error. Maybe use other place for all arg-checks - if ( (self.param_grid=={}) & (self.mode =='disc') ): - print('\nThis mode (', self.mode, ') needs a param_grid as a dictionary') - return -1 - - # commom for all modes - np.random.seed(seed = self.seed) - O = int(np.round(self.Nself.Mself.r0)) # number of occupied reefs - - # Binary mode - if self.mode =='bin': - A = np.random.randint(2, size=[O, self.L]) - B = np.zeros([( (self.Nself.M)-O), self.L], int) - REEFpob = np.concatenate([A,B]) # Population creation - REEF = np.array((REEFpob.any(axis=1)),int) - return (REEF, REEFpob) - - # Discrete mode - elif self.mode =='disc': - for key, value in self.param_grid.items(): - valmax = (value[1] - value[0] + 1) - A = np.random.randint(valmax, size=[O, self.L]) + value[0] - B = np.zeros([( (self.Nself.M)-O), self.L], int) - REEFpob = np.concatenate([A,B]) # Population creation - REEF = np.array((REEFpob.any(axis=1)),int) - return (REEF, REEFpob) - - else: - print('\nThis mode (', self.mode, ') is not available') - return -1 + np.random.seed(seed = self.seed) # commom for all modes + REEF, REEFpob = self.reefinit_function(self.M, self.N, self.r0, self.L, param_grid=self.param_grid) + return REEF, REEFpob def fitness(self, REEFpob): """ @@ -163,8 +146,8 @@ class CRO(object): pos = np.random.randint(brooders.shape[1], size=(npolyps, nbrooders)) - larvaemutation_function = get_larvaemutation_function(self.mode) - brooders = larvaemutation_function(brooders, pos, delta=1, param_grid=self.param_grid, seed=self.seed) + brooders = self.larvaemutation_function(brooders, pos, delta=1, + param_grid=self.param_grid, seed=self.seed) return brooders @@ -384,8 +367,7 @@ class CRO(object): Bestfitness.append(self.opt_multipliernp.min(REEFfitness)) Meanfitness.append(self.opt_multipliernp.mean(REEFfitness)) - if verbose: - print('Reef initialization:', self.opt_multipliernp.min(REEFfitness)) + logging.info('Reef initialization: %s', self.opt_multipliernp.min(REEFfitness)) for n in range(Ngen): @@ -413,14 +395,13 @@ class CRO(object): Meanfitness.append(self.opt_multipliernp.mean(REEFfitness)) if all([n%10 == 0, n != Ngen, verbose]): - print('Best-fitness:', self.opt_multipliernp.min(REEFfitness), '\n', str(n/Ngen100) + '% completado \n' ); + logging.info('Best-fitness: %s, (%.2f%% completado)', self.opt_multipliernp.min(REEFfitness), n/Ngen100) - if verbose: - print('Best-fitness:', self.opt_multipliernp.min(REEFfitness), '\n', str(100) + '% completado \n' ) + logging.info('Best-fitness: %s. (100%% completado)', self.opt_multipliernp.min(REEFfitness)) ind_best = np.where(REEFfitness == np.min(REEFfitness))[0][0] self.plot_results(Bestfitness, Meanfitness) print('Best coral: ', REEFpob[ind_best, :]) - print('Best solution:', self.opt_multiplierREEFfitness[ind_best]) + print('Best solution: ', self.opt_multiplierREEFfitness[ind_best]) return (REEF, REEFpob, REEFfitness, ind_best, Bestfitness, Meanfitness) diff --git a/cro/larvaemutation.py b/cro/larvaemutation.py index 835e7f6..20211a7 100644 --- a/cro/larvaemutation.py +++ b/cro/larvaemutation.py @@ -87,6 +87,6 @@ def get_larvaemutation_function(mode): logging.info("Using {}".format(name)) else: name, func = mode_functions[0] - logging.info("Using {} for initializing the reef".format(name)) + logging.info("Using {} for the brooding operator".format(name)) - return func \ No newline at end of file + return func diff --git a/cro/reef_initialization.py b/cro/reef_initialization.py new file mode 100644 index 0000000..211b87f --- /dev/null +++ b/cro/reef_initialization.py @@ -0,0 +1,86 @@ +""" +Module that contains all the functions that perform the reef +initialization. + +Every function should start with the mode name it performs, +followed by an underscore and the function name. + +It should accept the following arguments: + - M: Reef size + - N: Reef size + - r0: occupied/total ratio + - L: coral length + - kwargs: extra arguments that the function might need (see + https://stackoverflow.com/a/1769475 for an + explanation on kwargs) + +It should return a tuple with (REEF, REEFpob) +""" +import logging + +import numpy as np + +from .utils import get_module_functions + +def bin_binary(M, N, r0, L, *kwargs): + """ + Each value in each coral in the reef is a boolean value, i.e, + either a 0 or a 1 + """ + O = int(np.round(NMr0)) # number of occupied reefs + A = np.random.randint(2, size=[O, L]) + B = np.zeros([((NM)-O), L], int) + REEFpob = np.concatenate([A, B]) # Population creation + REEF = np.array((REEFpob.any(axis=1)),int) + return (REEF, REEFpob) + +def disc_equal_range(M, N, r0, L, *kwargs): + """ + Each value in each coral in the reef is an integer in the range + specified by the keyword argument `param_grid`. `param_grid` + must have the next format: + + >>> param_grid = { + "x": [2, 10] + } + + where "x" can be basically anything, and its value is a list + with both minimum and maximum value. + In this example each coral will contain integers between 2 and 10 + """ + try: + param_grid = kwargs["param_grid"] + except KeyError: + raise ValueError("disc mode needs a param_grid as a dictionary") + + O = int(np.round(NMr0)) # number of occupied reefs + for _, value in param_grid.items(): + valmax = (value[1] - value[0] + 1) + A = np.random.randint(valmax, size=[O, L]) + value[0] + B = np.zeros([((NM)-O), L], int) + REEFpob = np.concatenate([A,B]) # Population creation + REEF = np.array((REEFpob.any(axis=1)),int) + return (REEF, REEFpob) + +""""" +UTILS +""""" +def get_reefinit_function(mode): + """ + Returns the init function for the given mode. + If more than one function exists, return one randomly. + """ + reef_init_functions = get_module_functions(__name__) + mode_functions = [(name, func) for name, func in reef_init_functions.items() + if name.startswith(mode)] + if not mode_functions: + raise ValueError("No initialization function for mode {}".format(mode)) + elif len(mode_functions) > 1: + logging.warning("More than one initialization function for mode {}".format(mode)) + name, func = mode_functions[0] + logging.info("Using {}".format(name)) + else: + name, func = mode_functions[0] + logging.info("Using {} for initializing the reef".format(name)) + + return func diff --git a/cro/utils.py b/cro/utils.py index 5ffd7ff..980e657 100644 --- a/cro/utils.py +++ b/cro/utils.py @@ -31,5 +31,3 @@ def get_module_functions(module_name): """ current_module = sys.modules[module_name] return dict(getmembers(current_module, predicate=isfunction)) - - diff --git a/examples/example_advanced.py b/examples/example_advanced.py index 9b5d55b..39e1378 100644 --- a/examples/example_advanced.py +++ b/examples/example_advanced.py @@ -90,9 +90,9 @@ if __name__ == '__main__': get_prediction=lambda gbr, X: gbr.predict(X), metric=mean_squared_error) start = time.time() - cro = CRO(Ngen, N, M, Fb, Fa, Fd, r0, k, Pd, fitness_coral, opt, L, verbose=True) + cro = CRO(Ngen, N, M, Fb, Fa, Fd, r0, k, Pd, fitness_coral, opt, L, seed=13, verbose=True) (REEF, REEFpob, REEFfitness, ind_best, Bestfitness, Meanfitness) = cro.fit(X, y, gbr) print("Example II: feature selection, regression (min mse): ", time.time() - start, "seconds.") names = np.array(['CRIM', 'ZN', 'INDUS', 'CHAS', 'NOX', 'RM', 'AGE', 'DIS', 'RAD', 'TAX', 'PTRATIO', 'B', 'LSTAT']) - print(names[REEFpob[ind_best, :]>0]) \ No newline at end of file + print(names[REEFpob[ind_best, :]>0])	VictorPelaez/coral-reef-optimization-algorithm	bc0b2fd006187f3e269c6e1898241866f502bd25	diff --git a/tests/__init__.py b/tests/__init__.py index e69de29..1581836 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -0,0 +1,4 @@ +import sys +import os + +sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) diff --git a/tests/test_cro.py b/tests/test_cro.py index f71a78f..5c8a9ed 100644 --- a/tests/test_cro.py +++ b/tests/test_cro.py @@ -3,11 +3,6 @@ ############################################################################### # run with: # python -m pytest tests/test_cro.py - -import sys -import os -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) - import numpy as np from cro.cro import CRO @@ -119,7 +114,6 @@ def test_larvaesettling_nonemptyreef(): """ Due to the passed seed, [1,0,0,0] will be placed in the empty coral (index 0) - Then, larva [0,1,1,0] will try to settle in indices [0,3,1], settling in the third try (index 1) Larva [0,1,0,0] will try in indices [0,3,3], being discarded Larva [1,0,0,1] will try in indices [3,3,1], settling in the third try (index 1) @@ -176,4 +170,4 @@ def test_settle_larvae(): assert REEF_res[indices] == 1 np.testing.assert_almost_equal(REEFpob_res[indices, :], larvae) - np.testing.assert_almost_equal(REEFfitness_res[indices], larvaefitness) \ No newline at end of file + np.testing.assert_almost_equal(REEFfitness_res[indices], larvaefitness) diff --git a/tests/test_fitness.py b/tests/test_fitness.py index 30f0a0e..73eafe7 100644 --- a/tests/test_fitness.py +++ b/tests/test_fitness.py @@ -3,11 +3,6 @@ ############################################################################### # run with: # python -m pytest tests/test_fitness.py - -import sys -import os -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) - import numpy as np from cro.fitness import max_ones @@ -37,4 +32,4 @@ def test_feature_selection(): """ To be added """ - pass \ No newline at end of file + pass diff --git a/tests/test_larvaemutation.py b/tests/test_larvaemutation.py index 9713491..c564422 100644 --- a/tests/test_larvaemutation.py +++ b/tests/test_larvaemutation.py @@ -3,11 +3,6 @@ ############################################################################### # run with: # python -m pytest tests/test_larvaemutation.py - -import sys -import os -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) - import numpy as np from cro.larvaemutation import get_larvaemutation_function @@ -79,4 +74,4 @@ def test_get_larvaemutation_function(): f = get_larvaemutation_function('bin') assert 'function bin_larvaemutation' in str(f) f = get_larvaemutation_function('disc') - assert 'function disc_larvaemutation' in str(f) \ No newline at end of file + assert 'function disc_larvaemutation' in str(f) diff --git a/tests/test_reefinitialization.py b/tests/test_reefinitialization.py index 567c7dd..198f6bd 100644 --- a/tests/test_reefinitialization.py +++ b/tests/test_reefinitialization.py @@ -3,28 +3,28 @@ ############################################################################### # run with: # python -m pytest tests/test_larvaemutation.py - -import sys -import os -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) - import numpy as np -#from cro.reefinitialization import bin_binary, disc_equal_range +from cro.reef_initialization import bin_binary, disc_equal_range # ------------------------------------------------------ # reefinitialization module # ------------------------------------------------------ - def test_bin_binary(): """ Test that corals in the population only contain values in {0, 1} """ - pass - - + M, N, r0, L = 2, 2, 0.6, 8 + REEF, REEFpob = bin_binary(M, N, r0, L) + assert set(REEFpob.ravel()) == {0, 1} + def test_disc_equal_range(): """ Test that corals in population contain values specified in the grid """ - pass \ No newline at end of file + M, N, r0, L = 2, 2, 0.6, 8 + grid = {'x': [2, 10]} # Discrete values between 2 and 10 + + REEF, REEFpob = disc_equal_range(M, N, r0, L, param_grid=grid) + p = sum(REEFpob[np.where(REEFpob!=0)]<grid['x'][0]) + sum(REEFpob[np.where(REEFpob!=0)]>grid['x'][1]) + assert p == 0	Refactor Reef initialization To improve the code architecture, a module with different initialization functions should be considered: one function per mode that accepts all the parameters it needs (`M`, `N`, `L`, `param_grid`, ...) and have it return `REEFpob`. This way we could add documentation for each initialization explaining how it is done and which parameters it needs. Also each function could be easily testable.	bc0b2fd006187f3e269c6e1898241866f502bd25	[ "tests/test_cro.py::test_croCreation", "tests/test_cro.py::test_croInit", "tests/test_cro.py::test_reefinitializationDisc", "tests/test_cro.py::test_larvaesettling_emptyreef", "tests/test_cro.py::test_larvaesettling_nonemptyreef", "tests/test_cro.py::test_brooding", "tests/test_cro.py::test_settle_larvae", "tests/test_fitness.py::test_max_ones", "tests/test_fitness.py::test_feature_selection", "tests/test_larvaemutation.py::test_bin_larvaemutattion", "tests/test_larvaemutation.py::test_disc_larvaemutattion", "tests/test_larvaemutation.py::test_cont_larvaemutattion", "tests/test_larvaemutation.py::test_get_larvaemutation_function", "tests/test_reefinitialization.py::test_bin_binary", "tests/test_reefinitialization.py::test_disc_equal_range" ]	[]	{ "failed_lite_validators": [ "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2017-11-02 21:28:47+00:00	mit	823
Vipul-Cariappa__py-utility-7	diff --git a/README.md b/README.md index e6336ee..47feb7f 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,8 @@ Utility functions for managing and monitoring python resources. ## installation <pre><code>pip install py-utility</code></pre> -## Decorator Function + +## Documentation ### memoryit memoryit returns the total memory used by the function at runtime in bytes. @@ -12,25 +13,32 @@ memoryit returns the total memory used by the function at runtime in bytes. Example Code: <br> <pre><code>from pyutility import memoryit -@memoryit + def prime_check(x): for i in range(2, x): if x % i == 0: return False - return True</code></pre> + return True + +if __name__ == "__main__": + ... + memoryit(prime_check, args=(89,)) + ... + + </code></pre> ### limit_memory -limit_memory limits the memory consumption of function at runtime. It takes the limit in MB. You will find unexpected behaviour if too low value is set. The default value is 25 MB. It is throw MemoryError if it exceeds the limit. +limit_memory limits the memory consumption of function at runtime. It takes the limit in MB. You will find unexpected behaviour if too low value is set. The default value is 25 MB. It throws MemoryError if it exceeds the limit. <br> Example Code: <br> <pre><code>from pyutility import limit_memory -@limit_memory(30) -def prime_check(x): - for i in range(2, x): - if x % i == 0: - return False - return True</code></pre> + +if __name__ == "__main__": + ... + limit_memory(prime_check, memory=30, args=(89,)) + ... + </code></pre> ### timeit timeit returns the total time take to execute the function in seconds. @@ -38,12 +46,11 @@ timeit returns the total time take to execute the function in seconds. Example Code: <br> <pre><code>from pyutility import timeit -@timeit -def prime_check(x): - for i in range(2, x): - if x % i == 0: - return False - return True</code></pre> + +if __name__ == "__main__": + ... + timeit(prime_check, args=(89,)) + ...</code></pre> ### limit_time limit_time limits the time used to execute the function. It takes limit as seconds. The default value is 10 seconds. It throws TimeoutError if it exceeds the limit. @@ -51,12 +58,12 @@ limit_time limits the time used to execute the function. It takes limit as secon Example Code: <br> <pre><code>from pyutility import limit_time -@limit_time(30) -def prime_check(x): - for i in range(2, x): - if x % i == 0: - return False - return True</code></pre> + +if __name__ == "__main__": + ... + limit_time(prime_check, time=2, args=(89,)) + ...</code></pre> ## Contribution All contributions are welcomed. If it is a bug fix or new feature, creating new issue is highly recommend before any pull request. + If you want any new feature to be included create new issue asking for the feature with a use case and example code if possible. diff --git a/pyutility/memoryutil.py b/pyutility/memoryutil.py index 29c5f3f..ca8d3ed 100644 --- a/pyutility/memoryutil.py +++ b/pyutility/memoryutil.py @@ -4,7 +4,7 @@ import resource def me_worker(func, storage, args, kwargs): - """measures the peak memory consumption of given function; should be run by memoryit decorator as a new process + """measures the peak memory consumption of given function Args: func (`function`): function to execute @@ -30,11 +30,11 @@ def me_worker(func, storage, args, *kwargs): def li_worker(func, limit, storage, args, *kwargs): - """limits the memory consumption of given function; should be run by limit_memory decorator as a new process + """limits the memory consumption of given function Args: func (`function`): function to execute - limit (`int`): maximum allowed memory consuption + limit (`int`): maximum allowed memory consumption storage (`list`): multiprocessing.Manager().List() to store the peak memory args (`tuple`): arguments for the function kwargs(`dict`): keyword arguments for the function @@ -57,53 +57,51 @@ def li_worker(func, limit, storage, args, *kwargs): return 0 -def memoryit(func): - """decorator function to measures the peak memory consumption of given function +def memoryit(func, args=(), kwargs={}): + """measures the peak memory consumption of given function Args: func (`function`): function to execute + args (`tuple`): arguments for the function + kwargs(`dict`): keyword arguments for the function Return: peak memory used during the execution of given function in bytes (`int`) """ - def wrapper(args, *kwargs): - ctx = mp.get_context('spawn') - manager = ctx.Manager() - com_obj = manager.list() - p = ctx.Process(target=me_worker, args=( - func, com_obj, args), kwargs=kwargs) - p.start() - p.join() - - return com_obj[-1] + ctx = mp.get_context('spawn') + manager = ctx.Manager() + com_obj = manager.list() + p = ctx.Process(target=me_worker, args=( + func, com_obj, args), kwargs=kwargs) + p.start() + p.join() - return wrapper + return com_obj[-1] -def limit_memory(value=15): - """decorator function to limits the memory consumption of given function +def limit_memory(func, memory=25, args=(), kwargs={}): + """limits the memory consumption of given function. + If limit set is very low it will not behave in expected way. Args: - value (`int`): maximum allowed memory consumption in MB func (`function`): function to execute + limit (`int`): maximum allowed memory consumption in MB default is 25 MB + args (`tuple`): arguments for the function + kwargs(`dict`): keyword arguments for the function Return: return value of function or MemoryError """ - def decorator(func): - def wrapper(args, *kwargs): - ctx = mp.get_context('spawn') - manager = ctx.Manager() - com_obj = manager.list() - p = ctx.Process(target=li_worker, args=( - func, value, com_obj, args), kwargs=kwargs) - p.start() - p.join() - - if isinstance(com_obj[-1], Exception): - raise com_obj[-1] - else: - return com_obj[-1] - - return wrapper - return decorator + + ctx = mp.get_context('spawn') + manager = ctx.Manager() + com_obj = manager.list() + p = ctx.Process(target=li_worker, args=( + func, memory, com_obj, args), kwargs=kwargs) + p.start() + p.join() + + if isinstance(com_obj[-1], Exception): + raise com_obj[-1] + else: + return com_obj[-1] diff --git a/pyutility/timeutil.py b/pyutility/timeutil.py index 325830a..dc2c0bd 100644 --- a/pyutility/timeutil.py +++ b/pyutility/timeutil.py @@ -4,8 +4,7 @@ import signal def me_worker(func, storage, args, *kwargs): - """measures the time taken to execute given function should be run by timeit decorator as a new process - + """measures the time taken to execute given function Args: func (`function`): function to execute storage (`list`): multiprocessing.Manager().List() to store the time taken to excute @@ -13,7 +12,7 @@ def me_worker(func, storage, args, *kwargs): kwargs(`dict`): keyword arguments for the function Return: - time taken to execute the given function in seconds (`int`) + time taken to execute the given function in seconds (`float`) """ t1 = time() func(args, *kwargs) @@ -23,7 +22,7 @@ def me_worker(func, storage, args, *kwargs): def li_worker(func, time, storage, args, *kwargs): - """limits the time taken for exection of given function; should be run by limit_time decorator as a new process + """limits the time taken for exection of given function Args: func (`function`): function to execute @@ -52,53 +51,51 @@ def li_worker(func, time, storage, args, *kwargs): return 0 -def timeit(func): - """decorator function to measure time taken to execute a given function in new process +def timeit(func, args=(), kwargs={}): + """measures the time taken to execute given function Args: func (`function`): function to execute + args (`tuple`): arguments for the function + kwargs(`dict`): keyword arguments for the function Return: - time taken to execute the given function in seconds (`int`) + time taken to execute the given function in seconds (`float`) """ - def wrapper(args, *kwargs): - ctx = mp.get_context('spawn') - manager = ctx.Manager() - com_obj = manager.list() - p = ctx.Process(target=me_worker, args=( - func, com_obj, args), kwargs=kwargs) - p.start() - p.join() - return com_obj[-1] - return wrapper + ctx = mp.get_context('spawn') + manager = ctx.Manager() + com_obj = manager.list() + p = ctx.Process(target=me_worker, args=( + func, com_obj, args), kwargs=kwargs) + p.start() + p.join() + + return com_obj[-1] -def limit_time(time=10): - """decorator function to limits the time taken to execute given function +def limit_time(func, time=10, args=(), kwargs={}): + """limits the time taken for exection of given function Args: - value (`int`): maximum allowed time in seconds func (`function`): function to execute + limit (`int`): maximum allowed time in seconds, default is 10 + args (`tuple`): arguments for the function + kwargs(`dict`): keyword arguments for the function Return: return value of function or TimeoutError """ - def inner(func): - def wrapper(args, *kwargs): - - ctx = mp.get_context('spawn') - manager = ctx.Manager() - com_obj = manager.list() - p = ctx.Process(target=li_worker, args=( - func, time, com_obj, args), kwargs=kwargs) - p.start() - p.join() - - if isinstance(com_obj[-1], Exception): - raise com_obj[-1] - else: - return com_obj[-1] - - return wrapper - return inner + + ctx = mp.get_context('spawn') + manager = ctx.Manager() + com_obj = manager.list() + p = ctx.Process(target=li_worker, args=( + func, time, com_obj, args), kwargs=kwargs) + p.start() + p.join() + + if isinstance(com_obj[-1], Exception): + raise com_obj[-1] + else: + return com_obj[-1] diff --git a/pyutility/utility.py b/pyutility/utility.py index d0eefbc..841fd7e 100644 --- a/pyutility/utility.py +++ b/pyutility/utility.py @@ -15,7 +15,7 @@ def me_worker(func, storage, args, *kwargs): kwargs(`dict`): keyword arguments for the function Return: - peak memory used, time taken during the execution of given function in bytes (`list` of 'int', 'float') + peak memory used, time taken for the execution of given function (`list` of 'int', 'float') """ tm.start() @@ -74,58 +74,54 @@ def li_worker(func, storage, time, memory, args, *kwargs): return 0 -def measureit(func): - """decorator function to measures the peak memory consumption and time taken to execute given function +def measureit(func, args=(), kwargs={}): + """measures the peak memory consumption and time taken for execution of given function Args: func (`function`): function to execute + args (`tuple`): arguments for the function + kwargs(`dict`): keyword arguments for the function Return: - peak memory used, time taken during the execution of given function in bytes (`tuple` of 'int', 'float') + peak memory used (MB), time taken (seconds) during the execution of given function (`list` of 'int', 'float') """ - def wrapper(args, *kwargs): - ctx = mp.get_context('spawn') - manager = ctx.Manager() - com_obj = manager.list() - p = ctx.Process(target=me_worker, args=( - func, com_obj, args), kwargs=kwargs) - p.start() - p.join() - - if len(com_obj) == 2: - return tuple(com_obj) - - # else - raise com_obj[-1] + ctx = mp.get_context('spawn') + manager = ctx.Manager() + com_obj = manager.list() + p = ctx.Process(target=me_worker, args=( + func, com_obj, args), kwargs=kwargs) + p.start() + p.join() - return wrapper + if len(com_obj) == 2: + return tuple(com_obj) + # else + raise com_obj[-1] -def limit_resource(time=10, memory=25): - """decorator function to limits the memory consumption and time taken to execute given function + +def limit_resource(func, time=10, memory=25, args=(), kwargs={}): + """limits the memory consumption and time taken to execute given function Args: - time (`int`): maximum allowed time consuption in seconds - memory (`int`): maximum allowed memory consuption in MB func (`function`): function to execute + time (`int`): maximum allowed time in seconds, default is 10 + memory (`int`): maximum allowed memory consumption in MB, default is 25 + args (`tuple`): arguments for the function + kwargs(`dict`): keyword arguments for the function Return: return value of function or MemoryError or TimeoutError """ - def decorator(func): - def wrapper(args, *kwargs): - ctx = mp.get_context('spawn') - manager = ctx.Manager() - com_obj = manager.list() - p = ctx.Process(target=li_worker, args=( - func, com_obj, time, memory, args), kwargs=kwargs) - p.start() - p.join() - - if isinstance(com_obj[-1], Exception): - raise com_obj[-1] - else: - return com_obj[-1] - - return wrapper - return decorator + ctx = mp.get_context('spawn') + manager = ctx.Manager() + com_obj = manager.list() + p = ctx.Process(target=li_worker, args=( + func, com_obj, time, memory, *args), kwargs=kwargs) + p.start() + p.join() + + if isinstance(com_obj[-1], Exception): + raise com_obj[-1] + # else + return com_obj[-1]	Vipul-Cariappa/py-utility	8f66fc1fc569c34798865ab063f1da4e7753c9d5	diff --git a/tests/func.py b/tests/func.py new file mode 100644 index 0000000..cbe21ea --- /dev/null +++ b/tests/func.py @@ -0,0 +1,20 @@ +def memory(x): + x = [i for i in range(x)] + return -1 + + +def time(x): + # recursive function to find xth fibonacci number + if x < 3: + return 1 + return time(x-1) + time(x-2) + + +def error(x=None): + # error function + return "a" / 2 + + +def return_check(args, kwagrs): + # args and kwargs function + return list(args) + list(kwagrs.values()) diff --git a/tests/test_memory.py b/tests/test_memory.py index c5b3197..437a8ac 100644 --- a/tests/test_memory.py +++ b/tests/test_memory.py @@ -1,50 +1,46 @@ from unittest import TestCase from pyutility import limit_memory, memoryit - -def func1(x): - x = [i for i in range(x)] - return -1 - - -def func2(): - # error function - return "a" / 2 - - -def func3(args, *kwagrs): - # args and kwargs function - return list(args) + list(kwagrs.values()) +from .func import memory, error, return_check class MemoryitTest(TestCase): - def setUp(self): - self.er_func = memoryit(func2) - self.func = memoryit(func1) - self.ka_func = memoryit(func3) - def test_memoryit_1(self): - self.assertIsInstance(self.func(5), int) + def test_memoryit1(self): + v = memoryit(memory, args=(5,)) + self.assertIsInstance(v, int) - def test_memoryit_2(self): - self.assertRaises(Exception, self.er_func) + def test_memoryit2(self): + self.assertRaises(Exception, memoryit, error, 5) class LimitMemoryTest(TestCase): - def setUp(self): - self.er_func = limit_memory()(func2) - self.func = limit_memory()(func1) - self.ka_func = limit_memory()(func3) def test_limit_memory_1(self): - self.assertEqual(self.func(3), -1) + v = limit_memory(memory, args=(10,)) + self.assertEqual(v, -1) def test_limit_memory_2(self): - self.assertRaises(Exception, self.er_func) + self.assertRaises( + Exception, + limit_memory, + error, + args=(100_000_000,) + ) def test_limit_memory_3(self): - self.assertRaises(MemoryError, self.func, 100_000_000) + self.assertRaises( + MemoryError, + limit_memory, + memory, + args=(500_000_000,) + ) def test_limit_memory_4(self): - self.assertEqual(self.ka_func( - 1, 2, 3, four=4, five=5), [1, 2, 3, 4, 5]) + v = limit_memory( + return_check, + args=(1, 2, 3), + kwargs={"four": 4, "five": 5} + ) + + self.assertEqual(v, [1, 2, 3, 4, 5]) diff --git a/tests/test_time.py b/tests/test_time.py index ce5ec03..78bbd2c 100644 --- a/tests/test_time.py +++ b/tests/test_time.py @@ -1,52 +1,49 @@ from unittest import TestCase from pyutility import limit_time, timeit - -def func1(x): - # recursive function to find xth fibonacci number - if x < 3: - return 1 - return func1(x-1) + func1(x-2) - - -def func2(): - # error function - return "a" / 2 - - -def func3(args, *kwagrs): - # args and kwargs function - return list(args) + list(kwagrs.values()) +from .func import time, error, return_check class TimeitTest(TestCase): - def setUp(self): - self.er_func = timeit(func2) - self.func = timeit(func1) - self.ka_func = timeit(func3) def test_timeit1(self): - self.assertIsInstance(self.func(5), float) + v = timeit(time, args=(5,)) + self.assertIsInstance(v, float) def test_timeit2(self): - self.assertRaises(Exception, self.er_func) + self.assertRaises(Exception, timeit, error, 5) class LimitTimeTest(TestCase): - def setUp(self): - self.er_func = limit_time(2)(func2) - self.func = limit_time(2)(func1) - self.ka_func = limit_time(2)(func3) def test_limit_time_1(self): - self.assertEqual(self.func(10), 55) + v = limit_time(time, time=2, args=(10,)) + self.assertEqual(v, 55) def test_limit_time_2(self): - self.assertRaises(Exception, self.er_func) + self.assertRaises( + Exception, + limit_time, + error, + time=2, + args=(2,) + ) def test_limit_time_3(self): - self.assertRaises(TimeoutError, self.func, 50) + self.assertRaises( + TimeoutError, + limit_time, + time, + time=2, + args=(50,) + ) def test_limit_time_4(self): - self.assertEqual(self.ka_func( - 1, 2, 3, four=4, five=5), [1, 2, 3, 4, 5]) + v = limit_time( + return_check, + time=2, + args=(1, 2, 3), + kwargs={"four": 4, "five": 5} + ) + + self.assertEqual(v, [1, 2, 3, 4, 5]) diff --git a/tests/test_utility.py b/tests/test_utility.py index 603316a..266cdfa 100644 --- a/tests/test_utility.py +++ b/tests/test_utility.py @@ -1,73 +1,65 @@ from unittest import TestCase from pyutility import limit_resource, measureit - -def func1a(x): - x = [i for i in range(x)] - return -1 - - -def func1b(x): - # recursive function to find xth fibonacci number - if x < 3: - return 1 - return func1b(x-1) + func1b(x-2) - - -def func2(): - # error function - return "a" / 2 - - -def func3(args, **kwagrs): - # args and kwargs function - return list(args) + list(kwagrs.values()) +from .func import memory, time, return_check, error class MeasureitTest(TestCase): - def setUp(self): - self.er_func = measureit(func2) - self.func_m = measureit(func1a) - self.func_t = measureit(func1b) - self.ka_func = measureit(func3) def test_measureit_1(self): - self.assertIsInstance(self.func_m(100), tuple) + v = measureit(memory, args=(100,)) + self.assertIsInstance(v, tuple) def test_measureit_2(self): - x = self.func_t(10) - self.assertIsInstance(x[0], int) - self.assertIsInstance(x[1], float) + v = measureit(time, args=(15,)) + self.assertIsInstance(v[0], int) + self.assertIsInstance(v[1], float) def test_measureit_3(self): - self.assertIsInstance(self.func_t(15), tuple) + v = measureit(time, args=(15,)) + self.assertIsInstance(v, tuple) def test_measureit_4(self): - self.assertRaises(Exception, self.er_func) + self.assertRaises(Exception, measureit, error, 100) class LimitResourceTest(TestCase): - def setUp(self): - self.er_func = limit_resource(time=2)(func2) - self.func_m = limit_resource(time=2)(func1a) - self.func_t = limit_resource(time=2)(func1b) - self.ka_func = limit_resource(time=2)(func3) def test_limit_resource_1(self): - self.assertEqual(self.func_m(300), -1) + v = limit_resource(memory, time=2, args=(300,)) + self.assertEqual(v, -1) def test_limit_resource_2(self): - self.assertEqual(self.func_t(3), 2) + v = limit_resource(time, time=2, args=(3,)) + self.assertEqual(v, 2) def test_limit_resource_3(self): - self.assertRaises(Exception, self.er_func) + self.assertRaises(Exception, error) def test_limit_resource_4(self): - self.assertRaises(MemoryError, self.func_m, 100_000_000) + self.assertRaises( + MemoryError, + limit_resource, + memory, + args=(100_000_000,), + time=2 + ) def test_limit_resource_5(self): - self.assertRaises(TimeoutError, self.func_t, 50) + self.assertRaises( + TimeoutError, + limit_resource, + time, + args=(50,), + time=2 + ) def test_limit_resource_6(self): - self.assertEqual(self.ka_func( - 1, 2, 3, four=4, five=5), [1, 2, 3, 4, 5]) + v = limit_resource( + return_check, + time=2, + args=(1, 2, 3), + kwargs={"four": 4, "five": 5} + ) + + self.assertEqual(v, [1, 2, 3, 4, 5])	Multiprocessing Errors Python throws EOFError and RuntimeError, when decorator is used. Even when `__name__ == __main__` if statement is present it throws PicklingError. This is because multiprocessing is using spawn to create new processes. Some details can be found here: [StackOverFlow Question](https://stackoverflow.com/questions/41385708/multiprocessing-example-giving-attributeerror) Either using other method to create new process or changing it to function may resolve the problem.	8f66fc1fc569c34798865ab063f1da4e7753c9d5	[ "tests/test_memory.py::MemoryitTest::test_memoryit1", "tests/test_memory.py::LimitMemoryTest::test_limit_memory_1", "tests/test_memory.py::LimitMemoryTest::test_limit_memory_3", "tests/test_memory.py::LimitMemoryTest::test_limit_memory_4", "tests/test_time.py::TimeitTest::test_timeit1", "tests/test_time.py::LimitTimeTest::test_limit_time_1", "tests/test_time.py::LimitTimeTest::test_limit_time_3", "tests/test_time.py::LimitTimeTest::test_limit_time_4", "tests/test_utility.py::MeasureitTest::test_measureit_1", "tests/test_utility.py::MeasureitTest::test_measureit_2", "tests/test_utility.py::MeasureitTest::test_measureit_3", "tests/test_utility.py::LimitResourceTest::test_limit_resource_1", "tests/test_utility.py::LimitResourceTest::test_limit_resource_2", "tests/test_utility.py::LimitResourceTest::test_limit_resource_4", "tests/test_utility.py::LimitResourceTest::test_limit_resource_5", "tests/test_utility.py::LimitResourceTest::test_limit_resource_6" ]	[ "tests/test_memory.py::MemoryitTest::test_memoryit2", "tests/test_memory.py::LimitMemoryTest::test_limit_memory_2", "tests/test_time.py::TimeitTest::test_timeit2", "tests/test_time.py::LimitTimeTest::test_limit_time_2", "tests/test_utility.py::MeasureitTest::test_measureit_4", "tests/test_utility.py::LimitResourceTest::test_limit_resource_3" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2020-12-05 14:07:56+00:00	mit	824
VirtusLab__git-machete-179	diff --git a/git_machete/cmd.py b/git_machete/cmd.py index 03f722b..9772a79 100644 --- a/git_machete/cmd.py +++ b/git_machete/cmd.py @@ -89,7 +89,7 @@ class MacheteClient: def read_definition_file(self, verify_branches: bool = True) -> None: with open(self._definition_file_path) as f: - lines: List[str] = [line.rstrip() for line in f.readlines() if not line.isspace()] + lines: List[str] = [line.rstrip() for line in f.readlines()] at_depth = {} last_depth = -1 @@ -98,6 +98,8 @@ class MacheteClient: invalid_branches: List[str] = [] for index, line in enumerate(lines): + if line == "" or line.isspace(): + continue prefix = "".join(itertools.takewhile(str.isspace, line)) if prefix and not self.__indent: self.__indent = prefix @@ -1819,7 +1821,6 @@ def launch(orig_args: List[str]) -> None: cli_opts = CommandLineOptions() git = GitContext(cli_opts) - machete_client = MacheteClient(cli_opts, git) if sys.version_info.major == 2 or (sys.version_info.major == 3 and sys.version_info.minor < 6): version_str = f"{sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}" @@ -1967,6 +1968,7 @@ def launch(orig_args: List[str]) -> None: return in_args[0] try: + machete_client = MacheteClient(cli_opts, git) cmd = None # Let's first extract the common options like `--help` or `--verbose` that might appear BEFORE the command, # as in e.g. `git machete --verbose status`.	VirtusLab/git-machete	974914523542045104806e52be8135027603f771	diff --git a/git_machete/tests/functional/test_machete.py b/git_machete/tests/functional/test_machete.py index f549acf..fb587a0 100644 --- a/git_machete/tests/functional/test_machete.py +++ b/git_machete/tests/functional/test_machete.py @@ -10,8 +10,10 @@ from contextlib import redirect_stdout from typing import Iterable from git_machete import cmd +from git_machete.exceptions import MacheteException from git_machete.git_operations import GitContext from git_machete.options import CommandLineOptions +from git_machete.utils import fmt cli_opts: CommandLineOptions = CommandLineOptions() git: GitContext = GitContext(cli_opts) @@ -92,6 +94,12 @@ class MacheteTester(unittest.TestCase): git.flush_caches() return out.getvalue() + @staticmethod + def rewrite_definition_file(new_body: str) -> None: + definition_file_path = git.get_git_subpath("machete") + with open(os.path.join(os.getcwd(), definition_file_path), 'w') as def_file: + def_file.writelines(new_body) + def assert_command(self, cmds: Iterable[str], expected_result: str) -> None: self.assertEqual(self.launch_command(*cmds), self.adapt(expected_result)) @@ -175,6 +183,25 @@ class MacheteTester(unittest.TestCase): """, ) + def test_branch_reappers_in_definition(self) -> None: + body: str = \ + """master + \tdevelop + \t\n + develop + """ + expected_error_msg: str = fmt('.git/machete, line 5: branch `develop` re-appears in the tree definition. Edit the definition file manually with `git machete edit`') + + self.repo_sandbox.new_branch("root") + self.rewrite_definition_file(body) + + machete_client = cmd.MacheteClient(cli_opts, git) # Only to workaround sys.exit while calling launch(['status']) + try: + machete_client.read_definition_file() + except MacheteException as e: + if e.parameter != expected_error_msg: + self.fail(f'Actual Exception message: {e} \nis not equal to expected message: {expected_error_msg}') + def test_show(self) -> None: self.setup_discover_standard_tree()	Line numbers displayed in errors refer to non-empty lines, not all lines .git/machete file: ``` master develop develop ``` The empty lines lead to an error in `git machete status`: `.git/machete, line 3: branch develop re-appears in the tree definition. Edit the definition file manually with git machete edit` while it should say: `.git/machete, line 5: branch develop re-appears in the tree definition. Edit the definition file manually with git machete edit` This is due to how `read_definition_file` is implemented, should be pretty easy to fix.	974914523542045104806e52be8135027603f771	[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_branch_reappers_in_definition" ]	[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_few_possible_downstream_branches_and_yes_option", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_no_downstream_branches", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_one_downstream_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_discover_traverse_squash", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_with_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_without_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_help", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_first", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_next", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_prev", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_merge", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_override", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_untracked", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_not_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_specified" ]	{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-08-19 13:47:27+00:00	mit	825
VirtusLab__git-machete-330	diff --git a/git_machete/cli.py b/git_machete/cli.py index 19a6a38..8824ec9 100644 --- a/git_machete/cli.py +++ b/git_machete/cli.py @@ -358,15 +358,25 @@ def create_cli_parser() -> argparse.ArgumentParser: def update_cli_opts_using_parsed_args( cli_opts: git_machete.options.CommandLineOptions, parsed_args: argparse.Namespace) -> None: + + # Warning: In mypy, Arguments that come from untyped functions/variables are silently treated by mypy as Any. + # Since argparse is not typed, everything that comes from argparse.Namespace will be taken as Any :( + # Even if we add type=LocalBranchShortName into argument parser for branch, + # python debugger will see branch as LocalBranchShortName but mypy always will see it as Any, + # until you specifically tell mypy what is the exact type by casting (right now it's done this way below, but casting does not solve all of the problems). + # + # The reasonable solution here would be to use Typed Argument Parser which is a wrapper over argparse with modernised solution for typing. + # But it would add external dependency to git-machete, so let's stick to current casting. + for opt, arg in vars(parsed_args).items(): if opt == "branch": - cli_opts.opt_branch = arg + cli_opts.opt_branch = LocalBranchShortName.of(arg) elif opt == "checked_out_since": cli_opts.opt_checked_out_since = arg elif opt == "color": cli_opts.opt_color = arg elif opt == "down_fork_point": - cli_opts.opt_down_fork_point = arg + cli_opts.opt_down_fork_point = AnyRevision.of(arg) elif opt == "debug": cli_opts.opt_debug = True elif opt == "draft": @@ -374,7 +384,7 @@ def update_cli_opts_using_parsed_args( elif opt == "fetch": cli_opts.opt_fetch = True elif opt == "fork_point": - cli_opts.opt_fork_point = arg + cli_opts.opt_fork_point = AnyRevision.of(arg) elif opt == "inferred": cli_opts.opt_inferred = True elif opt == "list_commits_with_hashes": @@ -397,7 +407,7 @@ def update_cli_opts_using_parsed_args( elif opt == "no_push_untracked": cli_opts.opt_push_untracked = False elif opt == "onto": - cli_opts.opt_onto = arg + cli_opts.opt_onto = LocalBranchShortName.of(arg) elif opt == "override_to": cli_opts.opt_override_to = arg elif opt == "override_to_inferred": @@ -412,7 +422,7 @@ def update_cli_opts_using_parsed_args( elif opt == "as_root": cli_opts.opt_as_root = True elif opt == "roots": - cli_opts.opt_roots = arg.split(",") + cli_opts.opt_roots = list(map(LocalBranchShortName.of, arg.split(","))) elif opt == "return_to": cli_opts.opt_return_to = arg elif opt == "stat":	VirtusLab/git-machete	18f7e32640cab8483c32a231a478c23c1a50ec67	diff --git a/git_machete/tests/functional/test_machete.py b/git_machete/tests/functional/test_machete.py index e6f934d..36165d7 100644 --- a/git_machete/tests/functional/test_machete.py +++ b/git_machete/tests/functional/test_machete.py @@ -2647,3 +2647,31 @@ class MacheteTester(unittest.TestCase): roots_only_commit_hash, log_content, msg="Verify that commits from parent branch are not visible when " "executing `git machete log`.") + + @mock.patch('git_machete.utils.run_cmd', mock_run_cmd) # to hide git outputs in tests + def test_add(self) -> None: + """ + Verify behaviour of a 'git machete add' command. + """ + ( + self.repo_sandbox.new_branch("master") + .commit("master commit.") + .new_branch("develop") + .commit("develop commit.") + .new_branch("feature") + .commit("feature commit.") + .check_out("develop") + .commit("New commit on develop") + ) + self.launch_command("discover", "-y") + self.repo_sandbox.new_branch("bugfix/feature_fail") + + self.assert_command(['add', '-y', 'bugfix/feature_fail'], 'Adding `bugfix/feature_fail` onto the inferred upstream (parent) branch `develop`\n' + 'Added branch `bugfix/feature_fail` onto `develop`\n', strip_indentation=False) + + # test with --onto option + self.repo_sandbox.new_branch("chore/remove_indentation") + + self.assert_command(['add', '--onto=feature'], + 'Added branch `chore/remove_indentation` onto `feature`\n', + strip_indentation=False)	`AttributeError: 'str' object has no attribute 'full_name'` due to (?) mistyped `CommandLineOptions.opt_branch` For an already existing, but not yet managed branch `foo/bar`: ``` $ git machete add foo/bar Traceback (most recent call last): File "/usr/local/bin/git-machete", line 4, in <module> __import__('pkg_resources').run_script('git-machete==3.5.0', 'git-machete') File "/usr/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1469, in run_script exec(script_code, namespace, namespace) File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/EGG-INFO/scripts/git-machete", line 19, in <module> File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/git_machete/cli.py", line 803, in main File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/git_machete/cli.py", line 522, in launch File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/git_machete/client.py", line 263, in add File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/git_machete/client.py", line 1502, in __infer_upstream File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/git_machete/client.py", line 1479, in __match_log_to_filtered_reflogs File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/git_machete/git_operations.py", line 495, in spoonfeed_log_shas File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/git_machete/git_operations.py", line 487, in __get_log_shas AttributeError: 'str' object has no attribute 'full_name' ``` This is most likely due to assignment `cli_opts.opt_branch = arg`, with `arg` being `str`-typed (?)... not sure why it passed mypy in the first place, pls investigate. Also, regression test + preferable a systematic solution against this kind of errors would be very useful.	18f7e32640cab8483c32a231a478c23c1a50ec67	[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_add" ]	[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_few_possible_downstream_branches_and_yes_option", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_no_downstream_branches", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_one_downstream_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_anno_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_branch_reappers_in_definition", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_freshly_cloned", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_from_fork_with_deleted_repo", "git_machete/tests/functional/test_machete.py::MacheteTester::test_discover_traverse_squash", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_with_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_without_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_help", "git_machete/tests/functional/test_machete.py::MacheteTester::test_log", "git_machete/tests/functional/test_machete.py::MacheteTester::test_retarget_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_first", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_next", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_prev", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_down_fork_point_and_multiple_children_of_last_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_invalid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_valid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_merge", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_invalid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_valid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_override", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_untracked", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_not_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_invalid_fork_point" ]	{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-11-03 12:50:09+00:00	mit	826
VirtusLab__git-machete-348	diff --git a/git_machete/client.py b/git_machete/client.py index 556fa3d..d1d9146 100644 --- a/git_machete/client.py +++ b/git_machete/client.py @@ -1631,6 +1631,7 @@ class MacheteClient: *, branch: LocalBranchShortName, is_called_from_traverse: bool, + is_called_from_create_pr: bool, opt_push_untracked: bool, opt_push_tracked: bool, opt_yes: bool @@ -1654,6 +1655,7 @@ class MacheteClient: new_remote=rems[index], branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=is_called_from_create_pr, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes) @@ -1667,12 +1669,13 @@ class MacheteClient: new_remote: str, branch: LocalBranchShortName, is_called_from_traverse: bool, + is_called_from_create_pr: bool, opt_push_untracked: bool, opt_push_tracked: bool, opt_yes: bool ) -> None: rems: List[str] = self.__git.get_remotes() - can_pick_other_remote = len(rems) > 1 + can_pick_other_remote = len(rems) > 1 and not is_called_from_create_pr other_remote_choice = "o[ther-remote]" if can_pick_other_remote else "" remote_branch = RemoteBranchShortName.of(f"{new_remote}/{branch}") if not self.__git.get_commit_sha_by_revision(remote_branch): @@ -1694,6 +1697,7 @@ class MacheteClient: self.__pick_remote( branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=is_called_from_create_pr, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes) @@ -1708,6 +1712,7 @@ class MacheteClient: self.__pick_remote( branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=is_called_from_create_pr, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes) @@ -1783,6 +1788,7 @@ class MacheteClient: self.__pick_remote( branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=is_called_from_create_pr, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes) @@ -1994,9 +2000,24 @@ class MacheteClient: self.flush_caches() base: Optional[LocalBranchShortName] = self.up_branch.get(LocalBranchShortName.of(head)) + if not base: + raise MacheteException(f'Could not determine base branch for PR. Branch `{head}` is a root branch.') org: str repo: str - _, (org, repo) = self.__derive_remote_and_github_org_and_repo() + remote, (org, repo) = self.__derive_remote_and_github_org_and_repo() + print(f"Fetching {remote}...") + self.__git.fetch_remote(remote) + if '/'.join([remote, base]) not in self.__git.get_remote_branches(): + warn(f'Base branch for this PR (`{base}`) is not found on remote, pushing...') + self.handle_untracked_branch( + branch=base, + new_remote=remote, + is_called_from_traverse=False, + is_called_from_create_pr=True, + opt_push_tracked=False, + opt_push_untracked=True, + opt_yes=False) + current_user: Optional[str] = git_machete.github.derive_current_user_login() debug(f'create_github_pr({head})', f'organization is {org}, repository is {repo}') debug(f'create_github_pr({head})', 'current GitHub user is ' + (current_user or '<none>')) @@ -2079,13 +2100,16 @@ class MacheteClient: new_remote=rmt, branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=False, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes) elif len(rems) == 1: self.handle_untracked_branch( - new_remote=rems[0], branch=branch, + new_remote=rems[0], + branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=False, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes) @@ -2094,6 +2118,7 @@ class MacheteClient: new_remote="origin", branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=False, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes) @@ -2103,6 +2128,7 @@ class MacheteClient: self.__pick_remote( branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=False, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes)	VirtusLab/git-machete	931fd2c58aaebdc325e1fd2c9ceacecee80f72e7	diff --git a/git_machete/tests/functional/test_machete.py b/git_machete/tests/functional/test_machete.py index 36165d7..55749e7 100644 --- a/git_machete/tests/functional/test_machete.py +++ b/git_machete/tests/functional/test_machete.py @@ -1927,6 +1927,8 @@ class MacheteTester(unittest.TestCase): git_api_state_for_test_create_pr = MockGithubAPIState([{'head': {'ref': 'ignore-trailing', 'repo': mock_repository_info}, 'user': {'login': 'github_user'}, 'base': {'ref': 'hotfix/add-trigger'}, 'number': '3', 'html_url': 'www.github.com', 'state': 'open'}], issues=[{'number': '4'}, {'number': '5'}, {'number': '6'}]) + # We need to mock GITHUB_REMOTE_PATTERNS in the tests for `test_github_create_pr` due to `git fetch` executed by `create-pr` subcommand. + @mock.patch('git_machete.github.GITHUB_REMOTE_PATTERNS', FAKE_GITHUB_REMOTE_PATTERNS) @mock.patch('git_machete.utils.run_cmd', mock_run_cmd) # to hide git outputs in tests @mock.patch('git_machete.options.CommandLineOptions', FakeCommandLineOptions) @mock.patch('git_machete.client.MacheteClient.ask_if', mock_ask_if) @@ -2093,6 +2095,47 @@ class MacheteTester(unittest.TestCase): self.assertEqual(e.exception.parameter, expected_error_message, 'Verify that expected error message has appeared when creating PR from root branch.') + git_api_state_for_test_create_pr_missing_base_branch_on_remote = MockGithubAPIState([{'head': {'ref': 'chore/redundant_checks', 'repo': mock_repository_info}, 'user': {'login': 'github_user'}, 'base': {'ref': 'restrict_access'}, 'number': '18', 'html_url': 'www.github.com', 'state': 'open'}]) + + # We need to mock GITHUB_REMOTE_PATTERNS in the tests for `test_github_create_pr` due to `git fetch` executed by `create-pr` subcommand. + @mock.patch('git_machete.github.GITHUB_REMOTE_PATTERNS', FAKE_GITHUB_REMOTE_PATTERNS) + @mock.patch('git_machete.utils.run_cmd', mock_run_cmd) # to hide git outputs in tests + @mock.patch('git_machete.options.CommandLineOptions', FakeCommandLineOptions) + @mock.patch('git_machete.client.MacheteClient.ask_if', mock_ask_if) + @mock.patch('urllib.request.urlopen', MockContextManager) + @mock.patch('urllib.request.Request', git_api_state_for_test_create_pr_missing_base_branch_on_remote.new_request()) + def test_github_create_pr_missing_base_branch_on_remote(self) -> None: + ( + self.repo_sandbox.new_branch("root") + .commit("initial commit") + .new_branch("develop") + .commit("first commit on develop") + .push() + .new_branch("feature/api_handling") + .commit("Introduce GET and POST methods on API") + .new_branch("feature/api_exception_handling") + .commit("catch exceptions coming from API") + .push() + .delete_branch("root") + ) + + self.launch_command('discover') + + expected_msg = ("Fetching origin...\n" + "Warn: Base branch for this PR (`feature/api_handling`) is not found on remote, pushing...\n" + "Creating a PR from `feature/api_exception_handling` to `feature/api_handling`... OK, see www.github.com\n") + self.assert_command(['github', 'create-pr'], expected_msg, strip_indentation=False) + self.assert_command( + ['status'], + """ + develop + \| + o-feature/api_handling + \| + o-feature/api_exception_handling * PR #19 + """, + ) + git_api_state_for_test_checkout_prs = MockGithubAPIState([ {'head': {'ref': 'chore/redundant_checks', 'repo': mock_repository_info}, 'user': {'login': 'github_user'}, 'base': {'ref': 'restrict_access'}, 'number': '18', 'html_url': 'www.github.com', 'state': 'open'}, {'head': {'ref': 'restrict_access', 'repo': mock_repository_info}, 'user': {'login': 'github_user'}, 'base': {'ref': 'allow-ownership-link'}, 'number': '17', 'html_url': 'www.github.com', 'state': 'open'},	`github create-pr`: check if base branch for PR exists in remote Attempt to create a pull request with base branch being already deleted from remote ends up with `Unprocessable Entity` error. (example in #332). Proposed solution: Perform `git fetch <remote>` at the beginning of `create-pr`. if base branch is not present in remote branches, perform `handle_untracked_branch` with relevant remote for missing base branch.	931fd2c58aaebdc325e1fd2c9ceacecee80f72e7	[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr_missing_base_branch_on_remote" ]	[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_add", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_few_possible_downstream_branches_and_yes_option", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_no_downstream_branches", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_one_downstream_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_anno_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_branch_reappers_in_definition", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_freshly_cloned", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_from_fork_with_deleted_repo", "git_machete/tests/functional/test_machete.py::MacheteTester::test_discover_traverse_squash", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_with_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_without_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_help", "git_machete/tests/functional/test_machete.py::MacheteTester::test_log", "git_machete/tests/functional/test_machete.py::MacheteTester::test_retarget_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_first", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_next", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_prev", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_down_fork_point_and_multiple_children_of_last_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_invalid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_valid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_merge", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_invalid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_valid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_override", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_untracked", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_not_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_invalid_fork_point" ]	{ "failed_lite_validators": [ "has_issue_reference", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-11-16 14:09:49+00:00	mit	827
VirtusLab__git-machete-350	diff --git a/git_machete/exceptions.py b/git_machete/exceptions.py index a1f9893..ae09ea3 100644 --- a/git_machete/exceptions.py +++ b/git_machete/exceptions.py @@ -21,7 +21,7 @@ class UnprocessableEntityHTTPError(MacheteException): or creating a pull request for a branch that already has a PR. """ def __init__(self, msg: str) -> None: - self.msg: str = 'UnprocessableEntityHTTPError: ' + msg + self.msg: str = msg def __str__(self) -> str: return str(self.msg) diff --git a/git_machete/github.py b/git_machete/github.py index 031bcb5..8b246d4 100644 --- a/git_machete/github.py +++ b/git_machete/github.py @@ -9,9 +9,9 @@ import subprocess from pathlib import Path from typing import Any, Dict, List, Optional, Tuple import urllib.request -from urllib.error import HTTPError +import urllib.error -from git_machete.utils import debug, fmt, find_or_none +from git_machete.utils import debug, fmt from git_machete.exceptions import MacheteException, UnprocessableEntityHTTPError from git_machete.git_operations import GitContext, LocalBranchShortName @@ -158,7 +158,7 @@ def __fire_github_api_request(method: str, path: str, token: Optional[str], requ with urllib.request.urlopen(http_request) as response: parsed_response_body: Any = json.loads(response.read().decode()) return parsed_response_body - except HTTPError as err: + except urllib.error.HTTPError as err: if err.code == http.HTTPStatus.UNPROCESSABLE_ENTITY: error_response = json.loads(err.read().decode()) error_reason: str = __extract_failure_info_from_422(error_response) @@ -193,13 +193,8 @@ def create_pull_request(org: str, repo: str, head: str, base: str, title: str, d 'body': description, 'draft': draft } - prs: List[GitHubPullRequest] = derive_pull_requests(org, repo) - pr_found: Optional[GitHubPullRequest] = find_or_none(lambda pr: pr.base == base and pr.head == head, prs) - if not pr_found: - pr = __fire_github_api_request('POST', f'/repos/{org}/{repo}/pulls', token, request_body) - return __parse_pr_json(pr) - else: - raise MacheteException(f'Pull request for branch {head} is already created under link {pr_found.html_url}!\nPR details: {pr_found}') + pr = __fire_github_api_request('POST', f'/repos/{org}/{repo}/pulls', token, request_body) + return __parse_pr_json(pr) def add_assignees_to_pull_request(org: str, repo: str, number: int, assignees: List[str]) -> None:	VirtusLab/git-machete	5c5bef4a52ef72bdb4bc095210d15acdc1826ffd	diff --git a/git_machete/tests/functional/test_machete.py b/git_machete/tests/functional/test_machete.py index 55749e7..24e5542 100644 --- a/git_machete/tests/functional/test_machete.py +++ b/git_machete/tests/functional/test_machete.py @@ -174,6 +174,9 @@ class MockGithubAPIRequest: def update_pull_request(self) -> "MockGithubAPIResponse": pull_no: str = self.find_number(self.parsed_url.path, 'pulls') if not pull_no: + if self.is_pull_created(): + return self.make_response_object(HTTPStatus.UNPROCESSABLE_ENTITY, {'message': 'Validation Failed', 'errors': [ + {'message': f'A pull request already exists for test_repo:{json.loads(self.json_data)["head"]}.'}]}) return self.create_pull_request() pull: Dict[str, Any] = self.github_api_state.get_pull(pull_no) return self.fill_pull_request_data(json.loads(self.json_data), pull) @@ -221,6 +224,17 @@ class MockGithubAPIRequest: self.github_api_state.issues.append(issue) return self.make_response_object(HTTPStatus.CREATED, issue) + def is_pull_created(self) -> bool: + deserialized_json_data = json.loads(self.json_data) + head: str = deserialized_json_data['head'] + base: str = deserialized_json_data['base'] + for pull in self.github_api_state.pulls: + pull_head: str = pull['head']['ref'] + pull_base: str = pull['base']['ref'] + if (head, base) == (pull_head, pull_base): + return True + return False + @staticmethod def get_index_or_none(entity: Dict[str, Any], base: List[Dict[str, Any]]) -> Optional[int]: try: @@ -245,6 +259,15 @@ class MockGithubAPIRequest: return str(max(numbers) + 1) +class MockHTTPError(HTTPError): + def __init__(self, url: str, code: int, msg: Any, hdrs: Dict[str, str], fp: Any) -> None: + super().__init__(url, code, msg, hdrs, fp) + self.msg = msg + + def read(self, n: int = 1) -> bytes: + return json.dumps(self.msg).encode() + + class MockContextManager: def __init__(self, obj: MockGithubAPIResponse) -> None: self.obj = obj @@ -252,6 +275,8 @@ class MockContextManager: def __enter__(self) -> MockGithubAPIResponse: if self.obj.status_code == HTTPStatus.NOT_FOUND: raise HTTPError(None, 404, 'Not found', None, None) + elif self.obj.status_code == HTTPStatus.UNPROCESSABLE_ENTITY: + raise MockHTTPError(None, 422, self.obj.response_data, None, None) return self.obj def __exit__(self, *args: Any) -> None: @@ -1927,6 +1952,7 @@ class MacheteTester(unittest.TestCase): git_api_state_for_test_create_pr = MockGithubAPIState([{'head': {'ref': 'ignore-trailing', 'repo': mock_repository_info}, 'user': {'login': 'github_user'}, 'base': {'ref': 'hotfix/add-trigger'}, 'number': '3', 'html_url': 'www.github.com', 'state': 'open'}], issues=[{'number': '4'}, {'number': '5'}, {'number': '6'}]) + @mock.patch('urllib.error.HTTPError', MockHTTPError) # need to provide read() method, which does not actually reads error from url # We need to mock GITHUB_REMOTE_PATTERNS in the tests for `test_github_create_pr` due to `git fetch` executed by `create-pr` subcommand. @mock.patch('git_machete.github.GITHUB_REMOTE_PATTERNS', FAKE_GITHUB_REMOTE_PATTERNS) @mock.patch('git_machete.utils.run_cmd', mock_run_cmd) # to hide git outputs in tests @@ -2062,12 +2088,12 @@ class MacheteTester(unittest.TestCase): ) # check against attempt to create already existing pull request machete_client = MacheteClient(git) - expected_error_message = "Pull request for branch hotfix/add-trigger is already created under link www.github.com!\nPR details: PR #6 by github_user: hotfix/add-trigger -> master" + expected_error_message = "A pull request already exists for test_repo:hotfix/add-trigger." machete_client.read_definition_file() with self.assertRaises(MacheteException) as e: machete_client.create_github_pr(head=LocalBranchShortName.of('hotfix/add-trigger'), opt_draft=False, opt_onto=None) if e: - self.assertEqual(e.exception.parameter, expected_error_message, + self.assertEqual(e.exception.msg, expected_error_message, # type: ignore 'Verify that expected error message has appeared when given pull request to create is already created.') # check against head branch is ancestor or equal to base branch	Is the check for PR existence still needed now that we read the body of 422 response? `git_machete.github.create_pull_request`: ``` prs: List[GitHubPullRequest] = derive_pull_requests(org, repo) pr_found: Optional[GitHubPullRequest] = find_or_none(lambda pr: pr.base == base and pr.head == head, prs) if not pr_found: pr = __fire_github_api_request('POST', f'/repos/{org}/{repo}/pulls', token, request_body) return __parse_pr_json(pr) else: raise MacheteException(f'Pull request for branch {head} is already created under link {pr_found.html_url}!\nPR details: {pr_found}') ``` Maybe we can skip one request to the API (`derive_pull_requests`) and rely on our new handling for 422 now?	5c5bef4a52ef72bdb4bc095210d15acdc1826ffd	[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr" ]	[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_add", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_few_possible_downstream_branches_and_yes_option", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_no_downstream_branches", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_one_downstream_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_anno_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_branch_reappers_in_definition", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_freshly_cloned", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_from_fork_with_deleted_repo", "git_machete/tests/functional/test_machete.py::MacheteTester::test_discover_traverse_squash", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr_missing_base_branch_on_remote", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_with_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_without_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_help", "git_machete/tests/functional/test_machete.py::MacheteTester::test_log", "git_machete/tests/functional/test_machete.py::MacheteTester::test_retarget_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_first", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_next", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_prev", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_down_fork_point_and_multiple_children_of_last_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_invalid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_valid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_merge", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_invalid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_valid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_override", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_untracked", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_not_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_invalid_fork_point" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2021-11-18 14:42:19+00:00	mit	828
VirtusLab__git-machete-353	diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index 4cb7056..395fed7 100644 --- a/RELEASE_NOTES.md +++ b/RELEASE_NOTES.md @@ -1,5 +1,9 @@ # Release notes +## New in git-machete 3.6.0 + +- added: `t` alias for `traverse` command + ## New in git-machete 3.5.0 - added: new way of acquiring the github token (from `~/.github-token`) diff --git a/docs/source/cli_help/traverse.rst b/docs/source/cli_help/traverse.rst index 8b23310..d74e384 100644 --- a/docs/source/cli_help/traverse.rst +++ b/docs/source/cli_help/traverse.rst @@ -13,10 +13,10 @@ traverse .. code-block:: shell - git machete traverse [-F\|--fetch] [-l\|--list-commits] [-M\|--merge] - [-n\|--no-edit-merge\|--no-interactive-rebase] [--no-detect-squash-merges] - [--[no-]push] [--[no-]push-untracked] - [--return-to=WHERE] [--start-from=WHERE] [-w\|--whole] [-W] [-y\|--yes] + git machete t[raverse] [-F\|--fetch] [-l\|--list-commits] [-M\|--merge] + [-n\|--no-edit-merge\|--no-interactive-rebase] [--no-detect-squash-merges] + [--[no-]push] [--[no-]push-untracked] + [--return-to=WHERE] [--start-from=WHERE] [-w\|--whole] [-W] [-y\|--yes] Traverses the branch dependency tree in pre-order (i.e. simply in the order as they occur in the definition file). By default traverse starts from current branch, however this behaviour can be customized using options: ``--start-from=``, ``--whole`` or ``-w``, ``-W``. diff --git a/git_machete/__init__.py b/git_machete/__init__.py index bf5afe7..826cf62 100644 --- a/git_machete/__init__.py +++ b/git_machete/__init__.py @@ -1,1 +1,1 @@ -__version__ = '3.5.1' +__version__ = '3.6.0' diff --git a/git_machete/cli.py b/git_machete/cli.py index 0a4398c..34d369c 100644 --- a/git_machete/cli.py +++ b/git_machete/cli.py @@ -26,7 +26,8 @@ alias_by_command: Dict[str, str] = { "edit": "e", "go": "g", "log": "l", - "status": "s" + "status": "s", + "traverse": "t" } command_groups: List[Tuple[str, List[str]]] = [ @@ -316,6 +317,7 @@ def create_cli_parser() -> argparse.ArgumentParser: traverse_parser = subparsers.add_parser( 'traverse', + aliases=['t'], argument_default=argparse.SUPPRESS, usage=argparse.SUPPRESS, add_help=False, @@ -748,7 +750,7 @@ def launch(orig_args: List[str]) -> None: opt_list_commits=cli_opts.opt_list_commits, opt_list_commits_with_hashes=cli_opts.opt_list_commits_with_hashes, opt_no_detect_squash_merges=cli_opts.opt_no_detect_squash_merges) - elif cmd == "traverse": + elif cmd in {"traverse", alias_by_command["traverse"]}: if cli_opts.opt_start_from not in {"here", "root", "first-root"}: raise MacheteException( "Invalid argument for `--start-from`. " diff --git a/git_machete/docs.py b/git_machete/docs.py index 513561d..803bb3d 100644 --- a/git_machete/docs.py +++ b/git_machete/docs.py @@ -606,10 +606,10 @@ long_docs: Dict[str, str] = { when detecting if a branch is merged into its upstream (parent). """, "traverse": """ - <b>Usage: git machete traverse [-F\|--fetch] [-l\|--list-commits] [-M\|--merge] - [-n\|--no-edit-merge\|--no-interactive-rebase] [--no-detect-squash-merges] - [--[no-]push] [--[no-]push-untracked] - [--return-to=WHERE] [--start-from=WHERE] [-w\|--whole] [-W] [-y\|--yes]</b> + <b>Usage: git machete t[raverse] [-F\|--fetch] [-l\|--list-commits] [-M\|--merge] + [-n\|--no-edit-merge\|--no-interactive-rebase] [--no-detect-squash-merges] + [--[no-]push] [--[no-]push-untracked] + [--return-to=WHERE] [--start-from=WHERE] [-w\|--whole] [-W] [-y\|--yes]</b> Traverses the branch dependency tree in pre-order (i.e. simply in the order as they occur in the definition file). By default traverse starts from current branch, however this behaviour can be customized using options: `--starts-from=`, `--whole` or `-w`, `-W`.	VirtusLab/git-machete	b5ce4b7f67ea347ff0e1357a61d5412027218a87	diff --git a/git_machete/tests/functional/test_machete.py b/git_machete/tests/functional/test_machete.py index 24e5542..53cef1e 100644 --- a/git_machete/tests/functional/test_machete.py +++ b/git_machete/tests/functional/test_machete.py @@ -538,8 +538,39 @@ class MacheteTester(unittest.TestCase): @mock.patch('git_machete.utils.run_cmd', mock_run_cmd) # to hide git outputs in tests def test_traverse_no_push_override(self) -> None: self.setup_discover_standard_tree() + self.repo_sandbox.check_out("hotfix/add-trigger") + self.launch_command("t", "-Wy", "--no-push", "--push", "--start-from=here") + self.assert_command( + ["status", "-l"], + """ + develop + \| + \| Allow ownership links + \| 1st round of fixes + x-allow-ownership-link (ahead of origin) + \| \| + \| \| Build arbitrarily long chains + \| x-build-chain (untracked) + \| + \| Call web service + \| 1st round of fixes + \| 2nd round of fixes + o-call-ws (ahead of origin) + \| + \| Drop unneeded SQL constraints + x-drop-constraint (untracked) - self.launch_command("traverse", "-Wy", "--no-push", "--push") + master + \| + \| HOTFIX Add the trigger (amended) + o-hotfix/add-trigger * + \| + \| Ignore trailing data (amended) + o-ignore-trailing + """, + ) + self.repo_sandbox.check_out("ignore-trailing") + self.launch_command("t", "-Wy", "--no-push", "--push") self.assert_command( ["status", "-l"], """	Add `t` as an alias for `traverse` (just as `s` is for `status`)	b5ce4b7f67ea347ff0e1357a61d5412027218a87	[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_override" ]	[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_add", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_few_possible_downstream_branches_and_yes_option", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_no_downstream_branches", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_one_downstream_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_anno_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_branch_reappers_in_definition", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_freshly_cloned", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_from_fork_with_deleted_repo", "git_machete/tests/functional/test_machete.py::MacheteTester::test_discover_traverse_squash", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr_missing_base_branch_on_remote", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_with_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_without_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_help", "git_machete/tests/functional/test_machete.py::MacheteTester::test_log", "git_machete/tests/functional/test_machete.py::MacheteTester::test_retarget_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_first", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_next", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_prev", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_down_fork_point_and_multiple_children_of_last_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_invalid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_valid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_merge", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_invalid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_valid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_untracked", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_not_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_invalid_fork_point" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-11-22 09:53:54+00:00	mit	829
VirtusLab__git-machete-463	diff --git a/git_machete/client.py b/git_machete/client.py index b8a55b1..0e44ae6 100644 --- a/git_machete/client.py +++ b/git_machete/client.py @@ -1947,28 +1947,27 @@ class MacheteClient: if pr_from_github: result.append(pr_from_github) else: - if len(prs_list) > 1: - warn(f"PR #{pr_no} is not found in repository `{org}/{repo}`, skipping.") - else: - raise MacheteException(f"PR #{pr_no} is not found in repository `{org}/{repo}`") + raise MacheteException(f"PR #{pr_no} is not found in repository `{org}/{repo}`") if not result: raise MacheteException( f"Given PRs: {', '.join(map(str, prs_list))} are not found in repository `{org}/{repo}`") return result if all: if not all_opened_prs_from_github: - raise MacheteException(f"Currently there is not any pull request opened in repository `{org}/{repo}`") + warn(f"Currently there are no pull requests opened in repository `{org}/{repo}`") + return [] return all_opened_prs_from_github elif my and user: result = [pr for pr in all_opened_prs_from_github if pr.user == user] if not result: - raise MacheteException( - f"Current user {user} has no open pull request in repository `{org}/{repo}`") + warn(f"Current user `{user}` has no open pull request in repository `{org}/{repo}`") + return [] return result elif by: result = [pr for pr in all_opened_prs_from_github if pr.user == by] if not result: - raise MacheteException(f"User {by} has no open pull request in repository `{org}/{repo}`") + warn(f"User `{by}` has no open pull request in repository `{org}/{repo}`") + return [] return result return []	VirtusLab/git-machete	d5093f1a6f16a6f834fe71ddae9e4e63a2b18a03	diff --git a/git_machete/tests/functional/test_machete.py b/git_machete/tests/functional/test_machete.py index fc4d788..7718ce8 100644 --- a/git_machete/tests/functional/test_machete.py +++ b/git_machete/tests/functional/test_machete.py @@ -2220,6 +2220,7 @@ class MacheteTester(unittest.TestCase): @mock.patch('git_machete.github.GITHUB_REMOTE_PATTERNS', FAKE_GITHUB_REMOTE_PATTERNS) @mock.patch('git_machete.options.CommandLineOptions', FakeCommandLineOptions) @mock.patch('git_machete.utils.run_cmd', mock_run_cmd) # to hide git outputs in tests + @mock.patch('git_machete.github.__get_github_token', mock__get_github_token) @mock.patch('urllib.request.Request', git_api_state_for_test_checkout_prs.new_request()) @mock.patch('urllib.request.urlopen', MockContextManager) def test_github_checkout_prs(self) -> None: @@ -2416,6 +2417,16 @@ class MacheteTester(unittest.TestCase): self.assertEqual(e.exception.parameter, expected_error_message, 'Verify that expected error message has appeared when given pull request to checkout does not exists.') + with self.assertRaises(MacheteException) as e: + self.launch_command('github', 'checkout-prs', '19', '100') + if e: + self.assertEqual(e.exception.parameter, expected_error_message, + 'Verify that expected error message has appeared when one of the given pull requests to checkout does not exists.') + + # check against user with no open pull requests + expected_msg = f"Warn: User `tester` has no open pull request in repository `{org}/{repo}`\n" + self.assert_command(['github', 'checkout-prs', '--by', 'tester'], expected_msg, strip_indentation=False) + # Check against closed pull request with head branch deleted from remote local_path = popen("mktemp -d") self.repo_sandbox.new_repo(GitRepositorySandbox.second_remote_path)	`checkout_github_prs()` should NOT fail if no PRs for the given criteria are found	d5093f1a6f16a6f834fe71ddae9e4e63a2b18a03	[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_checkout_prs" ]	[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_add", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_few_possible_downstream_branches_and_yes_option", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_no_downstream_branches", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_one_downstream_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_anno_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_branch_reappears_in_definition", "git_machete/tests/functional/test_machete.py::MacheteTester::test_discover_traverse_squash", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_checkout_prs_freshly_cloned", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_checkout_prs_from_fork_with_deleted_repo", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr_missing_base_branch_on_remote", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_with_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_without_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_help", "git_machete/tests/functional/test_machete.py::MacheteTester::test_log", "git_machete/tests/functional/test_machete.py::MacheteTester::test_retarget_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_first", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_next", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_prev", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_down_fork_point_and_multiple_children_of_last_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_invalid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_valid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_merge", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_invalid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_valid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_override", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_untracked", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_not_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_invalid_fork_point" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2022-03-08 10:15:24+00:00	mit	830
VirtusLab__git-machete-483	diff --git a/docs/source/cli_help/github.rst b/docs/source/cli_help/github.rst index 0bfdb25..a5cef47 100644 --- a/docs/source/cli_help/github.rst +++ b/docs/source/cli_help/github.rst @@ -25,7 +25,7 @@ Creates, checks out and manages GitHub PRs while keeping them reflected in branc Check out the head branch of the given pull requests (specified by number), also traverse chain of pull requests upwards, adding branches one by one to git-machete and check them out locally. Once the specified pull requests are checked out locally, annotate local branches with corresponding pull request numbers. - If only one PR is given, then switch the local repository's HEAD to its head branch. + If only one PR has been checked out, then switch the local repository's HEAD to its head branch. Options: diff --git a/git_machete/cli.py b/git_machete/cli.py index d90f1a2..ec291d9 100644 --- a/git_machete/cli.py +++ b/git_machete/cli.py @@ -546,7 +546,9 @@ def launch(orig_args: List[str]) -> None: branch=branch, opt_onto=cli_opts.opt_onto, opt_as_root=cli_opts.opt_as_root, - opt_yes=cli_opts.opt_yes) + opt_yes=cli_opts.opt_yes, + verbose=True, + switch_head_if_new_branch=True) elif cmd == "advance": machete_client.read_definition_file(perform_interactive_slide_out=should_perform_interactive_slide_out) git.expect_no_operation_in_progress() diff --git a/git_machete/client.py b/git_machete/client.py index 7871c51..1a42aa7 100644 --- a/git_machete/client.py +++ b/git_machete/client.py @@ -219,7 +219,8 @@ class MacheteClient: opt_onto: Optional[LocalBranchShortName], opt_as_root: bool, opt_yes: bool, - verbose: bool = True + verbose: bool, + switch_head_if_new_branch: bool ) -> None: if branch in self.managed_branches: raise MacheteException( @@ -237,7 +238,7 @@ class MacheteClient: msg = common_line + f"Check out `{branch}` locally?" + get_pretty_choices('y', 'N') opt_yes_msg = common_line + f"Checking out `{branch}` locally..." if self.ask_if(msg, opt_yes_msg, opt_yes=opt_yes, verbose=verbose) in ('y', 'yes'): - self.__git.create_branch(branch, remote_branch.full_name()) + self.__git.create_branch(branch, remote_branch.full_name(), switch_head=switch_head_if_new_branch) else: return # Not dealing with `onto` here. If it hasn't been explicitly @@ -256,7 +257,7 @@ class MacheteClient: current_branch = self.__git.get_current_branch_or_none() if current_branch and current_branch in self.managed_branches: opt_onto = current_branch - self.__git.create_branch(branch, out_of) + self.__git.create_branch(branch, out_of, switch_head=switch_head_if_new_branch) else: return @@ -1913,21 +1914,23 @@ class MacheteClient: opt_as_root=True, opt_onto=None, opt_yes=True, - verbose=verbose) + verbose=verbose, + switch_head_if_new_branch=False) else: self.add( branch=branch, opt_onto=reversed_path[index - 1], opt_as_root=False, opt_yes=True, - verbose=verbose) + verbose=verbose, + switch_head_if_new_branch=False) if pr not in checked_out_prs: print(fmt(f"Pull request `#{pr.number}` checked out at local branch `{pr.head}`")) checked_out_prs.append(pr) debug('Current GitHub user is ' + (current_user or '<none>')) self.__sync_annotations_to_definition_file(all_open_prs, current_user, verbose=verbose) - if pr and len(applicable_prs) == 1 and len(checked_out_prs) == 1: + if pr and len(checked_out_prs) == 1: self.__git.checkout(LocalBranchShortName.of(pr.head)) if verbose: print(fmt(f"Switched to local branch `{pr.head}`")) @@ -2266,7 +2269,12 @@ class MacheteClient: current_branch = self.__git.get_current_branch() if current_branch not in self.managed_branches: - self.add(branch=current_branch, opt_onto=opt_onto, opt_as_root=False, opt_yes=opt_yes) + self.add(branch=current_branch, + opt_onto=opt_onto, + opt_as_root=False, + opt_yes=opt_yes, + verbose=True, + switch_head_if_new_branch=True) if current_branch not in self.managed_branches: raise MacheteException( "Command `github create-pr` can NOT be executed on the branch" diff --git a/git_machete/docs.py b/git_machete/docs.py index f6ad05e..b697234 100644 --- a/git_machete/docs.py +++ b/git_machete/docs.py @@ -351,7 +351,7 @@ long_docs: Dict[str, str] = { Check out the head branch of the given pull requests (specified by number), also traverse chain of pull requests upwards, adding branches one by one to git-machete and check them out locally. Once the specified pull requests are checked out locally, annotate local branches with corresponding pull request numbers. - If only one PR is given, then switch the local repository's HEAD to its head branch. + If only one PR has been checked out, then switch the local repository's HEAD to its head branch. <b>Options:</b> <b>--all</b> Checkout all open PRs. diff --git a/git_machete/git_operations.py b/git_machete/git_operations.py index d83eaed..ca3a753 100644 --- a/git_machete/git_operations.py +++ b/git_machete/git_operations.py @@ -580,8 +580,10 @@ class GitContext: )) return self.__reflogs_cached[branch] - def create_branch(self, branch: LocalBranchShortName, out_of_revision: AnyRevision) -> None: - self._run_git("checkout", "-b", branch, out_of_revision) + def create_branch(self, branch: LocalBranchShortName, out_of_revision: AnyRevision, switch_head: bool) -> None: + self._run_git("branch", branch, out_of_revision) + if switch_head: + self._run_git("checkout", branch) self.flush_caches() # the repository state has changed because of a successful branch creation, let's defensively flush all the caches def flush_caches(self) -> None:	VirtusLab/git-machete	5a2b68e1a7a7fff7e226f2e6ff96f7936bf98439	diff --git a/git_machete/tests/functional/test_machete.py b/git_machete/tests/functional/test_machete.py index b76db02..38a3d45 100644 --- a/git_machete/tests/functional/test_machete.py +++ b/git_machete/tests/functional/test_machete.py @@ -50,8 +50,7 @@ def mock_exit_script(status_code: Optional[int] = None, error: Optional[BaseExce def mock_fetch_ref(cls: Any, remote: str, ref: str) -> None: branch: LocalBranchShortName = LocalBranchShortName.of(ref[ref.index(':') + 1:]) - git.create_branch(branch, get_current_commit_hash()) - git.checkout(branch) + git.create_branch(branch, get_current_commit_hash(), switch_head=True) def mock_run_cmd(cmd: str, args: str, kwargs: Any) -> int: @@ -2404,13 +2403,13 @@ class MacheteTester(unittest.TestCase): \| \| \| o-chore/redundant_checks PR #18 (github_user) \| - o-enhance/add_user PR #19 (github_user) + o-enhance/add_user PR #19 (github_user) bugfix/add_user \| o-testing/add_user PR #22 (github_user) \| - o-chore/comments PR #24 (github_user) + o-chore/comments * PR #24 (github_user) """ )	`github checkout-prs --by=...` switches to ALL checked out branches one by one Installed version from PR #435 (commit `6ee6681e33cf037e8c86b1cf340a443b4d77fcee`). Testing on this very repo: ``` ➜ 12:29 ~/git-machete develop $ g m s master v3.7.2 │ └─develop v3.8.0 ➜ 12:29 ~/git-machete develop $ gb * develop master ➜ 12:30 ~/git-machete develop $ g m github checkout-prs --by=amalota Checking for open GitHub PRs... branch 'feature/command_clean' set up to track 'origin/feature/command_clean'. Switched to a new branch 'feature/command_clean' Pull request #435 checked out at local branch feature/command_clean branch 'code_quality/github_token_msg' set up to track 'origin/code_quality/github_token_msg'. Switched to a new branch 'code_quality/github_token_msg' Pull request #469 checked out at local branch code_quality/github_token_msg branch 'feature/advance_with_push_to_remote' set up to track 'origin/feature/advance_with_push_to_remote'. Switched to a new branch 'feature/advance_with_push_to_remote' Pull request #473 checked out at local branch feature/advance_with_push_to_remote ➜ 12:30 ~/git-machete feature/advance_with_push_to_remote PR #473 (amalota) $ ``` So... first HEAD hsa been switched to `feature/command_clean`, then to `code_quality/github_token_msg`, finally to `feature/advance_with_push_to_remote`. This is contrary to docs in github.rst: ``` If only one PR is given, then switch the local repository's HEAD to its head branch. ``` In fact, the doc should probably say: ``` If only one PR has been checked out, then switch the local repository's HEAD to its head branch. ``` and `github checkout-prs` should behave adequately (i.e. for the sample above, it should never switch HEAD). Pls provide regression tests as well.	5a2b68e1a7a7fff7e226f2e6ff96f7936bf98439	[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_checkout_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_checkout_prs_from_fork_with_deleted_repo" ]	[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_add", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_few_possible_downstream_branches_and_yes_option", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_no_downstream_branches", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_one_downstream_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_anno_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_branch_reappears_in_definition", "git_machete/tests/functional/test_machete.py::MacheteTester::test_clean", "git_machete/tests/functional/test_machete.py::MacheteTester::test_discover_traverse_squash", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_checkout_prs_freshly_cloned", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr_missing_base_branch_on_remote", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_sync", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_with_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_without_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_help", "git_machete/tests/functional/test_machete.py::MacheteTester::test_log", "git_machete/tests/functional/test_machete.py::MacheteTester::test_retarget_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_first", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_next", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_prev", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_down_fork_point_and_multiple_children_of_last_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_invalid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_valid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_merge", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_invalid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_valid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_override", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_untracked", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_not_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_invalid_fork_point" ]	{ "failed_lite_validators": [ "has_issue_reference", "has_git_commit_hash", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-04-05 12:58:57+00:00	mit	831
VirtusLab__git-machete-534	diff --git a/git_machete/client.py b/git_machete/client.py index d063583..19ef0c4 100644 --- a/git_machete/client.py +++ b/git_machete/client.py @@ -2109,7 +2109,7 @@ class MacheteClient: description_path = self.__git.get_main_git_subpath('info', 'description') description: str = utils.slurp_file_or_empty(description_path) - ok_str = ' <green><b>OK</b></green>' + ok_str = ' <green>-> <b>OK</b></green>' print(fmt(f'Creating a {"draft " if opt_draft else ""}PR from `{head}` to `{base}`...'), end='', flush=True) pr: GitHubPullRequest = create_pull_request(org, repo, head=head, base=base, title=commits[0].subject, description=description, draft=opt_draft) diff --git a/git_machete/github.py b/git_machete/github.py index f8dc8c4..49f089b 100644 --- a/git_machete/github.py +++ b/git_machete/github.py @@ -181,8 +181,9 @@ def __fire_github_api_request(method: str, path: str, token: Optional[str], requ 'Visit `https://github.com/settings/tokens` to generate a new one.') elif err.code == http.HTTPStatus.NOT_FOUND: raise MacheteException( - f'Given endpoint: {url}, not found in GitHub or you don\'t have' - f' the permission to access it (expired token?).') # TODO (#164): make dedicated exception here + f'`{method} {url}` request ended up in 404 response from GitHub. A valid GitHub API token is required.\n' + f'Provide a GitHub API token with `repo` access via one of the: {get_github_token_possible_providers()} ' + 'Visit `https://github.com/settings/tokens` to generate a new one.') # TODO (#164): make dedicated exception here else: first_line = fmt(f'GitHub API returned {err.code} HTTP status with error message: `{err.reason}`\n') raise MacheteException(first_line + "Please open an issue regarding this topic under link: https://github.com/VirtusLab/git-machete/issues/new")	VirtusLab/git-machete	7a72f615bfa9bd8e9c436dfb726216dfa07d0839	diff --git a/tests/test_github.py b/tests/test_github.py index 90fe555..d8fce10 100644 --- a/tests/test_github.py +++ b/tests/test_github.py @@ -454,7 +454,7 @@ class TestGithub: expected_msg = ("Fetching origin...\n" "Warn: Base branch for this PR (`feature/api_handling`) is not found on remote, pushing...\n" - "Creating a PR from `feature/api_exception_handling` to `feature/api_handling`... OK, see www.github.com\n") + "Creating a PR from `feature/api_exception_handling` to `feature/api_handling`... -> OK, see www.github.com\n") assert_command(['github', 'create-pr'], expected_msg, strip_indentation=False) assert_command( ['status'],	Does `/pulls` endpoint for a public GitHub repository really require authentication? As @mkondratek reported: I've tried to use `create-pr` with that result: ```sh mikko@mikko-MS-7C91:~/IdeaProjects/git-machete-intellij-plugin$ git machete github create-pr Fetching origin... Creating a PR from hook-executors-improvements to develop...Given endpoint: https://api.github.com/repos/VirtusLab/git-machete-intellij-plugin/pulls, not found in GitHub or you don't have the permission to access it (expired token?). ``` I have no token (generated and) set so that's the reason. After that - works. _Originally posted by @mkondratek in https://github.com/VirtusLab/git-machete/issues/493#issuecomment-1113174706_ --- My addition: note that https://api.github.com/repos/VirtusLab/git-machete-intellij-plugin/pulls can be readily accessed from browser and returns legit results. Let's check why this error happens when accessing GitHub API from git-machete CLI. If this can't be circumvented (e.g. for private repos), let's at least improve the error message (since it doesn't even clearly state that the token might be missing, only mentions expiry) :thinking:	7a72f615bfa9bd8e9c436dfb726216dfa07d0839	[ "tests/test_github.py::TestGithub::test_github_create_pr_missing_base_branch_on_remote" ]	[ "tests/test_github.py::TestGithub::test_github_retarget_pr", "tests/test_github.py::TestGithub::test_github_anno_prs", "tests/test_github.py::TestGithub::test_github_create_pr", "tests/test_github.py::TestGithub::test_github_checkout_prs", "tests/test_github.py::TestGithub::test_github_checkout_prs_freshly_cloned", "tests/test_github.py::TestGithub::test_github_checkout_prs_from_fork_with_deleted_repo", "tests/test_github.py::TestGithub::test_github_sync" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2022-05-27 10:32:01+00:00	mit	832
WIPACrepo__iceprod-339	diff --git a/iceprod/core/functions.py b/iceprod/core/functions.py index 964f20b9..619cc991 100644 --- a/iceprod/core/functions.py +++ b/iceprod/core/functions.py @@ -270,16 +270,11 @@ def get_local_ip_address(): def gethostname(): """Get hostname of this computer.""" ret = socket.getfqdn() - try: - resp = requests.get('http://simprod.icecube.wisc.edu/downloads/getip.php', timeout=1) - resp.raise_for_status() - logging.info('getip: %r', resp.text) - ret2 = resp.text.split(' ')[-1] - if len(ret2.split('.')) > 1: - ret = '.'.join(ret.split('.')[:1]+ret2.split('.')[1:]) - except Exception: - logging.info('error getting global ip', exc_info=True) - return ret + ret2 = socket.gethostname() + if len(ret2) > len(ret): + return ret2 + else: + return ret @contextmanager	WIPACrepo/iceprod	168fdf0ddea222567e6c87401d11b121d7369927	diff --git a/tests/core/functions_test.py b/tests/core/functions_test.py index ffe9f4ac..9ece4946 100644 --- a/tests/core/functions_test.py +++ b/tests/core/functions_test.py @@ -672,29 +672,25 @@ class functions_test(AsyncTestCase): logging.info('%s',e) @patch('socket.getfqdn') - @requests_mock.mock() + @patch('socket.gethostname') @unittest_reporter - def test_301_gethostname(self, fqdn, http_mock): + def test_301_gethostname(self, fqdn, hostname): fqdn.return_value = 'myhost' - http_mock.get('/downloads/getip.php', text='123 myhost') + hostname.return_value = 'myhost' host = iceprod.core.functions.gethostname() self.assertEqual(host, 'myhost') - self.assertEqual(http_mock.call_count, 1) - http_mock.get('/downloads/getip.php', text='123 dyn.test.com') + hostname.return_value = 'myhost.test.com' host = iceprod.core.functions.gethostname() self.assertEqual(host, 'myhost.test.com') - self.assertEqual(http_mock.call_count, 2) fqdn.return_value = 'myhost.foo.bar' host = iceprod.core.functions.gethostname() self.assertEqual(host, 'myhost.test.com') - self.assertEqual(http_mock.call_count, 3) fqdn.return_value = 'myhost.foo.bar.baz' host = iceprod.core.functions.gethostname() - self.assertEqual(host, 'myhost.test.com') - self.assertEqual(http_mock.call_count, 4) + self.assertEqual(host, 'myhost.foo.bar.baz') @unittest_reporter def test_302_isurl(self):	remove getip.php request This request: http://simprod.icecube.wisc.edu/downloads/getip.php is on an old SL6 server. We'd like to decommission that server. Replace this lookup with something else, or remove entirely.	168fdf0ddea222567e6c87401d11b121d7369927	[ "tests/core/functions_test.py::functions_test::test_301_gethostname" ]	[ "tests/core/functions_test.py::functions_test::test_001_uncompress", "tests/core/functions_test.py::functions_test::test_002_uncompress_tar", "tests/core/functions_test.py::functions_test::test_003_uncompress_tar", "tests/core/functions_test.py::functions_test::test_020_iscompressed", "tests/core/functions_test.py::functions_test::test_021_istarred", "tests/core/functions_test.py::functions_test::test_100_md5sum", "tests/core/functions_test.py::functions_test::test_101_check_md5sum", "tests/core/functions_test.py::functions_test::test_102_sha1sum", "tests/core/functions_test.py::functions_test::test_103_check_sha1sum", "tests/core/functions_test.py::functions_test::test_104_sha256sum", "tests/core/functions_test.py::functions_test::test_105_check_sha256sum", "tests/core/functions_test.py::functions_test::test_106_sha512sum", "tests/core/functions_test.py::functions_test::test_107_check_sha512sum", "tests/core/functions_test.py::functions_test::test_200_removedirs", "tests/core/functions_test.py::functions_test::test_201_copy", "tests/core/functions_test.py::functions_test::test_300_getInterfaces", "tests/core/functions_test.py::functions_test::test_302_isurl", "tests/core/functions_test.py::functions_test::test_304_download", "tests/core/functions_test.py::functions_test::test_305_download", "tests/core/functions_test.py::functions_test::test_320_download", "tests/core/functions_test.py::functions_test::test_404_upload", "tests/core/functions_test.py::functions_test::test_405_upload", "tests/core/functions_test.py::functions_test::test_410_upload", "tests/core/functions_test.py::functions_test::test_420_upload", "tests/core/functions_test.py::functions_test::test_504_delete", "tests/core/functions_test.py::functions_test::test_505_delete", "tests/core/functions_test.py::functions_test::test_510_delete" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }	2023-04-19 18:14:54+00:00	mit	833
WPI-MMR__gym_solo-38	diff --git a/examples/solo8_vanilla/interactive_pos_control.py b/examples/solo8_vanilla/interactive_pos_control.py index 8773e53..446e3c4 100644 --- a/examples/solo8_vanilla/interactive_pos_control.py +++ b/examples/solo8_vanilla/interactive_pos_control.py @@ -17,8 +17,7 @@ if __name__ == '__main__': env.obs_factory.register_observation(obs.TorsoIMU(env.robot)) env.reward_factory.register_reward(1,rewards.UprightReward(env.robot)) - env.termination_factory.register_termination( - terms.TimeBasedTermination(10000000)) + env.termination_factory.register_termination(terms.PerpetualTermination()) joint_params = [] num_joints = env.client.getNumJoints(env.robot) diff --git a/examples/solo8_vanilla/observation_dump.py b/examples/solo8_vanilla/observation_dump.py index 68bdde0..3dc3df9 100644 --- a/examples/solo8_vanilla/observation_dump.py +++ b/examples/solo8_vanilla/observation_dump.py @@ -19,8 +19,7 @@ if __name__ == '__main__': env.obs_factory.register_observation(obs.TorsoIMU(env.robot)) env.reward_factory.register_reward(1,rewards.UprightReward(env.robot)) - env.termination_factory.register_termination( - terms.TimeBasedTermination(100000000)) + env.termination_factory.register_termination(terms.PerpetualTermination()) try: print("""\n diff --git a/gym_solo/core/termination.py b/gym_solo/core/termination.py index 6135f8a..72a7b33 100644 --- a/gym_solo/core/termination.py +++ b/gym_solo/core/termination.py @@ -80,4 +80,19 @@ class TimeBasedTermination(Termination): Otherwise return false. """ self.step_delta += 1 - return self.step_delta > self.max_step_delta \ No newline at end of file + return self.step_delta > self.max_step_delta + + +class PerpetualTermination(Termination): + """Termination condition that never ends. Useful for demos / testing.""" + def reset(self): + """Unneeded.""" + pass + + def is_terminated(self) -> bool: + """Always returns that the episode is not terminated. + + Returns: + bool: False + """ + return False \ No newline at end of file	WPI-MMR/gym_solo	fdf8acff06a8d143e0d9890eb15d86fc643a6843	diff --git a/gym_solo/core/test_termination_conditions.py b/gym_solo/core/test_termination_conditions.py index bad6698..a6979b4 100644 --- a/gym_solo/core/test_termination_conditions.py +++ b/gym_solo/core/test_termination_conditions.py @@ -27,4 +27,13 @@ class TestTimeBasedTermination(unittest.TestCase): self.assertEqual(i+1, term.step_delta) self.assertEqual(True, term.is_terminated()) - self.assertEqual(max_step_delta + 1, term.step_delta) \ No newline at end of file + self.assertEqual(max_step_delta + 1, term.step_delta) + + +class TestPerpetualTermination(unittest.TestCase): + def test_is_terminated(self): + term = termination.PerpetualTermination() + + # Arbitrary count, just need to ensure that always returns False + for i in range(1000): + self.assertFalse(term.is_terminated()) \ No newline at end of file	Create Never Ending Termination A couple of PRs have this issue (#33, #35), but if a user wants to run gym indefinitely, they would need to create a `TimeBasedTermination` with a really big number. While that works, it's pretty jank and we should just make a `NoTermination` which just goes on forever instead.	fdf8acff06a8d143e0d9890eb15d86fc643a6843	[ "gym_solo/core/test_termination_conditions.py::TestPerpetualTermination::test_is_terminated" ]	[ "gym_solo/core/test_termination_conditions.py::TestTimeBasedTermination::test_attributes", "gym_solo/core/test_termination_conditions.py::TestTimeBasedTermination::test_is_terminated", "gym_solo/core/test_termination_conditions.py::TestTimeBasedTermination::test_reset" ]	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2021-01-16 19:53:13+00:00	mit	834
WPI-MMR__gym_solo-6	diff --git a/gym_solo/core/rewards.py b/gym_solo/core/rewards.py new file mode 100644 index 0000000..d364f98 --- /dev/null +++ b/gym_solo/core/rewards.py @@ -0,0 +1,63 @@ +from abc import ABC, abstractmethod +from dataclasses import dataclass +from typing import List + +from gym_solo import solo_types + + +class Reward(ABC): + @abstractmethod + def compute(self) -> solo_types.reward: + """Compute the reward for the current state. + + Returns: + solo_types.reward: The reward evalulated at the current state. + """ + pass + + +@dataclass +class _WeightedReward: + reward: Reward + weight: float + + +class RewardFactory: + """A factory to dynamically create rewards. + + Note that this factory is currently implemented to combined rewards via + a linear combination. For example, if the user wanted to register rewards + r1, r2, and r3, the final reward would be r1 + r2 + r3. + + Obviously, you can add coefficients to the rewards, and that functionality + is further explained in register_reward() below. + + If you need more functionality then a linear combination (exponential + temporal decay), then it's probably in your best interest to implement that + in a custom Reward. + """ + def __init__(self): + """Create a new RewardFactory.""" + self._rewards: List[_WeightedReward] = [] + + def register_reward(self, weight: float, reward: Reward): + """Register a reward to be computed per state. + + Args: + weight (float): The weight to be applied to this reward when it is + is combined linearly with the other rewards. The domain for this + value is (-∞, ∞). + reward (Reward): A Reward object which .compute() will be called on at + reward computation time. + """ + self._rewards.append(_WeightedReward(reward=reward, weight=weight)) + + def get_reward(self) -> float: + """Evaluate the current state and get the combined reward. + + Returns: + float: The reward from the current state. Note that this reward is a + combination of multiple atomic sub-rewards, as explained by the + strategies earlier. + """ + return sum(wr.weight * wr.reward.compute() for wr in self._rewards) \ No newline at end of file diff --git a/gym_solo/solo_types.py b/gym_solo/solo_types.py index 85dc7ae..365d7e8 100644 --- a/gym_solo/solo_types.py +++ b/gym_solo/solo_types.py @@ -3,4 +3,7 @@ from typing import List import numpy as np # A state observation -obs = np.ndarray \ No newline at end of file +obs = np.ndarray + +# A reward after a step +reward = float \ No newline at end of file	WPI-MMR/gym_solo	e4bcb11fb1b18da997494d56acf95bdd512a076a	diff --git a/gym_solo/core/test_rewards_factory.py b/gym_solo/core/test_rewards_factory.py new file mode 100644 index 0000000..fd70bea --- /dev/null +++ b/gym_solo/core/test_rewards_factory.py @@ -0,0 +1,35 @@ +import unittest +from gym_solo.core import rewards + +from parameterized import parameterized + + +class TestReward(rewards.Reward): + def __init__(self, return_value): + self._return_value = return_value + + def compute(self): + return self._return_value + + +class TestRewardsFactory(unittest.TestCase): + def test_empty(self): + rf = rewards.RewardFactory() + self.assertListEqual(rf._rewards, []) + + @parameterized.expand([ + ('single', {1: 2.5}, 2.5), + ('two_happy', {1: 1, 2: 2}, 5), + ('0-weight', {0: 1, 2: 2}, 4), + ('negative-weight', {-1: 1, 2: 2}, 3), + ('three', {1: 1, 2: 2, 3: 3}, 14), + ]) + def test_register_and_compute(self, name, rewards_dict, expected_reward): + rf = rewards.RewardFactory() + for weight, reward in rewards_dict.items(): + rf.register_reward(weight, TestReward(reward)) + self.assertEqual(rf.get_reward(), expected_reward) + + +if __name__ == '__main__': + unittest.main() \ No newline at end of file	Create Rewards Factory Similar to the observation factory. The reward factory should be able to take in `Reward` objects, similar to an `Observation` object, evaluate the rewards for the state, and combine them. I'm thinking of making the final reward a linear combination of the registered rewards. With that in mind, consider the following example: ```python r1 = Reward() r2 = Reward() r3 = Reward() rf = RewardFactory() r1.register_reward(-1, r1) r1.register_reward(.1, r2) r1.register_reward(.9, r3) ``` Notice that `register_reward()` has two args: `weight: float` and `reward: gym_solo.core.rewards.Reward`. Thus, the final reward would evaluate to: `-r1() + 0.1 * r2() + 0.9 * r3()`. Figure that if you need functionality more elaborate than a linear combination, you should be offloading that processing into a `Reward` class. @mahajanrevant thoughts on this? lmk if you think we need anything stronger than linear combinations in the `RewardFactory`.	e4bcb11fb1b18da997494d56acf95bdd512a076a	[ "gym_solo/core/test_rewards_factory.py::TestRewardsFactory::test_empty", "gym_solo/core/test_rewards_factory.py::TestRewardsFactory::test_register_and_compute_0_single", "gym_solo/core/test_rewards_factory.py::TestRewardsFactory::test_register_and_compute_1_two_happy", "gym_solo/core/test_rewards_factory.py::TestRewardsFactory::test_register_and_compute_2_0_weight", "gym_solo/core/test_rewards_factory.py::TestRewardsFactory::test_register_and_compute_3_negative_weight", "gym_solo/core/test_rewards_factory.py::TestRewardsFactory::test_register_and_compute_4_three" ]	[]	{ "failed_lite_validators": [ "has_added_files" ], "has_test_patch": true, "is_lite": false }	2020-10-27 21:14:37+00:00	mit	835
Workday__prism-python-8	diff --git a/.travis.yml b/.travis.yml index 4da15ef..478c235 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,4 +7,4 @@ python: install: - pip install . script: -- echo "skipping tests" +- pytest diff --git a/environment.yml b/environment.yml index de104b0..9049cf6 100644 --- a/environment.yml +++ b/environment.yml @@ -4,3 +4,4 @@ channels: dependencies: - python=3.7 - requests + - pytest diff --git a/prism/data/schema.json b/prism/data/schema.json new file mode 100644 index 0000000..896c055 --- /dev/null +++ b/prism/data/schema.json @@ -0,0 +1,42 @@ +{ + "fields": [ + { + "defaultValue": "textField", + "description": "this is a Text Field", + "name": "State2", + "parseFormat": "", + "precision": 0, + "ordinal": 1, + "scale": 0, + "type": { + "id": "Schema_Field_Type=Text" + } + }, + { + "defaultValue": "0", + "description": "this is an Integer Field", + "name": "Population2", + "parseFormat": "", + "precision": 9, + "ordinal": 2, + "scale": 0, + "type": { + "id": "Schema_Field_Type=Numeric" + } + } + ], + "parseOptions": { + "charset": { + "id": "Encoding=UTF-8" + }, + "fieldsDelimitedBy": ",", + "fieldsEnclosedBy": "\"", + "headerLinesToIgnore": 1, + "type": { + "id": "Schema_File_Type=Delimited" + } + }, + "schemaVersion": { + "id": "Schema_Version=1.0" + } +} \ No newline at end of file diff --git a/setup.py b/setup.py index f8e5ce8..5ea16f2 100644 --- a/setup.py +++ b/setup.py @@ -13,7 +13,13 @@ setup( author_email='[email protected]', url='https://github.com/Workday/prism-python', packages=['prism'], + package_data={'prism': ['data/*']}, install_requires=requirements, + extras_require={ + 'dev': [ + 'pytest', + ] + }, keywords='prism', classifiers=[ 'Programming Language :: Python :: 3.6',	Workday/prism-python	11b6c089a2d2c5b65e4ecc1caf57ccf30e426612	diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..317f19d --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,11 @@ +import os +import pytest + [email protected] +def rootdir(): + return os.path.join(os.path.dirname(os.path.abspath(__file__)), '..') + [email protected] +def schema_file(rootdir): + """Path to example JSON schema""" + return os.path.join(rootdir, 'prism', 'data', 'schema.json') diff --git a/tests/test_prism.py b/tests/test_prism.py new file mode 100644 index 0000000..bfaad2f --- /dev/null +++ b/tests/test_prism.py @@ -0,0 +1,5 @@ +import prism + +def test_load_schema(schema_file): + schema = prism.load_schema(schema_file) + assert type(schema) is dict	Add PyTest Add a simple unit test to make sure the package successfully imports. Unit tests can be expanded in the future to offer greater coverage.	11b6c089a2d2c5b65e4ecc1caf57ccf30e426612	[ "tests/test_prism.py::test_load_schema" ]	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_added_files", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2019-12-09 23:44:53+00:00	apache-2.0	836
WorksApplications__SudachiPy-158	diff --git a/sudachipy/dictionarylib/dictionarybuilder.py b/sudachipy/dictionarylib/dictionarybuilder.py index 5f3512a..bde5871 100644 --- a/sudachipy/dictionarylib/dictionarybuilder.py +++ b/sudachipy/dictionarylib/dictionarybuilder.py @@ -334,7 +334,7 @@ class DictionaryBuilder(object): @staticmethod def __is_id(text): - return re.match(r'U?\d+', text) + return re.match(r'U?\d+$', text) def parse_id(self, text): if text.startswith('U'): diff --git a/sudachipy/dictionarylib/doublearraylexicon.py b/sudachipy/dictionarylib/doublearraylexicon.py index 6e1a7ce..fb77ee8 100644 --- a/sudachipy/dictionarylib/doublearraylexicon.py +++ b/sudachipy/dictionarylib/doublearraylexicon.py @@ -78,14 +78,22 @@ class DoubleArrayLexicon(Lexicon): return self.word_params.size def get_word_id(self, headword: str, pos_id: int, reading_form: str) -> int: + for wid, _ in self.lookup(headword.encode('utf-8'), 0): + if self._compare_word_id(wid, headword, pos_id, reading_form): + return wid + for wid in range(self.word_infos.size()): - info = self.word_infos.get_word_info(wid) - if info.surface == headword \ - and info.pos_id == pos_id \ - and info.reading_form == reading_form: + if self._compare_word_id(wid, headword, pos_id, reading_form): return wid + return -1 + def _compare_word_id(self, wid: int, headword: str, pos_id: int, reading_form: str) -> bool: + info = self.word_infos.get_word_info(wid) + return info.surface == headword \ + and info.pos_id == pos_id \ + and info.reading_form == reading_form + def get_dictionary_id(self, word_id: int) -> int: return 0	WorksApplications/SudachiPy	7e5b501111920cef057b821412af595db248a7b8	diff --git a/tests/dictionarylib/test_dictionarybuilder.py b/tests/dictionarylib/test_dictionarybuilder.py index f1ead7a..a07a647 100644 --- a/tests/dictionarylib/test_dictionarybuilder.py +++ b/tests/dictionarylib/test_dictionarybuilder.py @@ -39,6 +39,8 @@ class TestDictionaryBuilder(TestCase): wf.write("東京都,0,0,0,東京都,名詞,固有名詞,地名,一般,,,ヒガシキョウト,東京都,,B,\"東,名詞,普通名詞,一般,,,,ヒガシ/2\",,1/2,1/2\n") wf.write("東,-1,-1,0,東,名詞,普通名詞,一般,,,,ヒガシ,ひがし,,A,,,,\n") wf.write("京都,0,0,0,京都,名詞,固有名詞,地名,一般,,,キョウト,京都,,A,,,,\n") + wf.write("1,-1,-1,0,1,名詞,数詞,,,,,イチ,1,,A,,,,\n") + wf.write("東1,0,0,0,東1,名詞,普通名詞,一般,,,,ヒガシイチ,東1,,C,\"東,名詞,普通名詞,一般,,,,ヒガシ/1,名詞,数詞,,,,,イチ\",\"東,名詞,普通名詞,一般,,,,ヒガシ/U3\",") self.logger = getLogger() self.logger.disabled = True @@ -218,13 +220,13 @@ class TestDictionaryBuilder(TestCase): self.assertEqual('test', header.description) # grammar - self.assertEqual(2, grammar.get_part_of_speech_size()) + self.assertEqual(3, grammar.get_part_of_speech_size()) self.assertEqual(["名詞", "固有名詞", "地名", "一般", "", ""], grammar.get_part_of_speech_string(0)) self.assertEqual(["名詞", "普通名詞", "一般", "", "", "*"], grammar.get_part_of_speech_string(1)) self.assertEqual(200, grammar.get_connect_cost(0, 0)) # lexicon - self.assertEqual(3, lexicon.size()) + self.assertEqual(5, lexicon.size()) self.assertEqual(0, lexicon.get_cost(0)) wi = lexicon.get_word_info(0) self.assertEqual('東京都', wi.surface)	Slow building of user dictionary with surface form split info It seems take 30+ seconds per entry to build user dictionary, if its words have split info with word info (構成語情報). ``` $ sudachipy ubuild user.csv -o user.dic reading the source file...1 words writing the POS table...2 bytes writing the connection matrix...4 bytes building the trie...done writing the trie...1028 bytes writing the word-ID table...9 bytes writing the word parameters...10 bytes writing the word_infos...70 bytes writing word_info offsets...4 bytes real 0m38.654s user 0m38.499s sys 0m0.139s ``` user.csv: ```csv 舞台藝術,5146,5146,8000,舞台藝術,名詞,普通名詞,一般,,,,ブタイゲイジュツ,舞台芸術,,C,"舞台,名詞,普通名詞,一般,,,,ブタイ/藝術,名詞,普通名詞,一般,,,,ゲイジュツ","舞台,名詞,普通名詞,一般,,,,ブタイ/藝術,名詞,普通名詞,一般,,,,ゲイジュツ","舞台,名詞,普通名詞,一般,,,,ブタイ/藝術,名詞,普通名詞,一般,,,,ゲイジュツ",* ``` If I have two lines then it takes 1m. ※ No problem with word id split info ```csv 舞台藝術,5146,5146,8000,舞台藝術,名詞,普通名詞,一般,,,,ブタイゲイジュツ,舞台芸術,,C,647312/659236,647312/659236,647312/659236,* ``` ``` $ sudachipy ubuild user.csv -o user.dic real 0m0.925s user 0m0.776s sys 0m0.159s ``` ---- ``` $ sudachipy --version sudachipy 0.5.2 ```	7e5b501111920cef057b821412af595db248a7b8	[ "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_build" ]	[ "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_add_to_trie", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_convert_matrix", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_convert_postable", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_decode", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_line_empty_headword", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_line_invalid_columns", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_line_same_readingform", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_line_toolong_headword", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_line_toomany_split", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_splitinfo", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_splitinfo_invalid_system_wordid_in_userdict", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_splitinfo_invalid_wordid", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_splitinfo_invalid_wordid_userdict", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parseline", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_write_intarray", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_write_string" ]	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2021-06-24 03:14:56+00:00	apache-2.0	837
Wortmeister-HQ__zahlwort2num-6	diff --git a/zahlwort2num/__init__.py b/zahlwort2num/__init__.py index cacf7d9..2e0a2b5 100644 --- a/zahlwort2num/__init__.py +++ b/zahlwort2num/__init__.py @@ -12,6 +12,7 @@ class ZahlConverter: 'eine': 1, 'er': 1, 'zwei': 2, + 'zwo': 2, 'drei': 3, 'drit': 3, 'vier': 4,	Wortmeister-HQ/zahlwort2num	325417a06bc6f79ca13605bb54b0dbc6d45c8f6e	diff --git a/zahlwort2num/tests/test_convert.py b/zahlwort2num/tests/test_convert.py index 91fd15f..905ec5c 100644 --- a/zahlwort2num/tests/test_convert.py +++ b/zahlwort2num/tests/test_convert.py @@ -6,6 +6,7 @@ class TestConverter(TestCase): def test_hardcoded_values_upto_100(self): self.assertTrue(w2n.convert('eins') == 1) self.assertTrue(w2n.convert('zwei') == 2) + self.assertTrue(w2n.convert('zwo') == 2) self.assertTrue(w2n.convert('drei') == 3) self.assertTrue(w2n.convert('vier') == 4) self.assertTrue(w2n.convert('fünf') == 5) @@ -128,12 +129,14 @@ class TestConverter(TestCase): 'zwei milliarden', 'eintausend', 'null', - 'neunundvierzig' + 'neunundvierzig', + 'zwohundertzwoundzwanzig', + 'zwotausend' ] numbers = [7, 99, 1000, 200000, 4504, 4511, 225, 3625, 12854, 653521, 99, 500002, 1004000, 700000000009001009001, 9000000000000000000000000011, - 2000000000, 1000, 0, 49] + 2000000000, 1000, 0, 49, 222, 2000] self.compare_sets(numbers, words)	Does not work with alternative pronunciation "zwo" ```py >>> from zahlwort2num import convert >>> convert("zwo") Traceback (most recent call last): File "<stdin>", line 1, in <module> File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 137, in convert return c.convert() File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 123, in convert return self.ordBn(number) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 108, in ordBn return self.ordWithBN(number, 0) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 88, in ordWithBN return self.convOrd(number) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 81, in convOrd return self.convt2(number) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 129, in <lambda> self.convt2 = lambda number: self.mult(number, 'tausend', 1000, self.convh2) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 60, in mult return fun(spliter[0]) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 130, in <lambda> self.convh2 = lambda number: self.mult(number, 'hundert', 100, self.convu2) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 60, in mult return fun(spliter[0]) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 131, in <lambda> self.convu2 = lambda number: self.mult(number, 'und', 1, lambda word: self.CONST_NUMS[word]) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 60, in mult return fun(spliter[0]) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 131, in <lambda> self.convu2 = lambda number: self.mult(number, 'und', 1, lambda word: self.CONST_NUMS[word]) KeyError: 'zwo' ```	325417a06bc6f79ca13605bb54b0dbc6d45c8f6e	[ "zahlwort2num/tests/test_convert.py::TestConverter::test_hardcoded_values_upto_100", "zahlwort2num/tests/test_convert.py::TestConverter::test_more_specific" ]	[ "zahlwort2num/tests/test_convert.py::TestConverter::test_bugs_found_by_users", "zahlwort2num/tests/test_convert.py::TestConverter::test_negative_values", "zahlwort2num/tests/test_convert.py::TestConverter::test_negative_with_ordinal", "zahlwort2num/tests/test_convert.py::TestConverter::test_ordinal_numbers", "zahlwort2num/tests/test_convert.py::TestConverter::test_swiss_variant", "zahlwort2num/tests/test_convert.py::TestConverter::test_yet_another_ordinal_edge_case" ]	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2022-10-28 09:45:02+00:00	mit	838
XKNX__xknx-1008	diff --git a/docs/changelog.md b/docs/changelog.md index 98a4c42b..9a9e0700 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -6,6 +6,12 @@ nav_order: 2 # Changelog +## Unreleased changes + +### Internal + +- Fix DPT2ByteFloat numeric range issues + ## 0.22.1 Wrong delivery 2022-07-29 ### Management diff --git a/xknx/dpt/dpt_2byte_float.py b/xknx/dpt/dpt_2byte_float.py index ead6abdc..c5858011 100644 --- a/xknx/dpt/dpt_2byte_float.py +++ b/xknx/dpt/dpt_2byte_float.py @@ -49,33 +49,23 @@ class DPT2ByteFloat(DPTNumeric): @classmethod def to_knx(cls, value: float) -> tuple[int, int]: """Serialize to KNX/IP raw data.""" - - def calc_exponent(float_value: float, sign: bool) -> tuple[int, int]: - """Return float exponent.""" - exponent = 0 - significand = abs(int(float_value * 100)) - - while significand < -2048 or significand > 2048: - exponent += 1 - significand >>= 1 - - if sign: - significand ^= 0x7FF # invert - significand += 1 # and add 1 - - return exponent, significand - try: knx_value = float(value) if not cls._test_boundaries(knx_value): raise ValueError - sign = knx_value < 0 - exponent, significand = calc_exponent(knx_value, sign) + value = knx_value * 100 + exponent = 0 + while value < -2048 or value > 2047: + exponent += 1 + value /= 2 + + mantisse = int(round(value)) & 0x7FF + msb = exponent << 3 \| mantisse >> 8 + if value < 0: + msb \|= 0x80 - return (sign << 7) \| (exponent << 3) \| ( - significand >> 8 - ), significand & 0xFF + return msb, mantisse & 0xFF except ValueError: raise ConversionError(f"Could not serialize {cls.__name__}", value=value) diff --git a/xknx/secure/keyring.py b/xknx/secure/keyring.py index e23bc7e7..1727e5e9 100644 --- a/xknx/secure/keyring.py +++ b/xknx/secure/keyring.py @@ -222,7 +222,7 @@ class XMLDevice(AttributeReader): class Keyring(AttributeReader): """Class for loading and decrypting knxkeys XML files.""" - backbone: XMLBackbone + backbone: XMLBackbone \| None = None interfaces: list[XMLInterface] group_addresses: list[XMLGroupAddress] devices: list[XMLDevice]	XKNX/xknx	180ec53481c40f8bebf4b9fcaad2b450857d7109	diff --git a/requirements/testing.txt b/requirements/testing.txt index 76aac084..ee9c39d4 100644 --- a/requirements/testing.txt +++ b/requirements/testing.txt @@ -8,6 +8,6 @@ pylint==2.14.5 pytest==7.1.2 pytest-asyncio==0.19.0 pytest-cov==3.0.0 -setuptools==63.4.2 +setuptools==64.0.1 tox==3.25.1 mypy==0.971 diff --git a/test/dpt_tests/dpt_float_test.py b/test/dpt_tests/dpt_float_test.py index 0a9dc336..083fa7c1 100644 --- a/test/dpt_tests/dpt_float_test.py +++ b/test/dpt_tests/dpt_float_test.py @@ -79,6 +79,13 @@ class TestDPTFloat: assert DPT2ByteFloat.to_knx(DPT2ByteFloat.value_max) == (0x7F, 0xFF) assert DPT2ByteFloat.from_knx((0x7F, 0xFF)) == DPT2ByteFloat.value_max + def test_close_to_limit(self): + """Test parsing and streaming of DPT2ByteFloat with numeric limit.""" + assert DPT2ByteFloat.to_knx(20.48) == (0x0C, 0x00) + assert DPT2ByteFloat.from_knx((0x0C, 0x00)) == 20.48 + assert DPT2ByteFloat.to_knx(-20.48) == (0x80, 0x00) + assert DPT2ByteFloat.from_knx((0x80, 0x00)) == -20.48 + def test_min(self): """Test parsing and streaming of DPT2ByteFloat with minimum value.""" assert DPT2ByteFloat.to_knx(DPT2ByteFloat.value_min) == (0xF8, 0x00)	AttributeError: 'Keyring' object has no attribute 'backbone' Hi. My ETS generates a .knxkeys file that doesn't have a "backbone" parameter: ``` <?xml version="1.0" encoding="utf-8"?> <Keyring Project="Apartment" CreatedBy="ETS 5.7.4 (Build 1093)" Created="2022-08-09T15:53:32" Signature="yaIT..." xmlns="http://knx.org/xml/keyring/1"> <Interface Type="Tunneling" Host="1.1.251" UserID="2" Password="HIDDEN" IndividualAddress="HIDDEN" Authentication="HIDDEN" /> <Interface Type="Tunneling" Host="1.1.251" UserID="3" Password="HIDDEN" IndividualAddress="HIDDEN" Authentication="HIDDEN" /> <Interface Type="Tunneling" Host="1.1.251" UserID="4" Password="HIDDEN" IndividualAddress="HIDDEN" Authentication="HIDDEN" /> <Interface Type="Tunneling" Host="1.1.251" UserID="5" Password="HIDDEN" IndividualAddress="HIDDEN" Authentication="HIDDEN" /> <Devices> <Device IndividualAddress="1.1.251" SequenceNumber="24" /> </Devices> </Keyring> ``` Because of that i get the following error: ``` There was an error during loading the knxkeys file. Traceback (most recent call last): File "/opt/homebrew/lib/python3.9/site-packages/xknx/secure/keyring.py", line 316, in load_key_ring keyring.decrypt(password) File "/opt/homebrew/lib/python3.9/site-packages/xknx/secure/keyring.py", line 299, in decrypt if self.backbone is not None: AttributeError: 'Keyring' object has no attribute 'backbone' Traceback (most recent call last): File "/opt/homebrew/lib/python3.9/site-packages/xknx/secure/keyring.py", line 316, in load_key_ring keyring.decrypt(password) File "/opt/homebrew/lib/python3.9/site-packages/xknx/secure/keyring.py", line 299, in decrypt if self.backbone is not None: AttributeError: 'Keyring' object has no attribute 'backbone' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/max/Projects/KNX/example_telegram_monitor.py", line 69, in <module> asyncio.run(main(sys.argv[1:])) File "/opt/homebrew/Cellar/[email protected]/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/runners.py", line 44, in run return loop.run_until_complete(main) File "/opt/homebrew/Cellar/[email protected]/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete return future.result() File "/Users/max/Projects/KNX/example_telegram_monitor.py", line 65, in main await monitor(address_filters) File "/Users/max/Projects/KNX/example_telegram_monitor.py", line 47, in monitor await xknx.start() File "/opt/homebrew/lib/python3.9/site-packages/xknx/xknx.py", line 128, in start await self.knxip_interface.start() File "/opt/homebrew/lib/python3.9/site-packages/xknx/io/knxip_interface.py", line 69, in start await self._start() File "/opt/homebrew/lib/python3.9/site-packages/xknx/io/knxip_interface.py", line 105, in _start keyring: Keyring = load_key_ring( File "/opt/homebrew/lib/python3.9/site-packages/xknx/secure/keyring.py", line 321, in load_key_ring raise InvalidSecureConfiguration() from exception xknx.exceptions.exception.InvalidSecureConfiguration ``` I get the same error in the standalone version of XKNX and in Home Assistant when using the "TCP with IP Secure" connection mode. My code: ``` connection_config = ConnectionConfig( connection_type=ConnectionType.TUNNELING_TCP_SECURE, gateway_ip="192.168.11.24", secure_config=SecureConfig( user_id=3, knxkeys_file_path="/Users/max/KNX/Deployment/Apartment.knxkeys", knxkeys_password="HIDDEN", ), ) xknx = XKNX(connection_config=connection_config, daemon_mode=True) ``` As a temporary fix i've applied the following patch: ``` --- xknx/secure/keyring.py 2022-08-09 19:49:28.000000000 +0300 +++ xknx/secure/keyring_fixed.py 2022-08-09 20:27:51.000000000 +0300 @@ -233,6 +233,7 @@ def __init__(self) -> None: """Initialize the Keyring.""" + self.backbone = None self.interfaces = [] self.devices = [] self.group_addresses = [] ``` - [X] using xknx standalone - [X] using Home-Assistant knx integration Version information: - Standalone xknx: 0.22.1 - xknx / Home-Assistant release with the issue: 2022.7.7 KNX installation: ETS 5.7.4 KNX IP Interface: MDT SCN-IP000.03	180ec53481c40f8bebf4b9fcaad2b450857d7109	[ "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_close_to_limit" ]	[ "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_value_from_documentation", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_value_taken_from_live_thermostat", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_zero_value", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_room_temperature", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_high_temperature", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_minor_negative_temperature", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_very_cold_temperature", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_max", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_min", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_close_to_max", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_close_to_min", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_to_knx_min_exceeded", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_to_knx_max_exceeded", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_to_knx_wrong_parameter", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_from_knx_wrong_parameter", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_from_knx_wrong_parameter2", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_temperature_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_temperature_assert_min_exceeded", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_temperature_assert_min_exceeded_from_knx", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_lux_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_lux_assert_min_exceeded", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_humidity_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_humidity_assert_min_exceeded", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_enthalpy_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_partspermillion_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_voltage_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_float_values_from_power_meter", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_14_033", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_14_055", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_14_057", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_float_values_from_voltage_meter", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_float_zero_value", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_float_special_value", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_float_to_knx_wrong_parameter", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_float_from_knx_wrong_parameter", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_float_from_knx_wrong_parameter2", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_flaot_from_knx_unpack_error", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_electric_current_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_electric_potential_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_power_settings" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2022-08-10 08:07:07+00:00	mit	839
XKNX__xknx-1114	diff --git a/docs/changelog.md b/docs/changelog.md index 2cc605ca..b056f7de 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -12,6 +12,10 @@ nav_order: 2 - ExposeSensor: Add `cooldown` option to allow rate-limiting of sent telegrams. +### Connection + +- Disconnect when tunnelling sequence number (UDP) gets out of sync. + ### Internals - Add `task.done()` to TaskRegistry tasks. diff --git a/xknx/io/tunnel.py b/xknx/io/tunnel.py index 20833f81..e57c871d 100644 --- a/xknx/io/tunnel.py +++ b/xknx/io/tunnel.py @@ -607,6 +607,9 @@ class UDPTunnel(_Tunnel): self.expected_sequence_number, tunneling_request, ) + # Tunnelling server should repeat that frame and disconnect after that was also not ACKed. + # some don't seem to initiate disconnection here so we take a shortcut and disconnect ourselves + self._tunnel_lost() def _send_tunnelling_ack( self, communication_channel_id: int, sequence_counter: int	XKNX/xknx	d1d6085102331fe9430004e55085612fd993b2f7	diff --git a/requirements/testing.txt b/requirements/testing.txt index 7954b357..e07b3e32 100644 --- a/requirements/testing.txt +++ b/requirements/testing.txt @@ -1,13 +1,13 @@ -r production.txt -pre-commit==2.20.0 -isort==5.11.3 +pre-commit==2.21.0 +isort==5.11.4 flake8==6.0.0 -flake8-isort==5.0.3 +flake8-isort==6.0.0 pydocstyle==6.1.1 pylint==2.15.9 pytest==7.2.0 pytest-asyncio==0.20.3 pytest-cov==4.0.0 setuptools==65.6.3 -tox==4.0.16 +tox==4.0.17 mypy==0.991 diff --git a/test/io_tests/tunnel_test.py b/test/io_tests/tunnel_test.py index cd177980..53178978 100644 --- a/test/io_tests/tunnel_test.py +++ b/test/io_tests/tunnel_test.py @@ -155,7 +155,9 @@ class TestUDPTunnel: assert self.tunnel.expected_sequence_number == 11 assert self.tg_received_mock.call_count == 1 # wrong sequence number - no ACK, not processed - self.tunnel._request_received(test_frame_9, None, None) + # reconnect if `auto_reconnect` was True + with pytest.raises(CommunicationError): + self.tunnel._request_received(test_frame_9, None, None) await time_travel(0) assert self.tunnel.transport.send.call_args_list == [] self.tunnel.transport.send.reset_mock()	'TunnellingRequest with sequence number not equal to expected' error every few hours Every few hours 'Received TunnellingRequest with sequence number not equal to expected' error is stuck while the sequence finally loops around. During that time messages are sent but not read. - [ ] using xknx standalone - [x] using Home-Assistant knx integration Version information: - xknx / Home-Assistant release with the issue: 1.2.1 - last working xknx / Home-Assistant release (if known): unknown KNX installation: `configuration.yaml` [knx.yaml.txt](https://github.com/XKNX/xknx/files/10067390/knx.yaml.txt) Diagnostic data of the config entry (only when Home Assistant is used) [config_entry-knx-ed093e5771cbc5d18e4307a64fd3a504.json.txt](https://github.com/XKNX/xknx/files/10067378/config_entry-knx-ed093e5771cbc5d18e4307a64fd3a504.json.txt) Traceback (if applicable): [log.txt](https://github.com/XKNX/xknx/files/10067435/log.txt)	d1d6085102331fe9430004e55085612fd993b2f7	[ "test/io_tests/tunnel_test.py::TestUDPTunnel::test_repeated_tunnel_request" ]	[ "test/io_tests/tunnel_test.py::TestUDPTunnel::test_tunnel_request_received[\\x06\\x10\\x04", "test/io_tests/tunnel_test.py::TestUDPTunnel::test_tunnel_request_received_callback", "test/io_tests/tunnel_test.py::TestUDPTunnel::test_tunnel_request_received_cemi_too_small", "test/io_tests/tunnel_test.py::TestUDPTunnel::test_tunnel_request_received_apci_unsupported", "test/io_tests/tunnel_test.py::TestUDPTunnel::test_tunnel_connect_send_disconnect[False-data_endpoint_addr0-local_endpoint0]", "test/io_tests/tunnel_test.py::TestUDPTunnel::test_tunnel_connect_send_disconnect[True-None-local_endpoint1]", "test/io_tests/tunnel_test.py::TestUDPTunnel::test_tunnel_request_description", "test/io_tests/tunnel_test.py::TestTCPTunnel::test_tunnel_heartbeat", "test/io_tests/tunnel_test.py::TestTCPTunnel::test_tunnel_heartbeat_no_answer", "test/io_tests/tunnel_test.py::TestTCPTunnel::test_tunnel_heartbeat_error" ]	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2022-12-21 21:20:28+00:00	mit	840
XKNX__xknx-1190	diff --git a/docs/changelog.md b/docs/changelog.md index 03b50890..5834d7d3 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -17,6 +17,7 @@ nav_order: 2 - Parse Data Secure credentials form Keyring from non-IP-Secure interfaces. - Parse Data Secure credentials from Keyrings exported for specific interfaces. +- Fix callback for Cover target position when called with same value consecutively. - Fix Windows TCP transport bug when using IP Secure Tunnelling. ### Protocol diff --git a/xknx/devices/cover.py b/xknx/devices/cover.py index 750913e1..489c1364 100644 --- a/xknx/devices/cover.py +++ b/xknx/devices/cover.py @@ -360,7 +360,7 @@ class Cover(Device): await self._stop_position_update() await self.position_current.process(telegram, always_callback=True) - await self.position_target.process(telegram) + await self.position_target.process(telegram, always_callback=True) await self.angle.process(telegram) await self.locked.process(telegram)	XKNX/xknx	88fc1ead4cdb10bdacee6824905540365588bf9d	diff --git a/test/devices_tests/cover_test.py b/test/devices_tests/cover_test.py index 2617622e..9dbe67ad 100644 --- a/test/devices_tests/cover_test.py +++ b/test/devices_tests/cover_test.py @@ -830,6 +830,9 @@ class TestCover: ("1/2/1", DPTBinary(1), "long"), ("1/2/2", DPTBinary(1), "short"), ("1/2/4", DPTArray(42), "position"), + ("1/2/3", DPTBinary(1), "stop"), + # call position with same value again to make sure `always_callback` is set for target position + ("1/2/4", DPTArray(42), "position"), ("1/2/5", DPTArray(42), "position state"), ("1/2/6", DPTArray(42), "angle"), ("1/2/7", DPTArray(51), "angle state"),	Cover update callback stops in some special case Hello! My intention is to use `device_updated_cb` callback for Cover to process some logic during its movement etc.. I faced the problem when callback stops working in some special case, for example: Pretend the blind initial position is 0% and we need to move it to 90% 1) start moving the blind to some position `await cover.set_position(90)` 2) send Stop during movement `cover.stop()` 3) then continue to move it to the previously given position `await cover.set_position(90)` Here the `device_updated_cb` stops 4) if then or instead to send the blind to any other position but except 90%, the callback gets back to work, for example, sending to any of 0-89 or 91-100% . Not sure if I'm doing something not correctly. Here is the reduced example: ` async def cover_update_cb(cover: Cover): print('Something inside cover update callback') cover: Cover = None async def test(): global cover await asyncio.sleep(1) await cover.set_position(90) await asyncio.sleep(4) print('STOP command') await cover.stop() await asyncio.sleep(2) print(f'Continue to move to 90') await cover.set_position(90) # here cover_update_cb stops. If instead set any different position from a position that the blind started moving from at the beginning (in our case 90) then callback will work. async def main(): global cover xknx = XKNX(daemon_mode=True) cover = Cover( xknx, 'Cover', group_address_stop = "1/1/2", group_address_position = "1/1/3", group_address_position_state = "1/1/4", device_updated_cb=cover_update_cb ) loop = asyncio.get_running_loop() loop.create_task(test()) await xknx.start() await xknx.stop() asyncio.run(main()) `	88fc1ead4cdb10bdacee6824905540365588bf9d	[ "test/devices_tests/cover_test.py::TestCover::test_process_callback" ]	[ "test/devices_tests/cover_test.py::TestCover::test_supports_stop_true", "test/devices_tests/cover_test.py::TestCover::test_supports_stop_false", "test/devices_tests/cover_test.py::TestCover::test_supports_position_true", "test/devices_tests/cover_test.py::TestCover::test_supports_position_false", "test/devices_tests/cover_test.py::TestCover::test_supports_angle_true", "test/devices_tests/cover_test.py::TestCover::test_support_angle_false", "test/devices_tests/cover_test.py::TestCover::test_support_locked", "test/devices_tests/cover_test.py::TestCover::test_sync", "test/devices_tests/cover_test.py::TestCover::test_sync_state", "test/devices_tests/cover_test.py::TestCover::test_sync_angle", "test/devices_tests/cover_test.py::TestCover::test_sync_angle_state", "test/devices_tests/cover_test.py::TestCover::test_set_up", "test/devices_tests/cover_test.py::TestCover::test_set_short_down", "test/devices_tests/cover_test.py::TestCover::test_set_down_inverted", "test/devices_tests/cover_test.py::TestCover::test_set_short_up", "test/devices_tests/cover_test.py::TestCover::test_set_up_inverted", "test/devices_tests/cover_test.py::TestCover::test_set_down", "test/devices_tests/cover_test.py::TestCover::test_stop", "test/devices_tests/cover_test.py::TestCover::test_stop_angle", "test/devices_tests/cover_test.py::TestCover::test_position", "test/devices_tests/cover_test.py::TestCover::test_position_without_binary", "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_up", "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_down", "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_uninitialized_up", "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_uninitialized_down", "test/devices_tests/cover_test.py::TestCover::test_angle", "test/devices_tests/cover_test.py::TestCover::test_angle_not_supported", "test/devices_tests/cover_test.py::TestCover::test_process_position", "test/devices_tests/cover_test.py::TestCover::test_process_angle", "test/devices_tests/cover_test.py::TestCover::test_process_locked", "test/devices_tests/cover_test.py::TestCover::test_process_up", "test/devices_tests/cover_test.py::TestCover::test_process_down", "test/devices_tests/cover_test.py::TestCover::test_process_stop", "test/devices_tests/cover_test.py::TestCover::test_process_short_stop", "test/devices_tests/cover_test.py::TestCover::test_is_traveling", "test/devices_tests/cover_test.py::TestCover::test_auto_stop", "test/devices_tests/cover_test.py::TestCover::test_periodic_update", "test/devices_tests/cover_test.py::TestCover::test_has_group_address" ]	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2023-02-11 06:57:04+00:00	mit	841
XKNX__xknx-234	diff --git a/examples/example_light_rgbw.py b/examples/example_light_rgbw.py new file mode 100644 index 00000000..dd060c98 --- /dev/null +++ b/examples/example_light_rgbw.py @@ -0,0 +1,49 @@ +"""Example for setting different colors on a RGBW light.""" +import asyncio + +from xknx import XKNX +from xknx.devices import RemoteValueColorRGBW + + +async def main(): + """Connect to KNX/IP bus and set different colors.""" + xknx = XKNX() + await xknx.start() + + rgbw = RemoteValueColorRGBW(xknx, + group_address='1/1/40', + group_address_state='1/1/41', + device_name="RGBWLight") + + await rgbw.set([255, 255, 255, 0, 15]) # cold-white + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 255, 15]) # warm-white + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 0, 15]) # off + await asyncio.sleep(1) + + await rgbw.set([255, 0, 0, 0]) # red + await asyncio.sleep(1) + await rgbw.set([0, 255, 0, 0]) # green + await asyncio.sleep(1) + await rgbw.set([0, 0, 255, 0]) # blue + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 0, 15]) # off + await asyncio.sleep(1) + + await rgbw.set([255, 255, 0, 0, 15]) + await asyncio.sleep(1) + await rgbw.set([0, 255, 255, 0, 15]) + await asyncio.sleep(1) + await rgbw.set([255, 0, 255, 0, 15]) + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 0, 15]) # off + await asyncio.sleep(1) + + await xknx.stop() + + +# pylint: disable=invalid-name +loop = asyncio.get_event_loop() +loop.run_until_complete(main()) +loop.close() diff --git a/xknx/devices/remote_value_color_rgbw.py b/xknx/devices/remote_value_color_rgbw.py index 6c2e436e..beea0ca9 100644 --- a/xknx/devices/remote_value_color_rgbw.py +++ b/xknx/devices/remote_value_color_rgbw.py @@ -35,19 +35,23 @@ class RemoteValueColorRGBW(RemoteValue): Convert value (4-6 bytes) to payload (6 bytes). * Structure of DPT 251.600 - Bytes 0, 1: - * Bit 0-11: 0 - * Bit 12,13,14,15: R,G,B,W value valid? - Byte 2: R value - Byte 3: G value - Byte 4: B value - Byte 5: W value + Byte 0: R value + Byte 1: G value + Byte 2: B value + Byte 3: W value + Byte 4: 0x00 (reserved) + Byte 5: + * Bit 0: W value valid? + * Bit 1: B value valid? + * Bit 2: G value valid? + * Bit 3: R value valid? + * Bit 4-7: 0 In case we receive * > 6 bytes: error * 6 bytes: all bytes are passed through - * 5 bytes: 0x00 left padding - * 4 bytes: 0x000f left padding + * 5 bytes: 0x00?? fill up to 6 bytes + * 4 bytes: 0x000f right padding to 6 bytes * < 4 bytes: error """ if not isinstance(value, (list, tuple)): @@ -56,12 +60,16 @@ class RemoteValueColorRGBW(RemoteValue): if len(value) < 4 or len(value) > 6: raise ConversionError("Cannot serialize value to DPT 251.600 (wrong length, expecting list of 4-6 bytes)", value=value, type=type(value)) - rgbw = value[len(value)-4:] + rgbw = value[:4] if any(not isinstance(color, int) for color in rgbw) \ or any(color < 0 for color in rgbw) \ or any(color > 255 for color in rgbw): raise ConversionError("Cannot serialize DPT 251.600 (wrong RGBW values)", value=value) - return DPTArray([0x00, 0x0f][:6-len(value)] + list(value)) + if len(value) < 5: + return DPTArray(list(rgbw) + [0x00, 0x0f]) + if len(value) < 6: + return DPTArray(list(rgbw) + [0x00] + list(value[4:])) + return DPTArray(value) def from_knx(self, payload): """ @@ -72,7 +80,7 @@ class RemoteValueColorRGBW(RemoteValue): """ result = [] for i in range(0, len(payload.value) - 2): - valid = payload.value[1] & (0x08 >> i) != 0 - result.append(payload.value[2 + i] if valid else self.previous_value[i]) + valid = (payload.value[5] & (0x08 >> i)) != 0 # R,G,B,W value valid? + result.append(payload.value[i] if valid else self.previous_value[i]) self.previous_value = result return result diff --git a/xknx/exceptions/exception.py b/xknx/exceptions/exception.py index 879e14b2..626299bd 100644 --- a/xknx/exceptions/exception.py +++ b/xknx/exceptions/exception.py @@ -6,7 +6,15 @@ class XKNXException(Exception): def __eq__(self, other): """Equal operator.""" - return self.__dict__ == other.__dict__ + return repr(self) == repr(other) + + def __hash__(self): + """Hash function.""" + return hash(str(self)) + + def __repr__(self): + """Representation of object.""" + return str(self) class CouldNotParseTelegram(XKNXException): @@ -14,7 +22,7 @@ class CouldNotParseTelegram(XKNXException): def __init__(self, description, kwargs): """Initialize CouldNotParseTelegram class.""" - super().__init__("Could not parse Telegram") + super().__init__() self.description = description self.parameter = kwargs @@ -32,7 +40,7 @@ class CouldNotParseKNXIP(XKNXException): def __init__(self, description=""): """Initialize CouldNotParseTelegram class.""" - super().__init__("Could not parse KNXIP") + super().__init__() self.description = description def __str__(self): @@ -46,7 +54,7 @@ class ConversionError(XKNXException): def __init__(self, description, kwargs): """Initialize ConversionError class.""" - super().__init__("Conversion Error") + super().__init__() self.description = description self.parameter = kwargs @@ -63,7 +71,7 @@ class CouldNotParseAddress(XKNXException): def __init__(self, address=None): """Initialize CouldNotParseAddress class.""" - super().__init__("Could not parse address") + super().__init__() self.address = address def __str__(self): @@ -76,7 +84,7 @@ class DeviceIllegalValue(XKNXException): def __init__(self, value, description): """Initialize DeviceIllegalValue class.""" - super().__init__("Illegal value for device") + super().__init__() self.value = value self.description = description	XKNX/xknx	4b71c28db4cde694695da3dfad0072dd5383717f	diff --git a/test/core_tests/exceptions_test.py b/test/core_tests/exceptions_test.py new file mode 100644 index 00000000..41fc1b74 --- /dev/null +++ b/test/core_tests/exceptions_test.py @@ -0,0 +1,51 @@ +"""Unit tests for exceptions""" +import pytest + +from xknx.exceptions import ( + ConversionError, CouldNotParseAddress, CouldNotParseKNXIP, + CouldNotParseTelegram, DeviceIllegalValue, XKNXException) + + [email protected]( + "base,equal,diff", + [ + ( + ConversionError("desc1"), + ConversionError("desc1"), + ConversionError("desc2"), + ), + ( + CouldNotParseAddress(123), + CouldNotParseAddress(123), + CouldNotParseAddress(321), + ), + ( + CouldNotParseKNXIP("desc1"), + CouldNotParseKNXIP("desc1"), + CouldNotParseKNXIP("desc2"), + ), + ( + CouldNotParseTelegram("desc", arg1=1, arg2=2), + CouldNotParseTelegram("desc", arg1=1, arg2=2), + CouldNotParseTelegram("desc", arg1=2, arg2=1), + ), + ( + DeviceIllegalValue("value1", "desc"), + DeviceIllegalValue("value1", "desc"), + DeviceIllegalValue("value1", "desc2"), + ), + ( + XKNXException("desc1"), + XKNXException("desc1"), + XKNXException("desc2"), + ), + ], +) +def test_exceptions(base, equal, diff): + """Test hashability and repr of exceptions.""" + assert hash(base) == hash(equal) + assert hash(base) != hash(diff) + assert base == equal + assert base != diff + assert repr(base) == repr(equal) + assert repr(base) != repr(diff) diff --git a/test/devices_tests/light_test.py b/test/devices_tests/light_test.py index b6283672..5de6eddf 100644 --- a/test/devices_tests/light_test.py +++ b/test/devices_tests/light_test.py @@ -318,7 +318,7 @@ class TestLight(unittest.TestCase): self.assertEqual(xknx.telegrams.qsize(), 1) telegram = xknx.telegrams.get_nowait() self.assertEqual(telegram, - Telegram(GroupAddress('1/2/5'), payload=DPTArray((0, 15, 23, 24, 25, 26)))) + Telegram(GroupAddress('1/2/5'), payload=DPTArray((23, 24, 25, 26, 0, 15)))) self.assertEqual(light.current_color, ([23, 24, 25], 26)) def test_set_color_rgbw_not_possible(self): @@ -489,7 +489,7 @@ class TestLight(unittest.TestCase): group_address_color='1/2/4', group_address_rgbw='1/2/5') self.assertEqual(light.current_color, (None, None)) - telegram = Telegram(GroupAddress('1/2/5'), payload=DPTArray((0, 15, 23, 24, 25, 26))) + telegram = Telegram(GroupAddress('1/2/5'), payload=DPTArray((23, 24, 25, 26, 0, 15))) self.loop.run_until_complete(asyncio.Task(light.process(telegram))) self.assertEqual(light.current_color, ([23, 24, 25], 26)) diff --git a/test/devices_tests/remote_value_color_rgbw_test.py b/test/devices_tests/remote_value_color_rgbw_test.py index 2a56d3b0..d352c299 100644 --- a/test/devices_tests/remote_value_color_rgbw_test.py +++ b/test/devices_tests/remote_value_color_rgbw_test.py @@ -26,32 +26,32 @@ class TestRemoteValueColorRGBW(unittest.TestCase): remote_value = RemoteValueColorRGBW(xknx) input_list = [100, 101, 102, 127] input_tuple = (100, 101, 102, 127) - expected = DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x7f)) + expected = DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x0f)) self.assertEqual(remote_value.to_knx(input_tuple), expected) self.assertEqual(remote_value.to_knx(input_list), expected) - self.assertEqual(remote_value.to_knx((15,) + input_tuple), expected) - self.assertEqual(remote_value.to_knx([15] + input_list), expected) - self.assertEqual(remote_value.to_knx((0, 15) + input_tuple), expected) - self.assertEqual(remote_value.to_knx([0, 15] + input_list), expected) + self.assertEqual(remote_value.to_knx(input_tuple + (15,)), expected) + self.assertEqual(remote_value.to_knx(input_list + [15]), expected) + self.assertEqual(remote_value.to_knx(input_tuple + (0, 15)), expected) + self.assertEqual(remote_value.to_knx(input_list + [0, 15]), expected) def test_from_knx(self): """Test from_knx function with normal operation.""" xknx = XKNX(loop=self.loop) remote_value = RemoteValueColorRGBW(xknx) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x00, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x00))), [0, 0, 0, 0]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x0f))), [100, 101, 102, 127]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x00, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x00))), [100, 101, 102, 127]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x09, 0xff, 0x65, 0x66, 0xff))), + remote_value.from_knx(DPTArray((0xff, 0x65, 0x66, 0xff, 0x00, 0x09))), [255, 101, 102, 255]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x01, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x01))), [255, 101, 102, 127]) def test_to_knx_error(self): @@ -90,7 +90,7 @@ class TestRemoteValueColorRGBW(unittest.TestCase): telegram, Telegram( GroupAddress('1/2/3'), - payload=DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x67)))) + payload=DPTArray((0x64, 0x65, 0x66, 0x67, 0x00, 0x0f)))) self.loop.run_until_complete(asyncio.Task(remote_value.set((100, 101, 104, 105)))) self.assertEqual(xknx.telegrams.qsize(), 1) telegram = xknx.telegrams.get_nowait() @@ -98,7 +98,7 @@ class TestRemoteValueColorRGBW(unittest.TestCase): telegram, Telegram( GroupAddress('1/2/3'), - payload=DPTArray((0x00, 0x0f, 0x64, 0x65, 0x68, 0x69)))) + payload=DPTArray((0x64, 0x65, 0x68, 0x69, 0x00, 0x0f)))) def test_process(self): """Test process telegram.""" @@ -108,7 +108,7 @@ class TestRemoteValueColorRGBW(unittest.TestCase): group_address=GroupAddress("1/2/3")) telegram = Telegram( group_address=GroupAddress("1/2/3"), - payload=DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x67))) + payload=DPTArray((0x64, 0x65, 0x66, 0x67, 0x00, 0x0f))) self.loop.run_until_complete(asyncio.Task(remote_value.process(telegram))) self.assertEqual(remote_value.value, [100, 101, 102, 103])	XKNXException is an unhashable exception Description of problem: Seem the XKNXException exception is not hashable causing problems with python traceback module: https://bugs.python.org/issue28603. Oddly that aught to have been solved already. - [ ] using xknx standalone - [X] using Home-Assistant knx plugin Version information: - xknx / Home-Assistant release with the issue: - last working xknx / Home-Assistant release (if known): 0.98 KNX installation: <!-- Please provide details about your installation. - Manufacturer and model of relevant actors, sensors or interfaces. - if you have access to ETS: - provide relevant group address parameters (DPT, Flags) - if applicable: excerpt of bus monitor output --> Problem-relevant `xknx.yaml` or `configuration.yaml` entries (fill out even if it seems unimportant): Traceback (if applicable): Aug 22 08:18:24 hass hass[35975]: TypeError: unhashable type: 'XKNXException' Aug 22 08:18:24 hass hass[35975]: _seen.add(exc_value) Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/traceback.py", line 462, in __init__ Aug 22 08:18:24 hass hass[35975]: type(value), value, tb, limit=limit).format(chain=chain): Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/traceback.py", line 100, in print_exception Aug 22 08:18:24 hass hass[35975]: traceback.print_exception(ei[0], ei[1], tb, None, sio) Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/logging/__init__.py", line 533, in formatException Aug 22 08:18:24 hass hass[35975]: record.exc_text = self.formatException(record.exc_info) Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/logging/__init__.py", line 583, in format Aug 22 08:18:24 hass hass[35975]: return fmt.format(record) Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/logging/__init__.py", line 838, in format Aug 22 08:18:24 hass hass[35975]: msg = self.format(record) Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/logging/__init__.py", line 992, in emit	4b71c28db4cde694695da3dfad0072dd5383717f	[ "test/core_tests/exceptions_test.py::test_exceptions[base0-equal0-diff0]", "test/core_tests/exceptions_test.py::test_exceptions[base1-equal1-diff1]", "test/core_tests/exceptions_test.py::test_exceptions[base2-equal2-diff2]", "test/core_tests/exceptions_test.py::test_exceptions[base3-equal3-diff3]", "test/core_tests/exceptions_test.py::test_exceptions[base4-equal4-diff4]", "test/core_tests/exceptions_test.py::test_exceptions[base5-equal5-diff5]", "test/devices_tests/light_test.py::TestLight::test_process_color_rgbw", "test/devices_tests/light_test.py::TestLight::test_set_color_rgbw", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_from_knx", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_process", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_set", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_to_knx" ]	[ "test/devices_tests/light_test.py::TestLight::test_do", "test/devices_tests/light_test.py::TestLight::test_has_group_address", "test/devices_tests/light_test.py::TestLight::test_process_color", "test/devices_tests/light_test.py::TestLight::test_process_color_temperature", "test/devices_tests/light_test.py::TestLight::test_process_color_temperature_payload_invalid_length", "test/devices_tests/light_test.py::TestLight::test_process_color_temperature_wrong_payload", "test/devices_tests/light_test.py::TestLight::test_process_dimm", "test/devices_tests/light_test.py::TestLight::test_process_dimm_payload_invalid_length", "test/devices_tests/light_test.py::TestLight::test_process_dimm_wrong_payload", "test/devices_tests/light_test.py::TestLight::test_process_switch", "test/devices_tests/light_test.py::TestLight::test_process_switch_callback", "test/devices_tests/light_test.py::TestLight::test_process_tunable_white", "test/devices_tests/light_test.py::TestLight::test_process_tunable_white_payload_invalid_length", "test/devices_tests/light_test.py::TestLight::test_process_tunable_white_wrong_payload", "test/devices_tests/light_test.py::TestLight::test_set_brightness", "test/devices_tests/light_test.py::TestLight::test_set_brightness_not_dimmable", "test/devices_tests/light_test.py::TestLight::test_set_color", "test/devices_tests/light_test.py::TestLight::test_set_color_not_possible", "test/devices_tests/light_test.py::TestLight::test_set_color_rgbw_not_possible", "test/devices_tests/light_test.py::TestLight::test_set_color_temp", "test/devices_tests/light_test.py::TestLight::test_set_color_temp_unsupported", "test/devices_tests/light_test.py::TestLight::test_set_off", "test/devices_tests/light_test.py::TestLight::test_set_on", "test/devices_tests/light_test.py::TestLight::test_set_tw", "test/devices_tests/light_test.py::TestLight::test_set_tw_unsupported", "test/devices_tests/light_test.py::TestLight::test_supports_color_false", "test/devices_tests/light_test.py::TestLight::test_supports_color_temp_false", "test/devices_tests/light_test.py::TestLight::test_supports_color_temp_true", "test/devices_tests/light_test.py::TestLight::test_supports_color_true", "test/devices_tests/light_test.py::TestLight::test_supports_dimm_no", "test/devices_tests/light_test.py::TestLight::test_supports_dimm_yes", "test/devices_tests/light_test.py::TestLight::test_supports_rgbw_false", "test/devices_tests/light_test.py::TestLight::test_supports_rgbw_true", "test/devices_tests/light_test.py::TestLight::test_supports_tw_no", "test/devices_tests/light_test.py::TestLight::test_supports_tw_yes", "test/devices_tests/light_test.py::TestLight::test_sync", "test/devices_tests/light_test.py::TestLight::test_sync_state_address", "test/devices_tests/light_test.py::TestLight::test_wrong_do", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_to_knx_error", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_to_process_error" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2019-09-10 16:14:51+00:00	mit	842
XKNX__xknx-235	diff --git a/examples/example_light_rgbw.py b/examples/example_light_rgbw.py new file mode 100644 index 00000000..dd060c98 --- /dev/null +++ b/examples/example_light_rgbw.py @@ -0,0 +1,49 @@ +"""Example for setting different colors on a RGBW light.""" +import asyncio + +from xknx import XKNX +from xknx.devices import RemoteValueColorRGBW + + +async def main(): + """Connect to KNX/IP bus and set different colors.""" + xknx = XKNX() + await xknx.start() + + rgbw = RemoteValueColorRGBW(xknx, + group_address='1/1/40', + group_address_state='1/1/41', + device_name="RGBWLight") + + await rgbw.set([255, 255, 255, 0, 15]) # cold-white + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 255, 15]) # warm-white + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 0, 15]) # off + await asyncio.sleep(1) + + await rgbw.set([255, 0, 0, 0]) # red + await asyncio.sleep(1) + await rgbw.set([0, 255, 0, 0]) # green + await asyncio.sleep(1) + await rgbw.set([0, 0, 255, 0]) # blue + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 0, 15]) # off + await asyncio.sleep(1) + + await rgbw.set([255, 255, 0, 0, 15]) + await asyncio.sleep(1) + await rgbw.set([0, 255, 255, 0, 15]) + await asyncio.sleep(1) + await rgbw.set([255, 0, 255, 0, 15]) + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 0, 15]) # off + await asyncio.sleep(1) + + await xknx.stop() + + +# pylint: disable=invalid-name +loop = asyncio.get_event_loop() +loop.run_until_complete(main()) +loop.close() diff --git a/xknx/devices/remote_value_color_rgbw.py b/xknx/devices/remote_value_color_rgbw.py index 6c2e436e..beea0ca9 100644 --- a/xknx/devices/remote_value_color_rgbw.py +++ b/xknx/devices/remote_value_color_rgbw.py @@ -35,19 +35,23 @@ class RemoteValueColorRGBW(RemoteValue): Convert value (4-6 bytes) to payload (6 bytes). * Structure of DPT 251.600 - Bytes 0, 1: - * Bit 0-11: 0 - * Bit 12,13,14,15: R,G,B,W value valid? - Byte 2: R value - Byte 3: G value - Byte 4: B value - Byte 5: W value + Byte 0: R value + Byte 1: G value + Byte 2: B value + Byte 3: W value + Byte 4: 0x00 (reserved) + Byte 5: + * Bit 0: W value valid? + * Bit 1: B value valid? + * Bit 2: G value valid? + * Bit 3: R value valid? + * Bit 4-7: 0 In case we receive * > 6 bytes: error * 6 bytes: all bytes are passed through - * 5 bytes: 0x00 left padding - * 4 bytes: 0x000f left padding + * 5 bytes: 0x00?? fill up to 6 bytes + * 4 bytes: 0x000f right padding to 6 bytes * < 4 bytes: error """ if not isinstance(value, (list, tuple)): @@ -56,12 +60,16 @@ class RemoteValueColorRGBW(RemoteValue): if len(value) < 4 or len(value) > 6: raise ConversionError("Cannot serialize value to DPT 251.600 (wrong length, expecting list of 4-6 bytes)", value=value, type=type(value)) - rgbw = value[len(value)-4:] + rgbw = value[:4] if any(not isinstance(color, int) for color in rgbw) \ or any(color < 0 for color in rgbw) \ or any(color > 255 for color in rgbw): raise ConversionError("Cannot serialize DPT 251.600 (wrong RGBW values)", value=value) - return DPTArray([0x00, 0x0f][:6-len(value)] + list(value)) + if len(value) < 5: + return DPTArray(list(rgbw) + [0x00, 0x0f]) + if len(value) < 6: + return DPTArray(list(rgbw) + [0x00] + list(value[4:])) + return DPTArray(value) def from_knx(self, payload): """ @@ -72,7 +80,7 @@ class RemoteValueColorRGBW(RemoteValue): """ result = [] for i in range(0, len(payload.value) - 2): - valid = payload.value[1] & (0x08 >> i) != 0 - result.append(payload.value[2 + i] if valid else self.previous_value[i]) + valid = (payload.value[5] & (0x08 >> i)) != 0 # R,G,B,W value valid? + result.append(payload.value[i] if valid else self.previous_value[i]) self.previous_value = result return result diff --git a/xknx/exceptions/exception.py b/xknx/exceptions/exception.py index 879e14b2..626299bd 100644 --- a/xknx/exceptions/exception.py +++ b/xknx/exceptions/exception.py @@ -6,7 +6,15 @@ class XKNXException(Exception): def __eq__(self, other): """Equal operator.""" - return self.__dict__ == other.__dict__ + return repr(self) == repr(other) + + def __hash__(self): + """Hash function.""" + return hash(str(self)) + + def __repr__(self): + """Representation of object.""" + return str(self) class CouldNotParseTelegram(XKNXException): @@ -14,7 +22,7 @@ class CouldNotParseTelegram(XKNXException): def __init__(self, description, kwargs): """Initialize CouldNotParseTelegram class.""" - super().__init__("Could not parse Telegram") + super().__init__() self.description = description self.parameter = kwargs @@ -32,7 +40,7 @@ class CouldNotParseKNXIP(XKNXException): def __init__(self, description=""): """Initialize CouldNotParseTelegram class.""" - super().__init__("Could not parse KNXIP") + super().__init__() self.description = description def __str__(self): @@ -46,7 +54,7 @@ class ConversionError(XKNXException): def __init__(self, description, kwargs): """Initialize ConversionError class.""" - super().__init__("Conversion Error") + super().__init__() self.description = description self.parameter = kwargs @@ -63,7 +71,7 @@ class CouldNotParseAddress(XKNXException): def __init__(self, address=None): """Initialize CouldNotParseAddress class.""" - super().__init__("Could not parse address") + super().__init__() self.address = address def __str__(self): @@ -76,7 +84,7 @@ class DeviceIllegalValue(XKNXException): def __init__(self, value, description): """Initialize DeviceIllegalValue class.""" - super().__init__("Illegal value for device") + super().__init__() self.value = value self.description = description diff --git a/xknx/knxip/cemi_frame.py b/xknx/knxip/cemi_frame.py index ec925a83..3f023c62 100644 --- a/xknx/knxip/cemi_frame.py +++ b/xknx/knxip/cemi_frame.py @@ -105,7 +105,10 @@ class CEMIFrame(KNXIPBody): def from_knx(self, raw): """Parse/deserialize from KNX/IP raw data.""" - self.code = CEMIMessageCode(raw[0]) + try: + self.code = CEMIMessageCode(raw[0]) + except ValueError: + raise CouldNotParseKNXIP("Could not understand CEMIMessageCode: {0} ".format(raw[0])) if self.code == CEMIMessageCode.L_DATA_IND or \ self.code == CEMIMessageCode.L_Data_REQ or \ @@ -140,7 +143,11 @@ class CEMIFrame(KNXIPBody): tpci_apci = cemi[9 + addil] * 256 + cemi[10 + addil] - self.cmd = APCICommand(tpci_apci & 0xFFC0) + try: + self.cmd = APCICommand(tpci_apci & 0xFFC0) + except ValueError: + raise CouldNotParseKNXIP( + "APCI not supported: {0:#012b}".format(tpci_apci & 0xFFC0)) apdu = cemi[10 + addil:] if len(apdu) != self.mpdu_len:	XKNX/xknx	4b71c28db4cde694695da3dfad0072dd5383717f	diff --git a/test/core_tests/exceptions_test.py b/test/core_tests/exceptions_test.py new file mode 100644 index 00000000..41fc1b74 --- /dev/null +++ b/test/core_tests/exceptions_test.py @@ -0,0 +1,51 @@ +"""Unit tests for exceptions""" +import pytest + +from xknx.exceptions import ( + ConversionError, CouldNotParseAddress, CouldNotParseKNXIP, + CouldNotParseTelegram, DeviceIllegalValue, XKNXException) + + [email protected]( + "base,equal,diff", + [ + ( + ConversionError("desc1"), + ConversionError("desc1"), + ConversionError("desc2"), + ), + ( + CouldNotParseAddress(123), + CouldNotParseAddress(123), + CouldNotParseAddress(321), + ), + ( + CouldNotParseKNXIP("desc1"), + CouldNotParseKNXIP("desc1"), + CouldNotParseKNXIP("desc2"), + ), + ( + CouldNotParseTelegram("desc", arg1=1, arg2=2), + CouldNotParseTelegram("desc", arg1=1, arg2=2), + CouldNotParseTelegram("desc", arg1=2, arg2=1), + ), + ( + DeviceIllegalValue("value1", "desc"), + DeviceIllegalValue("value1", "desc"), + DeviceIllegalValue("value1", "desc2"), + ), + ( + XKNXException("desc1"), + XKNXException("desc1"), + XKNXException("desc2"), + ), + ], +) +def test_exceptions(base, equal, diff): + """Test hashability and repr of exceptions.""" + assert hash(base) == hash(equal) + assert hash(base) != hash(diff) + assert base == equal + assert base != diff + assert repr(base) == repr(equal) + assert repr(base) != repr(diff) diff --git a/test/devices_tests/light_test.py b/test/devices_tests/light_test.py index b6283672..5de6eddf 100644 --- a/test/devices_tests/light_test.py +++ b/test/devices_tests/light_test.py @@ -318,7 +318,7 @@ class TestLight(unittest.TestCase): self.assertEqual(xknx.telegrams.qsize(), 1) telegram = xknx.telegrams.get_nowait() self.assertEqual(telegram, - Telegram(GroupAddress('1/2/5'), payload=DPTArray((0, 15, 23, 24, 25, 26)))) + Telegram(GroupAddress('1/2/5'), payload=DPTArray((23, 24, 25, 26, 0, 15)))) self.assertEqual(light.current_color, ([23, 24, 25], 26)) def test_set_color_rgbw_not_possible(self): @@ -489,7 +489,7 @@ class TestLight(unittest.TestCase): group_address_color='1/2/4', group_address_rgbw='1/2/5') self.assertEqual(light.current_color, (None, None)) - telegram = Telegram(GroupAddress('1/2/5'), payload=DPTArray((0, 15, 23, 24, 25, 26))) + telegram = Telegram(GroupAddress('1/2/5'), payload=DPTArray((23, 24, 25, 26, 0, 15))) self.loop.run_until_complete(asyncio.Task(light.process(telegram))) self.assertEqual(light.current_color, ([23, 24, 25], 26)) diff --git a/test/devices_tests/remote_value_color_rgbw_test.py b/test/devices_tests/remote_value_color_rgbw_test.py index 2a56d3b0..d352c299 100644 --- a/test/devices_tests/remote_value_color_rgbw_test.py +++ b/test/devices_tests/remote_value_color_rgbw_test.py @@ -26,32 +26,32 @@ class TestRemoteValueColorRGBW(unittest.TestCase): remote_value = RemoteValueColorRGBW(xknx) input_list = [100, 101, 102, 127] input_tuple = (100, 101, 102, 127) - expected = DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x7f)) + expected = DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x0f)) self.assertEqual(remote_value.to_knx(input_tuple), expected) self.assertEqual(remote_value.to_knx(input_list), expected) - self.assertEqual(remote_value.to_knx((15,) + input_tuple), expected) - self.assertEqual(remote_value.to_knx([15] + input_list), expected) - self.assertEqual(remote_value.to_knx((0, 15) + input_tuple), expected) - self.assertEqual(remote_value.to_knx([0, 15] + input_list), expected) + self.assertEqual(remote_value.to_knx(input_tuple + (15,)), expected) + self.assertEqual(remote_value.to_knx(input_list + [15]), expected) + self.assertEqual(remote_value.to_knx(input_tuple + (0, 15)), expected) + self.assertEqual(remote_value.to_knx(input_list + [0, 15]), expected) def test_from_knx(self): """Test from_knx function with normal operation.""" xknx = XKNX(loop=self.loop) remote_value = RemoteValueColorRGBW(xknx) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x00, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x00))), [0, 0, 0, 0]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x0f))), [100, 101, 102, 127]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x00, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x00))), [100, 101, 102, 127]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x09, 0xff, 0x65, 0x66, 0xff))), + remote_value.from_knx(DPTArray((0xff, 0x65, 0x66, 0xff, 0x00, 0x09))), [255, 101, 102, 255]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x01, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x01))), [255, 101, 102, 127]) def test_to_knx_error(self): @@ -90,7 +90,7 @@ class TestRemoteValueColorRGBW(unittest.TestCase): telegram, Telegram( GroupAddress('1/2/3'), - payload=DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x67)))) + payload=DPTArray((0x64, 0x65, 0x66, 0x67, 0x00, 0x0f)))) self.loop.run_until_complete(asyncio.Task(remote_value.set((100, 101, 104, 105)))) self.assertEqual(xknx.telegrams.qsize(), 1) telegram = xknx.telegrams.get_nowait() @@ -98,7 +98,7 @@ class TestRemoteValueColorRGBW(unittest.TestCase): telegram, Telegram( GroupAddress('1/2/3'), - payload=DPTArray((0x00, 0x0f, 0x64, 0x65, 0x68, 0x69)))) + payload=DPTArray((0x64, 0x65, 0x68, 0x69, 0x00, 0x0f)))) def test_process(self): """Test process telegram.""" @@ -108,7 +108,7 @@ class TestRemoteValueColorRGBW(unittest.TestCase): group_address=GroupAddress("1/2/3")) telegram = Telegram( group_address=GroupAddress("1/2/3"), - payload=DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x67))) + payload=DPTArray((0x64, 0x65, 0x66, 0x67, 0x00, 0x0f))) self.loop.run_until_complete(asyncio.Task(remote_value.process(telegram))) self.assertEqual(remote_value.value, [100, 101, 102, 103]) diff --git a/test/knxip_tests/cemi_frame_test.py b/test/knxip_tests/cemi_frame_test.py new file mode 100644 index 00000000..dae3f63c --- /dev/null +++ b/test/knxip_tests/cemi_frame_test.py @@ -0,0 +1,71 @@ +"""Tests for the CEMIFrame object""" + +from unittest.mock import MagicMock + +from pytest import fixture, raises + +from xknx.exceptions import CouldNotParseKNXIP +from xknx.knx import DPTBinary, PhysicalAddress +from xknx.knxip.cemi_frame import CEMIFrame +from xknx.knxip.knxip_enum import APCICommand, CEMIMessageCode + + +def get_data(code, adil, flags, src, dst, mpdu_len, tpci_apci, payload): + return [ + code, + adil, # adil + (flags >> 8) & 255, # flags + flags & 255, # flags + (src >> 8) & 255, # src + src & 255, # src + (dst >> 8) & 255, # dst + dst & 255, # dst + mpdu_len, # mpdu_len + (tpci_apci >> 8) & 255, # tpci_apci + tpci_apci & 255, # tpci_apci + payload, # payload + ] + + +@fixture(name="frame") +def fixture_frame(): + """Fixture to get a simple mocked frame""" + xknx = MagicMock() + return CEMIFrame(xknx) + + +def test_valid_command(frame): + """Test for valid frame parsing""" + packet_len = frame.from_knx(get_data(0x29, 0, 0, 0, 0, 1, 0, [])) + assert frame.code == CEMIMessageCode.L_DATA_IND + assert frame.cmd == APCICommand.GROUP_READ + assert frame.flags == 0 + assert frame.mpdu_len == 1 + assert frame.payload == DPTBinary(0) + assert frame.src_addr == PhysicalAddress(0) + assert frame.dst_addr == PhysicalAddress(0) + assert packet_len == 11 + + +def test_invalid_tpci_apci(frame): + """Test for invalid APCICommand""" + with raises(CouldNotParseKNXIP, match=r".APCI not supported: ."): + frame.from_knx(get_data(0x29, 0, 0, 0, 0, 1, 0xFFC0, [])) + + +def test_invalid_apdu_len(frame): + """Test for invalid apdu len""" + with raises(CouldNotParseKNXIP, match=r".APDU LEN should be ."): + frame.from_knx(get_data(0x29, 0, 0, 0, 0, 2, 0, [])) + + +def test_invalid_invalid_len(frame): + """Test for invalid cemi len""" + with raises(CouldNotParseKNXIP, match=r".CEMI too small"): + frame.from_knx(get_data(0x29, 0, 0, 0, 0, 2, 0, [])[:5]) + + +def test_invalid_invalid_code(frame): + """Test for invalid cemi code""" + with raises(CouldNotParseKNXIP, match=r".*Could not understand CEMIMessageCode"): + frame.from_knx(get_data(0x0, 0, 0, 0, 0, 2, 0, []))	ValueError: [448,256] is not a valid APCICommand Description of problem: Exception during processing of messages, likely while ETS is communicating with new Secure IP Interface. - [ ] using xknx standalone - [X] using Home-Assistant knx plugin Version information: - xknx / Home-Assistant release with the issue: 0.98 - last working xknx / Home-Assistant release (if known): None KNX installation: <!-- Please provide details about your installation. - Manufacturer and model of relevant actors, sensors or interfaces. - if you have access to ETS: - provide relevant group address parameters (DPT, Flags) - if applicable: excerpt of bus monitor output --> ETS 5.7.2 Problem-relevant `xknx.yaml` or `configuration.yaml` entries (fill out even if it seems unimportant): Traceback (if applicable): ``` Aug 19 19:09:24 hass hass[32967]: Traceback (most recent call last): Aug 19 19:09:24 hass hass[32967]: File "/usr/lib/python3.6/asyncio/events.py", line 127, in _run Aug 19 19:09:24 hass hass[32967]: self._callback(*self._args) Aug 19 19:09:24 hass hass[32967]: File "/usr/lib/python3.6/asyncio/selector_events.py", line 1078, in _read_ready Aug 19 19:09:24 hass hass[32967]: self._protocol.datagram_received(data, addr) Aug 19 19:09:24 hass hass[32967]: File "/home/homeassistant/env/lib/python3.6/site-packages/xknx/io/udp_client.py", line 55, in datagram_received Aug 19 19:09:24 hass hass[32967]: self.data_received_callback(data) Aug 19 19:09:24 hass hass[32967]: File "/home/homeassistant/env/lib/python3.6/site-packages/xknx/io/udp_client.py", line 87, in data_received_callback Aug 19 19:09:24 hass hass[32967]: knxipframe.from_knx(raw) Aug 19 19:09:24 hass hass[32967]: File "/home/homeassistant/env/lib/python3.6/site-packages/xknx/knxip/knxip.py", line 78, in from_knx Aug 19 19:09:24 hass hass[32967]: pos += self.body.from_knx(data[pos:]) Aug 19 19:09:24 hass hass[32967]: File "/home/homeassistant/env/lib/python3.6/site-packages/xknx/knxip/tunnelling_request.py", line 48, in from_knx Aug 19 19:09:24 hass hass[32967]: pos += self.cemi.from_knx(raw[pos:]) Aug 19 19:09:24 hass hass[32967]: File "/home/homeassistant/env/lib/python3.6/site-packages/xknx/knxip/cemi_frame.py", line 113, in from_knx Aug 19 19:09:24 hass hass[32967]: return self.from_knx_data_link_layer(raw) Aug 19 19:09:24 hass hass[32967]: File "/home/homeassistant/env/lib/python3.6/site-packages/xknx/knxip/cemi_frame.py", line 143, in from_knx_data_link_layer Aug 19 19:09:24 hass hass[32967]: self.cmd = APCICommand(tpci_apci & 0xFFC0) Aug 19 19:09:24 hass hass[32967]: File "/usr/lib/python3.6/enum.py", line 291, in __call__ Aug 19 19:09:24 hass hass[32967]: return cls.__new__(cls, value) Aug 19 19:09:24 hass hass[32967]: File "/usr/lib/python3.6/enum.py", line 533, in __new__ Aug 19 19:09:24 hass hass[32967]: return cls._missing_(value) Aug 19 19:09:24 hass hass[32967]: File "/usr/lib/python3.6/enum.py", line 546, in _missing_ Aug 19 19:09:24 hass hass[32967]: raise ValueError("%r is not a valid %s" % (value, cls.__name__)) Aug 19 19:09:24 hass hass[32967]: ValueError: 448 is not a valid APCICommand ``` ``` Aug 22 08:15:49 hass hass[35975]: ValueError: 256 is not a valid APCICommand Aug 22 08:15:49 hass hass[35975]: raise ValueError("%r is not a valid %s" % (value, cls.__name__)) Aug 22 08:15:49 hass hass[35975]: File "/usr/lib/python3.6/enum.py", line 546, in _missing_ Aug 22 08:15:49 hass hass[35975]: return cls._missing_(value) Aug 22 08:15:49 hass hass[35975]: File "/usr/lib/python3.6/enum.py", line 533, in __new__ Aug 22 08:15:49 hass hass[35975]: return cls.__new__(cls, value) Aug 22 08:15:49 hass hass[35975]: File "/usr/lib/python3.6/enum.py", line 291, in __call__ Aug 22 08:15:49 hass hass[35975]: self.cmd = APCICommand(tpci_apci & 0xFFC0) Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/asyncio/base_events.py", line 1426, in _run_once Aug 22 08:18:24 hass hass[35975]: self._run_once() Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/asyncio/base_events.py", line 421, in run_forever Aug 22 08:18:24 hass hass[35975]: self.run_forever() Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/asyncio/base_events.py", line 454, in run_until_complete Aug 22 08:18:24 hass hass[35975]: return loop.run_until_complete(main) Aug 22 08:18:24 hass hass[35975]: File "/home/homeassistant/env/lib/python3.6/site-packages/homeassistant/util/async_.py", line 37, in asyncio_run Aug 22 08:18:24 hass hass[35975]: exit_code = asyncio_run(setup_and_run_hass(config_dir, args)) Aug 22 08:18:24 hass hass[35975]: File "/home/homeassistant/env/lib/python3.6/site-packages/homeassistant/__main__.py", line 419, in main Aug 22 08:18:24 hass hass[35975]: sys.exit(main()) Aug 22 08:18:24 hass hass[35975]: File "/home/homeassistant/env/bin/hass", line 10, in <module> ```	4b71c28db4cde694695da3dfad0072dd5383717f	[ "test/core_tests/exceptions_test.py::test_exceptions[base0-equal0-diff0]", "test/core_tests/exceptions_test.py::test_exceptions[base1-equal1-diff1]", "test/core_tests/exceptions_test.py::test_exceptions[base2-equal2-diff2]", "test/core_tests/exceptions_test.py::test_exceptions[base3-equal3-diff3]", "test/core_tests/exceptions_test.py::test_exceptions[base4-equal4-diff4]", "test/core_tests/exceptions_test.py::test_exceptions[base5-equal5-diff5]", "test/devices_tests/light_test.py::TestLight::test_process_color_rgbw", "test/devices_tests/light_test.py::TestLight::test_set_color_rgbw", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_from_knx", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_process", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_set", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_to_knx", "test/knxip_tests/cemi_frame_test.py::test_invalid_tpci_apci", "test/knxip_tests/cemi_frame_test.py::test_invalid_invalid_code" ]	[ "test/devices_tests/light_test.py::TestLight::test_do", "test/devices_tests/light_test.py::TestLight::test_has_group_address", "test/devices_tests/light_test.py::TestLight::test_process_color", "test/devices_tests/light_test.py::TestLight::test_process_color_temperature", "test/devices_tests/light_test.py::TestLight::test_process_color_temperature_payload_invalid_length", "test/devices_tests/light_test.py::TestLight::test_process_color_temperature_wrong_payload", "test/devices_tests/light_test.py::TestLight::test_process_dimm", "test/devices_tests/light_test.py::TestLight::test_process_dimm_payload_invalid_length", "test/devices_tests/light_test.py::TestLight::test_process_dimm_wrong_payload", "test/devices_tests/light_test.py::TestLight::test_process_switch", "test/devices_tests/light_test.py::TestLight::test_process_switch_callback", "test/devices_tests/light_test.py::TestLight::test_process_tunable_white", "test/devices_tests/light_test.py::TestLight::test_process_tunable_white_payload_invalid_length", "test/devices_tests/light_test.py::TestLight::test_process_tunable_white_wrong_payload", "test/devices_tests/light_test.py::TestLight::test_set_brightness", "test/devices_tests/light_test.py::TestLight::test_set_brightness_not_dimmable", "test/devices_tests/light_test.py::TestLight::test_set_color", "test/devices_tests/light_test.py::TestLight::test_set_color_not_possible", "test/devices_tests/light_test.py::TestLight::test_set_color_rgbw_not_possible", "test/devices_tests/light_test.py::TestLight::test_set_color_temp", "test/devices_tests/light_test.py::TestLight::test_set_color_temp_unsupported", "test/devices_tests/light_test.py::TestLight::test_set_off", "test/devices_tests/light_test.py::TestLight::test_set_on", "test/devices_tests/light_test.py::TestLight::test_set_tw", "test/devices_tests/light_test.py::TestLight::test_set_tw_unsupported", "test/devices_tests/light_test.py::TestLight::test_supports_color_false", "test/devices_tests/light_test.py::TestLight::test_supports_color_temp_false", "test/devices_tests/light_test.py::TestLight::test_supports_color_temp_true", "test/devices_tests/light_test.py::TestLight::test_supports_color_true", "test/devices_tests/light_test.py::TestLight::test_supports_dimm_no", "test/devices_tests/light_test.py::TestLight::test_supports_dimm_yes", "test/devices_tests/light_test.py::TestLight::test_supports_rgbw_false", "test/devices_tests/light_test.py::TestLight::test_supports_rgbw_true", "test/devices_tests/light_test.py::TestLight::test_supports_tw_no", "test/devices_tests/light_test.py::TestLight::test_supports_tw_yes", "test/devices_tests/light_test.py::TestLight::test_sync", "test/devices_tests/light_test.py::TestLight::test_sync_state_address", "test/devices_tests/light_test.py::TestLight::test_wrong_do", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_to_knx_error", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_to_process_error", "test/knxip_tests/cemi_frame_test.py::test_valid_command", "test/knxip_tests/cemi_frame_test.py::test_invalid_apdu_len", "test/knxip_tests/cemi_frame_test.py::test_invalid_invalid_len" ]	{ "failed_lite_validators": [ "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2019-09-10 16:47:37+00:00	mit	843
XKNX__xknx-271	diff --git a/xknx/exceptions/__init__.py b/xknx/exceptions/__init__.py index 0875fb6f..95609fa0 100644 --- a/xknx/exceptions/__init__.py +++ b/xknx/exceptions/__init__.py @@ -2,4 +2,5 @@ # flake8: noqa from .exception import ( ConversionError, CouldNotParseAddress, CouldNotParseKNXIP, - CouldNotParseTelegram, DeviceIllegalValue, XKNXException) + CouldNotParseTelegram, DeviceIllegalValue, UnsupportedCEMIMessage, + XKNXException) diff --git a/xknx/exceptions/exception.py b/xknx/exceptions/exception.py index 626299bd..18702952 100644 --- a/xknx/exceptions/exception.py +++ b/xknx/exceptions/exception.py @@ -39,7 +39,7 @@ class CouldNotParseKNXIP(XKNXException): """Exception class for wrong KNXIP data.""" def __init__(self, description=""): - """Initialize CouldNotParseTelegram class.""" + """Initialize CouldNotParseKNXIP class.""" super().__init__() self.description = description @@ -49,6 +49,20 @@ class CouldNotParseKNXIP(XKNXException): .format(self.description) +class UnsupportedCEMIMessage(XKNXException): + """Exception class for unsupported CEMI Messages.""" + + def __init__(self, description=""): + """Initialize UnsupportedCEMIMessage class.""" + super().__init__() + self.description = description + + def __str__(self): + """Return object as readable string.""" + return '<UnsupportedCEMIMessage description="{0}" />' \ + .format(self.description) + + class ConversionError(XKNXException): """Exception class for error while converting one type to another.""" diff --git a/xknx/knxip/cemi_frame.py b/xknx/knxip/cemi_frame.py index 1fc80ead..dffa5064 100644 --- a/xknx/knxip/cemi_frame.py +++ b/xknx/knxip/cemi_frame.py @@ -12,7 +12,8 @@ Documentation within: File: AN117 v02.01 KNX IP Communication Medium DV.pdf """ from xknx.dpt import DPTArray, DPTBinary -from xknx.exceptions import ConversionError, CouldNotParseKNXIP +from xknx.exceptions import ( + ConversionError, CouldNotParseKNXIP, UnsupportedCEMIMessage) from xknx.telegram import GroupAddress, PhysicalAddress, Telegram, TelegramType from .body import KNXIPBody @@ -106,20 +107,25 @@ class CEMIFrame(KNXIPBody): def from_knx(self, raw): """Parse/deserialize from KNX/IP raw data.""" try: - self.code = CEMIMessageCode(raw[0]) - except ValueError: - raise CouldNotParseKNXIP("Could not understand CEMIMessageCode: {0} ".format(raw[0])) - - if self.code == CEMIMessageCode.L_DATA_IND or \ - self.code == CEMIMessageCode.L_Data_REQ or \ - self.code == CEMIMessageCode.L_DATA_CON: - return self.from_knx_data_link_layer(raw) - raise CouldNotParseKNXIP("Could not understand CEMIMessageCode: {0} / {1}".format(self.code, raw[0])) + try: + self.code = CEMIMessageCode(raw[0]) + except ValueError: + raise UnsupportedCEMIMessage("CEMIMessageCode not implemented: {0} ".format(raw[0])) + + if self.code == CEMIMessageCode.L_DATA_IND or \ + self.code == CEMIMessageCode.L_Data_REQ or \ + self.code == CEMIMessageCode.L_DATA_CON: + return self.from_knx_data_link_layer(raw) + raise UnsupportedCEMIMessage("Could not handle CEMIMessageCode: {0} / {1}".format(self.code, raw[0])) + except UnsupportedCEMIMessage as unsupported_cemi_err: + self.xknx.logger.warning("Ignoring not implemented CEMI: %s", unsupported_cemi_err) + return len(raw) def from_knx_data_link_layer(self, cemi): """Parse L_DATA_IND, CEMIMessageCode.L_Data_REQ, CEMIMessageCode.L_DATA_CON.""" if len(cemi) < 11: - raise CouldNotParseKNXIP("CEMI too small") + # eg. ETS Line-Scan issues L_DATA_IND with length 10 + raise UnsupportedCEMIMessage("CEMI too small. Length: {0}; CEMI: {1}".format(len(cemi), cemi)) # AddIL (Additional Info Length), as specified within # KNX Chapter 3.6.3/4.1.4.3 "Additional information." @@ -146,7 +152,7 @@ class CEMIFrame(KNXIPBody): try: self.cmd = APCICommand(tpci_apci & 0xFFC0) except ValueError: - raise CouldNotParseKNXIP( + raise UnsupportedCEMIMessage( "APCI not supported: {0:#012b}".format(tpci_apci & 0xFFC0)) apdu = cemi[10 + addil:]	XKNX/xknx	9790cdb696285b5700ec06c571193a7feeb96a39	diff --git a/test/knxip_tests/cemi_frame_test.py b/test/knxip_tests/cemi_frame_test.py index b305a3b3..711762ec 100644 --- a/test/knxip_tests/cemi_frame_test.py +++ b/test/knxip_tests/cemi_frame_test.py @@ -5,7 +5,7 @@ from unittest.mock import MagicMock from pytest import fixture, raises from xknx.dpt import DPTBinary -from xknx.exceptions import CouldNotParseKNXIP +from xknx.exceptions import CouldNotParseKNXIP, UnsupportedCEMIMessage from xknx.knxip.cemi_frame import CEMIFrame from xknx.knxip.knxip_enum import APCICommand, CEMIMessageCode from xknx.telegram import PhysicalAddress @@ -50,8 +50,8 @@ def test_valid_command(frame): def test_invalid_tpci_apci(frame): """Test for invalid APCICommand""" - with raises(CouldNotParseKNXIP, match=r".APCI not supported: ."): - frame.from_knx(get_data(0x29, 0, 0, 0, 0, 1, 0xFFC0, [])) + with raises(UnsupportedCEMIMessage, match=r".APCI not supported: ."): + frame.from_knx_data_link_layer(get_data(0x29, 0, 0, 0, 0, 1, 0xFFC0, [])) def test_invalid_apdu_len(frame): @@ -62,11 +62,5 @@ def test_invalid_apdu_len(frame): def test_invalid_invalid_len(frame): """Test for invalid cemi len""" - with raises(CouldNotParseKNXIP, match=r".CEMI too small"): - frame.from_knx(get_data(0x29, 0, 0, 0, 0, 2, 0, [])[:5]) - - -def test_invalid_invalid_code(frame): - """Test for invalid cemi code""" - with raises(CouldNotParseKNXIP, match=r".Could not understand CEMIMessageCode"): - frame.from_knx(get_data(0x0, 0, 0, 0, 0, 2, 0, [])) + with raises(UnsupportedCEMIMessage, match=r".CEMI too small."): + frame.from_knx_data_link_layer(get_data(0x29, 0, 0, 0, 0, 2, 0, [])[:5])	Error when reading group addresses with timers I have an extensive KNX installation with all kinds of actors, sensors, switches, etc. My integration with Home Assistant works perfect, but I do get the following error in the logs when input is detected on an object linked to a timer: > Error doing job: Exception in callback UDPTransport._on_read_ready Traceback (most recent call last): File "uvloop/cbhandles.pyx", line 69, in uvloop.loop.Handle._run File "uvloop/handles/udp.pyx", line 64, in uvloop.loop.UDPTransport._on_read_ready File "/usr/local/lib/python3.6/site-packages/xknx/io/udp_client.py", line 55, in datagram_received self.data_received_callback(data) File "/usr/local/lib/python3.6/site-packages/xknx/io/udp_client.py", line 85, in data_received_callback knxipframe.from_knx(raw) File "/usr/local/lib/python3.6/site-packages/xknx/knxip/knxip.py", line 78, in from_knx pos += self.body.from_knx(data[pos:]) File "/usr/local/lib/python3.6/site-packages/xknx/knxip/tunnelling_request.py", line 48, in from_knx pos += self.cemi.from_knx(raw[pos:]) File "/usr/local/lib/python3.6/site-packages/xknx/knxip/cemi_frame.py", line 116, in from_knx return self.from_knx_data_link_layer(raw) File "/usr/local/lib/python3.6/site-packages/xknx/knxip/cemi_frame.py", line 147, in from_knx_data_link_layer self.cmd = APCICommand(tpci_apci & 0xFFC0) File "/usr/local/lib/python3.6/enum.py", line 291, in __call__ return cls.__new__(cls, value) File "/usr/local/lib/python3.6/enum.py", line 533, in __new__ return cls._missing_(value) File "/usr/local/lib/python3.6/enum.py", line 546, in _missing_ raise ValueError("%r is not a valid %s" % (value, cls.__name__)) ValueError: 960 is not a valid APCICommand Two minutes after this error I then receive: `Error: reading rading group address from KNX bus failed: ErrorCode.E_CONNECTION_ID`	9790cdb696285b5700ec06c571193a7feeb96a39	[ "test/knxip_tests/cemi_frame_test.py::test_valid_command", "test/knxip_tests/cemi_frame_test.py::test_invalid_tpci_apci", "test/knxip_tests/cemi_frame_test.py::test_invalid_apdu_len", "test/knxip_tests/cemi_frame_test.py::test_invalid_invalid_len" ]	[]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-03-22 23:56:49+00:00	mit	844
XKNX__xknx-406	diff --git a/xknx/devices/weather.py b/xknx/devices/weather.py index 8b155818..48791d01 100644 --- a/xknx/devices/weather.py +++ b/xknx/devices/weather.py @@ -189,7 +189,7 @@ class Weather(Device): xknx, group_address_state=group_address_air_pressure, sync_state=sync_state, - value_type="pressure", + value_type="pressure_2byte", device_name=self.name, feature_name="Air pressure", after_update_cb=self.after_update,	XKNX/xknx	5a3bbc5c493fd18761b3d0b3b383d3a35b3efa54	diff --git a/test/devices_tests/weather_test.py b/test/devices_tests/weather_test.py index b3956b46..02312d17 100644 --- a/test/devices_tests/weather_test.py +++ b/test/devices_tests/weather_test.py @@ -79,16 +79,9 @@ class TestWeather(unittest.TestCase): """Test resolve state with pressure.""" xknx = XKNX(loop=self.loop) weather = Weather(name="weather", xknx=xknx, group_address_air_pressure="1/3/4") - weather._air_pressure.payload = DPTArray( - ( - 0xC5, - 0xE6, - 0xE6, - 0x63, - ) - ) + weather._air_pressure.payload = DPTArray((0x6C, 0xAD)) - self.assertEqual(weather.air_pressure, -7388.79833984375) + self.assertEqual(weather.air_pressure, 98058.24) self.assertEqual(weather._air_pressure.unit_of_measurement, "Pa") self.assertEqual(weather._air_pressure.ha_device_class, "pressure")	KNX Weather entity payload error for air pressure Description of problem: I set up the new weather entity. For the air pressure the HA log shows an error due to an invalid payload. - [ ] using xknx standalone - [X] using Home-Assistant knx plugin Version information: - xknx / Home-Assistant release with the issue: 0.13.0 KNX installation: Jung Weather Station 2225 WSU - communication object: Air Pressure DPT 9.006 ![image](https://user-images.githubusercontent.com/53949754/93705737-df789100-fb1f-11ea-8c3a-058d1cefed00.png) Problem-relevant `xknx.yaml` or `configuration.yaml` entries (fill out even if it seems unimportant): ```` - name: 'Dach' address_temperature: '6/5/11' address_brightness_south: '6/5/6' address_brightness_west: '6/5/7' address_brightness_east: '6/5/5' address_wind_speed: '6/5/0' address_rain_alarm: '6/5/37' # address_frost_alarm: "7/0/6" address_wind_alarm: '6/5/29' # address_day_night: "7/0/8" address_air_pressure: '6/5/13' address_humidity: '6/5/12' expose_sensors: False sync_state: True ```` Traceback (if applicable): ``` 2020-09-19 10:35:51 ERROR (MainThread) [homeassistant] Error doing job: Task exception was never retrieved Traceback (most recent call last): File "/usr/local/lib/python3.8/site-packages/xknx/remote_value/remote_value.py", line 151, in read_state await self.process(telegram) File "/usr/local/lib/python3.8/site-packages/xknx/remote_value/remote_value.py", line 92, in process raise CouldNotParseTelegram("payload invalid", xknx.exceptions.exception.CouldNotParseTelegram: <CouldNotParseTelegram description="payload invalid" device_name="Dach" feature_name="Value" group_address="6/5/13" payload="<DPTArray value="[0x6c,0xad]" />"/> ```	5a3bbc5c493fd18761b3d0b3b383d3a35b3efa54	[ "test/devices_tests/weather_test.py::TestWeather::test_pressure" ]	[ "test/devices_tests/weather_test.py::TestWeather::test_brightness", "test/devices_tests/weather_test.py::TestWeather::test_cloudy_summer", "test/devices_tests/weather_test.py::TestWeather::test_cloudy_winter", "test/devices_tests/weather_test.py::TestWeather::test_day_night", "test/devices_tests/weather_test.py::TestWeather::test_expose_sensor", "test/devices_tests/weather_test.py::TestWeather::test_has_group_address", "test/devices_tests/weather_test.py::TestWeather::test_humidity", "test/devices_tests/weather_test.py::TestWeather::test_iter_remote_values", "test/devices_tests/weather_test.py::TestWeather::test_rain_alarm", "test/devices_tests/weather_test.py::TestWeather::test_state_lightning", "test/devices_tests/weather_test.py::TestWeather::test_state_snowy_rainy", "test/devices_tests/weather_test.py::TestWeather::test_sunny_summer", "test/devices_tests/weather_test.py::TestWeather::test_sunny_winter", "test/devices_tests/weather_test.py::TestWeather::test_temperature", "test/devices_tests/weather_test.py::TestWeather::test_weather_default", "test/devices_tests/weather_test.py::TestWeather::test_weather_state_attributes", "test/devices_tests/weather_test.py::TestWeather::test_wind_alarm", "test/devices_tests/weather_test.py::TestWeather::test_wind_speed" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_media" ], "has_test_patch": true, "is_lite": false }	2020-09-20 12:20:12+00:00	mit	845
XKNX__xknx-454	diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index f470c332..29b7fbe0 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -2,33 +2,33 @@ You are awesome! Thanks for contributing to our project! Please, DO NOT DELETE ANY TEXT from this template!. --> - +## Description <!-- Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context. List any dependencies that are required for this change. --> -## Description - Fixes # (issue) +## Type of change <!-- Please tick the applicable options. NOTE: Ticking multiple options most likely indicates that your change is to big and it is suggested to split it into several smaller PRs. --> -## Type of change - [ ] Bug fix (non-breaking change which fixes an issue) - [ ] New feature (non-breaking change which adds functionality) - [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected) - [ ] This change requires a documentation update -# Checklist: +## Checklist: - [ ] I have performed a self-review of my own code -- [ ] I have made corresponding changes to the documentation -- [ ] My changes generate no new warnings -- [ ] I have added tests that prove my fix is effective or that my feature works +- [ ] The documentation has been adjusted accordingly +- [ ] The changes generate no new warnings +- [ ] Tests have been added that prove the fix is effective or that the feature works +- [ ] The changes are documented in the changelog +- [ ] The Homeassistant plugin has been adjusted in case of new config options diff --git a/home-assistant-plugin/custom_components/xknx/const.py b/home-assistant-plugin/custom_components/xknx/const.py index 8bb99529..b5bdd447 100644 --- a/home-assistant-plugin/custom_components/xknx/const.py +++ b/home-assistant-plugin/custom_components/xknx/const.py @@ -18,6 +18,7 @@ DOMAIN = "xknx" CONF_STATE_ADDRESS = "state_address" CONF_SYNC_STATE = "sync_state" +CONF_RESET_AFTER = "reset_after" class ColorTempModes(Enum): diff --git a/home-assistant-plugin/custom_components/xknx/factory.py b/home-assistant-plugin/custom_components/xknx/factory.py index 157565c4..9e721817 100644 --- a/home-assistant-plugin/custom_components/xknx/factory.py +++ b/home-assistant-plugin/custom_components/xknx/factory.py @@ -202,6 +202,7 @@ def _create_switch(knx_module: XKNX, config: ConfigType) -> XknxSwitch: name=config[CONF_NAME], group_address=config[CONF_ADDRESS], group_address_state=config.get(SwitchSchema.CONF_STATE_ADDRESS), + reset_after=config.get(SwitchSchema.CONF_RESET_AFTER), ) diff --git a/home-assistant-plugin/custom_components/xknx/schema.py b/home-assistant-plugin/custom_components/xknx/schema.py index a224d9cb..89a6fac7 100644 --- a/home-assistant-plugin/custom_components/xknx/schema.py +++ b/home-assistant-plugin/custom_components/xknx/schema.py @@ -15,6 +15,7 @@ from homeassistant.const import ( import homeassistant.helpers.config_validation as cv from .const import ( + CONF_RESET_AFTER, CONF_STATE_ADDRESS, CONF_SYNC_STATE, OPERATION_MODES, @@ -86,7 +87,7 @@ class BinarySensorSchema: CONF_SYNC_STATE = CONF_SYNC_STATE CONF_IGNORE_INTERNAL_STATE = "ignore_internal_state" CONF_CONTEXT_TIMEOUT = "context_timeout" - CONF_RESET_AFTER = "reset_after" + CONF_RESET_AFTER = CONF_RESET_AFTER DEFAULT_NAME = "KNX Binary Sensor" @@ -253,6 +254,7 @@ class SwitchSchema: """Voluptuous schema for KNX switches.""" CONF_STATE_ADDRESS = CONF_STATE_ADDRESS + CONF_RESET_AFTER = CONF_RESET_AFTER DEFAULT_NAME = "KNX Switch" SCHEMA = vol.Schema( @@ -260,6 +262,7 @@ class SwitchSchema: vol.Required(CONF_ADDRESS): cv.string, vol.Optional(CONF_NAME, default=DEFAULT_NAME): cv.string, vol.Optional(CONF_STATE_ADDRESS): cv.string, + vol.Optional(CONF_RESET_AFTER): cv.positive_float, } ) diff --git a/xknx/devices/switch.py b/xknx/devices/switch.py index 670eb569..0a9dab20 100644 --- a/xknx/devices/switch.py +++ b/xknx/devices/switch.py @@ -6,6 +6,7 @@ It provides functionality for * switching 'on' and 'off'. * reading the current state from KNX bus. """ +import asyncio import logging from xknx.remote_value import RemoteValueSwitch @@ -22,6 +23,7 @@ class Switch(Device): self, xknx, name, + reset_after=None, group_address=None, group_address_state=None, device_updated_cb=None, @@ -30,6 +32,10 @@ class Switch(Device): # pylint: disable=too-many-arguments super().__init__(xknx, name, device_updated_cb) + self.reset_after = reset_after + self._reset_task = None + self.state = False + self.switch = RemoteValueSwitch( xknx, group_address, @@ -42,6 +48,11 @@ class Switch(Device): """Iterate the devices RemoteValue classes.""" yield self.switch + def __del__(self): + """Destructor. Cleaning up if this was not done before.""" + if self._reset_task: + self._reset_task.cancel() + @classmethod def from_config(cls, xknx, name, config): """Initialize object from configuration structure.""" @@ -55,12 +66,6 @@ class Switch(Device): group_address_state=group_address_state, ) - @property - def state(self): - """Return the current switch state of the device.""" - # None will return False - return bool(self.switch.value) - async def set_on(self): """Switch on switch.""" await self.switch.on() @@ -82,7 +87,18 @@ class Switch(Device): async def process_group_write(self, telegram): """Process incoming and outgoing GROUP WRITE telegram.""" - await self.switch.process(telegram) + if await self.switch.process(telegram): + self.state = self.switch.value + if self.reset_after is not None and self.state: + if self._reset_task: + self._reset_task.cancel() + self._reset_task = asyncio.create_task( + self._reset_state(self.reset_after) + ) + + async def _reset_state(self, wait_seconds: float): + await asyncio.sleep(wait_seconds) + await self.set_off() def __str__(self): """Return object as readable string."""	XKNX/xknx	5b6766ed6f83b863e53b6b6b7d608930ea80718f	diff --git a/requirements/testing.txt b/requirements/testing.txt index 3c8a67ce..71727a7d 100644 --- a/requirements/testing.txt +++ b/requirements/testing.txt @@ -1,6 +1,6 @@ -r production.txt pre-commit==2.7.1 -isort==5.5.4 +isort==5.5.5 coveralls==2.1.2 flake8==3.8.4 flake8-isort==4.0.0 diff --git a/test/devices_tests/switch_test.py b/test/devices_tests/switch_test.py index 42f651b2..a9520431 100644 --- a/test/devices_tests/switch_test.py +++ b/test/devices_tests/switch_test.py @@ -76,6 +76,47 @@ class TestSwitch(unittest.TestCase): self.assertEqual(switch.state, False) + def test_process_reset_after(self): + """Test process reset_after.""" + xknx = XKNX() + reset_after_sec = 0.001 + switch = Switch( + xknx, "TestInput", group_address="1/2/3", reset_after=reset_after_sec + ) + telegram_on = Telegram( + group_address=GroupAddress("1/2/3"), payload=DPTBinary(1) + ) + + self.loop.run_until_complete(switch.process(telegram_on)) + self.assertTrue(switch.state) + self.assertEqual(xknx.telegrams.qsize(), 0) + self.loop.run_until_complete(asyncio.sleep(reset_after_sec * 2)) + self.assertEqual(xknx.telegrams.qsize(), 1) + self.loop.run_until_complete(switch.process(xknx.telegrams.get_nowait())) + self.assertFalse(switch.state) + + def test_process_reset_after_cancel_existing(self): + """Test process reset_after cancels existing reset tasks.""" + xknx = XKNX() + reset_after_sec = 0.01 + switch = Switch( + xknx, "TestInput", group_address="1/2/3", reset_after=reset_after_sec + ) + telegram_on = Telegram( + group_address=GroupAddress("1/2/3"), payload=DPTBinary(1) + ) + + self.loop.run_until_complete(switch.process(telegram_on)) + self.assertTrue(switch.state) + self.assertEqual(xknx.telegrams.qsize(), 0) + self.loop.run_until_complete(asyncio.sleep(reset_after_sec / 2)) + # half way through the reset timer + self.loop.run_until_complete(switch.process(telegram_on)) + self.assertTrue(switch.state) + + self.loop.run_until_complete(asyncio.sleep(reset_after_sec / 2)) + self.assertEqual(xknx.telegrams.qsize(), 0) + def test_process_callback(self): """Test process / reading telegrams from telegram queue. Test if callback was called.""" # pylint: disable=no-self-use	Switch: add auto-off function Sometimes it is required to s always send a "OFF" right after sending a "ON" eg. for door openers. I suggest to add a `reset_after` option to Switch, just like BinarySensor, to send the "OFF" telegram after a timer is finished.	5b6766ed6f83b863e53b6b6b7d608930ea80718f	[ "test/devices_tests/switch_test.py::TestSwitch::test_process_reset_after", "test/devices_tests/switch_test.py::TestSwitch::test_process_reset_after_cancel_existing" ]	[ "test/devices_tests/switch_test.py::TestSwitch::test_do", "test/devices_tests/switch_test.py::TestSwitch::test_has_group_address", "test/devices_tests/switch_test.py::TestSwitch::test_process", "test/devices_tests/switch_test.py::TestSwitch::test_process_callback", "test/devices_tests/switch_test.py::TestSwitch::test_set_off", "test/devices_tests/switch_test.py::TestSwitch::test_set_on", "test/devices_tests/switch_test.py::TestSwitch::test_sync", "test/devices_tests/switch_test.py::TestSwitch::test_sync_state_address", "test/devices_tests/switch_test.py::TestSwitch::test_wrong_do" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-10-07 19:40:38+00:00	mit	846
XKNX__xknx-469	diff --git a/changelog.md b/changelog.md index 97c850a5..7fdd1b95 100644 --- a/changelog.md +++ b/changelog.md @@ -4,6 +4,7 @@ ### Devices +- Sensor: add `always_callback` option - ClimateMode: Refactor climate modes in operation_mode and controller_mode, also fixes a bug for binary operation modes where the mode would be set to AWAY no matter what value was sent to the bus. ### Internals diff --git a/docs/sensor.md b/docs/sensor.md index c741e111..22ae2581 100644 --- a/docs/sensor.md +++ b/docs/sensor.md @@ -15,6 +15,7 @@ Sensors are monitoring temperature, air humidity, pressure etc. from KNX bus. sensor = Sensor( xknx=xknx, name='DiningRoom.Temperature.Sensor', + always_callback=False, group_address_state='6/2/1', sync_state=True, value_type='temperature' @@ -25,6 +26,7 @@ Sensors are monitoring temperature, air humidity, pressure etc. from KNX bus. * `xknx` is the XKNX object. * `name` is the name of the object. +* `always_callback` defines if a callback/update should always be triggered no matter if the previous and the new state are identical. * `group_address_state` is the KNX group address of the sensor device. * `sync_state` defines if the value should be actively read from the bus. If `False` no GroupValueRead telegrams will be sent to its group address. Defaults to `True` * `value_type` controls how the value should be rendered in a human readable representation. The attribut may have may have the values `percent`, `temperature`, `illuminance`, `speed_ms` or `current`. diff --git a/home-assistant-plugin/custom_components/xknx/factory.py b/home-assistant-plugin/custom_components/xknx/factory.py index de552ff2..005d24d5 100644 --- a/home-assistant-plugin/custom_components/xknx/factory.py +++ b/home-assistant-plugin/custom_components/xknx/factory.py @@ -214,6 +214,7 @@ def _create_sensor(knx_module: XKNX, config: ConfigType) -> XknxSensor: name=config[CONF_NAME], group_address_state=config[SensorSchema.CONF_STATE_ADDRESS], sync_state=config[SensorSchema.CONF_SYNC_STATE], + always_callback=config[SensorSchema.CONF_ALWAYS_CALLBACK], value_type=config[CONF_TYPE], ) diff --git a/home-assistant-plugin/custom_components/xknx/schema.py b/home-assistant-plugin/custom_components/xknx/schema.py index 9c628bed..d97a532a 100644 --- a/home-assistant-plugin/custom_components/xknx/schema.py +++ b/home-assistant-plugin/custom_components/xknx/schema.py @@ -306,6 +306,7 @@ class NotifySchema: class SensorSchema: """Voluptuous schema for KNX sensors.""" + CONF_ALWAYS_CALLBACK = "always_callback" CONF_STATE_ADDRESS = CONF_STATE_ADDRESS CONF_SYNC_STATE = CONF_SYNC_STATE DEFAULT_NAME = "KNX Sensor" @@ -318,6 +319,7 @@ class SensorSchema: cv.boolean, cv.string, ), + vol.Optional(CONF_ALWAYS_CALLBACK, default=False): cv.boolean, vol.Required(CONF_STATE_ADDRESS): cv.string, vol.Required(CONF_TYPE): vol.Any(int, float, str), } diff --git a/xknx/devices/sensor.py b/xknx/devices/sensor.py index 1ac1471e..de62ec95 100644 --- a/xknx/devices/sensor.py +++ b/xknx/devices/sensor.py @@ -19,14 +19,15 @@ class Sensor(Device): xknx, name, group_address_state=None, - sync_state=True, - value_type=None, + sync_state: bool = True, + always_callback: bool = False, + value_type: str = None, device_updated_cb=None, ): """Initialize Sensor class.""" # pylint: disable=too-many-arguments super().__init__(xknx, name, device_updated_cb) - + self.always_callback = always_callback self.sensor_value = RemoteValueSensor( xknx, group_address_state=group_address_state, @@ -45,6 +46,7 @@ class Sensor(Device): """Initialize object from configuration structure.""" group_address_state = config.get("group_address_state") sync_state = config.get("sync_state", True) + always_callback = config.get("always_callback", False) value_type = config.get("value_type") return cls( @@ -52,11 +54,16 @@ class Sensor(Device): name, group_address_state=group_address_state, sync_state=sync_state, + always_callback=always_callback, value_type=value_type, ) async def process_group_write(self, telegram): """Process incoming and outgoing GROUP WRITE telegram.""" + await self.sensor_value.process(telegram, always_callback=self.always_callback) + + async def process_group_response(self, telegram): + """Process incoming GroupValueResponse telegrams.""" await self.sensor_value.process(telegram) def unit_of_measurement(self):	XKNX/xknx	715856fdb69deceba4d54afe4ccf3f7ad304c5ec	diff --git a/test/devices_tests/sensor_test.py b/test/devices_tests/sensor_test.py index 2043eb3c..5875ea4e 100644 --- a/test/devices_tests/sensor_test.py +++ b/test/devices_tests/sensor_test.py @@ -47,6 +47,55 @@ class TestSensor(unittest.TestCase): self.assertEqual(sensor.unit_of_measurement(), "K") self.assertEqual(sensor.ha_device_class(), None) + def test_always_callback_sensor(self): + """Test always callback sensor.""" + xknx = XKNX() + sensor = Sensor( + xknx, + "TestSensor", + group_address_state="1/2/3", + always_callback=False, + value_type="volume_liquid_litre", + ) + + after_update_callback = Mock() + + async def async_after_update_callback(device): + """Async callback.""" + after_update_callback(device) + + sensor.register_device_updated_cb(async_after_update_callback) + + payload = DPTArray( + ( + 0x00, + 0x00, + 0x01, + 0x00, + ) + ) + + # set initial payload of sensor + sensor.sensor_value.payload = payload + + telegram = Telegram(group_address=GroupAddress("1/2/3"), payload=payload) + + # verify not called when always_callback is False + self.loop.run_until_complete(sensor.process(telegram)) + after_update_callback.assert_not_called() + after_update_callback.reset_mock() + + sensor.always_callback = True + + # verify called when always_callback is True + self.loop.run_until_complete(sensor.process(telegram)) + after_update_callback.assert_called_once() + after_update_callback.reset_mock() + + # verify not called when processing read responses + self.loop.run_until_complete(sensor.process_group_response(telegram)) + after_update_callback.assert_not_called() + def test_str_acceleration(self): """Test resolve state with acceleration sensor.""" xknx = XKNX()	Feature request: add the "ignore_internal_state" property to "Sensors" the same way it works already for "Binary Sensors" Hi, In the last release the property "ignore_internal_state" was added to the knx "binary sensor", and it would be great to have this property for knx "sensors" as well. For example I am using a sensor with type "scene_number" together with an automation in order to execute some actions within HA when a knx scene number is called, but if the same scene is called two times without any other scene number in between, the value of the HA sensor state is not changed and the automation is not called again. Note : the KNX scene entity is no help in this case as its state in HA does not change when triggered (it stays on "scening") and is only used the other way around (make HA to trigger a KNX scene). Thank you very much in advance !	715856fdb69deceba4d54afe4ccf3f7ad304c5ec	[ "test/devices_tests/sensor_test.py::TestSensor::test_always_callback_sensor" ]	[ "test/devices_tests/sensor_test.py::TestSensor::test_has_group_address", "test/devices_tests/sensor_test.py::TestSensor::test_process", "test/devices_tests/sensor_test.py::TestSensor::test_process_callback", "test/devices_tests/sensor_test.py::TestSensor::test_str_absolute_temperature", "test/devices_tests/sensor_test.py::TestSensor::test_str_acceleration", "test/devices_tests/sensor_test.py::TestSensor::test_str_acceleration_angular", "test/devices_tests/sensor_test.py::TestSensor::test_str_activation_energy", "test/devices_tests/sensor_test.py::TestSensor::test_str_active_energy", "test/devices_tests/sensor_test.py::TestSensor::test_str_active_energy_kwh", "test/devices_tests/sensor_test.py::TestSensor::test_str_activity", "test/devices_tests/sensor_test.py::TestSensor::test_str_amplitude", "test/devices_tests/sensor_test.py::TestSensor::test_str_angle", "test/devices_tests/sensor_test.py::TestSensor::test_str_angle_deg", "test/devices_tests/sensor_test.py::TestSensor::test_str_angle_rad", "test/devices_tests/sensor_test.py::TestSensor::test_str_angular_frequency", "test/devices_tests/sensor_test.py::TestSensor::test_str_angular_momentum", "test/devices_tests/sensor_test.py::TestSensor::test_str_angular_velocity", "test/devices_tests/sensor_test.py::TestSensor::test_str_apparant_energy", "test/devices_tests/sensor_test.py::TestSensor::test_str_apparant_energy_kvah", "test/devices_tests/sensor_test.py::TestSensor::test_str_area", "test/devices_tests/sensor_test.py::TestSensor::test_str_brightness", "test/devices_tests/sensor_test.py::TestSensor::test_str_capacitance", "test/devices_tests/sensor_test.py::TestSensor::test_str_charge_density_surface", "test/devices_tests/sensor_test.py::TestSensor::test_str_charge_density_volume", "test/devices_tests/sensor_test.py::TestSensor::test_str_color_temperature", "test/devices_tests/sensor_test.py::TestSensor::test_str_common_temperature", "test/devices_tests/sensor_test.py::TestSensor::test_str_compressibility", "test/devices_tests/sensor_test.py::TestSensor::test_str_conductance", "test/devices_tests/sensor_test.py::TestSensor::test_str_counter_pulses", "test/devices_tests/sensor_test.py::TestSensor::test_str_current", "test/devices_tests/sensor_test.py::TestSensor::test_str_delta_time_hrs", "test/devices_tests/sensor_test.py::TestSensor::test_str_delta_time_min", "test/devices_tests/sensor_test.py::TestSensor::test_str_delta_time_ms", "test/devices_tests/sensor_test.py::TestSensor::test_str_delta_time_sec", "test/devices_tests/sensor_test.py::TestSensor::test_str_density", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_charge", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_current", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_current_density", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_dipole_moment", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_displacement", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_field_strength", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_flux_density", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_polarization", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_potential", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_potential_difference", "test/devices_tests/sensor_test.py::TestSensor::test_str_electrical_conductivity", "test/devices_tests/sensor_test.py::TestSensor::test_str_electromagnetic_moment", "test/devices_tests/sensor_test.py::TestSensor::test_str_electromotive_force", "test/devices_tests/sensor_test.py::TestSensor::test_str_energy", "test/devices_tests/sensor_test.py::TestSensor::test_str_enthalpy", "test/devices_tests/sensor_test.py::TestSensor::test_str_flow_rate_m3h", "test/devices_tests/sensor_test.py::TestSensor::test_str_force", "test/devices_tests/sensor_test.py::TestSensor::test_str_frequency", "test/devices_tests/sensor_test.py::TestSensor::test_str_heat_quantity", "test/devices_tests/sensor_test.py::TestSensor::test_str_heatcapacity", "test/devices_tests/sensor_test.py::TestSensor::test_str_heatflowrate", "test/devices_tests/sensor_test.py::TestSensor::test_str_humidity", "test/devices_tests/sensor_test.py::TestSensor::test_str_illuminance", "test/devices_tests/sensor_test.py::TestSensor::test_str_impedance", "test/devices_tests/sensor_test.py::TestSensor::test_str_kelvin_per_percent", "test/devices_tests/sensor_test.py::TestSensor::test_str_length", "test/devices_tests/sensor_test.py::TestSensor::test_str_length_mm", "test/devices_tests/sensor_test.py::TestSensor::test_str_light_quantity", "test/devices_tests/sensor_test.py::TestSensor::test_str_long_delta_timesec", "test/devices_tests/sensor_test.py::TestSensor::test_str_luminance", "test/devices_tests/sensor_test.py::TestSensor::test_str_luminous_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_luminous_intensity", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetic_field_strength", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetic_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetic_flux_density", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetic_moment", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetic_polarization", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetization", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetomotive_force", "test/devices_tests/sensor_test.py::TestSensor::test_str_mass", "test/devices_tests/sensor_test.py::TestSensor::test_str_mass_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_mol", "test/devices_tests/sensor_test.py::TestSensor::test_str_momentum", "test/devices_tests/sensor_test.py::TestSensor::test_str_percent", "test/devices_tests/sensor_test.py::TestSensor::test_str_percent_u8", "test/devices_tests/sensor_test.py::TestSensor::test_str_percent_v16", "test/devices_tests/sensor_test.py::TestSensor::test_str_percent_v8", "test/devices_tests/sensor_test.py::TestSensor::test_str_phaseangledeg", "test/devices_tests/sensor_test.py::TestSensor::test_str_phaseanglerad", "test/devices_tests/sensor_test.py::TestSensor::test_str_power", "test/devices_tests/sensor_test.py::TestSensor::test_str_power_2byte", "test/devices_tests/sensor_test.py::TestSensor::test_str_power_density", "test/devices_tests/sensor_test.py::TestSensor::test_str_powerfactor", "test/devices_tests/sensor_test.py::TestSensor::test_str_ppm", "test/devices_tests/sensor_test.py::TestSensor::test_str_pressure", "test/devices_tests/sensor_test.py::TestSensor::test_str_pressure_2byte", "test/devices_tests/sensor_test.py::TestSensor::test_str_pulse", "test/devices_tests/sensor_test.py::TestSensor::test_str_rain_amount", "test/devices_tests/sensor_test.py::TestSensor::test_str_reactance", "test/devices_tests/sensor_test.py::TestSensor::test_str_reactive_energy", "test/devices_tests/sensor_test.py::TestSensor::test_str_reactive_energy_kvarh", "test/devices_tests/sensor_test.py::TestSensor::test_str_resistance", "test/devices_tests/sensor_test.py::TestSensor::test_str_resistivity", "test/devices_tests/sensor_test.py::TestSensor::test_str_rotation_angle", "test/devices_tests/sensor_test.py::TestSensor::test_str_scene_number", "test/devices_tests/sensor_test.py::TestSensor::test_str_self_inductance", "test/devices_tests/sensor_test.py::TestSensor::test_str_solid_angle", "test/devices_tests/sensor_test.py::TestSensor::test_str_sound_intensity", "test/devices_tests/sensor_test.py::TestSensor::test_str_speed", "test/devices_tests/sensor_test.py::TestSensor::test_str_stress", "test/devices_tests/sensor_test.py::TestSensor::test_str_surface_tension", "test/devices_tests/sensor_test.py::TestSensor::test_str_temperature", "test/devices_tests/sensor_test.py::TestSensor::test_str_temperature_a", "test/devices_tests/sensor_test.py::TestSensor::test_str_temperature_difference", "test/devices_tests/sensor_test.py::TestSensor::test_str_temperature_difference_2byte", "test/devices_tests/sensor_test.py::TestSensor::test_str_temperature_f", "test/devices_tests/sensor_test.py::TestSensor::test_str_thermal_capacity", "test/devices_tests/sensor_test.py::TestSensor::test_str_thermal_conductivity", "test/devices_tests/sensor_test.py::TestSensor::test_str_thermoelectric_power", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_1", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_2", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_100msec", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_10msec", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_hrs", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_min", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_msec", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_sec", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_seconds", "test/devices_tests/sensor_test.py::TestSensor::test_str_torque", "test/devices_tests/sensor_test.py::TestSensor::test_str_voltage", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_flow", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_liquid_litre", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_m3", "test/devices_tests/sensor_test.py::TestSensor::test_str_weight", "test/devices_tests/sensor_test.py::TestSensor::test_str_wind_speed_kmh", "test/devices_tests/sensor_test.py::TestSensor::test_str_wind_speed_ms", "test/devices_tests/sensor_test.py::TestSensor::test_str_work", "test/devices_tests/sensor_test.py::TestSensor::test_sync" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-10-17 20:17:34+00:00	mit	847
XKNX__xknx-470	diff --git a/changelog.md b/changelog.md index 97c850a5..26bbe12a 100644 --- a/changelog.md +++ b/changelog.md @@ -4,11 +4,12 @@ ### Devices +- Sensor: add `always_callback` option - ClimateMode: Refactor climate modes in operation_mode and controller_mode, also fixes a bug for binary operation modes where the mode would be set to AWAY no matter what value was sent to the bus. ### Internals -- StateUpdater: Only request one GA at a time. +- StateUpdater: Only request 3 GAs at a time. ## 0.15.1 bugfix for binary sensors diff --git a/docs/sensor.md b/docs/sensor.md index c741e111..22ae2581 100644 --- a/docs/sensor.md +++ b/docs/sensor.md @@ -15,6 +15,7 @@ Sensors are monitoring temperature, air humidity, pressure etc. from KNX bus. sensor = Sensor( xknx=xknx, name='DiningRoom.Temperature.Sensor', + always_callback=False, group_address_state='6/2/1', sync_state=True, value_type='temperature' @@ -25,6 +26,7 @@ Sensors are monitoring temperature, air humidity, pressure etc. from KNX bus. * `xknx` is the XKNX object. * `name` is the name of the object. +* `always_callback` defines if a callback/update should always be triggered no matter if the previous and the new state are identical. * `group_address_state` is the KNX group address of the sensor device. * `sync_state` defines if the value should be actively read from the bus. If `False` no GroupValueRead telegrams will be sent to its group address. Defaults to `True` * `value_type` controls how the value should be rendered in a human readable representation. The attribut may have may have the values `percent`, `temperature`, `illuminance`, `speed_ms` or `current`. diff --git a/home-assistant-plugin/custom_components/xknx/factory.py b/home-assistant-plugin/custom_components/xknx/factory.py index de552ff2..005d24d5 100644 --- a/home-assistant-plugin/custom_components/xknx/factory.py +++ b/home-assistant-plugin/custom_components/xknx/factory.py @@ -214,6 +214,7 @@ def _create_sensor(knx_module: XKNX, config: ConfigType) -> XknxSensor: name=config[CONF_NAME], group_address_state=config[SensorSchema.CONF_STATE_ADDRESS], sync_state=config[SensorSchema.CONF_SYNC_STATE], + always_callback=config[SensorSchema.CONF_ALWAYS_CALLBACK], value_type=config[CONF_TYPE], ) diff --git a/home-assistant-plugin/custom_components/xknx/schema.py b/home-assistant-plugin/custom_components/xknx/schema.py index 9c628bed..d97a532a 100644 --- a/home-assistant-plugin/custom_components/xknx/schema.py +++ b/home-assistant-plugin/custom_components/xknx/schema.py @@ -306,6 +306,7 @@ class NotifySchema: class SensorSchema: """Voluptuous schema for KNX sensors.""" + CONF_ALWAYS_CALLBACK = "always_callback" CONF_STATE_ADDRESS = CONF_STATE_ADDRESS CONF_SYNC_STATE = CONF_SYNC_STATE DEFAULT_NAME = "KNX Sensor" @@ -318,6 +319,7 @@ class SensorSchema: cv.boolean, cv.string, ), + vol.Optional(CONF_ALWAYS_CALLBACK, default=False): cv.boolean, vol.Required(CONF_STATE_ADDRESS): cv.string, vol.Required(CONF_TYPE): vol.Any(int, float, str), } diff --git a/xknx/core/state_updater.py b/xknx/core/state_updater.py index 268730df..db7df306 100644 --- a/xknx/core/state_updater.py +++ b/xknx/core/state_updater.py @@ -14,12 +14,12 @@ logger = logging.getLogger("xknx.state_updater") class StateUpdater: """Class for keeping the states of RemoteValues up to date.""" - def __init__(self, xknx): + def __init__(self, xknx, parallel_reads: int = 3): """Initialize StateUpdater class.""" self.xknx = xknx self.started = False self._workers = {} - self._one_by_one = asyncio.Lock() + self._semaphore = asyncio.Semaphore(value=parallel_reads) def register_remote_value(self, remote_value: RemoteValue, tracker_options=True): """Register a RemoteValue to initialize its state and/or track for expiration.""" @@ -77,7 +77,7 @@ class StateUpdater: async def read_state_mutex(): """Schedule to read the state from the KNX bus - one at a time.""" - async with self._one_by_one: + async with self._semaphore: # wait until there is nothing else to send to the bus await self.xknx.telegram_queue.outgoing_queue.join() logger.debug( diff --git a/xknx/devices/sensor.py b/xknx/devices/sensor.py index 1ac1471e..de62ec95 100644 --- a/xknx/devices/sensor.py +++ b/xknx/devices/sensor.py @@ -19,14 +19,15 @@ class Sensor(Device): xknx, name, group_address_state=None, - sync_state=True, - value_type=None, + sync_state: bool = True, + always_callback: bool = False, + value_type: str = None, device_updated_cb=None, ): """Initialize Sensor class.""" # pylint: disable=too-many-arguments super().__init__(xknx, name, device_updated_cb) - + self.always_callback = always_callback self.sensor_value = RemoteValueSensor( xknx, group_address_state=group_address_state, @@ -45,6 +46,7 @@ class Sensor(Device): """Initialize object from configuration structure.""" group_address_state = config.get("group_address_state") sync_state = config.get("sync_state", True) + always_callback = config.get("always_callback", False) value_type = config.get("value_type") return cls( @@ -52,11 +54,16 @@ class Sensor(Device): name, group_address_state=group_address_state, sync_state=sync_state, + always_callback=always_callback, value_type=value_type, ) async def process_group_write(self, telegram): """Process incoming and outgoing GROUP WRITE telegram.""" + await self.sensor_value.process(telegram, always_callback=self.always_callback) + + async def process_group_response(self, telegram): + """Process incoming GroupValueResponse telegrams.""" await self.sensor_value.process(telegram) def unit_of_measurement(self):	XKNX/xknx	715856fdb69deceba4d54afe4ccf3f7ad304c5ec	diff --git a/test/devices_tests/sensor_test.py b/test/devices_tests/sensor_test.py index 2043eb3c..5875ea4e 100644 --- a/test/devices_tests/sensor_test.py +++ b/test/devices_tests/sensor_test.py @@ -47,6 +47,55 @@ class TestSensor(unittest.TestCase): self.assertEqual(sensor.unit_of_measurement(), "K") self.assertEqual(sensor.ha_device_class(), None) + def test_always_callback_sensor(self): + """Test always callback sensor.""" + xknx = XKNX() + sensor = Sensor( + xknx, + "TestSensor", + group_address_state="1/2/3", + always_callback=False, + value_type="volume_liquid_litre", + ) + + after_update_callback = Mock() + + async def async_after_update_callback(device): + """Async callback.""" + after_update_callback(device) + + sensor.register_device_updated_cb(async_after_update_callback) + + payload = DPTArray( + ( + 0x00, + 0x00, + 0x01, + 0x00, + ) + ) + + # set initial payload of sensor + sensor.sensor_value.payload = payload + + telegram = Telegram(group_address=GroupAddress("1/2/3"), payload=payload) + + # verify not called when always_callback is False + self.loop.run_until_complete(sensor.process(telegram)) + after_update_callback.assert_not_called() + after_update_callback.reset_mock() + + sensor.always_callback = True + + # verify called when always_callback is True + self.loop.run_until_complete(sensor.process(telegram)) + after_update_callback.assert_called_once() + after_update_callback.reset_mock() + + # verify not called when processing read responses + self.loop.run_until_complete(sensor.process_group_response(telegram)) + after_update_callback.assert_not_called() + def test_str_acceleration(self): """Test resolve state with acceleration sensor.""" xknx = XKNX()	Use Semaphores in StateUpdater In https://github.com/XKNX/xknx/pull/457 we adjusted the state updater to update each value one by one. However, we should leverage the power of semaphores to update more than one state concurrently as the bus can handle more than one telegram per second. A value between 3 and 5 should be fine imho. But this would need further testing.	715856fdb69deceba4d54afe4ccf3f7ad304c5ec	[ "test/devices_tests/sensor_test.py::TestSensor::test_always_callback_sensor" ]	[ "test/devices_tests/sensor_test.py::TestSensor::test_has_group_address", "test/devices_tests/sensor_test.py::TestSensor::test_process", "test/devices_tests/sensor_test.py::TestSensor::test_process_callback", "test/devices_tests/sensor_test.py::TestSensor::test_str_absolute_temperature", "test/devices_tests/sensor_test.py::TestSensor::test_str_acceleration", "test/devices_tests/sensor_test.py::TestSensor::test_str_acceleration_angular", "test/devices_tests/sensor_test.py::TestSensor::test_str_activation_energy", "test/devices_tests/sensor_test.py::TestSensor::test_str_active_energy", "test/devices_tests/sensor_test.py::TestSensor::test_str_active_energy_kwh", "test/devices_tests/sensor_test.py::TestSensor::test_str_activity", "test/devices_tests/sensor_test.py::TestSensor::test_str_amplitude", "test/devices_tests/sensor_test.py::TestSensor::test_str_angle", "test/devices_tests/sensor_test.py::TestSensor::test_str_angle_deg", "test/devices_tests/sensor_test.py::TestSensor::test_str_angle_rad", "test/devices_tests/sensor_test.py::TestSensor::test_str_angular_frequency", "test/devices_tests/sensor_test.py::TestSensor::test_str_angular_momentum", "test/devices_tests/sensor_test.py::TestSensor::test_str_angular_velocity", "test/devices_tests/sensor_test.py::TestSensor::test_str_apparant_energy", "test/devices_tests/sensor_test.py::TestSensor::test_str_apparant_energy_kvah", "test/devices_tests/sensor_test.py::TestSensor::test_str_area", "test/devices_tests/sensor_test.py::TestSensor::test_str_brightness", "test/devices_tests/sensor_test.py::TestSensor::test_str_capacitance", "test/devices_tests/sensor_test.py::TestSensor::test_str_charge_density_surface", "test/devices_tests/sensor_test.py::TestSensor::test_str_charge_density_volume", "test/devices_tests/sensor_test.py::TestSensor::test_str_color_temperature", "test/devices_tests/sensor_test.py::TestSensor::test_str_common_temperature", "test/devices_tests/sensor_test.py::TestSensor::test_str_compressibility", "test/devices_tests/sensor_test.py::TestSensor::test_str_conductance", "test/devices_tests/sensor_test.py::TestSensor::test_str_counter_pulses", "test/devices_tests/sensor_test.py::TestSensor::test_str_current", "test/devices_tests/sensor_test.py::TestSensor::test_str_delta_time_hrs", "test/devices_tests/sensor_test.py::TestSensor::test_str_delta_time_min", "test/devices_tests/sensor_test.py::TestSensor::test_str_delta_time_ms", "test/devices_tests/sensor_test.py::TestSensor::test_str_delta_time_sec", "test/devices_tests/sensor_test.py::TestSensor::test_str_density", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_charge", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_current", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_current_density", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_dipole_moment", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_displacement", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_field_strength", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_flux_density", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_polarization", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_potential", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_potential_difference", "test/devices_tests/sensor_test.py::TestSensor::test_str_electrical_conductivity", "test/devices_tests/sensor_test.py::TestSensor::test_str_electromagnetic_moment", "test/devices_tests/sensor_test.py::TestSensor::test_str_electromotive_force", "test/devices_tests/sensor_test.py::TestSensor::test_str_energy", "test/devices_tests/sensor_test.py::TestSensor::test_str_enthalpy", "test/devices_tests/sensor_test.py::TestSensor::test_str_flow_rate_m3h", "test/devices_tests/sensor_test.py::TestSensor::test_str_force", "test/devices_tests/sensor_test.py::TestSensor::test_str_frequency", "test/devices_tests/sensor_test.py::TestSensor::test_str_heat_quantity", "test/devices_tests/sensor_test.py::TestSensor::test_str_heatcapacity", "test/devices_tests/sensor_test.py::TestSensor::test_str_heatflowrate", "test/devices_tests/sensor_test.py::TestSensor::test_str_humidity", "test/devices_tests/sensor_test.py::TestSensor::test_str_illuminance", "test/devices_tests/sensor_test.py::TestSensor::test_str_impedance", "test/devices_tests/sensor_test.py::TestSensor::test_str_kelvin_per_percent", "test/devices_tests/sensor_test.py::TestSensor::test_str_length", "test/devices_tests/sensor_test.py::TestSensor::test_str_length_mm", "test/devices_tests/sensor_test.py::TestSensor::test_str_light_quantity", "test/devices_tests/sensor_test.py::TestSensor::test_str_long_delta_timesec", "test/devices_tests/sensor_test.py::TestSensor::test_str_luminance", "test/devices_tests/sensor_test.py::TestSensor::test_str_luminous_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_luminous_intensity", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetic_field_strength", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetic_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetic_flux_density", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetic_moment", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetic_polarization", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetization", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetomotive_force", "test/devices_tests/sensor_test.py::TestSensor::test_str_mass", "test/devices_tests/sensor_test.py::TestSensor::test_str_mass_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_mol", "test/devices_tests/sensor_test.py::TestSensor::test_str_momentum", "test/devices_tests/sensor_test.py::TestSensor::test_str_percent", "test/devices_tests/sensor_test.py::TestSensor::test_str_percent_u8", "test/devices_tests/sensor_test.py::TestSensor::test_str_percent_v16", "test/devices_tests/sensor_test.py::TestSensor::test_str_percent_v8", "test/devices_tests/sensor_test.py::TestSensor::test_str_phaseangledeg", "test/devices_tests/sensor_test.py::TestSensor::test_str_phaseanglerad", "test/devices_tests/sensor_test.py::TestSensor::test_str_power", "test/devices_tests/sensor_test.py::TestSensor::test_str_power_2byte", "test/devices_tests/sensor_test.py::TestSensor::test_str_power_density", "test/devices_tests/sensor_test.py::TestSensor::test_str_powerfactor", "test/devices_tests/sensor_test.py::TestSensor::test_str_ppm", "test/devices_tests/sensor_test.py::TestSensor::test_str_pressure", "test/devices_tests/sensor_test.py::TestSensor::test_str_pressure_2byte", "test/devices_tests/sensor_test.py::TestSensor::test_str_pulse", "test/devices_tests/sensor_test.py::TestSensor::test_str_rain_amount", "test/devices_tests/sensor_test.py::TestSensor::test_str_reactance", "test/devices_tests/sensor_test.py::TestSensor::test_str_reactive_energy", "test/devices_tests/sensor_test.py::TestSensor::test_str_reactive_energy_kvarh", "test/devices_tests/sensor_test.py::TestSensor::test_str_resistance", "test/devices_tests/sensor_test.py::TestSensor::test_str_resistivity", "test/devices_tests/sensor_test.py::TestSensor::test_str_rotation_angle", "test/devices_tests/sensor_test.py::TestSensor::test_str_scene_number", "test/devices_tests/sensor_test.py::TestSensor::test_str_self_inductance", "test/devices_tests/sensor_test.py::TestSensor::test_str_solid_angle", "test/devices_tests/sensor_test.py::TestSensor::test_str_sound_intensity", "test/devices_tests/sensor_test.py::TestSensor::test_str_speed", "test/devices_tests/sensor_test.py::TestSensor::test_str_stress", "test/devices_tests/sensor_test.py::TestSensor::test_str_surface_tension", "test/devices_tests/sensor_test.py::TestSensor::test_str_temperature", "test/devices_tests/sensor_test.py::TestSensor::test_str_temperature_a", "test/devices_tests/sensor_test.py::TestSensor::test_str_temperature_difference", "test/devices_tests/sensor_test.py::TestSensor::test_str_temperature_difference_2byte", "test/devices_tests/sensor_test.py::TestSensor::test_str_temperature_f", "test/devices_tests/sensor_test.py::TestSensor::test_str_thermal_capacity", "test/devices_tests/sensor_test.py::TestSensor::test_str_thermal_conductivity", "test/devices_tests/sensor_test.py::TestSensor::test_str_thermoelectric_power", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_1", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_2", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_100msec", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_10msec", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_hrs", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_min", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_msec", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_sec", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_seconds", "test/devices_tests/sensor_test.py::TestSensor::test_str_torque", "test/devices_tests/sensor_test.py::TestSensor::test_str_voltage", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_flow", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_liquid_litre", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_m3", "test/devices_tests/sensor_test.py::TestSensor::test_str_weight", "test/devices_tests/sensor_test.py::TestSensor::test_str_wind_speed_kmh", "test/devices_tests/sensor_test.py::TestSensor::test_str_wind_speed_ms", "test/devices_tests/sensor_test.py::TestSensor::test_str_work", "test/devices_tests/sensor_test.py::TestSensor::test_sync" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-10-17 20:40:35+00:00	mit	848
XKNX__xknx-482	diff --git a/changelog.md b/changelog.md index b3ef0a15..5ed77445 100644 --- a/changelog.md +++ b/changelog.md @@ -12,6 +12,7 @@ ### Bugfixes - HA Switch entity: keep state without state_address +- Cover: fix `set_position` without writable position / auto_stop_if_necessary ## 0.15.2 Winter is coming diff --git a/xknx/devices/cover.py b/xknx/devices/cover.py index 4ff53c1a..7596c1e5 100644 --- a/xknx/devices/cover.py +++ b/xknx/devices/cover.py @@ -270,13 +270,20 @@ class Cover(Device): async def process_group_write(self, telegram): """Process incoming and outgoing GROUP WRITE telegram.""" + # call after_update to account for travelcalculator changes if await self.updown.process(telegram): - if self.updown.value == RemoteValueUpDown.Direction.UP: + if ( + not self.is_opening() + and self.updown.value == RemoteValueUpDown.Direction.UP + ): self.travelcalculator.start_travel_up() - else: + await self.after_update() + elif ( + not self.is_closing() + and self.updown.value == RemoteValueUpDown.Direction.DOWN + ): self.travelcalculator.start_travel_down() - # call after_update to account for travelcalculator changes - await self.after_update() + await self.after_update() # stop from bus if await self.stop_.process(telegram) or await self.step.process(telegram): if self.is_traveling():	XKNX/xknx	785d73b850a97a688a3b1a5e8baf34e82685d1b6	diff --git a/test/devices_tests/cover_test.py b/test/devices_tests/cover_test.py index 16e4547c..0865454c 100644 --- a/test/devices_tests/cover_test.py +++ b/test/devices_tests/cover_test.py @@ -397,6 +397,10 @@ class TestCover(unittest.TestCase): telegram, Telegram(GroupAddress("1/2/1"), payload=DPTBinary(0)) ) self.assertEqual(cover.travelcalculator.travel_to_position, 50) + self.assertTrue(cover.is_opening()) + # process the outgoing telegram to make sure it doesn't overwrite the target position + self.loop.run_until_complete(cover.process(telegram)) + self.assertEqual(cover.travelcalculator.travel_to_position, 50) def test_position_without_position_address_down(self): """Test moving cover down - with no absolute positioning supported.""" @@ -416,6 +420,10 @@ class TestCover(unittest.TestCase): telegram, Telegram(GroupAddress("1/2/1"), payload=DPTBinary(1)) ) self.assertEqual(cover.travelcalculator.travel_to_position, 80) + self.assertTrue(cover.is_closing()) + # process the outgoing telegram to make sure it doesn't overwrite the target position + self.loop.run_until_complete(cover.process(telegram)) + self.assertEqual(cover.travelcalculator.travel_to_position, 80) def test_position_without_position_address_uninitialized_up(self): """Test moving uninitialized cover to absolute position - with no absolute positioning supported."""	cover.set_cover_position not stopping with no position_address Description of problem: Dear xknx team, covers with no position_address do not longer stop when moving the slider in the ha frontpanel to a position e.g. 30%. I attached my according HA config as well as some debug log from HA. This was working in precious versions of Home Assistant for me ( version 0.111). The service cover.set_cover_position ist not stopping at this value. The services cover.close_cover; service cover.open_cover; cover.stop_cover are working currently. Maybe a bug to the reworked travelcalculator / cover.py? It seems to me, that there is no stop movement send to actor when the calculated position is reached. Remark: My covers do not have a positional feedback. But this applies not only to my knx config, this reproducible to other knx hardware setup with HA as well (a friend of mine reproduces this bug with his knx covers (which have a position_address). When deleting the position address in his config, this bug occurs as well. It would be great, to have this feature back / working again! Let me know, if i can assist you reproducing this bug. All the best Jan - [x ] using Home-Assistant knx plugin Version information: - xknx / Home-Assistant release with the issue: 0.116.4 - last working xknx / Home-Assistant release (if known): 0.111 KNX installation: <!-- - Manufacturer and model of relevant actors, sensors or interfaces. --> Problem-relevant `xknx.yaml` or `configuration.yaml` entries (fill out even if it seems unimportant): [LOG_ha.txt](https://github.com/XKNX/xknx/files/5434327/LOG_ha.txt) [knx_cover.yaml.txt](https://github.com/XKNX/xknx/files/5434337/knx_cover.yaml.txt) [knx.yaml.txt](https://github.com/XKNX/xknx/files/5434338/knx.yaml.txt) ![Log](https://user-images.githubusercontent.com/19536666/97102778-98466880-16a8-11eb-93fd-f1ca839db2ed.JPG)	785d73b850a97a688a3b1a5e8baf34e82685d1b6	[ "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_down", "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_up" ]	[ "test/devices_tests/cover_test.py::TestCover::test_angle", "test/devices_tests/cover_test.py::TestCover::test_angle_not_supported", "test/devices_tests/cover_test.py::TestCover::test_auto_stop", "test/devices_tests/cover_test.py::TestCover::test_do", "test/devices_tests/cover_test.py::TestCover::test_has_group_address", "test/devices_tests/cover_test.py::TestCover::test_is_traveling", "test/devices_tests/cover_test.py::TestCover::test_position", "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_uninitialized_down", "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_uninitialized_up", "test/devices_tests/cover_test.py::TestCover::test_process_angle", "test/devices_tests/cover_test.py::TestCover::test_process_callback", "test/devices_tests/cover_test.py::TestCover::test_process_down", "test/devices_tests/cover_test.py::TestCover::test_process_position", "test/devices_tests/cover_test.py::TestCover::test_process_short_stop", "test/devices_tests/cover_test.py::TestCover::test_process_stop", "test/devices_tests/cover_test.py::TestCover::test_process_up", "test/devices_tests/cover_test.py::TestCover::test_set_down", "test/devices_tests/cover_test.py::TestCover::test_set_down_inverted", "test/devices_tests/cover_test.py::TestCover::test_set_short_down", "test/devices_tests/cover_test.py::TestCover::test_set_short_up", "test/devices_tests/cover_test.py::TestCover::test_set_up", "test/devices_tests/cover_test.py::TestCover::test_set_up_inverted", "test/devices_tests/cover_test.py::TestCover::test_stop", "test/devices_tests/cover_test.py::TestCover::test_support_angle_false", "test/devices_tests/cover_test.py::TestCover::test_supports_angle_true", "test/devices_tests/cover_test.py::TestCover::test_supports_position_false", "test/devices_tests/cover_test.py::TestCover::test_supports_position_true", "test/devices_tests/cover_test.py::TestCover::test_supports_stop_false", "test/devices_tests/cover_test.py::TestCover::test_supports_stop_true", "test/devices_tests/cover_test.py::TestCover::test_sync", "test/devices_tests/cover_test.py::TestCover::test_sync_angle", "test/devices_tests/cover_test.py::TestCover::test_sync_angle_state", "test/devices_tests/cover_test.py::TestCover::test_sync_state", "test/devices_tests/cover_test.py::TestCover::test_wrong_do" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_media", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2020-10-25 20:45:25+00:00	mit	849
XKNX__xknx-572	diff --git a/changelog.md b/changelog.md index 8692b1d2..b8648063 100644 --- a/changelog.md +++ b/changelog.md @@ -2,6 +2,10 @@ ## Unreleased changes +### HA integration + +- knx_event: fire also for outgoing telegrams + ### Devices - BinarySensor: return `None` for `BinarySensor.counter` when context timeout is not used (and don't calculate it) diff --git a/home-assistant-plugin/custom_components/xknx/__init__.py b/home-assistant-plugin/custom_components/xknx/__init__.py index fab7ec68..f7f63d8d 100644 --- a/home-assistant-plugin/custom_components/xknx/__init__.py +++ b/home-assistant-plugin/custom_components/xknx/__init__.py @@ -368,6 +368,7 @@ class KNXModule: self.telegram_received_cb, address_filters=address_filters, group_addresses=[], + match_for_outgoing_telegrams=True, ) async def service_event_register_modify(self, call): diff --git a/xknx/core/telegram_queue.py b/xknx/core/telegram_queue.py index c793ebc4..ea68f572 100644 --- a/xknx/core/telegram_queue.py +++ b/xknx/core/telegram_queue.py @@ -37,15 +37,22 @@ class TelegramQueue: callback: "AsyncTelegramCallback", address_filters: Optional[List[AddressFilter]] = None, group_addresses: Optional[List[GroupAddress]] = None, + match_for_outgoing_telegrams: bool = False, ): """Initialize Callback class.""" self.callback = callback self._match_all = address_filters is None and group_addresses is None + self._match_outgoing = match_for_outgoing_telegrams self.address_filters = [] if address_filters is None else address_filters self.group_addresses = [] if group_addresses is None else group_addresses def is_within_filter(self, telegram: Telegram) -> bool: """Test if callback is filtering for group address.""" + if ( + not self._match_outgoing + and telegram.direction == TelegramDirection.OUTGOING + ): + return False if self._match_all: return True if isinstance(telegram.destination_address, GroupAddress): @@ -69,12 +76,14 @@ class TelegramQueue: telegram_received_cb: "AsyncTelegramCallback", address_filters: Optional[List[AddressFilter]] = None, group_addresses: Optional[List[GroupAddress]] = None, + match_for_outgoing: bool = False, ) -> Callback: - """Register callback for a telegram beeing received from KNX bus.""" + """Register callback for a telegram being received from KNX bus.""" callback = TelegramQueue.Callback( telegram_received_cb, address_filters=address_filters, group_addresses=group_addresses, + match_for_outgoing_telegrams=match_for_outgoing, ) self.telegram_received_cbs.append(callback) return callback @@ -165,6 +174,10 @@ class TelegramQueue: await self.xknx.knxip_interface.send_telegram(telegram) if isinstance(telegram.payload, GroupValueWrite): await self.xknx.devices.process(telegram) + + for telegram_received_cb in self.telegram_received_cbs: + if telegram_received_cb.is_within_filter(telegram): + await telegram_received_cb.callback(telegram) else: raise CommunicationError("No KNXIP interface defined")	XKNX/xknx	afa30c7e0acfa91ad68390eb89120e9f50e35b92	diff --git a/test/core_tests/telegram_queue_test.py b/test/core_tests/telegram_queue_test.py index 9543f66b..6ef23d1b 100644 --- a/test/core_tests/telegram_queue_test.py +++ b/test/core_tests/telegram_queue_test.py @@ -117,10 +117,62 @@ class TestTelegramQueue(unittest.TestCase): payload=GroupValueWrite(DPTBinary(1)), ) self.loop.run_until_complete( - xknx.telegram_queue.process_telegram_incoming(telegram) + xknx.telegram_queue.process_telegram_incoming(telegram), ) async_telegram_received_cb.assert_called_once_with(telegram) + @patch("xknx.io.KNXIPInterface") + def test_register_with_outgoing_telegrams(self, if_mock): + """Test telegram_received_callback with outgoing telegrams.""" + # pylint: disable=no-self-use + xknx = XKNX() + async_telegram_received_cb = AsyncMock() + + async_if_send_telegram = asyncio.Future() + async_if_send_telegram.set_result(None) + if_mock.send_telegram.return_value = async_if_send_telegram + + xknx.telegram_queue.register_telegram_received_cb( + async_telegram_received_cb, None, None, True + ) + + telegram = Telegram( + destination_address=GroupAddress("1/2/3"), + direction=TelegramDirection.OUTGOING, + payload=GroupValueWrite(DPTBinary(1)), + ) + + xknx.knxip_interface = if_mock + self.loop.run_until_complete( + xknx.telegram_queue.process_telegram_outgoing(telegram) + ) + async_telegram_received_cb.assert_called_once_with(telegram) + + @patch("xknx.io.KNXIPInterface") + def test_register_with_outgoing_telegrams_does_not_trigger(self, if_mock): + """Test telegram_received_callback with outgoing telegrams.""" + # pylint: disable=no-self-use + xknx = XKNX() + async_telegram_received_cb = AsyncMock() + + async_if_send_telegram = asyncio.Future() + async_if_send_telegram.set_result(None) + if_mock.send_telegram.return_value = async_if_send_telegram + + xknx.telegram_queue.register_telegram_received_cb(async_telegram_received_cb) + + telegram = Telegram( + destination_address=GroupAddress("1/2/3"), + direction=TelegramDirection.OUTGOING, + payload=GroupValueWrite(DPTBinary(1)), + ) + + xknx.knxip_interface = if_mock + self.loop.run_until_complete( + xknx.telegram_queue.process_telegram_outgoing(telegram) + ) + async_telegram_received_cb.assert_not_called() + # # TEST UNREGISTER #	Enhance HA knx_event There are some requests about updating the HA knx_event. Eg. https://github.com/home-assistant/core/issues/43256 Currently we just fire the `knx_event` for incoming telegrams, as stated in the documentation. We could - [ ] fire on outgoing telegrams too, not only on incoming - [x] add a parameter "direction" for incoming/outgoing - [x] add a parameter "source" for IA (eg. to identify which wall switch was used) - [x] add a parameter "type" for write or response (maybe also read) I'm still not very convinced about using the `knx_event` at all since we can't really decode the payload and dealing with raw payloads should not be a user-facing task in HA (besides maybe for DPT 1/2/3).	afa30c7e0acfa91ad68390eb89120e9f50e35b92	[ "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_register_with_outgoing_telegrams" ]	[ "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_callback_group_addresses", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_callback_negative_address_filters", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_callback_no_filters", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_callback_positive_address_filters", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_outgoing", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_process_all_telegrams", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_process_exception", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_process_to_callback", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_process_to_device", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_rate_limit", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_register", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_register_with_outgoing_telegrams_does_not_trigger", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_start", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_unregister" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-01-24 14:07:32+00:00	mit	850
XKNX__xknx-832	diff --git a/changelog.md b/changelog.md index e312e426..35e3c87c 100644 --- a/changelog.md +++ b/changelog.md @@ -4,7 +4,8 @@ ### Connection -- Fix rate limiter wait time. Don't add time waiting for ACK or L_DATA.con frames to the rate_limit. +- Handle separate Tunneling control and data endpoints +- Fix rate limiter wait time: don't add time waiting for ACK or L_DATA.con frames to the rate_limit ## Internals diff --git a/xknx/io/request_response/connect.py b/xknx/io/request_response/connect.py index ec97d58a..b5ae8696 100644 --- a/xknx/io/request_response/connect.py +++ b/xknx/io/request_response/connect.py @@ -27,6 +27,7 @@ class Connect(RequestResponse): self.route_back = route_back super().__init__(xknx, self.udp_client, ConnectResponse) self.communication_channel = 0 + self.data_endpoint = HPAI() self.identifier = 0 def create_knxipframe(self) -> KNXIPFrame: @@ -48,6 +49,6 @@ class Connect(RequestResponse): def on_success_hook(self, knxipframe: KNXIPFrame) -> None: """Set communication channel and identifier after having received a valid answer.""" assert isinstance(knxipframe.body, ConnectResponse) - assert isinstance(knxipframe.body.identifier, int) self.communication_channel = knxipframe.body.communication_channel + self.data_endpoint = knxipframe.body.data_endpoint self.identifier = knxipframe.body.identifier diff --git a/xknx/io/request_response/tunnelling.py b/xknx/io/request_response/tunnelling.py index 6a295bea..f7fc0e60 100644 --- a/xknx/io/request_response/tunnelling.py +++ b/xknx/io/request_response/tunnelling.py @@ -26,6 +26,7 @@ class Tunnelling(RequestResponse): self, xknx: XKNX, udp_client: UDPClient, + data_endpoint: tuple[str, int] \| None, telegram: Telegram, src_address: IndividualAddress, sequence_counter: int, @@ -34,6 +35,7 @@ class Tunnelling(RequestResponse): """Initialize Tunnelling class.""" self.xknx = xknx self.udp_client = udp_client + self.data_endpoint_addr = data_endpoint self.src_address = src_address super().__init__(xknx, self.udp_client, TunnellingAck) @@ -42,6 +44,10 @@ class Tunnelling(RequestResponse): self.sequence_counter = sequence_counter self.communication_channel_id = communication_channel_id + async def send_request(self) -> None: + """Build knxipframe (within derived class) and send via UDP.""" + self.udpclient.send(self.create_knxipframe(), addr=self.data_endpoint_addr) + def create_knxipframe(self) -> KNXIPFrame: """Create KNX/IP Frame object to be sent to device.""" cemi = CEMIFrame.init_from_telegram( diff --git a/xknx/io/tunnel.py b/xknx/io/tunnel.py index 65752e0a..cd555a13 100644 --- a/xknx/io/tunnel.py +++ b/xknx/io/tunnel.py @@ -69,6 +69,7 @@ class Tunnel(Interface): self.init_udp_client() self._src_address = xknx.own_address + self._data_endpoint_addr: tuple[str, int] \| None = None self.sequence_number = 0 self.communication_channel: int \| None = None self.number_heartbeat_failed = 0 @@ -144,6 +145,7 @@ class Tunnel(Interface): ) ) self.stop_heartbeat() + self._data_endpoint_addr = None if self.auto_reconnect: self._reconnect_task = asyncio.create_task(self._reconnect()) else: @@ -172,6 +174,7 @@ class Tunnel(Interface): XknxConnectionState.DISCONNECTED ) self.stop_heartbeat() + self._data_endpoint_addr = None self._stop_reconnect() await self._disconnect_request(False) await self.udp_client.stop() @@ -188,6 +191,11 @@ class Tunnel(Interface): await connect.start() if connect.success: self.communication_channel = connect.communication_channel + # assign data_endpoint received from server + self._data_endpoint_addr = ( + connect.data_endpoint.ip_addr, + connect.data_endpoint.port, + ) # Use the individual address provided by the tunnelling server self._src_address = IndividualAddress(connect.identifier) self.xknx.current_address = self._src_address @@ -274,6 +282,7 @@ class Tunnel(Interface): tunnelling = Tunnelling( self.xknx, self.udp_client, + self._data_endpoint_addr, telegram, self._src_address, self.sequence_number, @@ -355,7 +364,9 @@ class Tunnel(Interface): communication_channel_id=communication_channel_id, sequence_counter=sequence_counter, ) - self.udp_client.send(KNXIPFrame.init_from_body(ack)) + self.udp_client.send( + KNXIPFrame.init_from_body(ack), addr=self._data_endpoint_addr + ) def _disconnect_request_received( self, disconnect_request: DisconnectRequest diff --git a/xknx/io/udp_client.py b/xknx/io/udp_client.py index 2637a73f..1aeee391 100644 --- a/xknx/io/udp_client.py +++ b/xknx/io/udp_client.py @@ -116,7 +116,7 @@ class UDPClient: ) else: knx_logger.debug( - "Received from %s:%s at %s:\n%s", + "Received from %s:%s at %s:\n %s", source[0], source[1], time.time(), @@ -213,27 +213,28 @@ class UDPClient: (transport, _) = await loop.create_datagram_endpoint( lambda: udp_client_factory, local_addr=self.local_addr, - remote_addr=self.remote_addr, ) # TODO: typing - remove cast - loop.create_datagram_endpoint should return a DatagramTransport self.transport = cast(asyncio.DatagramTransport, transport) - def send(self, knxipframe: KNXIPFrame) -> None: + def send(self, knxipframe: KNXIPFrame, addr: tuple[str, int] \| None = None) -> None: """Send KNXIPFrame to socket.""" + _addr = addr or self.remote_addr knx_logger.debug( - "Sending to %s:%s at %s:\n%s", - self.remote_addr[0], - self.remote_addr[1], - time.time(), - knxipframe, + "Sending to %s:%s at %s:\n %s", _addr[0], _addr[1], time.time(), knxipframe ) if self.transport is None: raise XKNXException("Transport not connected") if self.multicast: + if addr is not None: + logger.warning( + "Multicast send to specific address is invalid. %s", + knxipframe, + ) self.transport.sendto(bytes(knxipframe.to_knx()), self.remote_addr) else: - self.transport.sendto(bytes(knxipframe.to_knx())) + self.transport.sendto(bytes(knxipframe.to_knx()), addr=_addr) def getsockname(self) -> tuple[str, int]: """Return socket IP and port.""" diff --git a/xknx/knxip/connect_response.py b/xknx/knxip/connect_response.py index 3f9c3835..865923ef 100644 --- a/xknx/knxip/connect_response.py +++ b/xknx/knxip/connect_response.py @@ -32,8 +32,8 @@ class ConnectResponse(KNXIPBodyResponse): communication_channel: int = 0, status_code: ErrorCode = ErrorCode.E_NO_ERROR, request_type: ConnectRequestType = ConnectRequestType.TUNNEL_CONNECTION, - control_endpoint: HPAI = HPAI(), - identifier: int \| None = None, + data_endpoint: HPAI = HPAI(), + identifier: int = 0, ): """Initialize ConnectResponse class.""" super().__init__(xknx) @@ -41,7 +41,7 @@ class ConnectResponse(KNXIPBodyResponse): self.communication_channel = communication_channel self.status_code = status_code self.request_type = request_type - self.control_endpoint = control_endpoint + self.data_endpoint = data_endpoint # identifier shall contain KNX Individual Address assigned to this KNXnet/IP Tunnelling connection self.identifier = identifier @@ -67,11 +67,11 @@ class ConnectResponse(KNXIPBodyResponse): pos = 2 if self.status_code == ErrorCode.E_NO_ERROR: - pos += self.control_endpoint.from_knx(raw[pos:]) + pos += self.data_endpoint.from_knx(raw[pos:]) pos += crd_from_knx(raw[pos:]) else: # do not parse HPAI and CRD in case of errors - just check length - pos += len(raw[pos:]) + pos = len(raw) return pos def to_knx(self) -> list[int]: @@ -91,7 +91,7 @@ class ConnectResponse(KNXIPBodyResponse): data = [] data.append(self.communication_channel) data.append(self.status_code.value) - data.extend(self.control_endpoint.to_knx()) + data.extend(self.data_endpoint.to_knx()) data.extend(crd_to_knx()) return data @@ -102,7 +102,7 @@ class ConnectResponse(KNXIPBodyResponse): "<ConnectResponse " f'communication_channel="{self.communication_channel}" ' f'status_code="{self.status_code}" ' - f'control_endpoint="{self.control_endpoint}" ' + f'data_endpoint="{self.data_endpoint}" ' f'request_type="{self.request_type}" ' f'identifier="{self.identifier}" />' ) diff --git a/xknx/knxip/knxip.py b/xknx/knxip/knxip.py index b5425a86..ed333e0a 100644 --- a/xknx/knxip/knxip.py +++ b/xknx/knxip/knxip.py @@ -101,7 +101,7 @@ class KNXIPFrame: data.extend(self.body.to_knx()) return data - def __str__(self) -> str: + def __repr__(self) -> str: """Return object as readable string.""" return f'<KNXIPFrame {self.header}\n body="{self.body}" />'	XKNX/xknx	e2f84405a5a62492c4cbf86de9e32abef043cecb	diff --git a/test/io_tests/tunnel_test.py b/test/io_tests/tunnel_test.py index 3615b9cd..d9d8aa48 100644 --- a/test/io_tests/tunnel_test.py +++ b/test/io_tests/tunnel_test.py @@ -1,14 +1,24 @@ """Unit test for KNX/IP Tunnelling Request/Response.""" import asyncio -from unittest.mock import Mock, patch +from unittest.mock import AsyncMock, Mock, patch import pytest from xknx import XKNX from xknx.dpt import DPTArray from xknx.io import Tunnel -from xknx.knxip import HPAI, CEMIFrame, KNXIPFrame, TunnellingAck, TunnellingRequest +from xknx.knxip import ( + HPAI, + CEMIFrame, + ConnectRequest, + ConnectResponse, + DisconnectRequest, + DisconnectResponse, + KNXIPFrame, + TunnellingAck, + TunnellingRequest, +) from xknx.knxip.knxip_enum import CEMIMessageCode -from xknx.telegram import Telegram, TelegramDirection +from xknx.telegram import IndividualAddress, Telegram, TelegramDirection from xknx.telegram.apci import GroupValueWrite @@ -103,3 +113,88 @@ class TestTunnel: # one call for the outgoing request and one for the ACK for the confirmation assert self.tunnel.udp_client.send.call_count == 2 await task + + async def test_tunnel_connect_send_disconnect(self, time_travel): + """Test initiating a tunnelling connection.""" + local_addr = ("192.168.1.1", 12345) + gateway_control_addr = ("192.168.1.2", 3671) + gateway_data_addr = ("192.168.1.2", 56789) + self.tunnel.udp_client.connect = AsyncMock() + self.tunnel.udp_client.getsockname = Mock(return_value=local_addr) + self.tunnel.udp_client.send = Mock() + self.tunnel.udp_client.stop = AsyncMock() + + # Connect + connect_request = ConnectRequest( + self.xknx, + control_endpoint=HPAI(local_addr), + data_endpoint=HPAI(local_addr), + ) + connect_frame = KNXIPFrame.init_from_body(connect_request) + + connection_task = asyncio.create_task(self.tunnel.connect()) + await time_travel(0) + self.tunnel.udp_client.connect.assert_called_once() + self.tunnel.udp_client.send.assert_called_once_with(connect_frame) + + connect_response_frame = KNXIPFrame.init_from_body( + ConnectResponse( + self.xknx, + communication_channel=23, + data_endpoint=HPAI(gateway_data_addr), + identifier=7, + ) + ) + self.tunnel.udp_client.handle_knxipframe( + connect_response_frame, gateway_control_addr + ) + await connection_task + assert self.tunnel._data_endpoint_addr == gateway_data_addr + assert self.tunnel._src_address == IndividualAddress(7) + + # Send - use data endpoint + self.tunnel.udp_client.send.reset_mock() + test_telegram = Telegram(payload=GroupValueWrite(DPTArray((1,)))) + test_telegram_frame = KNXIPFrame.init_from_body( + TunnellingRequest( + self.xknx, + communication_channel_id=23, + sequence_counter=0, + cemi=CEMIFrame.init_from_telegram( + self.xknx, + test_telegram, + code=CEMIMessageCode.L_DATA_REQ, + src_addr=IndividualAddress(7), + ), + ) + ) + asyncio.create_task(self.tunnel.send_telegram(test_telegram)) + await time_travel(0) + self.tunnel.udp_client.send.assert_called_once_with( + test_telegram_frame, addr=gateway_data_addr + ) + # skip ack and confirmation + + # Disconnect + self.tunnel.udp_client.send.reset_mock() + disconnect_request = DisconnectRequest( + self.xknx, communication_channel_id=23, control_endpoint=HPAI(local_addr) + ) + disconnect_frame = KNXIPFrame.init_from_body(disconnect_request) + + disconnection_task = asyncio.create_task(self.tunnel.disconnect()) + await time_travel(0) + self.tunnel.udp_client.send.assert_called_once_with(disconnect_frame) + + disconnect_response_frame = KNXIPFrame.init_from_body( + DisconnectResponse( + self.xknx, + communication_channel_id=23, + ) + ) + self.tunnel.udp_client.handle_knxipframe( + disconnect_response_frame, gateway_control_addr + ) + await disconnection_task + assert self.tunnel._data_endpoint_addr is None + self.tunnel.udp_client.stop.assert_called_once() diff --git a/test/io_tests/tunnelling_test.py b/test/io_tests/tunnelling_test.py index bfb4142c..b893e3cc 100644 --- a/test/io_tests/tunnelling_test.py +++ b/test/io_tests/tunnelling_test.py @@ -26,6 +26,7 @@ class TestTunnelling: """Test tunnelling from KNX bus.""" xknx = XKNX() communication_channel_id = 23 + data_endpoint = ("192.168.1.2", 4567) udp_client = UDPClient(xknx, ("192.168.1.1", 0), ("192.168.1.2", 1234)) telegram = Telegram( destination_address=GroupAddress("1/2/3"), @@ -36,6 +37,7 @@ class TestTunnelling: tunnelling = Tunnelling( xknx, udp_client, + data_endpoint, telegram, src_address, sequence_counter, @@ -60,7 +62,7 @@ class TestTunnelling: ) as mock_udp_getsockname: mock_udp_getsockname.return_value = ("192.168.1.3", 4321) await tunnelling.start() - mock_udp_send.assert_called_with(exp_knxipframe) + mock_udp_send.assert_called_with(exp_knxipframe, addr=data_endpoint) # Response KNX/IP-Frame with wrong type wrong_knxipframe = KNXIPFrame(xknx) diff --git a/test/knxip_tests/connect_response_test.py b/test/knxip_tests/connect_response_test.py index 71f61a4c..3bd85054 100644 --- a/test/knxip_tests/connect_response_test.py +++ b/test/knxip_tests/connect_response_test.py @@ -38,9 +38,7 @@ class TestKNXIPConnectResponse: assert isinstance(knxipframe.body, ConnectResponse) assert knxipframe.body.communication_channel == 1 assert knxipframe.body.status_code == ErrorCode.E_NO_ERROR - assert knxipframe.body.control_endpoint == HPAI( - ip_addr="192.168.42.10", port=3671 - ) + assert knxipframe.body.data_endpoint == HPAI(ip_addr="192.168.42.10", port=3671) assert knxipframe.body.request_type == ConnectRequestType.TUNNEL_CONNECTION assert knxipframe.body.identifier == 4607 @@ -49,7 +47,7 @@ class TestKNXIPConnectResponse: communication_channel=1, status_code=ErrorCode.E_NO_ERROR, request_type=ConnectRequestType.TUNNEL_CONNECTION, - control_endpoint=HPAI(ip_addr="192.168.42.10", port=3671), + data_endpoint=HPAI(ip_addr="192.168.42.10", port=3671), identifier=4607, ) knxipframe2 = KNXIPFrame.init_from_body(connect_response) @@ -151,7 +149,7 @@ class TestKNXIPConnectResponse: communication_channel=192, status_code=ErrorCode.E_NO_MORE_CONNECTIONS, request_type=ConnectRequestType.TUNNEL_CONNECTION, - control_endpoint=HPAI(ip_addr="10.1.0.41", port=3671), + data_endpoint=HPAI(ip_addr="10.1.0.41", port=3671), identifier=0, ) knxipframe2 = KNXIPFrame.init_from_body(connect_response) diff --git a/test/str_test.py b/test/str_test.py index 72c9ef56..3d34719f 100644 --- a/test/str_test.py +++ b/test/str_test.py @@ -526,12 +526,12 @@ class TestStringRepresentations: connect_response = ConnectResponse(xknx) connect_response.communication_channel = 13 connect_response.request_type = ConnectRequestType.TUNNEL_CONNECTION - connect_response.control_endpoint = HPAI(ip_addr="192.168.42.1", port=33941) + connect_response.data_endpoint = HPAI(ip_addr="192.168.42.1", port=33941) connect_response.identifier = 42 assert ( str(connect_response) == '<ConnectResponse communication_channel="13" status_code="ErrorCode.E_NO_ERROR" ' - 'control_endpoint="192.168.42.1:33941" ' + 'data_endpoint="192.168.42.1:33941" ' 'request_type="ConnectRequestType.TUNNEL_CONNECTION" identifier="42" />' )	Handle different Tunneling data and control endpoints correctly KNX tunneling servers can have different data and control endpoints (eg. Calimero does). `DisconnectRequest`s should be sent to the other device’s control endpoint instead of to the data endpoint. (see KNX specification 03_08_04 Tunneling §2.6 Frame confirmation) I have not found an other usecase for the control endpoint for us yet.	e2f84405a5a62492c4cbf86de9e32abef043cecb	[ "test/io_tests/tunnel_test.py::TestTunnel::test_tunnel_connect_send_disconnect", "test/io_tests/tunnelling_test.py::TestTunnelling::test_tunnelling", "test/knxip_tests/connect_response_test.py::TestKNXIPConnectResponse::test_connect_response", "test/knxip_tests/connect_response_test.py::TestKNXIPConnectResponse::test_connect_response_connection_error_gira", "test/str_test.py::TestStringRepresentations::test_connect_response" ]	[ "test/io_tests/tunnel_test.py::TestTunnel::test_tunnel_request_received", "test/io_tests/tunnel_test.py::TestTunnel::test_tunnel_request_received_cemi_too_small", "test/io_tests/tunnel_test.py::TestTunnel::test_tunnel_request_received_apci_unsupported", "test/knxip_tests/connect_response_test.py::TestKNXIPConnectResponse::test_from_knx_wrong_crd", "test/knxip_tests/connect_response_test.py::TestKNXIPConnectResponse::test_from_knx_wrong_crd2", "test/knxip_tests/connect_response_test.py::TestKNXIPConnectResponse::test_connect_response_connection_error_lox", "test/knxip_tests/connect_response_test.py::TestKNXIPConnectResponse::test_connect_response_connection_error_mdt", "test/str_test.py::TestStringRepresentations::test_remote_value", "test/str_test.py::TestStringRepresentations::test_binary_sensor", "test/str_test.py::TestStringRepresentations::test_climate", "test/str_test.py::TestStringRepresentations::test_climate_mode", "test/str_test.py::TestStringRepresentations::test_cover", "test/str_test.py::TestStringRepresentations::test_fan", "test/str_test.py::TestStringRepresentations::test_light", "test/str_test.py::TestStringRepresentations::test_light_dimmable", "test/str_test.py::TestStringRepresentations::test_light_color", "test/str_test.py::TestStringRepresentations::test_notification", "test/str_test.py::TestStringRepresentations::test_scene", "test/str_test.py::TestStringRepresentations::test_sensor", "test/str_test.py::TestStringRepresentations::test_expose_sensor", "test/str_test.py::TestStringRepresentations::test_switch", "test/str_test.py::TestStringRepresentations::test_weather", "test/str_test.py::TestStringRepresentations::test_datetime", "test/str_test.py::TestStringRepresentations::test_could_not_parse_telegramn_exception", "test/str_test.py::TestStringRepresentations::test_could_not_parse_telegramn_exception_parameter", "test/str_test.py::TestStringRepresentations::test_could_not_parse_knxip_exception", "test/str_test.py::TestStringRepresentations::test_conversion_error_exception", "test/str_test.py::TestStringRepresentations::test_conversion_error_exception_parameter", "test/str_test.py::TestStringRepresentations::test_could_not_parse_address_exception", "test/str_test.py::TestStringRepresentations::test_device_illegal_value_exception", "test/str_test.py::TestStringRepresentations::test_address", "test/str_test.py::TestStringRepresentations::test_dpt_array", "test/str_test.py::TestStringRepresentations::test_dpt_binary", "test/str_test.py::TestStringRepresentations::test_telegram", "test/str_test.py::TestStringRepresentations::test_dib_generic", "test/str_test.py::TestStringRepresentations::test_dib_supp_svc_families", "test/str_test.py::TestStringRepresentations::test_dib_device_informatio", "test/str_test.py::TestStringRepresentations::test_hpai", "test/str_test.py::TestStringRepresentations::test_header", "test/str_test.py::TestStringRepresentations::test_connect_request", "test/str_test.py::TestStringRepresentations::test_disconnect_request", "test/str_test.py::TestStringRepresentations::test_disconnect_response", "test/str_test.py::TestStringRepresentations::test_connectionstate_request", "test/str_test.py::TestStringRepresentations::test_connectionstate_response", "test/str_test.py::TestStringRepresentations::test_search_reqeust", "test/str_test.py::TestStringRepresentations::test_search_response", "test/str_test.py::TestStringRepresentations::test_tunnelling_request", "test/str_test.py::TestStringRepresentations::test_tunnelling_ack", "test/str_test.py::TestStringRepresentations::test_cemi_frame", "test/str_test.py::TestStringRepresentations::test_knxip_frame", "test/str_test.py::TestStringRepresentations::test_gateway_descriptor", "test/str_test.py::TestStringRepresentations::test_routing_indication_str" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-12-27 10:18:03+00:00	mit	851
XKNX__xknx-910	diff --git a/changelog.md b/changelog.md index aef5dcc2..b7f15948 100644 --- a/changelog.md +++ b/changelog.md @@ -6,10 +6,12 @@ - Add support for SearchRequestExtended to find interfaces that allow IP Secure - Use XKNX `state_updater` argument to set default method for StateUpdater. StateUpdater is always started - Device / RemoteValue can always opt in to use it, even if default is `False`. +- Add support for DPT 16.001 (DPT_String_8859_1) as `DPTLatin1` with value_type "latin_1". ### Bug fixes - Stop SecureSession keepalive_task when session is stopped (and don't restart it from sending STATUS_CLOSE) +- Fix encoding invalid characters for DPTString (value_type "string") ## 0.20.0 IP Secure 2022-03-29 diff --git a/xknx/dpt/__init__.py b/xknx/dpt/__init__.py index 669c6993..cea33e90 100644 --- a/xknx/dpt/__init__.py +++ b/xknx/dpt/__init__.py @@ -172,7 +172,7 @@ from .dpt_date import DPTDate from .dpt_datetime import DPTDateTime from .dpt_hvac_mode import DPTControllerStatus, DPTHVACContrMode, DPTHVACMode from .dpt_scaling import DPTAngle, DPTScaling -from .dpt_string import DPTString +from .dpt_string import DPTLatin1, DPTString from .dpt_time import DPTTime __all__ = [ @@ -249,6 +249,7 @@ __all__ = [ "DPTHVACMode", "DPTImpedance", "DPTKelvinPerPercent", + "DPTLatin1", "DPTLength", "DPTLengthMm", "DPTLightQuantity", diff --git a/xknx/dpt/dpt_string.py b/xknx/dpt/dpt_string.py index 0788bc33..faf33207 100644 --- a/xknx/dpt/dpt_string.py +++ b/xknx/dpt/dpt_string.py @@ -8,7 +8,7 @@ from .dpt import DPTBase class DPTString(DPTBase): """ - Abstraction for KNX 14 Octet ASCII String. + Abstraction for KNX 14 Octet ASCII string. DPT 16.000 """ @@ -19,15 +19,15 @@ class DPTString(DPTBase): value_type = "string" unit = "" + _encoding = "ascii" + @classmethod def from_knx(cls, raw: tuple[int, ...]) -> str: """Parse/deserialize from KNX/IP raw data.""" cls.test_bytesarray(raw) - value = "" - for byte in raw: - if byte != 0x00: - value += chr(byte) - return value + return bytes(byte for byte in raw if byte != 0x00).decode( + cls._encoding, errors="replace" + ) @classmethod def to_knx(cls, value: str) -> tuple[int, ...]: @@ -36,15 +36,26 @@ class DPTString(DPTBase): knx_value = str(value) if not cls._test_boundaries(knx_value): raise ValueError - raw = [ord(character) for character in knx_value] - raw.extend([0] * (cls.payload_length - len(raw))) - # replace invalid characters with question marks - # bytes(knx_value, 'ascii') would raise UnicodeEncodeError - return tuple(map(lambda char: char if char <= 0xFF else ord("?"), raw)) except ValueError: raise ConversionError(f"Could not serialize {cls.__name__}", value=value) + # replace invalid characters with question marks + raw_bytes = knx_value.encode(cls._encoding, errors="replace") + padding = bytes(cls.payload_length - len(raw_bytes)) + return tuple(raw_bytes + padding) @classmethod def _test_boundaries(cls, value: str) -> bool: """Test if value is within defined range for this object.""" return len(value) <= cls.payload_length + + +class DPTLatin1(DPTString): + """ + Abstraction for KNX 14 Octet Latin-1 (ISO 8859-1) string. + + DPT 16.001 + """ + + dpt_sub_number = 1 + value_type = "latin_1" + _encoding = "latin_1"	XKNX/xknx	cf242d29979d21f5433b3e9e36b35ea8b1d14356	diff --git a/test/dpt_tests/dpt_string_test.py b/test/dpt_tests/dpt_string_test.py index b73065ae..0cf820e5 100644 --- a/test/dpt_tests/dpt_string_test.py +++ b/test/dpt_tests/dpt_string_test.py @@ -1,167 +1,91 @@ """Unit test for KNX string object.""" import pytest -from xknx.dpt import DPTString +from xknx.dpt import DPTLatin1, DPTString from xknx.exceptions import ConversionError class TestDPTString: - """Test class for KNX float object.""" + """Test class for KNX ASCII string object.""" - def test_value_from_documentation(self): - """Test parsing and streaming Example from documentation.""" - raw = ( - 0x4B, - 0x4E, - 0x58, - 0x20, - 0x69, - 0x73, - 0x20, - 0x4F, - 0x4B, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - ) - string = "KNX is OK" - assert DPTString.to_knx(string) == raw - assert DPTString.from_knx(raw) == string - - def test_value_empty_string(self): - """Test parsing and streaming empty string.""" - raw = ( - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - ) - string = "" - assert DPTString.to_knx(string) == raw - assert DPTString.from_knx(raw) == string + @pytest.mark.parametrize( + "string,raw", + [ + ( + "KNX is OK", + (75, 78, 88, 32, 105, 115, 32, 79, 75, 0, 0, 0, 0, 0), + ), + ( + "", + (0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), + ), + ( + "AbCdEfGhIjKlMn", + (65, 98, 67, 100, 69, 102, 71, 104, 73, 106, 75, 108, 77, 110), + ), + ( + ".,:;-_!?$@&#%/", + (46, 44, 58, 59, 45, 95, 33, 63, 36, 64, 38, 35, 37, 47), + ), + ], + ) + @pytest.mark.parametrize("test_dpt", [DPTString, DPTLatin1]) + def test_values(self, string, raw, test_dpt): + """Test parsing and streaming strings.""" + assert test_dpt.to_knx(string) == raw + assert test_dpt.from_knx(raw) == string - def test_value_max_string(self): - """Test parsing and streaming large string.""" - raw = ( - 0x41, - 0x41, - 0x41, - 0x41, - 0x41, - 0x42, - 0x42, - 0x42, - 0x42, - 0x42, - 0x43, - 0x43, - 0x43, - 0x43, - ) - string = "AAAAABBBBBCCCC" - assert DPTString.to_knx(string) == raw - assert DPTString.from_knx(raw) == string - - def test_value_special_chars(self): - """Test parsing and streaming string with special chars.""" - raw = ( - 0x48, - 0x65, - 0x79, - 0x21, - 0x3F, - 0x24, - 0x20, - 0xC4, - 0xD6, - 0xDC, - 0xE4, - 0xF6, - 0xFC, - 0xDF, - ) - string = "Hey!?$ ÄÖÜäöüß" - assert DPTString.to_knx(string) == raw - assert DPTString.from_knx(raw) == string - - def test_to_knx_invalid_chars(self): - """Test streaming string with invalid chars.""" - raw = ( - 0x4D, - 0x61, - 0x74, - 0x6F, - 0x75, - 0x3F, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - ) - string = "Matouš" - knx_string = "Matou?" + @pytest.mark.parametrize( + "string,knx_string,raw", + [ + ( + "Matouš", + "Matou?", + (77, 97, 116, 111, 117, 63, 0, 0, 0, 0, 0, 0, 0, 0), + ), + ( + "Gänsefüßchen", + "G?nsef??chen", + (71, 63, 110, 115, 101, 102, 63, 63, 99, 104, 101, 110, 0, 0), + ), + ], + ) + def test_to_knx_ascii_invalid_chars(self, string, knx_string, raw): + """Test streaming ASCII string with invalid chars.""" assert DPTString.to_knx(string) == raw assert DPTString.from_knx(raw) == knx_string + @pytest.mark.parametrize( + "string,raw", + [ + ( + "Gänsefüßchen", + (71, 228, 110, 115, 101, 102, 252, 223, 99, 104, 101, 110, 0, 0), + ), + ( + "àáâãåæçèéêëìíî", + (224, 225, 226, 227, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238), + ), + ], + ) + def test_to_knx_latin_1(self, string, raw): + """Test streaming Latin-1 strings.""" + assert DPTLatin1.to_knx(string) == raw + assert DPTLatin1.from_knx(raw) == string + def test_to_knx_too_long(self): """Test serializing DPTString to KNX with wrong value (to long).""" with pytest.raises(ConversionError): DPTString.to_knx("AAAAABBBBBCCCCx") - def test_from_knx_wrong_parameter_too_large(self): - """Test parsing of KNX string with too many elements.""" - raw = ( - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - ) - with pytest.raises(ConversionError): - DPTString.from_knx(raw) - - def test_from_knx_wrong_parameter_too_small(self): - """Test parsing of KNX string with too less elements.""" - raw = ( - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - ) + @pytest.mark.parametrize( + "raw", + [ + ((0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),), + ((0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),), + ], + ) + def test_from_knx_wrong_parameter_length(self, raw): + """Test parsing of KNX string with wrong elements length.""" with pytest.raises(ConversionError): DPTString.from_knx(raw)	ISO 8859-1 String support (Latin-1) - support DPT 16.001 ISO 8859-1 strings currently we only support DPT 16.000 but I think we encode/decode it as Unicode (`char()`) instead of just ASCII.	cf242d29979d21f5433b3e9e36b35ea8b1d14356	[ "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTString-KNX", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTString--raw1]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTString-AbCdEfGhIjKlMn-raw2]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTString-.,:;-_!?$@&#%/-raw3]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTLatin1-KNX", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTLatin1--raw1]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTLatin1-AbCdEfGhIjKlMn-raw2]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTLatin1-.,:;-_!?$@&#%/-raw3]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_to_knx_ascii_invalid_chars[Matou\\u0161-Matou?-raw0]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_to_knx_ascii_invalid_chars[G\\xe4nsef\\xfc\\xdfchen-G?nsef??chen-raw1]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_to_knx_latin_1[G\\xe4nsef\\xfc\\xdfchen-raw0]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_to_knx_latin_1[\\xe0\\xe1\\xe2\\xe3\\xe5\\xe6\\xe7\\xe8\\xe9\\xea\\xeb\\xec\\xed\\xee-raw1]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_to_knx_too_long", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_from_knx_wrong_parameter_length[raw0]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_from_knx_wrong_parameter_length[raw1]" ]	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-04-05 14:17:08+00:00	mit	852
Yelp__pyramid-hypernova-15	diff --git a/pyramid_hypernova/batch.py b/pyramid_hypernova/batch.py index e4592f1..869b5ea 100644 --- a/pyramid_hypernova/batch.py +++ b/pyramid_hypernova/batch.py @@ -131,9 +131,9 @@ class BatchRequest(object): __, __, exc_traceback = sys.exc_info() error = HypernovaError( - repr(type(e)), + type(e).__name__, str(e), - traceback.format_tb(exc_traceback), + [line.rstrip('\n') for line in traceback.format_tb(exc_traceback)], ) self.plugin_controller.on_error(error, jobs) response = create_fallback_response(jobs, True, self.json_encoder, error)	Yelp/pyramid-hypernova	573e13042412461fa31bf046473c0033f9dc3fec	diff --git a/tests/batch_test.py b/tests/batch_test.py index 6a9dcf3..1b9f790 100644 --- a/tests/batch_test.py +++ b/tests/batch_test.py @@ -331,7 +331,7 @@ class TestBatchRequest(object): assert response == { token.identifier: JobResult( error=HypernovaError( - name="<class 'fido.exceptions.NetworkError'>", + name='NetworkError', message='oh no', stack=mock.ANY, ), @@ -475,16 +475,20 @@ class TestBatchRequestLifecycleMethods(object): with mock.patch( 'fido.fetch' ) as mock_fetch, mock.patch( - 'traceback.format_tb' - ) as mock_format_tb: + 'traceback.format_tb', + return_value=[ + 'Traceback:\n', + ' foo:\n', + ], + ): mock_fetch.return_value.wait.return_value.json.side_effect = NetworkError('oh no') batch_request.submit() spy_plugin_controller.on_error.assert_called_once_with( HypernovaError( - name="<class 'fido.exceptions.NetworkError'>", + name='NetworkError', message='oh no', - stack=mock_format_tb.return_value, + stack=['Traceback:', ' foo:'], ), batch_request.jobs, )	"stack" property on HypernovaError is formatted inconsistently When the error is a Python traceback, each element in the list has a trailing newline: ```python [' File "/nail/home/ckuehl/pg/yelp-main/virtualenv_run/lib/python2.7/site-packages/pyramid_hypernova/batch.py", line 116, in process_responses\n response_json = r.json()\n', ' File "/nail/home/ckuehl/pg/yelp-main/virtualenv_run/lib/python2.7/site-packages/fido/fido.py", line 98, in json\n return json.loads(self.body.decode(\'utf-8\'))\n', ' File "/usr/lib/python2.7/json/__init__.py", line 339, in loads\n return _default_decoder.decode(s)\n', [...] ``` When the error comes from the Hypernova server (a JS traceback), each element has no trailing newline: ```python [u'ReferenceError: Component "yelp_main__DEV__yelp_main__SearchApp__dynamic" not registered', u'at YOUR-COMPONENT-DID-NOT-REGISTER_yelp_main__DEV__yelp_main__SearchApp__dynamic:1:1', u'at notFound (/nail/home/ckuehl/proj/react_component_renderer/node_modules/hypernova/lib/utils/BatchManager.js:36:15)', u'at /nail/home/ckuehl/proj/react_component_renderer/node_modules/hypernova/lib/utils/BatchManager.js:186:35', u'at tryCatcher (/nail/home/ckuehl/proj/react_component_renderer/node_modules/bluebird/js/release/util.js:16:23)', u'at Promise._settlePromiseFromHandler (/nail/home/ckuehl/proj/react_component_renderer/node_modules/bluebird/js/release/promise.js:512:31)', [...] ``` Could we normalize these so that it's easier to print these out in a human-readable way?	573e13042412461fa31bf046473c0033f9dc3fec	[ "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data0-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data2-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data2-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data1-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data0-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data0-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data1-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data1-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data2-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data2-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data0-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data1-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data2-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data1-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data0-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data1-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data2-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data0-1]" ]	[ "tests/batch_test.py::TestBatchRequest::test_batch_request_with_component_errors[test_data0-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_component_errors[test_data1-2]", "tests/batch_test.py::TestBatchRequest::test_successful_batch_request[test_data0-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[2-test_data0]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data1-None]", "tests/batch_test.py::TestBatchRequest::test_successful_batch_request[test_data0-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data2-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data2-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_component_errors[test_data0-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data0-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[None-test_data0]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_component_errors[test_data2-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[None-test_data1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[1-test_data2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[1-test_data0]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data1-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_component_errors[test_data1-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data0-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[None-test_data2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[1-test_data1]", "tests/batch_test.py::TestBatchRequest::test_successful_batch_request[test_data1-1]", "tests/batch_test.py::TestBatchRequest::test_successful_batch_request[test_data1-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data0-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data1-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_component_errors[test_data2-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[2-test_data2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[2-test_data1]", "tests/batch_test.py::TestBatchRequest::test_successful_batch_request[test_data2-None]", 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"tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_get_view_data[test_data0-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error[test_data1-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data2-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_prepare_request[test_data0-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_will_send_request[test_data0-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data0-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_get_view_data[test_data0-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data1-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data0-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_after_response[test_data2-2]", 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"tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data0-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_get_view_data[test_data0-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data2-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data2-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error[test_data1-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_prepare_request[test_data1-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_will_send_request[test_data1-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_prepare_request[test_data0-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error[test_data1-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_get_view_data[test_data2-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_after_response[test_data1-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error[test_data2-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_will_send_request[test_data1-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_will_send_request[test_data2-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error[test_data2-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_after_response[test_data0-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_get_view_data[test_data2-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data1-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_will_send_request[test_data2-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_will_send_request[test_data0-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_prepare_request[test_data1-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_prepare_request[test_data0-1]", "tests/batch_test.py::test_create_fallback_response[jobs2-True-json_encoder2]", "tests/batch_test.py::test_create_fallback_response[jobs5-False-json_encoder5]", "tests/batch_test.py::test_create_job_groups[5-expected5]", "tests/batch_test.py::test_create_job_groups[1-expected1]", "tests/batch_test.py::test_create_jobs_payload", "tests/batch_test.py::test_create_job_groups[2-expected2]", "tests/batch_test.py::test_create_fallback_response[jobs1-False-json_encoder1]", "tests/batch_test.py::test_create_job_groups[None-expected0]", "tests/batch_test.py::test_create_fallback_response[jobs0-True-json_encoder0]", "tests/batch_test.py::test_create_job_groups[6-expected6]", "tests/batch_test.py::test_create_fallback_response[jobs3-False-json_encoder3]", "tests/batch_test.py::test_create_fallback_response[jobs4-True-json_encoder4]", "tests/batch_test.py::test_create_job_groups[4-expected4]", "tests/batch_test.py::test_create_job_groups[3-expected3]" ]	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2019-01-18 00:11:18+00:00	mit	853
Yelp__virtualenv-tools-22	diff --git a/tox.ini b/tox.ini index 43f5f76..fceab09 100644 --- a/tox.ini +++ b/tox.ini @@ -16,4 +16,4 @@ envdir = venv-{[tox]project} commands = [pep8] -ignore = E265,E501 +ignore = E265,E501,W504 diff --git a/virtualenv_tools.py b/virtualenv_tools.py index 2b3cfae..2f76a24 100644 --- a/virtualenv_tools.py +++ b/virtualenv_tools.py @@ -31,7 +31,7 @@ ACTIVATION_SCRIPTS = [ _pybin_match = re.compile(r'^python\d+\.\d+$') _pypy_match = re.compile(r'^\d+.\d+$') _activation_path_re = re.compile( - r'^(?:set -gx \|setenv \|)VIRTUAL_ENV[ =]"(.?)"\s$', + r'^(?:set -gx \|setenv \|)VIRTUAL_ENV[ =][\'"](.?)[\'"]\s$', ) VERBOSE = False MAGIC_LENGTH = 4 + 4 # magic length + 4 byte timestamp @@ -169,7 +169,11 @@ def update_pycs(lib_dir, new_path): for dirname, dirnames, filenames in os.walk(lib_dir): for filename in filenames: - if filename.endswith(('.pyc', '.pyo')): + if ( + filename.endswith(('.pyc', '.pyo')) and + # python 2, virtualenv 20.x symlinks os.pyc + not os.path.islink(os.path.join(dirname, filename)) + ): filename = os.path.join(dirname, filename) local_path = get_new_path(filename) update_pyc(filename, local_path) @@ -236,11 +240,13 @@ def get_orig_path(venv_path): with open(activate_path) as activate: for line in activate: - if line.startswith('VIRTUAL_ENV="'): - return line.split('"', 2)[1] + # virtualenv 20 changes the position + for possible in ('VIRTUAL_ENV="', "VIRTUAL_ENV='"): + if line.startswith(possible): + return line.split(possible[-1], 2)[1] else: raise AssertionError( - 'Could not find VIRTUAL_ENV=" in activation script: %s' % + 'Could not find VIRTUAL_ENV= in activation script: %s' % activate_path )	Yelp/virtualenv-tools	5247e0c8c39a584b217ae7de82bc9051903f863f	diff --git a/tests/virtualenv_tools_test.py b/tests/virtualenv_tools_test.py index e34d596..44fdc27 100644 --- a/tests/virtualenv_tools_test.py +++ b/tests/virtualenv_tools_test.py @@ -185,7 +185,7 @@ def test_verbose(venv, capsys): run(venv.before, venv.after, args=('--verbose',)) out, _ = capsys.readouterr() # Lots of output - assert len(out.splitlines()) > 25 + assert len(out.splitlines()) > 10 def test_non_absolute_error(capsys):	Unable to find the VIRTUAL_ENV variable in activate.sh for recent virtualenv versions. Starting in `virtualenv==20.0.0`, the `VIRTUAL_ENV` variable is now defined using single quotes instead of double quotes. This breaks `virtualenv-tools3` as it specifically searches for the string `VIRTUAL_ENV="` in `activate.sh`.	5247e0c8c39a584b217ae7de82bc9051903f863f	[ "tests/virtualenv_tools_test.py::test_bad_pyc", "tests/virtualenv_tools_test.py::test_already_up_to_date" ]	[ "tests/virtualenv_tools_test.py::test_help[helpargs1]", "tests/virtualenv_tools_test.py::test_not_a_virtualenv_missing_bindir", "tests/virtualenv_tools_test.py::test_help[helpargs0]", "tests/virtualenv_tools_test.py::test_not_a_virtualenv_missing_site_packages", "tests/virtualenv_tools_test.py::test_not_a_virtualenv_missing_activate_file", "tests/virtualenv_tools_test.py::test_not_a_virtualenv_missing_versioned_lib_directory", "tests/virtualenv_tools_test.py::test_non_absolute_error" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-02-12 00:45:18+00:00	bsd-3-clause	854
Zepmanbc__creopyson-2	diff --git a/creopyson/creo.py b/creopyson/creo.py index 890f29d..1d86c48 100755 --- a/creopyson/creo.py +++ b/creopyson/creo.py @@ -1,4 +1,5 @@ """Creo module.""" +from creopyson.exceptions import MissingKey def cd(client, dirname): @@ -108,7 +109,11 @@ def list_dirs(client, dirname=None): data = {"dirname": "*"} if dirname: data["dirname"] = dirname - return client._creoson_post("creo", "list_dirs", data, "dirlist") + try: + result = client._creoson_post("creo", "list_dirs", data, "dirlist") + except MissingKey: + result = [] + return result def list_files(client, filename=None):	Zepmanbc/creopyson	4a214ea618fba75d4200cc3dcbc6371d924765e6	diff --git a/tests/fixtures.py b/tests/fixtures.py index 8919eca..6d2ff6e 100644 --- a/tests/fixtures.py +++ b/tests/fixtures.py @@ -55,7 +55,7 @@ def mk_creoson_post_dict(monkeypatch): @pytest.fixture def mk_creoson_post_None(monkeypatch): """Mock _creoson_post return None.""" - def fake_func(client, command, function, data=None): + def fake_func(client, command, function, data=None, key_data=None): return None monkeypatch.setattr( creopyson.connection.Client, '_creoson_post', fake_func) @@ -64,7 +64,7 @@ def mk_creoson_post_None(monkeypatch): @pytest.fixture def mk_creoson_post_list(monkeypatch): """Mock _creoson_post return list.""" - def fake_func(client, command, function, data=None): + def fake_func(client, command, function, data=None, key_data=None): return ['information'] monkeypatch.setattr( creopyson.connection.Client, '_creoson_post', fake_func) diff --git a/tests/test_creo.py b/tests/test_creo.py index ccdb9fe..1398006 100644 --- a/tests/test_creo.py +++ b/tests/test_creo.py @@ -1,5 +1,6 @@ """Creo testing.""" import creopyson +from creopyson.exceptions import MissingKey from .fixtures import mk_creoson_post_dict, mk_creoson_post_None @@ -43,6 +44,23 @@ def test_creo_list_dirs(mk_creoson_post_dict): c = creopyson.Client() result = c.creo_list_dirs("filter_*") assert isinstance(result, (list)) + result = c.creo_list_dirs() + assert isinstance(result, (list)) + + +def test_creo_list_dirs_empty(monkeypatch): + """Correction issue #1. + + if there is no folder in directory, creoson does not return `data`. + Need to return an empty list. + """ + def fake_func(client, command, function, data=None, key_data=None): + raise MissingKey("Missing `data` in creoson return") + monkeypatch.setattr( + creopyson.connection.Client, '_creoson_post', fake_func) + c = creopyson.Client() + result = c.creo_list_dirs() + assert result == [] def test_creo_list_files(mk_creoson_post_dict):	Exception thrown in creo_list_dirs * Creopyson version: 0.3.1 * Python version: 3.6 * Operating System: Windows ### Description I tried to list the directories in the current session with `creo_list_dirs()` but I received an exception telling that Creoson did not return the right data. ### What I Did ``` >>> c.creo_list_dirs() Traceback (most recent call last): File "<stdin>", line 1, in <module> File "C:\Users\Tim\.virtualenvs\creopyson_test-yJfFsqNW\lib\site-packages\creopyson\creo.py", line 111, in list_dirs return client._creoson_post("creo", "list_dirs", data, "dirlist") File "C:\Users\Tim\.virtualenvs\creopyson_test-yJfFsqNW\lib\site-packages\creopyson\connection.py", line 81, in _creoson_post raise MissingKey("Missing `data` in creoson return") creopyson.exceptions.MissingKey: Missing `data` in creoson return ```	4a214ea618fba75d4200cc3dcbc6371d924765e6	[ "tests/test_creo.py::test_creo_list_dirs_empty" ]	[ "tests/test_creo.py::test_creo_cd", "tests/test_creo.py::test_creo_delete_files", "tests/test_creo.py::test_creo_get_config", "tests/test_creo.py::test_creo_get_std_color", "tests/test_creo.py::test_creo_list_dirs", "tests/test_creo.py::test_creo_list_files", "tests/test_creo.py::test_creo_mkdir", "tests/test_creo.py::test_creo_pwd", "tests/test_creo.py::test_creo_rmdir_ok", "tests/test_creo.py::test_creo_set_config_ok", "tests/test_creo.py::test_creo_set_std_color_ok" ]	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2019-07-03 19:45:24+00:00	mit	855
a2i2__surround-106	diff --git a/surround/cli.py b/surround/cli.py index e8922cb..f57dc50 100644 --- a/surround/cli.py +++ b/surround/cli.py @@ -93,6 +93,16 @@ def is_valid_dir(aparser, arg): else: return arg +def allowed_to_access_dir(path): + try: + os.makedirs(path, exist_ok=True) + except OSError: + print("error: can't write to " + path) + + if os.access(path, os.R_OK \| os.W_OK \| os.F_OK \| os.X_OK): + return True + return False + def is_valid_name(aparser, arg): if not arg.isalpha() or not arg.islower(): aparser.error("Name %s must be lowercase letters" % arg) @@ -229,26 +239,29 @@ def parse_tutorial_args(args): def parse_init_args(args): - if args.project_name: - project_name = args.project_name - else: - while True: - project_name = input("Name of project: ") - if not project_name.isalpha() or not project_name.islower(): - print("Project name requires lowercase letters only") - else: - break - - if args.description: - project_description = args.description - else: - project_description = input("What is the purpose of this project?: ") + if allowed_to_access_dir(args.path): + if args.project_name: + project_name = args.project_name + else: + while True: + project_name = input("Name of project: ") + if not project_name.isalpha() or not project_name.islower(): + print("error: project name requires lowercase letters only") + else: + break + + if args.description: + project_description = args.description + else: + project_description = input("What is the purpose of this project?: ") - new_dir = os.path.join(args.path, project_name) - if process(new_dir, PROJECTS["new"], project_name, project_description, "new"): - print("Project created at %s" % os.path.join(os.path.abspath(args.path), project_name)) + new_dir = os.path.join(args.path, project_name) + if process(new_dir, PROJECTS["new"], project_name, project_description, "new"): + print("info: project created at %s" % os.path.join(os.path.abspath(args.path), project_name)) + else: + print("error: directory %s already exists" % new_dir) else: - print("Directory %s already exists" % new_dir) + print("error: permission denied") def parse_tool_args(parsed_args, remote_parser, tool): if tool == "tutorial": @@ -278,10 +291,10 @@ def main(): tutorial_parser = sub_parser.add_parser('tutorial', help="Create the tutorial project") tutorial_parser.add_argument('tutorial', help="Create the Surround tutorial project", action='store_true') - tutorial_parser.add_argument('path', type=lambda x: is_valid_dir(parser, x), help="Path for creating the tutorial project", nargs='?', default="./") + tutorial_parser.add_argument('path', help="Path for creating the tutorial project", nargs='?', default="./") init_parser = sub_parser.add_parser('init', help="Initialise a new Surround project") - init_parser.add_argument('path', type=lambda x: is_valid_dir(parser, x), help="Path for creating a Surround project", nargs='?', default="./") + init_parser.add_argument('path', help="Path for creating a Surround project", nargs='?', default="./") init_parser.add_argument('-p', '--project-name', help="Name of the project", type=lambda x: is_valid_name(parser, x)) init_parser.add_argument('-d', '--description', help="A description for the project")	a2i2/surround	6e5a32dafc6ba858edc1b21cf6644fb2c6b77815	diff --git a/surround/tests/cli/project_cli/init_test.py b/surround/tests/cli/project_cli/init_test.py index 24d0f53..1bbce4e 100644 --- a/surround/tests/cli/project_cli/init_test.py +++ b/surround/tests/cli/project_cli/init_test.py @@ -9,13 +9,13 @@ class InitTest(unittest.TestCase): def test_happy_path(self): process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Project created at " + os.getcwd() + "/temp\n") + self.assertEqual(process.stdout, "info: project created at " + os.getcwd() + "/temp\n") is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp")) self.assertEqual(is_temp, True) process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Directory ./temp already exists\n") + self.assertEqual(process.stdout, "error: directory ./temp already exists\n") def tearDown(self): # Remove residual files diff --git a/surround/tests/cli/remote_cli/add_test.py b/surround/tests/cli/remote_cli/add_test.py index 07c9ea4..537a8d8 100644 --- a/surround/tests/cli/remote_cli/add_test.py +++ b/surround/tests/cli/remote_cli/add_test.py @@ -9,7 +9,7 @@ class AddTest(unittest.TestCase): def test_rejecting_path(self): process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Project created at " + os.getcwd() + "/temp\n") + self.assertEqual(process.stdout, "info: project created at " + os.getcwd() + "/temp\n") is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp")) self.assertEqual(is_temp, True) @@ -24,7 +24,7 @@ class AddTest(unittest.TestCase): def test_happy_path(self): process = subprocess.run(['surround', 'init', os.getcwd(), '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Project created at " + os.getcwd() + "/temp\n") + self.assertEqual(process.stdout, "info: project created at " + os.getcwd() + "/temp\n") is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp")) self.assertEqual(is_temp, True) diff --git a/surround/tests/cli/remote_cli/list_test.py b/surround/tests/cli/remote_cli/list_test.py index 71970eb..d993284 100644 --- a/surround/tests/cli/remote_cli/list_test.py +++ b/surround/tests/cli/remote_cli/list_test.py @@ -9,7 +9,7 @@ class ListTest(unittest.TestCase): def test_rejecting_path(self): process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Project created at " + os.getcwd() + "/temp\n") + self.assertEqual(process.stdout, "info: project created at " + os.getcwd() + "/temp\n") is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp")) self.assertEqual(is_temp, True) @@ -19,7 +19,7 @@ class ListTest(unittest.TestCase): def test_happy_path(self): process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Project created at " + os.getcwd() + "/temp\n") + self.assertEqual(process.stdout, "info: project created at " + os.getcwd() + "/temp\n") is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp")) self.assertEqual(is_temp, True) diff --git a/surround/tests/cli/remote_cli/remote_test.py b/surround/tests/cli/remote_cli/remote_test.py index e8ed4cd..7236530 100644 --- a/surround/tests/cli/remote_cli/remote_test.py +++ b/surround/tests/cli/remote_cli/remote_test.py @@ -12,7 +12,7 @@ class RemoteTest(unittest.TestCase): self.assertEqual(process.stdout, "error: not a surround project\nerror: goto project root directory\n") process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Project created at " + os.getcwd() + "/temp\n") + self.assertEqual(process.stdout, "info: project created at " + os.getcwd() + "/temp\n") is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp")) self.assertEqual(is_temp, True) @@ -22,7 +22,7 @@ class RemoteTest(unittest.TestCase): def test_remote_add(self): process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Project created at " + os.getcwd() + "/temp\n") + self.assertEqual(process.stdout, "info: project created at " + os.getcwd() + "/temp\n") is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp")) self.assertEqual(is_temp, True)	`surround tutorial` doesn't work if destination directory doesn't exist `surround tutorial <path>` doesn't work if the path doesn't exist. Not sure if this is intended behaviour, but it might be nice to follow what Git does, i.e. * Create the directory if it doesn't exist * Print error if the directory exists but isn't empty My experience below: ``` ➜ surround tutorial usage: surround tutorial [-h] path surround tutorial: error: the following arguments are required: path ➜ surround tutorial my-first-surround-app usage: surround [-h] {tutorial,init} ... surround: error: Invalid directory or can't write to my-first-surround-app ➜ mkdir surround-tutorial ➜ surround tutorial my-first-surround-app The tutorial project has been created. Start by reading the README.md file at: /home/rohan/Development/sandbox/my-first-surround-app/README.md ``` After doing the above, I ended up with all the files in `my-first-surround-app/tutorial`, instead of just in `my-first-surround-app` as I expected.	6e5a32dafc6ba858edc1b21cf6644fb2c6b77815	[ "surround/tests/cli/project_cli/init_test.py::InitTest::test_happy_path", "surround/tests/cli/remote_cli/add_test.py::AddTest::test_happy_path", "surround/tests/cli/remote_cli/add_test.py::AddTest::test_rejecting_path", "surround/tests/cli/remote_cli/list_test.py::ListTest::test_happy_path", "surround/tests/cli/remote_cli/list_test.py::ListTest::test_rejecting_path", "surround/tests/cli/remote_cli/remote_test.py::RemoteTest::test_remote", "surround/tests/cli/remote_cli/remote_test.py::RemoteTest::test_remote_add" ]	[]	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2019-04-04 06:46:13+00:00	bsd-3-clause	856
abantos__bolt-88	diff --git a/bolt/about.py b/bolt/about.py index 3c285ba..9b6ae95 100644 --- a/bolt/about.py +++ b/bolt/about.py @@ -8,4 +8,4 @@ A task runner written in Python copyright = u'2016 Abantos' author = u'Isaac Rodriguez' version = u'0.2' -release = u'0.2.2' +release = u'0.2.3' diff --git a/bolt/tasks/bolt_setup.py b/bolt/tasks/bolt_setup.py index 6190eb5..e10aa8b 100644 --- a/bolt/tasks/bolt_setup.py +++ b/bolt/tasks/bolt_setup.py @@ -26,8 +26,12 @@ configure the task. :: import distutils.core as dcore import logging +import bolt.errors as errors import bolt.utils as utilities + +class BuildSetupError(errors.TaskError): pass + DEFAULT_ARGUMENTS = ['build'] DEFAULT_SETUP_SCRIPT = 'setup.py' @@ -50,11 +54,13 @@ class ExecuteSetupTask(object): self.setup_script = DEFAULT_SETUP_SCRIPT generator = _SetupArgumentGenerator() self.args = generator.generate_from(config) - self._execute_setup() + result = self._execute_setup() + if not result.dist_files: + raise BuildSetupError() def _execute_setup(self): - dcore.run_setup(self.setup_script, self.args) + return dcore.run_setup(self.setup_script, self.args)	abantos/bolt	39a5db9fa29ec6c13dceb51480fb3e56574aa2a7	diff --git a/test/test_tasks/test_bolt_setup.py b/test/test_tasks/test_bolt_setup.py index d9a03b9..9e874cc 100644 --- a/test/test_tasks/test_bolt_setup.py +++ b/test/test_tasks/test_bolt_setup.py @@ -7,7 +7,7 @@ import _mocks as mck class TestExecuteSetupTask(unittest.TestCase): def setUp(self): - self. subject = ExecuteSetupTaskSpy() + self.subject = ExecuteSetupTaskSpy() return super(TestExecuteSetupTask, self).setUp() @@ -25,6 +25,12 @@ class TestExecuteSetupTask(unittest.TestCase): self.assertEqual(self.subject.setup_script, script) + def test_raises_exception_if_building_setup_fails(self): + self.subject.dist_files = [] + with self.assertRaises(bsetup.BuildSetupError): + self.given({}) + + def given(self, config): self.subject(config=config) @@ -36,9 +42,13 @@ class TestExecuteSetupTask(unittest.TestCase): class ExecuteSetupTaskSpy(bsetup.ExecuteSetupTask): + + def __init__(self): + super(ExecuteSetupTaskSpy, self).__init__() + self.dist_files = [('bdist_wheel', '3.5', '/some/colation/the.whl')] def _execute_setup(self): - pass + return self	Setup Task Swallows Errors Building Distribution ### Description The current implementation of the Setup task does not evaluate the return object from `distutils.core.run_setup()` and it just assumes it works. Unfortunately, some environments will not have the right tools to build a distribution; therefore, the task will silently fail. I found this problem in another project's pipeline where building a `wheel` inside the official Python 2.7 Docker container silently failed because the `wheel` package is not installed by default like when creating a virtual environment. ### Steps to Reproduce - Create a setup task that builds a simple distribution wheel. - Create a virtual environment, activate it, and uninstall the `wheel` package. - Run the setup task within the environment. - Check the dist folder, which will be empty. The current behavior shows that the return code from `distutils.core.run_setup()` invoked by the task is not evaluated, and the task seems to succeed; however, the `.whl` file has not been created. An exception is expected to be raised if the wheel doesn't succeed. ### Fix Analysis Looking at the implementation of `distutils.core.run_setup()`, you can see the function returns a `Distribution` instance. The instance exposes a `dist_files` property, which is empty if the distribution failed to build. If it succeeds, the return value is a list of tuples containing information about each distribution. This allow us to fix the problem, or at list report an error if no distribution was built, by checking the contents of `dist_files`; something like the following code: ```python # dcore is an alias to distutils.core. dist_info = dcore.run_setup(self.setup_script, self.args) if not dist_info.dist_files: raise DistributionBuildError() ``` > NOTE:I need to think on how to handle multiple distributions; although, I believe right now the task only supports one distribution per configuration. The following is an example of the contents of the `dist_files` property: ``` [('bdist_wheel', '3.5', 'D:\\Projects\\Abantos\\bolt\\dist\\bolt_ta-0.2.1-py2.py3-none-any.whl')] ``` ### Acceptance Criteria Raises exception if building the distribution fails.	39a5db9fa29ec6c13dceb51480fb3e56574aa2a7	[ "test/test_tasks/test_bolt_setup.py::TestExecuteSetupTask::test_raises_exception_if_building_setup_fails" ]	[ "test/test_tasks/test_bolt_setup.py::TestExecuteSetupTask::test_uses_default_if_empty_configuration", "test/test_tasks/test_bolt_setup.py::TestExecuteSetupTask::test_uses_specified_script", "test/test_tasks/test_bolt_setup.py::TestRegisterTasks::test_registers_setup" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2017-03-07 16:19:15+00:00	mit	857
abdullahselek__HerePy-25	diff --git a/README.rst b/README.rst index b6bd1b8..78d2e19 100644 --- a/README.rst +++ b/README.rst @@ -224,6 +224,14 @@ Calculate an MxN cost matrix for M start points and N destinations departure='2013-07-04T17:00:00+02', modes=[herepy.RouteMode.fastest, herepy.RouteMode.car]) +Calculate route providing names instead of coordinates + +.. code:: python + + response = routingApi.car_route([11.0, 12.0], + '200 S Mathilda Sunnyvale CA', + [herepy.RouteMode.car, herepy.RouteMode.fastest]) + GeocoderAutoCompleteApi ----------------------- diff --git a/herepy/routing_api.py b/herepy/routing_api.py index d188aaf..9a9fd52 100644 --- a/herepy/routing_api.py +++ b/herepy/routing_api.py @@ -5,12 +5,13 @@ import sys import json import requests +from herepy.geocoder_api import GeocoderApi from herepy.here_api import HEREApi from herepy.utils import Utils from herepy.error import HEREError from herepy.models import RoutingResponse, RoutingMatrixResponse from herepy.here_enum import RouteMode, MatrixSummaryAttribute -from typing import List +from typing import List, Union class RoutingApi(HEREApi): """A python interface into the HERE Routing API""" @@ -53,6 +54,10 @@ class RoutingApi(HEREApi): return str.format('geo!{0},{1}', waypoint_a[0], waypoint_a[1]) def _route(self, waypoint_a, waypoint_b, modes=None, departure=None, arrival=None): + if isinstance(waypoint_a, str): + waypoint_a = self._get_coordinates_for_location_name(waypoint_a) + if isinstance(waypoint_b, str): + waypoint_b = self._get_coordinates_for_location_name(waypoint_b) data = {'waypoint0': self.__array_to_waypoint(waypoint_a), 'waypoint1': self.__array_to_waypoint(waypoint_b), 'mode': self.__prepare_mode_values(modes), @@ -84,16 +89,18 @@ class RoutingApi(HEREApi): return response def bicycle_route(self, - waypoint_a: List[float], - waypoint_b: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], modes: List[RouteMode]=None, departure: str='now'): """Request a bicycle route between two points Args: - waypoint_a (array): - array including latitude and longitude in order. - waypoint_b (array): - array including latitude and longitude in order. + waypoint_a: + array including latitude and longitude in order + or string with the location name + waypoint_b: + array including latitude and longitude in order + or string with the location name. modes (array): array including RouteMode enums. departure (str): @@ -108,16 +115,18 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure) def car_route(self, - waypoint_a: List[float], - waypoint_b: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], modes: List[RouteMode]=None, departure: str='now'): """Request a driving route between two points Args: waypoint_a (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. waypoint_b (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. modes (array): array including RouteMode enums. departure (str): @@ -132,16 +141,18 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure) def pedastrian_route(self, - waypoint_a: List[float], - waypoint_b: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], modes: List[RouteMode]=None, departure: str='now'): """Request a pedastrian route between two points Args: waypoint_a (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. waypoint_b (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. modes (array): array including RouteMode enums. departure (str): @@ -156,19 +167,22 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure) def intermediate_route(self, - waypoint_a: List[float], - waypoint_b: List[float], - waypoint_c: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], + waypoint_c: Union[List[float], str], modes: List[RouteMode]=None, departure: str='now'): """Request a intermediate route from three points Args: waypoint_a (array): - Starting array including latitude and longitude in order. + Starting array including latitude and longitude in order + or string with the location name. waypoint_b (array): - Intermediate array including latitude and longitude in order. + Intermediate array including latitude and longitude in order + or string with the location name. waypoint_c (array): - Last array including latitude and longitude in order. + Last array including latitude and longitude in order + or string with the location name. modes (array): array including RouteMode enums. departure (str): @@ -183,17 +197,19 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure) def public_transport(self, - waypoint_a: List[float], - waypoint_b: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], combine_change: bool, modes: List[RouteMode]=None, departure='now'): """Request a public transport route between two points Args: waypoint_a (array): - Starting array including latitude and longitude in order. + Starting array including latitude and longitude in order + or string with the location name. waypoint_b (array): - Intermediate array including latitude and longitude in order. + Intermediate array including latitude and longitude in order + or string with the location name. combine_change (bool): Enables the change manuever in the route response, which indicates a public transit line change. @@ -211,8 +227,8 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure) def public_transport_timetable(self, - waypoint_a: List[float], - waypoint_b: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], combine_change: bool, modes: List[RouteMode]=None, departure: str=None, @@ -220,9 +236,11 @@ class RoutingApi(HEREApi): """Request a public transport route between two points based on timetables Args: waypoint_a (array): - Starting array including latitude and longitude in order. + Starting array including latitude and longitude in order + or string with the location name. waypoint_b (array): - Intermediate array including latitude and longitude in order. + Intermediate array including latitude and longitude in order + or string with the location name. combine_change (bool): Enables the change manuever in the route response, which indicates a public transit line change. @@ -242,16 +260,18 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure, arrival) def location_near_motorway(self, - waypoint_a: List[float], - waypoint_b: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], modes: List[RouteMode]=None, departure: str='now'): """Calculates the fastest car route between two location Args: waypoint_a (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. waypoint_b (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. modes (array): array including RouteMode enums. departure (str): @@ -266,16 +286,18 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure) def truck_route(self, - waypoint_a: List[float], - waypoint_b: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], modes: List[RouteMode]=None, departure: str='now'): """Calculates the fastest truck route between two location Args: waypoint_a (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. waypoint_b (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. modes (array): array including RouteMode enums. departure (str): @@ -290,8 +312,8 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure) def matrix(self, - start_waypoints: List[float], - destination_waypoints: List[float], + start_waypoints: Union[List[float], str], + destination_waypoints: Union[List[float], str], departure: str='now', modes: List[RouteMode]=[], summary_attributes: List[MatrixSummaryAttribute]=[]): @@ -299,8 +321,10 @@ class RoutingApi(HEREApi): Args: start_waypoints (array): array of arrays of coordinates [lat,long] of start waypoints. + or array of string with the location names. destination_waypoints (array): array of arrays of coordinates [lat,long] of destination waypoints. + or array of string with the location names. departure (str): time when travel is expected to start, e.g.: '2013-07-04T17:00:00+02' modes (array): @@ -320,12 +344,27 @@ class RoutingApi(HEREApi): 'summaryAttributes': ','.join([attribute.__str__() for attribute in summary_attributes]) } for i, start_waypoint in enumerate(start_waypoints): + if isinstance(start_waypoint, str): + start_waypoint = self._get_coordinates_for_location_name(start_waypoint) data['start' + str(i)] = self.__array_to_waypoint(start_waypoint) for i, destination_waypoint in enumerate(destination_waypoints): + if isinstance(destination_waypoint, str): + destination_waypoint = self._get_coordinates_for_location_name(destination_waypoint) data['destination' + str(i)] = self.__array_to_waypoint(destination_waypoint) response = self.__get(self.URL_CALCULATE_MATRIX, data, RoutingMatrixResponse) return response + def _get_coordinates_for_location_name(self, location_name: str) -> List[float]: + """Use the Geocoder API to resolve a location name to a set of coordinates.""" + + geocoder_api = GeocoderApi(self._api_key) + try: + geocoder_response = geocoder_api.free_form(location_name) + coordinates = geocoder_response.Response["View"][0]["Result"][0]["Location"]["NavigationPosition"][0] + return [coordinates["Latitude"], coordinates["Longitude"]] + except (HEREError) as here_error: + raise WaypointNotFoundError(here_error.message) + @staticmethod def _convert_datetime_to_isoformat(datetime_object): """Convert a datetime.datetime object to an ISO8601 string."""	abdullahselek/HerePy	8691e147549141dc8287ba16a4396a63ed09b73b	diff --git a/tests/test_routing_api.py b/tests/test_routing_api.py index db150bd..9239be6 100644 --- a/tests/test_routing_api.py +++ b/tests/test_routing_api.py @@ -455,6 +455,22 @@ class RoutingApiTest(unittest.TestCase): self.assertTrue(response) self.assertIsInstance(response, herepy.RoutingMatrixResponse) + @responses.activate + def test_matrix_multiple_start_names(self): + with codecs.open('testdata/models/routing_matrix_multiple_starts.json', mode='r', encoding='utf-8') as f: + server_response = f.read() + responses.add(responses.GET, 'https://matrix.route.ls.hereapi.com/routing/7.2/calculatematrix.json', + server_response, status=200) + with open('testdata/models/geocoder.json', 'r') as f: + expectedGeocoderResponse = f.read() + responses.add(responses.GET, 'https://geocoder.ls.hereapi.com/6.2/geocode.json', + expectedGeocoderResponse, status=200) + response = self._api.matrix( + start_waypoints=['Seattle', 'Kentucky'], + destination_waypoints=[[9.934574, -84.065544]]) + self.assertTrue(response) + self.assertIsInstance(response, herepy.RoutingMatrixResponse) + @responses.activate def test_matrix_multiple_destinations(self): with codecs.open('testdata/models/routing_matrix_multiple_destinations.json', mode='r', encoding='utf-8') as f: @@ -467,6 +483,22 @@ class RoutingApiTest(unittest.TestCase): self.assertTrue(response) self.assertIsInstance(response, herepy.RoutingMatrixResponse) + @responses.activate + def test_matrix_multiple_destinations(self): + with codecs.open('testdata/models/routing_matrix_multiple_destinations.json', mode='r', encoding='utf-8') as f: + server_response = f.read() + responses.add(responses.GET, 'https://matrix.route.ls.hereapi.com/routing/7.2/calculatematrix.json', + server_response, status=200) + with open('testdata/models/geocoder.json', 'r') as f: + expectedGeocoderResponse = f.read() + responses.add(responses.GET, 'https://geocoder.ls.hereapi.com/6.2/geocode.json', + expectedGeocoderResponse, status=200) + response = self._api.matrix( + start_waypoints=[[9.933231, -84.076831]], + destination_waypoints=['Seattle', 'Kentucky']) + self.assertTrue(response) + self.assertIsInstance(response, herepy.RoutingMatrixResponse) + @responses.activate def test_matrix_bad_request(self): with codecs.open('testdata/models/routing_matrix_bad_request.json', mode='r', encoding='utf-8') as f: @@ -500,4 +532,30 @@ class RoutingApiTest(unittest.TestCase): response = self._api.truck_route([11.0, 12.0], [22.0, 23.0], departure=date) - + + @responses.activate + def test_location_by_name(self): + with codecs.open('testdata/models/routing_truck_route_short.json', mode='r', encoding='utf-8') as f: + expectedRoutingResponse = f.read() + responses.add(responses.GET, 'https://route.ls.hereapi.com/routing/7.2/calculateroute.json', + expectedRoutingResponse, status=200) + with open('testdata/models/geocoder.json', 'r') as f: + expectedGeocoderResponse = f.read() + responses.add(responses.GET, 'https://geocoder.ls.hereapi.com/6.2/geocode.json', + expectedGeocoderResponse, status=200) + response = self._api.truck_route('200 S Mathilda Sunnyvale CA', + '200 S Mathilda Sunnyvale CA') + + @responses.activate + def test_location_by_name_throws_WaypointNotFoundError(self): + with codecs.open('testdata/models/routing_truck_route_short.json', mode='r', encoding='utf-8') as f: + expectedRoutingResponse = f.read() + responses.add(responses.GET, 'https://route.ls.hereapi.com/routing/7.2/calculateroute.json', + expectedRoutingResponse, status=200) + with open('testdata/models/geocoder_error.json', 'r') as f: + expectedGeocoderResponse = f.read() + responses.add(responses.GET, 'https://geocoder.ls.hereapi.com/6.2/geocode.json', + expectedGeocoderResponse, status=200) + with self.assertRaises(herepy.WaypointNotFoundError): + response = self._api.truck_route('200 S Mathilda Sunnyvale CA', + '200 S Mathilda Sunnyvale CA')	Combine routing api and geocoder to allow routing to/from names Add a new function to the routing api that takes names for the origin and destination. Call the geocoder api to resolve these to coordinates. I would be happy to create a PR for this if you would welcome this feature.	8691e147549141dc8287ba16a4396a63ed09b73b	[ "tests/test_routing_api.py::RoutingApiTest::test_location_by_name_throws_WaypointNotFoundError" ]	[ "tests/test_routing_api.py::RoutingApiTest::test_carroute_route_short", "tests/test_routing_api.py::RoutingApiTest::test_pedastrianroute_when_error_invalid_input_data_occured", "tests/test_routing_api.py::RoutingApiTest::test_matrix_multiple_start_names", "tests/test_routing_api.py::RoutingApiTest::test_pedastrianroute_when_error_no_route_found_occured", "tests/test_routing_api.py::RoutingApiTest::test_publictransport_when_error_invalid_input_data_occured", "tests/test_routing_api.py::RoutingApiTest::test_publictransport_when_error_no_route_found_occured", "tests/test_routing_api.py::RoutingApiTest::test_truckroute_when_error_no_route_found_occured", "tests/test_routing_api.py::RoutingApiTest::test_initiation", "tests/test_routing_api.py::RoutingApiTest::test_matrix_bad_request", "tests/test_routing_api.py::RoutingApiTest::test_location_by_name", "tests/test_routing_api.py::RoutingApiTest::test_publictransport_withdefaultmodes_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_pedastrianroute_when_error_invalid_credentials_occured", "tests/test_routing_api.py::RoutingApiTest::test_carroute_when_error_invalid_input_data_occured", "tests/test_routing_api.py::RoutingApiTest::test_departure_as_datetime", "tests/test_routing_api.py::RoutingApiTest::test_locationnearmotorway_when_error_no_route_found_occured", "tests/test_routing_api.py::RoutingApiTest::test_publictransport_route_short", "tests/test_routing_api.py::RoutingApiTest::test_departure_as_string", "tests/test_routing_api.py::RoutingApiTest::test_matrix_multiple_destinations", "tests/test_routing_api.py::RoutingApiTest::test_locationnearmotorway_withdefaultmodes_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_pedastrianroute_route_short", "tests/test_routing_api.py::RoutingApiTest::test_truckroute_when_error_invalid_credentials_occured", "tests/test_routing_api.py::RoutingApiTest::test_truckroute_withdefaultmodes_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_publictransport_when_error_invalid_credentials_occured", "tests/test_routing_api.py::RoutingApiTest::test_locationnearmotorway_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_carroute_withdefaultmodes_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_locationnearmotorway_when_error_invalid_credentials_occured", "tests/test_routing_api.py::RoutingApiTest::test_intermediateroute_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_truckroute_route_short", "tests/test_routing_api.py::RoutingApiTest::test_truckroute_when_error_invalid_input_data_occured", "tests/test_routing_api.py::RoutingApiTest::test_truckroute_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_intermediateroute_when_error_invalid_credentials_occured", "tests/test_routing_api.py::RoutingApiTest::test_intermediateroute_when_error_invalid_input_data_occured", "tests/test_routing_api.py::RoutingApiTest::test_carroute_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_locationnearmotorway_when_error_invalid_input_data_occured", "tests/test_routing_api.py::RoutingApiTest::test_matrix_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_intermediateroute_when_error_no_route_found_occured", "tests/test_routing_api.py::RoutingApiTest::test_matrix_multiple_starts", "tests/test_routing_api.py::RoutingApiTest::test_carroute_when_error_no_route_found_occured", "tests/test_routing_api.py::RoutingApiTest::test_bicycleroute_route_short", "tests/test_routing_api.py::RoutingApiTest::test_pedastrianroute_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_intermediateroute_withdefaultmodes_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_carroute_when_error_invalid_credentials_occured", "tests/test_routing_api.py::RoutingApiTest::test_publictransport_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_bicycleroute_withdefaultmodes_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_publictransporttimetable_route_short", "tests/test_routing_api.py::RoutingApiTest::test_pedastrianroute_withdefaultmodes_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_publictransporttimetable_withdefaultmodes_whensucceed" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2020-01-22 08:15:56+00:00	mit	858
abs-tudelft__vhdeps-21	diff --git a/vhdeps/targets/ghdl.py b/vhdeps/targets/ghdl.py index a354670..3e0e2b8 100644 --- a/vhdeps/targets/ghdl.py +++ b/vhdeps/targets/ghdl.py @@ -140,7 +140,7 @@ def _run_test_case(output_file, test_case, vcd_dir, ghdl_elaborate, ghdl_run): exit_code, _ = run_cmd( output_file, ghdl_elaborate, - '--work=%s' % test_case.lib, + '--work=%s' % test_case.file.lib, test_case.unit) if exit_code != 0: output_file.write('Elaboration for %s failed!\n' % test_case.unit) @@ -151,13 +151,13 @@ def _run_test_case(output_file, test_case, vcd_dir, ghdl_elaborate, ghdl_run): vcd_switch = [] if vcd_dir is not None: vcd_file = '%s/%s.%s.vcd' % ( - vcd_dir, test_case.lib, test_case.unit) + vcd_dir, test_case.file.lib, test_case.unit) vcd_switch.append('--vcd=%s' % vcd_file) exit_code, stdout, _ = run_cmd( output_file, ghdl_run, - '--work=' + test_case.lib, test_case.unit, - '--stop-time=' + test_case.get_timeout().replace(' ', ''), + '--work=' + test_case.file.lib, test_case.unit, + '--stop-time=' + test_case.file.get_timeout().replace(' ', ''), vcd_switch) if 'simulation stopped by --stop-time' in stdout: code = 1 diff --git a/vhdeps/targets/shared.py b/vhdeps/targets/shared.py index 6318ff2..7fd85b1 100644 --- a/vhdeps/targets/shared.py +++ b/vhdeps/targets/shared.py @@ -16,6 +16,7 @@ import sys import fnmatch +from collections import namedtuple def add_arguments_for_get_test_cases(parser): """Adds the appropriate command line arguments for the `get_test_cases()` @@ -33,6 +34,8 @@ def add_arguments_for_get_test_cases(parser): 'partial match. If no patterns are specified, the matcher defaults to ' 'a single \'_tc\' pattern.') +TestCase = namedtuple('TestCase', ('file', 'unit')) + def get_test_cases(vhd_list, pattern=None, _): """Filters the toplevel entities in `vhd_list` using the given pattern list, returning the resulting list.""" @@ -40,25 +43,21 @@ def get_test_cases(vhd_list, pattern=None, _): pattern = ['_tc'] test_cases = [] for top in vhd_list.top: - if top.unit is None: - raise NotImplementedError( - 'vhdeps\' test case runners currently do not support having ' - 'multiple test cases per VHDL file.\nThe offending file is ' - '"%s".' % top.fname) - include = False - for pat in pattern: - target = top.unit - if pat.startswith(':'): - target = top.fname - pat = pat[1:] - invert = False - if pat.startswith('!'): - invert = True - pat = pat[1:] - if fnmatch.fnmatchcase(target, pat): - include = not invert - if include: - test_cases.append(top) + for unit in top.entity_defs: + include = False + for pat in pattern: + target = unit + if pat.startswith(':'): + target = top.fname + pat = pat[1:] + invert = False + if pat.startswith('!'): + invert = True + pat = pat[1:] + if fnmatch.fnmatchcase(target, pat): + include = not invert + if include: + test_cases.append(TestCase(top, unit)) return test_cases def run_cmd(output_file, cmd, args): diff --git a/vhdeps/targets/vsim.py b/vhdeps/targets/vsim.py index 0e10b0a..a2984e3 100644 --- a/vhdeps/targets/vsim.py +++ b/vhdeps/targets/vsim.py @@ -381,11 +381,11 @@ def _write_tcl(vhd_list, tcl_file, kwargs): test_cases = get_test_cases(vhd_list, kwargs) for test_case in test_cases: tcl_file.write('lappend testcases [list %s %s "%s"]\n' % ( - test_case.lib, test_case.unit, test_case.get_timeout())) + test_case.file.lib, test_case.unit, test_case.file.get_timeout())) if len(test_cases) == 1: test_case = test_cases[0] tcl_file.write('simulate %s %s "%s"\n' % ( - test_case.lib, test_case.unit, test_case.get_timeout())) + test_case.file.lib, test_case.unit, test_case.file.get_timeout())) else: tcl_file.write('regression\n')	abs-tudelft/vhdeps	85fb3cccacdfa99132170c6ba8ae58d300b3ebfd	diff --git a/tests/test_ghdl.py b/tests/test_ghdl.py index f37a06d..a02b2a8 100644 --- a/tests/test_ghdl.py +++ b/tests/test_ghdl.py @@ -40,6 +40,16 @@ class TestGhdlSimple(TestCase): self.assertTrue('PASSED test_tc' in out) self.assertTrue('Test suite PASSED' in out) + def test_multiple_per_file(self): + """Test that multiple test cases can exist in one file (GHDL)""" + code, out, _ = run_vhdeps('ghdl', '-i', DIR+'/complex/multi-tc-per-file') + self.assertEqual(code, 0) + self.assertTrue('working!' in out) + self.assertTrue('PASSED foo_tc' in out) + self.assertTrue('PASSED bar_tc' in out) + self.assertFalse('baz' in out) + self.assertTrue('Test suite PASSED' in out) + def test_failure(self): """Test that a single failing test case results in failure (GHDL)""" code, out, _ = run_vhdeps('ghdl', '-i', DIR+'/simple/failure') diff --git a/tests/test_patterns.py b/tests/test_patterns.py index ebe47db..efa34b3 100644 --- a/tests/test_patterns.py +++ b/tests/test_patterns.py @@ -92,9 +92,14 @@ class TestPatterns(TestCase): self.assertFalse(bool(re.search(r'ghdl -r [^\n]baz', out))) def test_multi_tc_per_file(self): - """Test multiple test cases per file (not supported)""" + """Test multiple test cases per file""" with local.env(PATH=DIR+'/ghdl/fake-ghdl:' + local.env['PATH']): - code, _, err = run_vhdeps('ghdl', '-i', DIR+'/complex/multi-tc-per-file') - self.assertEqual(code, 1) - self.assertTrue('NotImplementedError: vhdeps\' test case runners currently do ' - 'not support having multiple test cases per VHDL file.' in err) + code, out, _ = run_vhdeps('ghdl', '-i', DIR+'/complex/multi-tc-per-file') + self.assertEqual(code, 0) + self.assertTrue(bool(re.search(r'ghdl -a [^\n]test_tc.vhd', out))) + self.assertTrue(bool(re.search(r'ghdl -e [^\n]foo_tc', out))) + self.assertTrue(bool(re.search(r'ghdl -e [^\n]bar_tc', out))) + self.assertFalse(bool(re.search(r'ghdl -e [^\n]baz', out))) + self.assertTrue(bool(re.search(r'ghdl -r [^\n]foo_tc', out))) + self.assertTrue(bool(re.search(r'ghdl -r [^\n]bar_tc', out))) + self.assertFalse(bool(re.search(r'ghdl -r [^\n]baz', out))) diff --git a/tests/test_vsim.py b/tests/test_vsim.py index 2ab1e48..3228735 100644 --- a/tests/test_vsim.py +++ b/tests/test_vsim.py @@ -27,6 +27,12 @@ class TestVsimReal(TestCase): self.assertEqual(code, 0) self.assertTrue('working!' in out) + def test_multiple_per_file(self): + """Test running vsim on a file with multiple test cases""" + code, out, _ = run_vhdeps('ghdl', '-i', DIR+'/complex/multi-tc-per-file') + self.assertEqual(code, 0) + self.assertTrue('working!' in out) + def test_failure(self): """Test running vsim on a single failing test case""" code, out, _ = run_vhdeps('vsim', '-i', DIR+'/simple/failure')	GHDL and vsim backends cannot handle multiple test cases in one file See title. Individual test cases are represented as `VhdFile` objects everywhere in these backends, making use of the `VhdFile.unit` attribute, which can be `None` when multiple are defined per file. This may be fixable by representing the test cases as two-tuples of the library and entity name.	85fb3cccacdfa99132170c6ba8ae58d300b3ebfd	[ "tests/test_patterns.py::TestPatterns::test_multi_tc_per_file" ]	[ "tests/test_ghdl.py::TestGhdlSpecific::test_analyze_error", "tests/test_ghdl.py::TestGhdlSpecific::test_elaborate_error", "tests/test_ghdl.py::TestGhdlSpecific::test_multi_version", "tests/test_ghdl.py::TestGhdlSpecific::test_no_ghdl", "tests/test_ghdl.py::TestGhdlSpecific::test_no_plumbum", "tests/test_ghdl.py::TestGhdlSpecific::test_no_wc", "tests/test_ghdl.py::TestGhdlSpecific::test_unknown_version", "tests/test_patterns.py::TestPatterns::test_negative_filename", "tests/test_patterns.py::TestPatterns::test_negative_name", "tests/test_patterns.py::TestPatterns::test_no_patterns", "tests/test_patterns.py::TestPatterns::test_positive_filename", "tests/test_patterns.py::TestPatterns::test_positive_name", "tests/test_vsim.py::TestVsimMocked::test_batch_no_tempdir", "tests/test_vsim.py::TestVsimMocked::test_gui_no_tempdir", "tests/test_vsim.py::TestVsimMocked::test_gui_tempdir", "tests/test_vsim.py::TestVsimMocked::test_no_plumbum", "tests/test_vsim.py::TestVsimMocked::test_no_vsim", "tests/test_vsim.py::TestVsimMocked::test_tcl_multi", "tests/test_vsim.py::TestVsimMocked::test_tcl_single", "tests/test_vsim.py::TestVsimMocked::test_tcl_to_file", "tests/test_vsim.py::TestVsimMocked::test_tcl_versions", "tests/test_vsim.py::TestVsimMocked::test_unsupported_version" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2019-07-12 09:11:14+00:00	apache-2.0	859
abs-tudelft__vhdeps-22	diff --git a/vhdeps/targets/ghdl.py b/vhdeps/targets/ghdl.py index 3e0e2b8..ff426a1 100644 --- a/vhdeps/targets/ghdl.py +++ b/vhdeps/targets/ghdl.py @@ -81,7 +81,22 @@ def add_arguments(parser): 'regardless of whether it passed or not. If there are multiple test ' 'cases, gtkwave is launched for the first failure.') -def _get_ghdl_cmds(vhd_list, ieee='synopsys', no_debug=False, coverage=None, _): + parser.add_argument( + '-W', action='append', metavar='#{#},<options>', dest='extra_args', + # It'd be great to use [] here ^^^ but Python devs managed to + # sufficiently bork argparse's internals to make that break before + # Python 3.8. Since it's completely asenine to require 3.8 for + # something like this, {} will have to do. + help='Pass comma-separated options to the command specified by #. The ' + 'first # can be \'a\' for the analysis command, \'e\' for the ' + 'elaboration command, and \'r\' for the run command. If a second ' + 'character is specified, <options> are chained to a \'-W#,<options>\' ' + 'option for the command specified by the first letter. For instance, ' + '\'-Wac,-O3\' passes -O3 to the GCC compiler during the analysis ' + 'phase.') + +def _get_ghdl_cmds(vhd_list, ieee='synopsys', no_debug=False, + coverage=None, extra_args=None, _): """Returns a three-tuple of the analyze, elaborate, and run commands for GHDL in plumbum form.""" @@ -130,6 +145,25 @@ def _get_ghdl_cmds(vhd_list, ieee='synopsys', no_debug=False, coverage=None, *_ ghdl_analyze = ghdl_analyze['-Wc,-fprofile-arcs', '-Wc,-ftest-coverage', '-Wc,-O3'] ghdl_elaborate = ghdl_elaborate['-Wl,-lgcov'] + # Add user-specified extra arguments. + if extra_args: + for extra_arg in extra_args: + if ',' not in extra_arg: + raise ValueError('invalid value for -W') + target, args = extra_arg.split(',') + if len(target) not in (1, 2): + raise ValueError('invalid value for -W') + if len(target) == 2: + args = ['-W%s,%s' % (target[1], ','.join(args))] + if target[0] == 'a': + ghdl_analyze = ghdl_analyze[args] + elif target[0] == 'e': + ghdl_elaborate = ghdl_elaborate[args] + elif target[0] == 'r': + ghdl_run = ghdl_run[args] + else: + raise ValueError('invalid value for -W') + return ghdl_analyze, ghdl_elaborate, ghdl_run def _run_test_case(output_file, test_case, vcd_dir, ghdl_elaborate, ghdl_run):	abs-tudelft/vhdeps	f2b55a77340e99d13e1adea753c63d10f2b06d79	diff --git a/tests/test_ghdl.py b/tests/test_ghdl.py index a02b2a8..9e16da5 100644 --- a/tests/test_ghdl.py +++ b/tests/test_ghdl.py @@ -2,6 +2,7 @@ from unittest import TestCase, skipIf from unittest.mock import patch +import re import os import tempfile from plumbum import local @@ -254,6 +255,22 @@ class TestGhdlSpecific(TestCase): code, _, _ = run_vhdeps('ghdl', '-i', DIR+'/simple/multiple-ok', '-j') self.assertEqual(code, 1) + def test_extra_options(self): + """Test the -W option for GHDL""" + with local.env(PATH=DIR+'/ghdl/fake-ghdl:' + local.env['PATH']): + self.assertNotEqual(run_vhdeps('ghdl', '-i', DIR+'/simple/all-good', '-W'), 0) + self.assertNotEqual(run_vhdeps('ghdl', '-i', DIR+'/simple/all-good', '-Wx'), 0) + self.assertNotEqual(run_vhdeps('ghdl', '-i', DIR+'/simple/all-good', '-W,x'), 0) + self.assertNotEqual(run_vhdeps('ghdl', '-i', DIR+'/simple/all-good', '-Wx,x'), 0) + code, out, _ = run_vhdeps( + 'ghdl', '-i', DIR+'/simple/all-good', + '-Wa,a,na,lyze', '-We,e,la,bo,rate', '-Wr,run', '-Wrx,a,b,c') + self.assertEqual(code, 0) + self.assertTrue(bool(re.search(r'ghdl -a [^\n]* a na lyze', out))) + self.assertTrue(bool(re.search(r'ghdl -e [^\n]* e la bo rate', out))) + self.assertTrue(bool(re.search(r'ghdl -r [^\n]* run', out))) + self.assertTrue(bool(re.search(r'ghdl -r [^\n]* -Wx,a,b,c', out))) + @skipIf( not coverage_supported(),	Passing arbitrary arguments to GHDL Sometimes one might want to pass some extra arguments to GHDL, especially with the GCC backend to pass additional compiler flags. There is currently no command-line syntax for this.	f2b55a77340e99d13e1adea753c63d10f2b06d79	[ "tests/test_ghdl.py::TestGhdlSpecific::test_extra_options" ]	[ "tests/test_ghdl.py::TestGhdlSpecific::test_analyze_error", "tests/test_ghdl.py::TestGhdlSpecific::test_elaborate_error", "tests/test_ghdl.py::TestGhdlSpecific::test_multi_version", "tests/test_ghdl.py::TestGhdlSpecific::test_no_ghdl", "tests/test_ghdl.py::TestGhdlSpecific::test_no_plumbum", "tests/test_ghdl.py::TestGhdlSpecific::test_no_wc", "tests/test_ghdl.py::TestGhdlSpecific::test_unknown_version" ]	{ "failed_lite_validators": [ "has_short_problem_statement" ], "has_test_patch": true, "is_lite": false }	2019-07-12 14:41:55+00:00	apache-2.0	860
absent1706__sqlalchemy-mixins-108	diff --git a/sqlalchemy_mixins/inspection.py b/sqlalchemy_mixins/inspection.py index 41d1ea6..bd2584e 100644 --- a/sqlalchemy_mixins/inspection.py +++ b/sqlalchemy_mixins/inspection.py @@ -5,12 +5,7 @@ from sqlalchemy.orm import RelationshipProperty, DeclarativeBase from .utils import classproperty -class Base(DeclarativeBase): - __abstract__ = True - - -class InspectionMixin(Base): - __abstract__ = True +class InspectionMixin: @classproperty def columns(cls): diff --git a/sqlalchemy_mixins/inspection.pyi b/sqlalchemy_mixins/inspection.pyi index ebc9da1..09582d8 100644 --- a/sqlalchemy_mixins/inspection.pyi +++ b/sqlalchemy_mixins/inspection.pyi @@ -1,18 +1,16 @@ from typing import List, Protocol, Dict from sqlalchemy.ext.hybrid import hybrid_method -from sqlalchemy.orm import Mapper, DeclarativeBase +from sqlalchemy.orm import Mapper from sqlalchemy.orm.interfaces import MapperProperty from sqlalchemy_mixins.utils import classproperty -class Base(DeclarativeBase): - __abstract__ = True class MappingProtocol(Protocol): __mapper__: Mapper -class InspectionMixin(Base): +class InspectionMixin: @classproperty def columns(cls) -> List[str]: ...	absent1706/sqlalchemy-mixins	4d4e5d575a3b8b3d72ee12b67b17741579ef26c1	diff --git a/sqlalchemy_mixins/tests/test_activerecord.py b/sqlalchemy_mixins/tests/test_activerecord.py index 901ac73..8284b2a 100644 --- a/sqlalchemy_mixins/tests/test_activerecord.py +++ b/sqlalchemy_mixins/tests/test_activerecord.py @@ -3,13 +3,16 @@ import unittest import sqlalchemy as sa from sqlalchemy import create_engine from sqlalchemy.ext.hybrid import hybrid_property -from sqlalchemy.orm import Query, Session, DeclarativeBase +from sqlalchemy.orm import Query, Session, DeclarativeBase, declarative_base from sqlalchemy_mixins import ActiveRecordMixin from sqlalchemy_mixins.activerecord import ModelNotFoundError class Base(DeclarativeBase): __abstract__ = True + +AlternativeBase = declarative_base() + engine = create_engine('sqlite:///:memory:', echo=False) sess = Session(engine) # sess = scoped_session(sessionmaker(bind=engine)) @@ -20,6 +23,9 @@ class BaseModel(Base, ActiveRecordMixin): pass +class BaseModelAlternative(AlternativeBase, ActiveRecordMixin): + __abstract__ = True + class User(BaseModel): __tablename__ = 'user' __repr_attrs__ = ['name'] @@ -29,6 +35,13 @@ class User(BaseModel): posts_viewonly = sa.orm.relationship('Post', viewonly=True) +class UserAlternative(BaseModelAlternative): + __tablename__ = 'user_alt' + __repr_attrs__ = ['name'] + id = sa.Column(sa.Integer, primary_key=True) + name = sa.Column(sa.String) + + class Post(BaseModel): __tablename__ = 'post' id = sa.Column(sa.Integer, primary_key=True) @@ -204,5 +217,21 @@ class TestActiveRecord(unittest.TestCase): _ = User.find_or_fail(123456789) +class TestActiveRecordAlternative(unittest.TestCase): + def setUp(self): + sess.rollback() + + BaseModelAlternative.set_session(None) + AlternativeBase.metadata.drop_all(engine) + AlternativeBase.metadata.create_all(engine) + + BaseModelAlternative.set_session(sess) + + def test_create(self): + u1 = UserAlternative.create(name='Bill u1') + self.assertEqual(u1, sess.query(UserAlternative).first()) + + + if __name__ == '__main__': # pragma: no cover unittest.main()	sqlalchemy.exc.ArgumentError: Class 'MyClass' already has a primary mapper defined. I have a project with SQLAlchemy 1.4 and sqlalchemy-mixins 1.5.3. I have upgraded SQLAlchemy to 2.0 and made the code work and passes the tests. Then, I tried to upgrade sqlalchemy-mixins to 2.0.3 but I get the error of the title. ``` File "/lib/MyClass.py", line 12, in <module> class MyClass(MyBaseClass): File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/decl_api.py", line 195, in __init__ _as_declarative(reg, cls, dict_) File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/decl_base.py", line 247, in _as_declarative return _MapperConfig.setup_mapping(registry, cls, dict_, None, {}) File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/decl_base.py", line 328, in setup_mapping return _ClassScanMapperConfig( File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/decl_base.py", line 520, in __init__ super().__init__(registry, cls_, mapper_kw) File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/decl_base.py", line 344, in __init__ instrumentation.register_class( File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/instrumentation.py", line 684, in register_class manager._update_state( File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/instrumentation.py", line 209, in _update_state registry._add_manager(self) File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/decl_api.py", line 1380, in _add_manager raise exc.ArgumentError( sqlalchemy.exc.ArgumentError: Class '<class 'lib.MyClass'>' already has a primary mapper defined. ``` MyBaseClass is defined as: ```python class MyBaseClass(AnotherBaseClass): __abstract__ = True #SOME CODE class AnotherBaseClass(Base, AllFeaturesMixin): __abstract__ = True #SOME OTHER CODE ``` Any idea of what may be happening or how to troubleshoot this?	4d4e5d575a3b8b3d72ee12b67b17741579ef26c1	[ "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_all", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_create", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_delete", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_destroy", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_fill_and_save", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_fill_wrong_attribute", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_find", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_find_or_fail", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_first", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_settable_attributes", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_update", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecordAlternative::test_create" ]	[]	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2023-07-25 20:54:25+00:00	mit	861
absent1706__sqlalchemy-mixins-110	diff --git a/sqlalchemy_mixins/activerecord.py b/sqlalchemy_mixins/activerecord.py index 7b082f1..122a60d 100644 --- a/sqlalchemy_mixins/activerecord.py +++ b/sqlalchemy_mixins/activerecord.py @@ -23,50 +23,56 @@ class ActiveRecordMixin(InspectionMixin, SessionMixin): return self - def save(self): + def save(self, commit=True): """Saves the updated model to the current entity db. + :param commit: where to commit the transaction """ - try: - self.session.add(self) - self.session.commit() - return self - except: - self.session.rollback() - raise + self.session.add(self) + if commit: + self._commit_or_fail() + return self @classmethod - def create(cls, kwargs): + def create(cls, commit=True, kwargs): """Create and persist a new record for the model + :param commit: where to commit the transaction :param kwargs: attributes for the record :return: the new model instance """ - return cls().fill(kwargs).save() + return cls().fill(kwargs).save(commit=commit) - def update(self, kwargs): + def update(self, commit=True, kwargs): """Same as :meth:`fill` method but persists changes to database. + :param commit: where to commit the transaction """ - return self.fill(kwargs).save() + return self.fill(kwargs).save(commit=commit) - def delete(self): + def delete(self, commit=True): """Removes the model from the current entity session and mark for deletion. + :param commit: where to commit the transaction """ + self.session.delete(self) + if commit: + self._commit_or_fail() + + def _commit_or_fail(self): try: - self.session.delete(self) self.session.commit() except: self.session.rollback() raise @classmethod - def destroy(cls, ids): + def destroy(cls, ids, commit=True): """Delete the records with the given ids :type ids: list :param ids: primary key ids of records + :param commit: where to commit the transaction """ for pk in ids: obj = cls.find(pk) if obj: - obj.delete() + obj.delete(commit=commit) cls.session.flush() @classmethod	absent1706/sqlalchemy-mixins	cbd35a6ac4d1ae641b08b5542fa13de22c2b74fb	diff --git a/sqlalchemy_mixins/tests/test_activerecord.py b/sqlalchemy_mixins/tests/test_activerecord.py index 8284b2a..1f8b0df 100644 --- a/sqlalchemy_mixins/tests/test_activerecord.py +++ b/sqlalchemy_mixins/tests/test_activerecord.py @@ -1,5 +1,6 @@ import unittest +import sqlalchemy import sqlalchemy as sa from sqlalchemy import create_engine from sqlalchemy.ext.hybrid import hybrid_property @@ -115,6 +116,30 @@ class TestActiveRecord(unittest.TestCase): self.assertEqual(p11, sess.query(Post).first()) self.assertEqual(p11.archived, True) + def test_save_commits(self): + with self.assertRaises(sqlalchemy.exc.InvalidRequestError): + with sess.begin(): + u1 = User() + u1.fill(name='Bill u1') + u1.save() + u2 = User() + u2.fill(name='Bill u2') + u2.save() + self.assertEqual([u1, u2], sess.query(User).order_by(User.id.asc()).all()) + # The first user is saved even when the block raises a Exception + self.assertEqual([u1], sess.query(User).order_by(User.id.asc()).all()) + + def test_save_do_not_commit(self): + with sess.begin(): + u1 = User() + u1.fill(name='Bill u1') + u1.save(commit=False) + u2 = User() + u2.fill(name='Bill u2') + u2.save(commit=False) + + self.assertEqual([u1,u2], sess.query(User).order_by(User.id.asc()).all()) + def test_create(self): u1 = User.create(name='Bill u1') self.assertEqual(u1, sess.query(User).first()) @@ -158,6 +183,16 @@ class TestActiveRecord(unittest.TestCase): self.assertEqual(sess.query(Post).get(11).public, True) self.assertEqual(sess.query(Post).get(11).user, u2) + def test_update_no_commit(self): + u1 = User(name='Bill', id=1) + u1.save() + u1.update(name='Joe', commit=False) + self.assertEqual('Joe', sess.query(User).where(User.id==1).first().name) + sess.rollback() + self.assertEqual('Bill', sess.query(User).where(User.id==1).first().name) + + + def test_fill_wrong_attribute(self): u1 = User(name='Bill u1') sess.add(u1) @@ -179,6 +214,15 @@ class TestActiveRecord(unittest.TestCase): u1.delete() self.assertEqual(sess.query(User).get(1), None) + def test_delete_without_commit(self): + u1 = User() + u1.save() + u1.delete(commit=False) + self.assertIsNone(sess.query(User).one_or_none()) + sess.rollback() + self.assertIsNotNone(sess.query(User).one_or_none()) + + def test_destroy(self): u1, u2, p11, p12, p13 = self._seed() @@ -186,6 +230,16 @@ class TestActiveRecord(unittest.TestCase): Post.destroy(11, 12) self.assertEqual(set(sess.query(Post).all()), {p13}) + + def test_destroy_no_commit(self): + u1, u2, p11, p12, p13 = self._seed() + sess.commit() + self.assertEqual(set(sess.query(Post).order_by(Post.id).all()), {p11, p12, p13}) + Post.destroy(11, 12, commit=False) + self.assertEqual(set(sess.query(Post).order_by(Post.id).all()), {p13}) + sess.rollback() + self.assertEqual(set(sess.query(Post).order_by(Post.id).all()), {p11, p12, p13}) + def test_all(self): u1, u2, p11, p12, p13 = self._seed() @@ -231,6 +285,12 @@ class TestActiveRecordAlternative(unittest.TestCase): u1 = UserAlternative.create(name='Bill u1') self.assertEqual(u1, sess.query(UserAlternative).first()) + def test_create_no_commit(self): + u1 = UserAlternative.create(name='Bill u1', commit=False) + self.assertEqual(u1, sess.query(UserAlternative).first()) + sess.rollback() + self.assertIsNone(sess.query(UserAlternative).one_or_none()) + if __name__ == '__main__': # pragma: no cover	save from Activerecord can commit external transactions I have some code in a transaction: ```python with session.begin(): an_object.save() another_object.save() ``` both objects have the ActiveRecordMixin. That code used to work, and even after going to sqlalchemy 2, it worked. But now with sqlalchemy-mixins 2.0.3, the save method commits the transaction, even when it wasn't the save method who opened it and that code is broken. I was thinking if it makes sense to check whether there is an active transaction an in that case don't commit. Something like this (of course more tidy): ``` python def save(self): """Saves the updated model to the current entity db. """ # If there is an active transaction, we are not responsible for commit or rollback. if self.session.get_transaction(): self.session.add(self) self.session.flush() return self try: self.session.add(self) self.session.commit() return self except: self.session.rollback() raise ``` I realized the same happens with delete	cbd35a6ac4d1ae641b08b5542fa13de22c2b74fb	[ "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_delete_without_commit", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_destroy_no_commit", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_save_do_not_commit", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_update_no_commit", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecordAlternative::test_create_no_commit" ]	[ "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_all", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_create", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_delete", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_destroy", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_fill_and_save", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_fill_wrong_attribute", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_find", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_find_or_fail", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_first", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_save_commits", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_settable_attributes", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_update", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecordAlternative::test_create" ]	{ "failed_lite_validators": [ "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2023-07-31 13:01:12+00:00	mit	862
aburrell__ocbpy-111	diff --git a/Changelog.rst b/Changelog.rst index 72966f5..30b8cf1 100644 --- a/Changelog.rst +++ b/Changelog.rst @@ -21,6 +21,7 @@ Summary of all changes made since the first stable release * ENH: Added function to select data along a satellite track * ENH: Changed attributes in VectorData into properties to ensure expected behaviour if altering the class data after initialisation +* ENH: Added IMAGE SI12, SI13, and WIC DMSP corrections to `harmonic` * MAINT: Removed support for Python 2.7, 3.5, and 3.6; added support for 3.10 * MAINT: Improved PEP8 compliance * MAINT: Updated pysat routines to v3.0.0 standards diff --git a/docs/citing.rst b/docs/citing.rst index 9a60f6a..f0da9fd 100644 --- a/docs/citing.rst +++ b/docs/citing.rst @@ -42,8 +42,8 @@ which may also be cited if a description of the package is desired. IMAGE FUV Boundaries -------------------- -Please cite both the papers discussing both the instrument and the boundary -retrieval method. +Please cite both the papers discussing the instrument and the appropriate +boundary retrieval method. * SI12/SI13: Mende, S., et al. Space Science Reviews (2000) 91: 287-318. http://doi.org/10.1023/A:1005292301251. @@ -53,6 +53,8 @@ retrieval method. high‐latitude ionospheric climatologies and empirical models, J. Geophys. Res. Space Physics, 122, 932–947, http://doi.org/10.1002/2016JA023235. +* OCB: Chisham, G. et al. (2022) Ionospheric Boundaries Derived from Auroral + Images. In Prep. * OCB: Chisham, G. (2017) Auroral Boundary Derived from IMAGE Satellite Mission Data (May 2000 - Oct 2002), Version 1.1, Polar Data Centre, Natural Environment Research Council, UK. diff --git a/docs/ocb_datasets.rst b/docs/ocb_datasets.rst index 56fdffb..08138a2 100644 --- a/docs/ocb_datasets.rst +++ b/docs/ocb_datasets.rst @@ -19,16 +19,24 @@ provided in the :py:mod:`ocbpy.boundaries.files` sub-module. IMAGE ----- -Data from three auroral instruments provide northern hemisphere OCB and EAB -locations for 3 May 2000 02:41:43 UT - 31 Oct 2002 20:05:16, though not all of -the times included in these files contain high-quality estimations of the -boundary locations. Recommended selection criteria are included as defaults in -the :py:class:`~ocbpy.OCBoundary` class. There are also boundary -files that combine the information from all instruments to obtain the OCB and -EAB. You can read more about the OCB determination, EAB determination, this -selection criteria, and the three auroral instruments (IMAGE Wideband Imaging -Camera (WIC) and FUV Spectrographic Imagers SI12 and SI13) in the articles -listed in :ref:`cite-image`. +Data from three auroral instruments provide northern hemisphere poleward auroral +boundary (PAB) and EAB locations for 3 May 2000 02:41:43 UT - 31 Oct 2002 +20:05:16, though not all of the times included in these files contain +high-quality estimations of the boundary locations. Recommended selection +criteria are included as defaults in the :py:class:`~ocbpy.OCBoundary` class. +There are also boundary files that combine the information from all instruments +to obtain the OCB and EAB. These combined files are the default boundaries for +the IMAGE time period. You can read more about the OCB determination, EAB +determination, this selection criteria, and the three auroral instruments +(IMAGE Wideband Imaging Camera (WIC) and FUV Spectrographic Imagers SI12 and +SI13) in the articles listed in :ref:`cite-image`. + +The most recent corrects for each instrument that add the DMSP particle +precipitation corrections to the PAB and EAB locations are included in +:py:mod:`ocbpy.ocb_correction`. These corrections should be applied to the +data used to obtain the circle fits included in the instrument files, not the +circle fits themselves. These data sets may be obtained from the British +Antarctic Survey. .. _bound-data-ampere: diff --git a/ocbpy/boundaries/README.md b/ocbpy/boundaries/README.md index ad99f4b..9d42e78 100644 --- a/ocbpy/boundaries/README.md +++ b/ocbpy/boundaries/README.md @@ -1,8 +1,8 @@ This directory contains files with Open Closed field line Boundaries obtained from different instruments -IMAGE (si12/si13/wic) File Format ---------------------------------- +IMAGE (image/si12/si13/wic) File Format +--------------------------------------- YR, SOY, NB, PHICENT, RCENT, R, A, R_ERR, R_MERIT YR : Year @@ -20,7 +20,9 @@ R_MERIT : Radial distance from the most typical pole location in degrees There are certain ranges for NB, RCENT, and R that you shouldn’t use that can be found (and explained) in Chisham (2017), doi:10.1002/2016JA023235. These ranges are the defaults in OCBoundary.get_next_good_ocb_ind. When using these -boundaries, remember to cite Chisham (2017). +boundaries, remember to cite Chisham (2017). From ocbpy version 0.3.0 onward, +the SI12, SI13, and WIC files contain uncorrected auroral boundary fits, while +the IMAGE file contains DMSP corrected average boundaries for the OCB and EAB. AMPERE (amp) File Format ------------------------ diff --git a/ocbpy/ocb_correction.py b/ocbpy/ocb_correction.py index ba7cf8a..b73a0e6 100644 --- a/ocbpy/ocb_correction.py +++ b/ocbpy/ocb_correction.py @@ -9,6 +9,8 @@ References ---------- .. [4] Burrell, A. G. et al.: AMPERE Polar Cap Boundaries, Ann. Geophys., 38, 481-490, doi:10.5194/angeo-38-481-2020, 2020. +.. [6] Chisham, G. et al.: Ionospheric Boundaries Derived from Auroral Images, + in prep, 2022. """ @@ -18,7 +20,7 @@ from ocbpy.ocb_time import hr2rad def circular(mlt, r_add=0.0): - """Return a circular boundary correction + """Return a circular boundary correction. Parameters ---------- @@ -42,7 +44,7 @@ def circular(mlt, r_add=0.0): def elliptical(mlt, instrument='ampere', method='median'): - """Return the results of an elliptical correction to the data boundary [4]_ + """Return the results of an elliptical correction to the data boundary. Parameters ---------- @@ -59,6 +61,10 @@ def elliptical(mlt, instrument='ampere', method='median'): r_corr : float or array-like Radius correction in degrees at this MLT + References + ---------- + Prefered AMPERE boundary correction validated in [4]_. + """ if instrument.lower() != 'ampere': @@ -81,7 +87,7 @@ def elliptical(mlt, instrument='ampere', method='median'): def harmonic(mlt, instrument='ampere', method='median'): - """Return the results of a harmonic fit correction to the data boundary [4]_ + """Return the results of a harmonic fit correction to the data boundary. Parameters ---------- @@ -91,38 +97,67 @@ def harmonic(mlt, instrument='ampere', method='median'): Data set's instrument name (default='ampere') method : str Method used to determine coefficients; accepts 'median' or - 'gaussian' (default='median') + 'gaussian' when `instrument` is 'ampere'. Otherwise, accepts 'eab' or + 'ocb'. (default='median') Returns ------- r_corr : float or array-like Radius correction in degrees at this MLT + References + ---------- + AMPERE boundaries obtained from [4]_. IMAGE boundaries obtained from [6]_. + """ - if instrument.lower() != 'ampere': + # Define the harmonic coefficients for each instrument and method/location + coeff = {'ampere': {'median': [3.31000535, -0.5452934, -1.24389141, + 2.42619653, -0.66677988, -1.03467488, + -0.30763009, 0.52426756, 0.04359299, + 0.60201848, 0.50618522, 1.04360529, + 0.25186405], + 'gaussian': [3.80100827, 0.98555723, -3.43760943, + 1.85084271, -0.36730751, -0.81975654, + -1.02823832, 1.30637288, -0.53599218, + 0.40380183, -1.22462708, -1.2733629, + -0.62743381]}, + 'si12': {'ocb': [0.0405, -1.5078, 1.0, 0.5095, 1.0, 0.9371, 1.0, + 0.0708, 1.0, 0.0, 1.0, 0.0, 1.0], + 'eab': [-0.1447, -1.9779, 1.0, 2.6799, 1.0, 0.5778, 1.0, + -1.2297, 1.0, 0.0, 1.0, 0.0, 1.0]}, + 'si13': {'ocb': [0.5797, -0.6837, 1.0, -0.5020, 1.0, 0.2971, 1.0, + -0.4173, 1.0, 0.0, 1.0, 0.0, 1.0], + 'eab': [0.2500, -2.9931, 1.0, 0.8818, 1.0, 0.8511, 1.0, + -0.6300, 1.0, 0.0, 1.0, 0.0, 1.0]}, + 'wic': {'ocb': [1.0298, -1.1249, 1.0, -0.7380, 1.0, 0.1838, 1.0, + -0.6171, 1.0, 0.0, 1.0, 0.0, 1.0], + 'eab': [-0.4935, -2.1186, 1.0, 0.3188, 1.0, 0.5749, 1.0, + -0.3118, 1.0, 0.0, 1.0, 0.0, 1.0]}} + + # Check the inputs + inst = instrument.lower() + if inst not in coeff.keys(): raise ValueError("no harmonic correction for {:}".format(instrument)) method = method.lower() - coeff = {'median': [3.31000535, -0.5452934, -1.24389141, 2.42619653, - -0.66677988, -1.03467488, -0.30763009, 0.52426756, - 0.04359299, 0.60201848, 0.50618522, 1.04360529, - 0.25186405], - 'gaussian': [3.80100827, 0.98555723, -3.43760943, 1.85084271, - -0.36730751, -0.81975654, -1.02823832, 1.30637288, - -0.53599218, 0.40380183, -1.22462708, -1.2733629, - -0.62743381]} - - if method not in coeff.keys(): - raise ValueError("unknown coefficient computation method") + if method not in coeff[inst].keys(): + raise ValueError("".join(["unknown coefficient computation method, ", + "expects one of: {:}".format( + coeff[inst].keys())])) + # Calculate the offset rad_mlt = hr2rad(mlt) - r_corr = coeff[method][0] \ - + coeff[method][1] * np.cos(rad_mlt + coeff[method][2]) \ - + coeff[method][3] * np.sin(rad_mlt + coeff[method][4]) \ - + coeff[method][5] * np.cos(2.0 * (rad_mlt + coeff[method][6])) \ - + coeff[method][7] * np.sin(2.0 * (rad_mlt + coeff[method][8])) \ - + coeff[method][9] * np.cos(3.0 * (rad_mlt + coeff[method][10])) \ - + coeff[method][11] * np.sin(3.0 * (rad_mlt + coeff[method][12])) + r_corr = coeff[inst][method][0] \ + + coeff[inst][method][1] * np.cos(rad_mlt + coeff[inst][method][2]) \ + + coeff[inst][method][3] * np.sin(rad_mlt + coeff[inst][method][4]) \ + + coeff[inst][method][5] * np.cos(2.0 * ( + rad_mlt + coeff[inst][method][6])) \ + + coeff[inst][method][7] * np.sin(2.0 * ( + rad_mlt + coeff[inst][method][8])) \ + + coeff[inst][method][9] * np.cos(3.0 * ( + rad_mlt + coeff[inst][method][10])) \ + + coeff[inst][method][11] * np.sin(3.0 * ( + rad_mlt + coeff[inst][method][12])) # Because this is a poleward shift, return the negative of the correction return -r_corr	aburrell/ocbpy	ce1ee978f2f1f31e8777bed474750dcef493ee31	diff --git a/ocbpy/tests/test_ocb_correction.py b/ocbpy/tests/test_ocb_correction.py index fc2f648..787cc62 100644 --- a/ocbpy/tests/test_ocb_correction.py +++ b/ocbpy/tests/test_ocb_correction.py @@ -3,8 +3,7 @@ # Copyright (C) 2017, AGB & GC # Full license can be found in License.md # ----------------------------------------------------------------------------- -""" Tests the ocboundary class and functions -""" +"""Tests the ocboundary class and functions.""" import numpy as np import unittest @@ -13,38 +12,48 @@ from ocbpy import ocb_correction as ocb_cor class TestOCBCorrectionFailure(unittest.TestCase): + """Unit tests for correction failure evaluations.""" + def setUp(self): - """ Set up the test runs """ + """Set up the test runs.""" self.mlt = 12.0 self.bad_kwarg = 'bad_kwarg' self.functions = {'elliptical': ocb_cor.elliptical, 'harmonic': ocb_cor.harmonic} self.bound = None + return def tearDown(self): - """ Tear down the test runs """ + """Tear down the test runs.""" del self.mlt, self.bad_kwarg, self.functions, self.bound + return def test_instrument_failure(self): - """ Test failure when an unknown instrument is provided """ + """Test failure when an unknown instrument is provided.""" for self.bound in self.functions.keys(): with self.subTest(bound=self.bound): - with self.assertRaises(ValueError): + msg = "no {:s} correction for".format(self.bound) + with self.assertRaisesRegex(ValueError, msg): self.functions[self.bound](self.mlt, instrument=self.bad_kwarg) + return def test_method_failure(self): - """ Test failure when an unknown method is provided """ + """Test failure when an unknown method is provided.""" + msg = "unknown coefficient computation method" for self.bound in self.functions.keys(): with self.subTest(bound=self.bound): - with self.assertRaises(ValueError): + with self.assertRaisesRegex(ValueError, msg): self.functions[self.bound](self.mlt, method=self.bad_kwarg) + return class TestOCBCorrection(unittest.TestCase): + """Unit tests for the boundary correction functions.""" + def setUp(self): - """ Set up test runs """ + """Set up test runs.""" self.functions = {'circular': ocb_cor.circular, 'elliptical': ocb_cor.elliptical, 'harmonic': ocb_cor.harmonic} @@ -56,36 +65,65 @@ class TestOCBCorrection(unittest.TestCase): -3.4392638193624325])} self.gaus_results = {'elliptical': -2.51643691301747, 'harmonic': -2.293294645880221} + self.image_results = {'si12': {'ocb': np.array([0.67103129, + -0.10084541]), + 'eab': np.array([0.31691853, + 2.68970685])}, + 'si13': {'ocb': np.array([0.71521016, + -0.86843608]), + 'eab': np.array([1.55220967, + -0.19812977])}, + 'wic': {'ocb': np.array([0.83660688, + -1.62097642]), + 'eab': np.array([1.89268527, + 0.13983824])}} self.bound = None + return def tearDown(self): - """ Clean up after each test """ + """Clean up after each test.""" del self.mlt, self.functions, self.def_results, self.gaus_results - del self.bound + del self.bound, self.image_results + return def test_default_float(self): - """ Test the boundary functions using a float and function defaults""" + """Test the boundary functions using a float and function defaults.""" for self.bound in self.functions.keys(): with self.subTest(bound=self.bound): self.assertEqual(self.functions[self.bound](self.mlt[0]), self.def_results[self.bound][0]) + return def test_default_arr(self): - """ Test the boundary functions using an array and function defaults""" + """Test the boundary functions using an array and function defaults.""" for self.bound in self.functions.keys(): with self.subTest(bound=self.bound): self.assertTrue(np.all( abs(self.functions[self.bound](self.mlt) - self.def_results[self.bound]) < 1.0e-7)) + return def test_circular_offset(self): - """ Test the circular boundary function with an offset """ + """Test the circular boundary function with an offset.""" self.assertEqual(ocb_cor.circular(self.mlt[0], r_add=1.0), 1.0) + return def test_gauss_method(self): - """ Test the boundary functions using an array and function defaults""" + """Test the boundary functions using an array and function defaults.""" for self.bound in self.gaus_results.keys(): with self.subTest(bound=self.bound): self.assertAlmostEqual( self.functions[self.bound](self.mlt[0], method='gaussian'), self.gaus_results[self.bound]) + return + + def test_image_harmonic(self): + """Test the IMAGE harmonic correction functions.""" + for self.bound in self.image_results.keys(): + for method in self.image_results[self.bound].keys(): + with self.subTest(bound=self.bound, method=method): + self.assertTrue(np.all( + abs(self.functions["harmonic"]( + self.mlt, instrument=self.bound, method=method) + - self.image_results[self.bound][method]) < 1.0e-7)) + return	BUG: individual IMAGE instrument OCBs Describe the bug The new individual IMAGE "ocb" files are actually the poleward edge of the auroral oval w/o the DMSP correction. Expected behavior A clear explanation of what they are. To Fix - [x] Update documentation	ce1ee978f2f1f31e8777bed474750dcef493ee31	[ "ocbpy/tests/test_ocb_correction.py::TestOCBCorrection::test_image_harmonic" ]	[ "ocbpy/tests/test_ocb_correction.py::TestOCBCorrectionFailure::test_instrument_failure", "ocbpy/tests/test_ocb_correction.py::TestOCBCorrectionFailure::test_method_failure", "ocbpy/tests/test_ocb_correction.py::TestOCBCorrection::test_circular_offset", "ocbpy/tests/test_ocb_correction.py::TestOCBCorrection::test_default_arr", "ocbpy/tests/test_ocb_correction.py::TestOCBCorrection::test_default_float", "ocbpy/tests/test_ocb_correction.py::TestOCBCorrection::test_gauss_method" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2022-04-05 19:29:16+00:00	bsd-3-clause	863
achabotl__popthings-4	diff --git a/popthings.py b/popthings.py index eeda9e6..4310e2d 100644 --- a/popthings.py +++ b/popthings.py @@ -24,7 +24,7 @@ what's possible. They would be added to Things as two separate projects. Note under project 1 - Task 1 @due($start + 1w) @$where A note under task 1 - - Task 2 @start($start) + - Task 2 @start($start - 1) - Checklist item under task 2 - Also a checklist item under task 2 Heading 1: @@ -40,9 +40,11 @@ Attributes ---------- """ +from datetime import datetime, timedelta from io import open import json import logging +import operator import re import sys try: @@ -87,6 +89,65 @@ PATTERN_TAG = re.compile(r"""(?:^\|\s+)@ # space and @ before tag # space or EOL """, re.VERBOSE) +# Patterns to match dates and dates with day offsets +ISO_DATE_RE = re.compile(r"^\d{4}-\d{2}-\d{2}$") +DATE_OFFSET_RE = re.compile(r""" + (?P<base_date>\d{4}-\d{2}-\d{2}) + \s* + (?P<op>[+-]) + \s* + (?P<offset_count>\d+) + """, re.X) + + +def compute_date(date_str): + """ + Compute new date string given dates with day offsets. + + Parameters + ========== + date_str : string + Text string representing a date. The format must be a standalone date: + 'YYYY-MM-DD', a date with a day offset: 'YYYY-MM-DD + 1' or 'YYYY-MM-DD + - 10'. Other values as just passed through, assuming Things knows how + to handled them, like 'today', 'tomorrow', 'evening', 'next month', + etc. + + Returns + ======= + new_date_str : string + Date where the offset has been added or subtracted from the date. + + """ + date_str = date_str.strip() + + # Simple ISO date + if ISO_DATE_RE.match(date_str): + return date_str + + elif DATE_OFFSET_RE.match(date_str): + # Precompute dates with offsets of days + m = DATE_OFFSET_RE.match(date_str) + if m is None: + raise ValueError(f"Unable to parse date '{date_str}' as 'YYYY-MM-DD+/-offset' date.") + + try: + op = { + '-': operator.sub, + '+': operator.add, + }.get(m.group('op')) + except KeyError: + raise ValueError(f"Unable to parse date {date_str} as YYYY-MM-DD +/- D date. The operator is wrong.") + + count = int(m.group('offset_count')) + date_delta = timedelta(count) + + date = datetime.strptime(m.group("base_date"), '%Y-%m-%d') + + return op(date, date_delta).strftime('%Y-%m-%d') + + return date_str + class TPNode(object): def __init__(self, line, text, indent, type, line_number=None, tags=None): @@ -442,8 +503,8 @@ class _ThingsRichObject(ThingsObject): """ super(_ThingsRichObject, self).__init__(title) self.notes = notes - self.when = when - self.deadline = deadline + self.when = compute_date(when) if when else when + self.deadline = compute_date(deadline) if deadline else deadline if tags is None: tags = [] self.tags = tags	achabotl/popthings	29523615476639f8e844768ef7730258bd7d13ad	diff --git a/tests/test_date_parsing.py b/tests/test_date_parsing.py new file mode 100644 index 0000000..127090a --- /dev/null +++ b/tests/test_date_parsing.py @@ -0,0 +1,33 @@ +from unittest import TestCase +from popthings import compute_date + + +class TestDateParsing(TestCase): + def test_iso_date(self): + """ ISO formatted dates: YYYY-MM-DD.""" + date = "2018-12-31" + self.assertEqual(date, compute_date(date)) + + def test_iso_date_with_space(self): + date = " 2018-12-31 " + self.assertEqual("2018-12-31", compute_date(date)) + + def test_invalid_date(self): + self.assertEqual("31/12/2018", compute_date("31/12/2018")) + + def test_iso_date_with_positive_offset(self): + date = "2018-12-30 + 1" + self.assertEqual("2018-12-31", compute_date(date)) + + def test_iso_date_with_negative_offset(self): + date = "2018-12-30 - 1" + self.assertEqual("2018-12-29", compute_date(date)) + + def test_iso_date_with_negative_large_offset(self): + date = "2018-12-30 - 10" + self.assertEqual("2018-12-20", compute_date(date)) + + def test_other_values(self): + for word in ('today', 'tomorrow', 'evening', 'anytime', 'someday', 'next month'): + with self.subTest(word=word): + self.assertEqual(word, compute_date(word))	Parse dates in popthings instead of Things.app As of Things 3.8, it still parse dates with a `-` as if it was a `+`, e.g., "Today - 1 day" is actually tomorrow… I could write my own, possible with the help of `dateutil`, or consider using [dateparser](https://dateparser.readthedocs.io/en/latest/) by [Scraping Hub](https://blog.scrapinghub.com/2015/11/09/parse-natural-language-dates-with-dateparser).	29523615476639f8e844768ef7730258bd7d13ad	[ "tests/test_date_parsing.py::TestDateParsing::test_invalid_date", "tests/test_date_parsing.py::TestDateParsing::test_iso_date", "tests/test_date_parsing.py::TestDateParsing::test_iso_date_with_negative_large_offset", "tests/test_date_parsing.py::TestDateParsing::test_iso_date_with_negative_offset", "tests/test_date_parsing.py::TestDateParsing::test_iso_date_with_positive_offset", "tests/test_date_parsing.py::TestDateParsing::test_iso_date_with_space", "tests/test_date_parsing.py::TestDateParsing::test_other_values" ]	[]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-03-25 13:01:13+00:00	mit	864
acorg__dark-matter-569	diff --git a/CHANGELOG.md b/CHANGELOG.md index 3aac224..4781caa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,20 @@ +## 2.0.4 April 29, 2018 + +* Added `--sampleIndexFilename` and `--pathogenIndexFilename` to + `proteins-to-pathogens.py`. These cause the writing of files containing + lines with an integer index, a space, then a sample or pathogen name. + These can be later used to identify the de-duplicated reads files for a + given sample or pathogen name. + +## 2.0.3 April 28, 2018 + +* Added number of identical and positive amino acid matches to BLAST and + DIAMOND hsps. + +## 2.0.2 April 23, 2018 + +* The protein grouper now de-duplicates read by id, not sequence. + ## 2.0.1 April 23, 2018 * Fixed HTML tiny formatting error in `toHTML` method of `ProteinGrouper` diff --git a/bin/proteins-to-pathogens.py b/bin/proteins-to-pathogens.py index 004263a..3a3ce34 100755 --- a/bin/proteins-to-pathogens.py +++ b/bin/proteins-to-pathogens.py @@ -83,6 +83,22 @@ if __name__ == '__main__': help=('An (optional) filename to write a pathogen-sample panel PNG ' 'image to.')) + parser.add_argument( + '--sampleIndexFilename', + help=('An (optional) filename to write a sample index file to. ' + 'Lines in the file will have an integer index, a space, and ' + 'then the sample name. Only produced if --html is used ' + '(because the pathogen-NNN-sample-MMM.fastq are only written ' + 'in that case).')) + + parser.add_argument( + '--pathogenIndexFilename', + help=('An (optional) filename to write a pathogen index file to. ' + 'Lines in the file will have an integer index, a space, and ' + 'then the pathogen name. Only produced if --html is used ' + '(because the pathogen-NNN-sample-MMM.fastq are only written ' + 'in that case).')) + parser.add_argument( '--html', default=False, action='store_true', help='If specified, output HTML instead of plain text.') @@ -123,6 +139,16 @@ if __name__ == '__main__': args = parser.parse_args() + if not args.html: + if args.sampleIndexFilename: + print('It does not make sense to use --sampleIndexFilename ' + 'without also using --html', file=sys.stderr) + sys.exit(1) + if args.pathogenIndexFilename: + print('It does not make sense to use --pathogenIndexFilename ' + 'without also using --html', file=sys.stderr) + sys.exit(1) + if args.proteinFastaFilename: # Flatten lists of lists that we get from using both nargs='+' and # action='append'. We use both because it allows people to use @@ -153,6 +179,8 @@ if __name__ == '__main__': if args.html: print(grouper.toHTML(args.pathogenPanelFilename, minProteinFraction=args.minProteinFraction, - pathogenType=args.pathogenType)) + pathogenType=args.pathogenType, + sampleIndexFilename=args.sampleIndexFilename, + pathogenIndexFilename=args.pathogenIndexFilename)) else: print(grouper.toStr()) diff --git a/dark/__init__.py b/dark/__init__.py index c8923d7..d0bf4db 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -5,4 +5,6 @@ if sys.version_info < (2, 7): # Note that the version string must have the following format, otherwise it # will not be found by the version() function in ../setup.py -__version__ = '2.0.3' +# +# Remember to update ../CHANGELOG.md describing what's new in each version. +__version__ = '2.0.4' diff --git a/dark/proteins.py b/dark/proteins.py index 6a1270f..8e6a850 100644 --- a/dark/proteins.py +++ b/dark/proteins.py @@ -178,6 +178,28 @@ class PathogenSampleFiles(object): sampleIndex = self._samples[sampleName] return self._readsFilenames[(pathogenIndex, sampleIndex)] + def writeSampleIndex(self, fp): + """ + Write a file of sample indices and names, sorted by index. + + @param fp: A file-like object, opened for writing. + """ + print('\n'.join( + '%d %s' % (index, name) for (index, name) in + sorted((index, name) for (name, index) in self._samples.items()) + ), file=fp) + + def writePathogenIndex(self, fp): + """ + Write a file of pathogen indices and names, sorted by index. + + @param fp: A file-like object, opened for writing. + """ + print('\n'.join( + '%d %s' % (index, name) for (index, name) in + sorted((index, name) for (name, index) in self._pathogens.items()) + ), file=fp) + class ProteinGrouper(object): """ @@ -387,7 +409,8 @@ class ProteinGrouper(object): return '\n'.join(result) def toHTML(self, pathogenPanelFilename=None, minProteinFraction=0.0, - pathogenType='viral'): + pathogenType='viral', sampleIndexFilename=None, + pathogenIndexFilename=None): """ Produce an HTML string representation of the pathogen summary. @@ -398,6 +421,12 @@ class ProteinGrouper(object): for that pathogen to be displayed. @param pathogenType: A C{str} giving the type of the pathogen involved, either 'bacterial' or 'viral'. + @param sampleIndexFilename: A C{str} filename to write a sample index + file to. Lines in the file will have an integer index, a space, and + then the sample name. + @param pathogenIndexFilename: A C{str} filename to write a pathogen + index file to. Lines in the file will have an integer index, a + space, and then the pathogen name. @return: An HTML C{str} suitable for printing. """ if pathogenType not in ('bacterial', 'viral'): @@ -411,6 +440,14 @@ class ProteinGrouper(object): if pathogenPanelFilename: self.pathogenPanel(pathogenPanelFilename) + if sampleIndexFilename: + with open(sampleIndexFilename, 'w') as fp: + self.pathogenSampleFiles.writeSampleIndex(fp) + + if pathogenIndexFilename: + with open(pathogenIndexFilename, 'w') as fp: + self.pathogenSampleFiles.writePathogenIndex(fp) + pathogenNames = sorted( pathogenName for pathogenName in self.pathogenNames if self.maxProteinFraction(pathogenName) >= minProteinFraction) @@ -494,7 +531,8 @@ class ProteinGrouper(object): proteinFieldsDescription = [ '<p>', - 'In all bullet point protein lists below, there are eight fields:', + 'In all bullet point protein lists below, there are the following ' + 'fields:', '<ol>', '<li>Coverage fraction.</li>', '<li>Median bit score.</li>',	acorg/dark-matter	bb55d862e66a923688c1f4db4fdfc9467c8210f4	diff --git a/test/test_proteins.py b/test/test_proteins.py index ed8c49f..81bcccb 100644 --- a/test/test_proteins.py +++ b/test/test_proteins.py @@ -917,3 +917,35 @@ class TestPathogenSampleFiles(TestCase): proteins['gi\|327410\| protein 77']['readLengths']) self.assertEqual((2, 7), proteins['gi\|327409\| ubiquitin']['readLengths']) + + def testWriteSampleIndex(self): + """ + The writeSampleIndex function must write a file with the expected + content. + """ + pathogenSampleFiles = PathogenSampleFiles(None) + pathogenSampleFiles._samples = { + 'NEO11': 500, + 'NEO33': 24, + 'NEO66': 333, + } + + fp = StringIO() + pathogenSampleFiles.writeSampleIndex(fp) + self.assertEqual('24 NEO33\n333 NEO66\n500 NEO11\n', fp.getvalue()) + + def testWritePathogenIndex(self): + """ + The writePatogenIndex function must write a file with the expected + content. + """ + pathogenSampleFiles = PathogenSampleFiles(None) + pathogenSampleFiles._pathogens = { + 'virus b': 4, + 'virus a': 3, + 'virus c': 9, + } + + fp = StringIO() + pathogenSampleFiles.writePathogenIndex(fp) + self.assertEqual('3 virus a\n4 virus b\n9 virus c\n', fp.getvalue())	The protein grouper should write a plain text index of pathogen index and name Right now after running `proteins-to-pathogens.py` we are left with files with names like `pathogen-219-sample-228.fastq` but there is no simple way to match a pathogen name with its index. That information is in the `index.html` file but should also be in a text file so we can know which file to look in to get reads when we just have a pathogen name (e.g., from a different pipeline run). The `toStr` method could perhaps print it?	bb55d862e66a923688c1f4db4fdfc9467c8210f4	[ "test/test_proteins.py::TestPathogenSampleFiles::testWritePathogenIndex", "test/test_proteins.py::TestPathogenSampleFiles::testWriteSampleIndex" ]	[ "test/test_proteins.py::TestSplitNames::testNestedBrackets", "test/test_proteins.py::TestSplitNames::testNoBrackets", "test/test_proteins.py::TestSplitNames::testNormalCase", "test/test_proteins.py::TestSplitNames::testTwoSetsOfBrackets", "test/test_proteins.py::TestSplitNames::testWhitespaceStripping", "test/test_proteins.py::TestGetPathogenProteinCounts::testNone", "test/test_proteins.py::TestProteinGrouper::testAssetDir", "test/test_proteins.py::TestProteinGrouper::testDuplicatePathogenProteinSample", "test/test_proteins.py::TestProteinGrouper::testNoAssetDir", "test/test_proteins.py::TestProteinGrouper::testNoFiles", "test/test_proteins.py::TestProteinGrouper::testNoFilesToStr", "test/test_proteins.py::TestProteinGrouper::testNoRegex", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesDifferentPathogens", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesDifferentPathogensTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogen", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogenTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFile", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileFASTQ", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileToStr", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileDifferentPathogens", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileSamePathogen", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testUnknownFormat", "test/test_proteins.py::TestProteinGrouper::testUnknownPathogenType", "test/test_proteins.py::TestPathogenSampleFiles::testUnknownFormat" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2018-04-29 11:55:47+00:00	mit	865
acorg__dark-matter-576	diff --git a/Makefile b/Makefile index 8bf842a..afdcfe8 100644 --- a/Makefile +++ b/Makefile @@ -1,10 +1,10 @@ .PHONY: check, pycodestyle, pyflakes, lint check: - python -m discover -v + env PYTHONPATH=. python -m discover -v tcheck: - trial --rterrors test + env PYTHONPATH=. trial --rterrors test pycodestyle: find . -path './.tox' -prune -o -path './build' -prune -o -path './dist' -prune -o -name '*.py' -print0 \| xargs -0 pycodestyle diff --git a/bin/proteins-to-pathogens.py b/bin/proteins-to-pathogens.py index 3a3ce34..726d4a9 100755 --- a/bin/proteins-to-pathogens.py +++ b/bin/proteins-to-pathogens.py @@ -137,6 +137,12 @@ if __name__ == '__main__': 'contain the lengths of all reads that match proteins for a ' 'pathogen.')) + parser.add_argument( + '--assetDir', default='out', + help=('The output directory where noninteractive-alignment-panel.py ' + 'puts its HTML, plots and FASTA or FASTQ files, needed for ' + 'using --html')) + args = parser.parse_args() if not args.html: @@ -162,7 +168,8 @@ if __name__ == '__main__': else: proteinFastaFilenames = None - grouper = ProteinGrouper(sampleNameRegex=args.sampleNameRegex, + grouper = ProteinGrouper(assetDir=args.assetDir, + sampleNameRegex=args.sampleNameRegex, format_=args.format, proteinFastaFilenames=proteinFastaFilenames, saveReadLengths=args.showReadLengths) diff --git a/dark/__init__.py b/dark/__init__.py index 0246a07..6a59296 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.5' +__version__ = '3.0.6' diff --git a/dark/filter.py b/dark/filter.py index 0665ffc..b0daa76 100644 --- a/dark/filter.py +++ b/dark/filter.py @@ -279,6 +279,23 @@ def addFASTAFilteringCommandLineOptions(parser): help=('A file of (1-based) sequence numbers to retain. Numbers must ' 'be one per line.')) + parser.add_argument( + '--idLambda', metavar='LAMBDA-FUNCTION', + help=('A one-argument function taking and returning a read id. ' + 'E.g., --idLambda "lambda id: id.split(\'_\')[0]" or ' + '--idLambda "lambda id: id[:10]". If the function returns None, ' + 'the read will be filtered out.')) + + parser.add_argument( + '--readLambda', metavar='LAMBDA-FUNCTION', + help=('A one-argument function taking and returning a read. ' + 'E.g., --readLambda "lambda r: Read(r.id.split(\'_\')[0], ' + 'r.sequence.strip(\'-\')". Make sure to also modify the quality ' + 'string if you change the length of a FASTQ sequence. If the ' + 'function returns None, the read will be filtered out. The ' + 'function will be passed to eval with the dark.reads classes ' + 'Read, DNARead, AARead, etc. all in scope.')) + # A mutually exclusive group for --keepSites, --keepSitesFile, # --removeSites, and --removeSitesFile. group = parser.add_mutually_exclusive_group() @@ -381,4 +398,5 @@ def parseFASTAFilteringCommandLineOptions(args, reads): randomSubset=args.randomSubset, trueLength=args.trueLength, sampleFraction=args.sampleFraction, sequenceNumbersFile=args.sequenceNumbersFile, + idLambda=args.idLambda, readLambda=args.readLambda, keepSites=keepSites, removeSites=removeSites) diff --git a/dark/proteins.py b/dark/proteins.py index 8e6a850..33e53eb 100644 --- a/dark/proteins.py +++ b/dark/proteins.py @@ -9,19 +9,9 @@ import numpy as np from textwrap import fill from collections import Counter -try: - import matplotlib - if not os.environ.get('DISPLAY'): - # Use non-interactive Agg backend - matplotlib.use('Agg') - import matplotlib.pyplot as plt -except ImportError: - import platform - if platform.python_implementation() == 'PyPy': - raise NotImplementedError( - 'matplotlib is not supported under pypy') - else: - raise +import matplotlib +matplotlib.use('PDF') +import matplotlib.pyplot as plt from dark.dimension import dimensionalIterator from dark.fasta import FastaReads diff --git a/dark/reads.py b/dark/reads.py index 42390e4..1074f78 100644 --- a/dark/reads.py +++ b/dark/reads.py @@ -740,8 +740,9 @@ class ReadFilter(object): sequence identity. @param removeDuplicatesById: If C{True} remove duplicated reads based only on read id. - @param removeDescriptions: If C{True} remove the description part of read - ids (i.e., the part following the first whitespace). + @param removeDescriptions: If C{True} remove the description (the part + following the first whitespace) from read ids. The description is + removed after applying the function specified by --idLambda (if any). @param modifier: If not C{None}, a function that is passed a read and which either returns a read or C{None}. If it returns a read, that read is passed through the filter. If it returns C{None}, @@ -791,6 +792,14 @@ class ReadFilter(object): file containing (1-based) sequence numbers, in ascending order, one per line. Only those sequences matching the given numbers will be kept. + @param idLambda: If not C{None}, a C{str} Python lambda function + specification to use to modify read ids. The function is applied + before removing the description (if --removeDescriptions is also + specified). + @param readLambda: If not C{None}, a C{str} Python lambda function + specification to use to modify reads. The function will be passed, + and must return, a single Read (or one of its subclasses). This + function is called after the --idLambda function, if any. @param keepSites: A set of C{int} 0-based sites (i.e., indices) in sequences that should be kept. If C{None} (the default), all sites are kept. @@ -819,7 +828,8 @@ class ReadFilter(object): removeDuplicates=False, removeDuplicatesById=False, removeDescriptions=False, modifier=None, randomSubset=None, trueLength=None, sampleFraction=None, - sequenceNumbersFile=None, keepSites=None, removeSites=None): + sequenceNumbersFile=None, idLambda=None, readLambda=None, + keepSites=None, removeSites=None): if randomSubset is not None: if sampleFraction is not None: @@ -929,6 +939,9 @@ class ReadFilter(object): sampleFraction = None self.sampleFraction = sampleFraction + self.idLambda = eval(idLambda) if idLambda else None + self.readLambda = eval(readLambda) if readLambda else None + def filter(self, read): """ Check if a read passes the filter. @@ -1038,6 +1051,20 @@ class ReadFilter(object): elif self.removeSites is not None: read = read.newFromSites(self.removeSites, exclude=True) + if self.idLambda: + newId = self.idLambda(read.id) + if newId is None: + return False + else: + read.id = newId + + if self.readLambda: + newRead = self.readLambda(read) + if newRead is None: + return False + else: + read = newRead + if self.removeDescriptions: read.id = read.id.split()[0] diff --git a/doc/mac.md b/doc/mac.md index ae0d13f..15b1c08 100644 --- a/doc/mac.md +++ b/doc/mac.md @@ -59,3 +59,24 @@ and follow the instructions in that file to install `numpy`. Then run the # Install a taxonomy database (optional) See [taxonomy.md](taxonomy.md) for details. + +# Running the tests + +If you run the tests using `make tcheck` you may encounter the following +error: + +``` +RuntimeError: Python is not installed as a framework. The Mac OS X backend +will not be able to function correctly if Python is not installed as a +framework. See the Python documentation for more information on installing +Python as a framework on Mac OS X. Please either reinstall Python as a +framework, or try one of the other backends. If you are using (Ana)Conda +please install python.app and replace the use of 'python' with 'pythonw'. See + 'Working with Matplotlib on OSX' in the Matplotlib FAQ for more information. +``` + +You can solve this by editing ~/.matplotlib/matplotlibrc (you may have to create the ~/.matplotlib directory) and inserting the following line: + +``` +backend: TkAgg +```	acorg/dark-matter	66f246ba9417430e3f00e94ca0abc88de59a92d4	diff --git a/test/test_proteins.py b/test/test_proteins.py index 81bcccb..5b0d5e9 100644 --- a/test/test_proteins.py +++ b/test/test_proteins.py @@ -255,6 +255,42 @@ class TestProteinGrouper(TestCase): }, pg.pathogenNames) + def testOneLineInOneFileWithDifferentAssetDir(self): + """ + If a protein grouper is given a different assetDir name, + the outDir needs to have that same name, as expected. + """ + fp = StringIO( + '0.77 46.6 48.1 5 6 74 gi\|327\|X\|I44.6 ubiquitin [Lausannevirus]\n') + pg = ProteinGrouper(assetDir='differentname') + pg.addFile('sample-filename', fp) + self.assertEqual( + { + 'Lausannevirus': { + 'sample-filename': { + 'proteins': { + 'gi\|327\|X\|I44.6 ubiquitin': { + 'bestScore': 48.1, + 'bluePlotFilename': 'differentname/0.png', + 'coverage': 0.77, + 'readsFilename': 'differentname/0.fasta', + 'hspCount': 6, + 'index': 0, + 'medianScore': 46.6, + 'outDir': 'differentname', + 'proteinLength': 74, + 'proteinName': 'gi\|327\|X\|I44.6 ubiquitin', + 'proteinURL': ( + 'http://www.ncbi.nlm.nih.gov/nuccore/I44'), + 'readCount': 5, + }, + }, + 'uniqueReadCount': None, + }, + } + }, + pg.pathogenNames) + def testOneLineInOneFileFASTQ(self): """ If a protein grouper is given one file with one line, its pathogenNames diff --git a/test/test_reads.py b/test/test_reads.py index 4e51442..5d9cd3e 100644 --- a/test/test_reads.py +++ b/test/test_reads.py @@ -3126,6 +3126,52 @@ class TestReadsFiltering(TestCase): six.assertRaisesRegex(self, ValueError, error, Reads().filter, keepSites={4}, removeSites={5}) + def testIdLambda(self): + """ + A passed idLambda function should produce the expected read ids. + """ + read = Read('id1', 'ATCGCC') + reads = Reads(initialReads=[read]) + result = reads.filter(idLambda='lambda id: "x-" + id.upper()') + self.assertEqual('x-ID1', list(result)[0].id) + + def testIdLambdaReturningNone(self): + """ + A passed idLambda function should produce the expected read ids, + including when it returns None. + """ + read1 = Read('id1', 'ATCGCC') + read2 = Read('id2', 'GGATCG') + reads = Reads(initialReads=[read1, read2]) + result = reads.filter( + idLambda='lambda id: "aa" if id.find("1") > -1 else None') + (result,) = list(result) + self.assertEqual('aa', result.id) + + def testReadLambda(self): + """ + A passed readLambda function should produce the expected reads. + """ + read = Read('id1', 'ATCGCC') + reads = Reads(initialReads=[read]) + result = reads.filter(readLambda='lambda r: Read("hey", "AAA")') + (result,) = list(result) + self.assertEqual(Read('hey', 'AAA'), result) + + def testReadLambdaReturningNone(self): + """ + A passed readLambda function should produce the expected reads, + including when it returns None. + """ + read1 = Read('xid1', 'ATCGCC') + read2 = Read('yid2', 'GGATCG') + reads = Reads(initialReads=[read1, read2]) + result = reads.filter( + readLambda=('lambda r: Read(r.id + "-x", r.sequence[:2]) ' + 'if r.id.startswith("x") else None')) + (result,) = list(result) + self.assertEqual(Read('xid1-x', 'AT'), result) + class TestReadsInRAM(TestCase): """	Add ability to give an anonymous Python function for read id conversion when filtering FASTA	66f246ba9417430e3f00e94ca0abc88de59a92d4	[ "test/test_reads.py::TestReadsFiltering::testIdLambda", "test/test_reads.py::TestReadsFiltering::testIdLambdaReturningNone", "test/test_reads.py::TestReadsFiltering::testReadLambda", "test/test_reads.py::TestReadsFiltering::testReadLambdaReturningNone" ]	[ "test/test_proteins.py::TestSplitNames::testNestedBrackets", "test/test_proteins.py::TestSplitNames::testNoBrackets", "test/test_proteins.py::TestSplitNames::testNormalCase", "test/test_proteins.py::TestSplitNames::testTwoSetsOfBrackets", "test/test_proteins.py::TestSplitNames::testWhitespaceStripping", "test/test_proteins.py::TestGetPathogenProteinCounts::testNone", "test/test_proteins.py::TestProteinGrouper::testAssetDir", "test/test_proteins.py::TestProteinGrouper::testDuplicatePathogenProteinSample", "test/test_proteins.py::TestProteinGrouper::testNoAssetDir", "test/test_proteins.py::TestProteinGrouper::testNoFiles", "test/test_proteins.py::TestProteinGrouper::testNoFilesToStr", "test/test_proteins.py::TestProteinGrouper::testNoRegex", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesDifferentPathogens", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesDifferentPathogensTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogen", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogenTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFile", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileFASTQ", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileToStr", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileWithDifferentAssetDir", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileDifferentPathogens", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileSamePathogen", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testUnknownFormat", "test/test_proteins.py::TestProteinGrouper::testUnknownPathogenType", "test/test_proteins.py::TestPathogenSampleFiles::testUnknownFormat", "test/test_proteins.py::TestPathogenSampleFiles::testWritePathogenIndex", "test/test_proteins.py::TestPathogenSampleFiles::testWriteSampleIndex", "test/test_reads.py::TestRead::testCasePreservation", "test/test_reads.py::TestRead::testCheckAlphabetAAReadMatchingReturnTrue", "test/test_reads.py::TestRead::testCheckAlphabetAAReadNotMatchingRaise", "test/test_reads.py::TestRead::testCheckAlphabetDNAReadMatchingReturnTrue", "test/test_reads.py::TestRead::testCheckAlphabetDNAReadNotMatchingRaise", "test/test_reads.py::TestRead::testCheckAlphabetwithReadMustBePermissive", "test/test_reads.py::TestRead::testEquality", "test/test_reads.py::TestRead::testEqualityWithDifferingIds", "test/test_reads.py::TestRead::testEqualityWithDifferingQuality", "test/test_reads.py::TestRead::testEqualityWithDifferingSequences", "test/test_reads.py::TestRead::testEqualityWithNoQuality", "test/test_reads.py::TestRead::testEqualityWithOneOmittedQuality", "test/test_reads.py::TestRead::testExpectedAttributes", "test/test_reads.py::TestRead::testFromDict", "test/test_reads.py::TestRead::testFromDictNoQuality", "test/test_reads.py::TestRead::testGetitemFullCopy", "test/test_reads.py::TestRead::testGetitemId", "test/test_reads.py::TestRead::testGetitemLength", "test/test_reads.py::TestRead::testGetitemQuality", "test/test_reads.py::TestRead::testGetitemReturnsNewRead", "test/test_reads.py::TestRead::testGetitemReversed", "test/test_reads.py::TestRead::testGetitemSequence", "test/test_reads.py::TestRead::testGetitemSingleIndex", "test/test_reads.py::TestRead::testGetitemWithStep", "test/test_reads.py::TestRead::testHashDiffersIfIdDiffers", "test/test_reads.py::TestRead::testHashDiffersIfQualityDiffers", "test/test_reads.py::TestRead::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestRead::testHashIdenticalNoQuality", "test/test_reads.py::TestRead::testHashIdenticalWithQuality", "test/test_reads.py::TestRead::testHashViaDict", "test/test_reads.py::TestRead::testHashViaSet", "test/test_reads.py::TestRead::testKeepSites", "test/test_reads.py::TestRead::testKeepSitesAllSites", "test/test_reads.py::TestRead::testKeepSitesNoSites", "test/test_reads.py::TestRead::testKeepSitesOutOfRange", "test/test_reads.py::TestRead::testKeepSitesWithQuality", "test/test_reads.py::TestRead::testLength", "test/test_reads.py::TestRead::testLowComplexityFraction", "test/test_reads.py::TestRead::testLowComplexityFractionEmptySequence", "test/test_reads.py::TestRead::testLowComplexityFractionOne", "test/test_reads.py::TestRead::testLowComplexityFractionZero", "test/test_reads.py::TestRead::testNoQuality", "test/test_reads.py::TestRead::testRemoveSites", "test/test_reads.py::TestRead::testRemoveSitesAllSites", "test/test_reads.py::TestRead::testRemoveSitesNoSites", "test/test_reads.py::TestRead::testRemoveSitesOutOfRange", "test/test_reads.py::TestRead::testRemoveSitesWithQuality", "test/test_reads.py::TestRead::testToDict", "test/test_reads.py::TestRead::testToDictNoQuality", "test/test_reads.py::TestRead::testToFASTA", "test/test_reads.py::TestRead::testToFASTAWithQuality", "test/test_reads.py::TestRead::testToFASTQ", "test/test_reads.py::TestRead::testToFASTQWithNoQuality", "test/test_reads.py::TestRead::testToUnknownFormat", "test/test_reads.py::TestRead::testUnequalLengths", "test/test_reads.py::TestRead::testWalkHSPExactMatch", "test/test_reads.py::TestRead::testWalkHSPExactMatchWithGap", "test/test_reads.py::TestRead::testWalkHSPLeftAndRightOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPLeftAndRightOverhangingMatchNoWhiskers", "test/test_reads.py::TestRead::testWalkHSPLeftOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPLeftOverhangingMatchNoWhiskers", "test/test_reads.py::TestRead::testWalkHSPRightOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPRightOverhangingMatchNoWhiskers", "test/test_reads.py::TestDNARead::testGetitemReturnsNewDNARead", "test/test_reads.py::TestDNARead::testReverseComplement", "test/test_reads.py::TestDNARead::testReverseComplementAmbiguous", "test/test_reads.py::TestDNARead::testReverseComplementReversesQuality", "test/test_reads.py::TestDNARead::testTranslationOfMultipleStopCodons", "test/test_reads.py::TestDNARead::testTranslationOfStartCodonATG", "test/test_reads.py::TestDNARead::testTranslationOfStopCodonTAG", "test/test_reads.py::TestDNARead::testTranslationOfStopCodonTGA", "test/test_reads.py::TestDNARead::testTranslations", "test/test_reads.py::TestDNARead::testTranslationsOfEmptySequence", "test/test_reads.py::TestDNARead::testTranslationsOfOneBaseSequence", "test/test_reads.py::TestDNARead::testTranslationsOfTwoBaseSequence", "test/test_reads.py::TestRNARead::testGetitemReturnsNewRNARead", "test/test_reads.py::TestRNARead::testReverseComplement", "test/test_reads.py::TestRNARead::testReverseComplementAmbiguous", "test/test_reads.py::TestRNARead::testTranslationOfStopCodonUAA", "test/test_reads.py::TestAARead::testCloseCloseORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseCloseORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseCloseORFWithJunk", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseOpenORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseOpenORFWithJunk", "test/test_reads.py::TestAARead::testCloseCloseThenCloseOpenORF", "test/test_reads.py::TestAARead::testCloseOpenORF", "test/test_reads.py::TestAARead::testCloseOpenORFWithMultipleStarts", "test/test_reads.py::TestAARead::testGetitemReturnsNewAARead", "test/test_reads.py::TestAARead::testNoStartCodon_GithubIssue239", "test/test_reads.py::TestAARead::testORFsEmptySequence", "test/test_reads.py::TestAARead::testORFsEmptySequenceWithStart", "test/test_reads.py::TestAARead::testORFsEmptySequenceWithStartStop", "test/test_reads.py::TestAARead::testORFsWithJustStartsAndStops", "test/test_reads.py::TestAARead::testORFsWithOneStopCodon", 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"test/test_reads.py::TestAAReadORF::testOpenClosedId", "test/test_reads.py::TestAAReadORF::testOpenLeft", "test/test_reads.py::TestAAReadORF::testOpenOpenId", "test/test_reads.py::TestAAReadORF::testOpenRight", "test/test_reads.py::TestAAReadORF::testSequence", "test/test_reads.py::TestAAReadORF::testStart", "test/test_reads.py::TestAAReadORF::testStartGreaterThanStop", "test/test_reads.py::TestAAReadORF::testStartNegative", "test/test_reads.py::TestAAReadORF::testStop", "test/test_reads.py::TestAAReadORF::testStopGreaterThanOriginalSequenceLength", "test/test_reads.py::TestAAReadORF::testToDict", "test/test_reads.py::TestSSAARead::testCorrectAttributes", "test/test_reads.py::TestSSAARead::testFromDict", "test/test_reads.py::TestSSAARead::testGetitemFullCopy", "test/test_reads.py::TestSSAARead::testGetitemId", "test/test_reads.py::TestSSAARead::testGetitemLength", "test/test_reads.py::TestSSAARead::testGetitemReturnsNewRead", "test/test_reads.py::TestSSAARead::testGetitemReversed", "test/test_reads.py::TestSSAARead::testGetitemSequence", "test/test_reads.py::TestSSAARead::testGetitemSingleIndex", "test/test_reads.py::TestSSAARead::testGetitemStructure", "test/test_reads.py::TestSSAARead::testGetitemWithStep", "test/test_reads.py::TestSSAARead::testHashDiffersIfIdDiffers", "test/test_reads.py::TestSSAARead::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestSSAARead::testHashDiffersIfStructureDiffers", "test/test_reads.py::TestSSAARead::testHashViaDict", "test/test_reads.py::TestSSAARead::testHashViaSet", "test/test_reads.py::TestSSAARead::testKeepSites", "test/test_reads.py::TestSSAARead::testKeepSitesAllSites", "test/test_reads.py::TestSSAARead::testKeepSitesNoSites", "test/test_reads.py::TestSSAARead::testKeepSitesOutOfRange", "test/test_reads.py::TestSSAARead::testReads", "test/test_reads.py::TestSSAARead::testRemoveSites", "test/test_reads.py::TestSSAARead::testRemoveSitesAllSites", "test/test_reads.py::TestSSAARead::testRemoveSitesNoSites", "test/test_reads.py::TestSSAARead::testRemoveSitesOutOfRange", "test/test_reads.py::TestSSAARead::testSequenceLengthMatchesStructureLength", "test/test_reads.py::TestSSAARead::testToDict", "test/test_reads.py::TestSSAARead::testToString", "test/test_reads.py::TestSSAARead::testToStringWithExplicitFastaFormat", "test/test_reads.py::TestSSAARead::testToStringWithExplicitFastaSSFormat", "test/test_reads.py::TestSSAARead::testToStringWithStructureSuffix", "test/test_reads.py::TestSSAARead::testToStringWithUnknownFormat", "test/test_reads.py::TestSSAAReadWithX::testCorrectAttributes", "test/test_reads.py::TestSSAAReadWithX::testFromDict", "test/test_reads.py::TestSSAAReadWithX::testGetitemFullCopy", "test/test_reads.py::TestSSAAReadWithX::testGetitemId", "test/test_reads.py::TestSSAAReadWithX::testGetitemLength", "test/test_reads.py::TestSSAAReadWithX::testGetitemReturnsNewRead", "test/test_reads.py::TestSSAAReadWithX::testGetitemReversed", "test/test_reads.py::TestSSAAReadWithX::testGetitemSequence", "test/test_reads.py::TestSSAAReadWithX::testGetitemSingleIndex", "test/test_reads.py::TestSSAAReadWithX::testGetitemStructure", "test/test_reads.py::TestSSAAReadWithX::testGetitemWithStep", "test/test_reads.py::TestSSAAReadWithX::testHashDiffersIfIdDiffers", "test/test_reads.py::TestSSAAReadWithX::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestSSAAReadWithX::testHashDiffersIfStructureDiffers", "test/test_reads.py::TestSSAAReadWithX::testHashViaDict", "test/test_reads.py::TestSSAAReadWithX::testHashViaSet", "test/test_reads.py::TestSSAAReadWithX::testKeepSites", "test/test_reads.py::TestSSAAReadWithX::testKeepSitesAllSites", "test/test_reads.py::TestSSAAReadWithX::testKeepSitesNoSites", "test/test_reads.py::TestSSAAReadWithX::testKeepSitesOutOfRange", "test/test_reads.py::TestSSAAReadWithX::testReads", "test/test_reads.py::TestSSAAReadWithX::testRemoveSites", "test/test_reads.py::TestSSAAReadWithX::testRemoveSitesAllSites", "test/test_reads.py::TestSSAAReadWithX::testRemoveSitesNoSites", "test/test_reads.py::TestSSAAReadWithX::testRemoveSitesOutOfRange", "test/test_reads.py::TestSSAAReadWithX::testSequenceContainingX", "test/test_reads.py::TestSSAAReadWithX::testSequenceLengthMatchesStructureLength", "test/test_reads.py::TestSSAAReadWithX::testToDict", "test/test_reads.py::TestSSAAReadWithX::testToString", "test/test_reads.py::TestSSAAReadWithX::testToStringWithExplicitFastaFormat", "test/test_reads.py::TestSSAAReadWithX::testToStringWithExplicitFastaSSFormat", "test/test_reads.py::TestSSAAReadWithX::testToStringWithStructureSuffix", "test/test_reads.py::TestSSAAReadWithX::testToStringWithUnknownFormat", "test/test_reads.py::TestTranslatedRead::testExpectedAttributes", "test/test_reads.py::TestTranslatedRead::testExpectedFrame", "test/test_reads.py::TestTranslatedRead::testFromDict", "test/test_reads.py::TestTranslatedRead::testId", "test/test_reads.py::TestTranslatedRead::testIdReverseComplemented", "test/test_reads.py::TestTranslatedRead::testMaximumORFLength", "test/test_reads.py::TestTranslatedRead::testMaximumORFLengthNoStops", "test/test_reads.py::TestTranslatedRead::testOutOfRangeFrame", "test/test_reads.py::TestTranslatedRead::testReverseComplemented", "test/test_reads.py::TestTranslatedRead::testSequence", "test/test_reads.py::TestTranslatedRead::testToDict", "test/test_reads.py::TestReadClassNameToClass::testNames", "test/test_reads.py::TestReads::testEmptyInitialReads", "test/test_reads.py::TestReads::testInitialReads", "test/test_reads.py::TestReads::testManuallyAddedReads", "test/test_reads.py::TestReads::testManuallyAddedReadsLength", "test/test_reads.py::TestReads::testNoReads", "test/test_reads.py::TestReads::testNoReadsLength", "test/test_reads.py::TestReads::testRepeatedIter", "test/test_reads.py::TestReads::testSaveAsFASTA", "test/test_reads.py::TestReads::testSaveAsFASTQ", "test/test_reads.py::TestReads::testSaveAsFASTQFailsOnReadWithNoQuality", "test/test_reads.py::TestReads::testSaveFASTAIsDefault", "test/test_reads.py::TestReads::testSaveReturnsReadCount", "test/test_reads.py::TestReads::testSaveToFileDescriptor", "test/test_reads.py::TestReads::testSaveWithUnknownFormat", "test/test_reads.py::TestReads::testSaveWithUppercaseFormat", "test/test_reads.py::TestReads::testSubclass", "test/test_reads.py::TestReads::testSubclassLength", "test/test_reads.py::TestReads::testSubclassWithAdditionalReads", "test/test_reads.py::TestReads::testUnfilteredLengthAdditionalReads", "test/test_reads.py::TestReads::testUnfilteredLengthAdditionalReadsAfterFiltering", "test/test_reads.py::TestReads::testUnfilteredLengthBeforeIterating", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReads", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReadsAfterFiltering", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReadsIsReads", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReadsIsReadsWithAdditional", "test/test_reads.py::TestReads::testUnfilteredLengthInitialSubclassThenFiltered", "test/test_reads.py::TestReads::testUnfilteredLengthInitialSubclassWithAdditionalThenFiltered", "test/test_reads.py::TestReads::testUnfilteredLengthInitialSubclassWithNoLen", "test/test_reads.py::TestReads::testUnfilteredLengthNoReads", "test/test_reads.py::TestReadsFiltering::testAddFiltersThenClearFilters", "test/test_reads.py::TestReadsFiltering::testFilterBlacklist", "test/test_reads.py::TestReadsFiltering::testFilterDoNotRemoveDescriptions", "test/test_reads.py::TestReadsFiltering::testFilterDuplicates", "test/test_reads.py::TestReadsFiltering::testFilterDuplicatesById", "test/test_reads.py::TestReadsFiltering::testFilterHead", "test/test_reads.py::TestReadsFiltering::testFilterHeadZero", "test/test_reads.py::TestReadsFiltering::testFilterKeepSequences", "test/test_reads.py::TestReadsFiltering::testFilterKeepSequencesNoSequences", "test/test_reads.py::TestReadsFiltering::testFilterNegativeRegex", "test/test_reads.py::TestReadsFiltering::testFilterNoArgs", "test/test_reads.py::TestReadsFiltering::testFilterOnLengthEverythingMatches", "test/test_reads.py::TestReadsFiltering::testFilterOnLengthNothingMatches", "test/test_reads.py::TestReadsFiltering::testFilterOnMaxLength", "test/test_reads.py::TestReadsFiltering::testFilterOnMinLength", "test/test_reads.py::TestReadsFiltering::testFilterPositiveRegex", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfFiveFromFiveReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfFiveFromOneRead", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfOneFromOneRead", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfTwoFromFiveReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfZeroReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetSizeZeroNoReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetSizeZeroTwoReads", "test/test_reads.py::TestReadsFiltering::testFilterRemoveDescriptions", "test/test_reads.py::TestReadsFiltering::testFilterRemoveGaps", "test/test_reads.py::TestReadsFiltering::testFilterRemoveGapsWithQuality", "test/test_reads.py::TestReadsFiltering::testFilterRemoveSequences", "test/test_reads.py::TestReadsFiltering::testFilterRemoveSequencesNoSequences", "test/test_reads.py::TestReadsFiltering::testFilterReturnsReadInstance", "test/test_reads.py::TestReadsFiltering::testFilterTruncateTitles", "test/test_reads.py::TestReadsFiltering::testFilterWhitelist", "test/test_reads.py::TestReadsFiltering::testFilterWithMinLengthEqualToMaxLength", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatChangesIds", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatOmits", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatOmitsAndChangesIds", "test/test_reads.py::TestReadsFiltering::testFilteredReadsInstanceHasExpectedLength", "test/test_reads.py::TestReadsFiltering::testKeepSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesAllSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesNoSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesOutOfRange", "test/test_reads.py::TestReadsFiltering::testKeepSitesWithQuality", "test/test_reads.py::TestReadsFiltering::testLineNumberFile", "test/test_reads.py::TestReadsFiltering::testLineNumberFileEmpty", "test/test_reads.py::TestReadsFiltering::testLineNumberFileFirstLineTooSmall", "test/test_reads.py::TestReadsFiltering::testLineNumberFileNonAscending", "test/test_reads.py::TestReadsFiltering::testLineNumberFileRunOutOfSequences", "test/test_reads.py::TestReadsFiltering::testRemoveAndKeepSites", "test/test_reads.py::TestReadsFiltering::testRemoveSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesAllSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesNoSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesOutOfRange", "test/test_reads.py::TestReadsFiltering::testRemoveSitesWithQuality", "test/test_reads.py::TestReadsFiltering::testSampleFractionAndNoTrueLengthRaisesValueError", "test/test_reads.py::TestReadsFiltering::testSampleFractionAndRandomSubsetRaisesValueError", "test/test_reads.py::TestReadsFiltering::testSampleFractionOne", "test/test_reads.py::TestReadsFiltering::testSampleFractionPointOne", "test/test_reads.py::TestReadsFiltering::testSampleFractionZero", "test/test_reads.py::TestReadsInRAM::testAdd", "test/test_reads.py::TestReadsInRAM::testFromReads", "test/test_reads.py::TestReadsInRAM::testNoReads", "test/test_reads.py::TestReadsInRAM::testOneReadIndex", "test/test_reads.py::TestReadsInRAM::testOneReadLength", "test/test_reads.py::TestReadsInRAM::testOneReadList", "test/test_reads.py::TestReadsInRAM::testSetItem", "test/test_reads.py::TestReadsInRAM::testTwoReadsIndex", "test/test_reads.py::TestReadsInRAM::testTwoReadsLength", "test/test_reads.py::TestReadsInRAM::testTwoReadsList", "test/test_reads.py::TestSummarizePosition::testCorrectFrequencies", "test/test_reads.py::TestSummarizePosition::testExcludeShortSequences", "test/test_reads.py::TestSummarizePosition::testFrequenciesNoReads", "test/test_reads.py::TestSummarizePosition::testIndexLargerThanSequenceLength", "test/test_reads.py::TestSummarizePosition::testNumberOfExclusionsNoReads", "test/test_reads.py::TestSitesMatching::testAllMatches", "test/test_reads.py::TestSitesMatching::testIgnoreCase", "test/test_reads.py::TestSitesMatching::testMatchCase", "test/test_reads.py::TestSitesMatching::testMultipleReadsAll", "test/test_reads.py::TestSitesMatching::testMultipleReadsAllWithDifferingLengths", "test/test_reads.py::TestSitesMatching::testMultipleReadsAny", "test/test_reads.py::TestSitesMatching::testMultipleReadsAnyWithDifferingLengths", "test/test_reads.py::TestSitesMatching::testNoMatches", "test/test_reads.py::TestSitesMatching::testPartialMatch" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2018-05-27 14:07:28+00:00	mit	866
acorg__dark-matter-610	diff --git a/CHANGELOG.md b/CHANGELOG.md index d7f91b4..add466a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +## 3.0.23 June 22, 2018 + +Changed the way reference sequence insertions are stored in a +`dark.sam.PaddedSAM` instance to make it possible to tell which query +sequences caused reference insertions. + ## 3.0.22 June 21, 2018 Made `dark/sam.py` properly deal with secondary alignments that are missing diff --git a/dark/__init__.py b/dark/__init__.py index db6691a..e3d166b 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.22' +__version__ = '3.0.23' diff --git a/dark/sam.py b/dark/sam.py index f0ffa19..2165ea6 100644 --- a/dark/sam.py +++ b/dark/sam.py @@ -29,12 +29,12 @@ class PaddedSAM(object): """ def __init__(self, filename): self.samfile = AlignmentFile(filename) - # self.referenceInsertions will be keyed by offset into the reference - # sequence. The inserted bases would need to begin at this offset. The - # value will be a Counter whose keys are the nucleotides proposed for - # insertion, with a value indicating how many times the nucleotide was - # proposed for insertion at that offset. - self.referenceInsertions = defaultdict(Counter) + # self.referenceInsertions will be keyed by query id (the query + # that would cause a reference insertion). The values will be lists + # of 2-tuples, with each 2-tuple containing an offset into the + # reference sequence and the C{str} of nucleotide that would be + # inserted starting at that offset. + self.referenceInsertions = defaultdict(list) def close(self): """ @@ -182,6 +182,16 @@ class PaddedSAM(object): if rcSuffix: read.query_name += rcSuffix + # Adjust the query id if it's a duplicate and we're not + # allowing duplicates. + if allowDuplicateIds: + queryId = read.query_name + else: + count = idCount[read.query_name] + idCount[read.query_name] += 1 + queryId = read.query_name + ( + '' if count == 0 else '/%d' % count) + referenceStart = read.reference_start atStart = True queryIndex = 0 @@ -205,9 +215,9 @@ class PaddedSAM(object): # query but record what would have been inserted into the # reference. atStart = False - for i in range(length): - self.referenceInsertions[referenceIndex + i][ - query[queryIndex + i]] += 1 + self.referenceInsertions[queryId].append( + (referenceIndex, + query[queryIndex:queryIndex + length])) elif operation == CDEL: # Delete from the reference. Some bases from the reference # would need to be deleted to continue the match. So we put @@ -293,14 +303,7 @@ class PaddedSAM(object): padChar * (referenceLength - (referenceStart + len(alignedSequence)))) - if allowDuplicateIds: - suffix = '' - else: - count = idCount[read.query_name] - idCount[read.query_name] += 1 - suffix = '' if count == 0 else '/%d' % count - - yield Read('%s%s' % (read.query_name, suffix), paddedSequence) + yield Read(queryId, paddedSequence) @contextmanager	acorg/dark-matter	d75630ac7a4f6f99bd0c4e87737290ff971b92d5	diff --git a/test/test_sam.py b/test/test_sam.py index e31f801..f8fd7e9 100644 --- a/test/test_sam.py +++ b/test/test_sam.py @@ -347,8 +347,32 @@ class TestPaddedSAM(TestCase): self.assertEqual(Read('query1', '-TCGG-----'), read) self.assertEqual( { - 3: {'T': 1}, - 4: {'A': 1}, + 'query1': [(3, 'TA')], + }, + ps.referenceInsertions) + ps.close() + + def testPrimaryAndSecondaryReferenceInsertion(self): + """ + A primary and secondary insertion into the reference (of the same + query) must result in the expected padded sequences and the expected + value in the referenceInsertions dictionary. + """ + data = '\n'.join([ + '@SQ SN:ref1 LN:10', + 'query1 0 ref1 2 60 2M2I2M * 0 0 TCTAGG ZZZZZZ', + 'query1 256 ref1 4 60 2M3I1M * 0 0 * *', + ]).replace(' ', '\t') + + with dataFile(data) as filename: + ps = PaddedSAM(filename) + (read1, read2) = list(ps.queries()) + self.assertEqual(Read('query1', '-TCGG-----'), read1) + self.assertEqual(Read('query1/1', '---TCG----'), read2) + self.assertEqual( + { + 'query1': [(3, 'TA')], + 'query1/1': [(5, 'TAG')], }, ps.referenceInsertions) ps.close()	SAM referenceInsertion should record what reads cause reference insertions The code currently records all reference insertions but doesn't keep track of which reads caused insertions. That makes it impossible to ignore insertions according to which read created it.	d75630ac7a4f6f99bd0c4e87737290ff971b92d5	[ "test/test_sam.py::TestPaddedSAM::testPrimaryAndSecondaryReferenceInsertion", "test/test_sam.py::TestPaddedSAM::testReferenceInsertion" ]	[ "test/test_sam.py::TestPaddedSAM::testAllMMatch", "test/test_sam.py::TestPaddedSAM::testAllowDuplicateIds", "test/test_sam.py::TestPaddedSAM::testDropDuplicates", "test/test_sam.py::TestPaddedSAM::testDropSecondary", "test/test_sam.py::TestPaddedSAM::testDropSupplementary", "test/test_sam.py::TestPaddedSAM::testDuplicateIdDisambiguation", "test/test_sam.py::TestPaddedSAM::testHardClipLeft", "test/test_sam.py::TestPaddedSAM::testHardClipRight", "test/test_sam.py::TestPaddedSAM::testKF414679SoftClipLeft", "test/test_sam.py::TestPaddedSAM::testKeepQualityControlFailures", "test/test_sam.py::TestPaddedSAM::testMinLength", "test/test_sam.py::TestPaddedSAM::testMinLengthWithReferenceDeletion", "test/test_sam.py::TestPaddedSAM::testMixedMatch", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReference", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReferenceButNoMatches", "test/test_sam.py::TestPaddedSAM::testNotSecondaryAndNotSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testQueryHardClipAndSoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesRight", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesLeftEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesRightEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipRight", "test/test_sam.py::TestPaddedSAM::testRcNeeded", "test/test_sam.py::TestPaddedSAM::testRcSuffix", "test/test_sam.py::TestPaddedSAM::testReferenceDeletion", "test/test_sam.py::TestPaddedSAM::testReferenceDeletionAlternateChar", "test/test_sam.py::TestPaddedSAM::testReferenceSkip", "test/test_sam.py::TestPaddedSAM::testReferenceSkipAlternateChar", "test/test_sam.py::TestPaddedSAM::testReferencesToStr", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testUnequalReferenceLengths", "test/test_sam.py::TestPaddedSAM::testUnknownReferences" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2018-06-22 17:31:59+00:00	mit	867
acorg__dark-matter-617	diff --git a/CHANGELOG.md b/CHANGELOG.md index 67af944..2065375 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,11 @@ +## 3.0.28 July 3, 2018 + +Added `alsoYieldAlignments` option to `PaddedSAM.queries` method to have +the returned generator also yield the `pysam.AlignedSegment` instance with +the gap-padded query sequence. This makes it possible to retrieve padded +queries from SAM/BAM and generate SAM/BAM (or FASTQ) of some subset of the +queries. + ## 3.0.27 June 30, 2018 Added `bin/filter-sam.py` script. diff --git a/bin/filter-sam.py b/bin/filter-sam.py index 18b5b47..363fed1 100755 --- a/bin/filter-sam.py +++ b/bin/filter-sam.py @@ -38,26 +38,26 @@ if __name__ == '__main__': 'error message is printed unless --quiet is used).')) parser.add_argument( - '--dropUnmapped', default=False, action='store_true', - help='If given, unmapped matches will not be output.') + '--dropUnmapped', default=False, action='store_true', + help='If given, unmapped matches will not be output.') parser.add_argument( - '--dropSecondary', default=False, action='store_true', - help='If given, secondary matches will not be output.') + '--dropSecondary', default=False, action='store_true', + help='If given, secondary matches will not be output.') parser.add_argument( - '--dropSupplementary', default=False, action='store_true', - help='If given, supplementary matches will not be output.') + '--dropSupplementary', default=False, action='store_true', + help='If given, supplementary matches will not be output.') parser.add_argument( - '--dropDuplicates', default=False, action='store_true', - help=('If given, matches flagged as optical or PCR duplicates will ' - 'not be output.')) + '--dropDuplicates', default=False, action='store_true', + help=('If given, matches flagged as optical or PCR duplicates will ' + 'not be output.')) parser.add_argument( - '--keepQCFailures', default=False, action='store_true', - help=('If given, reads that are considered quality control failures ' - 'will be included in the output.')) + '--keepQCFailures', default=False, action='store_true', + help=('If given, reads that are considered quality control failures ' + 'will be included in the output.')) parser.add_argument( '--referenceWhitelist', metavar='NAME', action='append', @@ -106,17 +106,17 @@ if __name__ == '__main__': if (filterRead(Read(alignment.query_name, alignment.query_sequence, - alignment.qual)) - and not ( - (alignment.is_unmapped and dropUnmapped) or - (alignment.is_secondary and dropSecondary) or - (alignment.is_supplementary and dropSupplementary) or - (alignment.is_duplicate and dropDuplicates) or - (alignment.is_qcfail and not keepQCFailures) or - (referenceWhitelist is not None and - alignment.reference_name not in referenceWhitelist) or - (referenceBlacklist is not None and - alignment.reference_name in referenceBlacklist))): + alignment.qual)) and + not ( + (alignment.is_unmapped and dropUnmapped) or + (alignment.is_secondary and dropSecondary) or + (alignment.is_supplementary and dropSupplementary) or + (alignment.is_duplicate and dropDuplicates) or + (alignment.is_qcfail and not keepQCFailures) or + (referenceWhitelist is not None and + alignment.reference_name not in referenceWhitelist) or + (referenceBlacklist is not None and + alignment.reference_name in referenceBlacklist))): kept += 1 save(alignment) out.close() diff --git a/dark/__init__.py b/dark/__init__.py index dabfdd7..2f8e41d 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.27' +__version__ = '3.0.28' diff --git a/dark/sam.py b/dark/sam.py index f2bb28b..a5d9363 100644 --- a/dark/sam.py +++ b/dark/sam.py @@ -61,7 +61,7 @@ class PaddedSAM(object): dropSecondary=False, dropSupplementary=False, dropDuplicates=False, allowDuplicateIds=False, keepQCFailures=False, rcNeeded=False, padChar='-', - queryInsertionChar='N'): + queryInsertionChar='N', alsoYieldAlignments=False): """ Produce padded (with gaps) queries according to the CIGAR string and reference sequence length for each matching query sequence. @@ -107,13 +107,18 @@ class PaddedSAM(object): is inserted as a 'missing' query character (i.e., a base that can be assumed to have been lost due to an error) whose existence is necessary for the match to continue. + @param alsoYieldAlignments: If C{True} the returned generator will + yield 2-tuples containing a padded query and the + C{pysam.AlignedSegment} for each query. @raises UnequalReferenceLengthError: If C{referenceName} is C{None} and the reference sequence lengths in the SAM/BAM file are not all identical. @raises UnknownReference: If C{referenceName} does not exist. @return: A generator that yields C{Read} instances that are padded with gap characters to align them to the length of the reference - sequence. + sequence. See C{alsoYieldAlignments}, above, to have the generator + yield tuples also containing the corresponding + C{pysam.AlignedSegment}. """ samfile = self.samfile @@ -142,24 +147,24 @@ class PaddedSAM(object): MATCH_OPERATIONS = {CMATCH, CEQUAL, CDIFF} lastQuery = None - for lineNumber, read in enumerate(samfile.fetch(), start=1): - if (read.is_unmapped or - (read.is_secondary and dropSecondary) or - (read.is_supplementary and dropSupplementary) or - (read.is_duplicate and dropDuplicates) or - (read.is_qcfail and not keepQCFailures) or + for lineNumber, alignment in enumerate(samfile.fetch(), start=1): + if (alignment.is_unmapped or + (alignment.is_secondary and dropSecondary) or + (alignment.is_supplementary and dropSupplementary) or + (alignment.is_duplicate and dropDuplicates) or + (alignment.is_qcfail and not keepQCFailures) or (referenceId is not None and - read.reference_id != referenceId)): + alignment.reference_id != referenceId)): continue - query = read.query_sequence + query = alignment.query_sequence # Secondary (and presumably supplementary) alignments may have # a '' (None in pysam) SEQ field, indicating that the previous # sequence should be used. This is best practice according to # section 2.5.2 of https://samtools.github.io/hts-specs/SAMv1.pdf if query is None: - if read.is_secondary or read.is_supplementary: + if alignment.is_secondary or alignment.is_supplementary: if lastQuery is None: raise ValueError( 'Query line %d has an empty SEQ field, but no ' @@ -176,29 +181,29 @@ class PaddedSAM(object): # due to it being reverse complimented for the alignment). lastQuery = query - if read.is_reverse: + if alignment.is_reverse: if rcNeeded: query = DNARead('id', query).reverseComplement().sequence if rcSuffix: - read.query_name += rcSuffix + alignment.query_name += rcSuffix # Adjust the query id if it's a duplicate and we're not # allowing duplicates. if allowDuplicateIds: - queryId = read.query_name + queryId = alignment.query_name else: - count = idCount[read.query_name] - idCount[read.query_name] += 1 - queryId = read.query_name + ( + count = idCount[alignment.query_name] + idCount[alignment.query_name] += 1 + queryId = alignment.query_name + ( '' if count == 0 else '/%d' % count) - referenceStart = read.reference_start + referenceStart = alignment.reference_start atStart = True queryIndex = 0 referenceIndex = referenceStart alignedSequence = '' - for operation, length in read.cigartuples: + for operation, length in alignment.cigartuples: # The operations are tested in the order they appear in # https://samtools.github.io/hts-specs/SAMv1.pdf It would be @@ -303,7 +308,11 @@ class PaddedSAM(object): padChar (referenceLength - (referenceStart + len(alignedSequence)))) - yield Read(queryId, paddedSequence) + read = Read(queryId, paddedSequence) + if alsoYieldAlignments: + yield (read, alignment) + else: + yield read @contextmanager	acorg/dark-matter	252de3e0a17525dde6a5f4167ea1e54a70ba91ee	diff --git a/test/test_sam.py b/test/test_sam.py index f8fd7e9..a6ee95a 100644 --- a/test/test_sam.py +++ b/test/test_sam.py @@ -706,3 +706,31 @@ class TestPaddedSAM(TestCase): queries = ps.queries() assertRaisesRegex(self, ValueError, error, list, queries) ps.close() + + def testAlsoYieldAlignments(self): + """ + A request for queries and their pysam alignments should have the + expected result. + """ + data = '\n'.join([ + '@SQ SN:ref1 LN:10', + 'query1 0 ref1 2 60 2=2X2M * 0 0 TCTAGG 123456', + 'query2 0 ref1 2 60 2= * 0 0 TC XY', + ]).replace(' ', '\t') + + with dataFile(data) as filename: + ps = PaddedSAM(filename) + ((read1, alignment1), + (read2, alignment2)) = list(ps.queries(alsoYieldAlignments=True)) + + self.assertEqual(Read('query1', '-TCTAGG---'), read1) + self.assertEqual('TCTAGG', alignment1.query_sequence) + self.assertEqual('123456', ''.join( + map(lambda x: chr(x + 33), alignment1.query_qualities))) + + self.assertEqual(Read('query2', '-TC-------'), read2) + self.assertEqual('TC', alignment2.query_sequence) + self.assertEqual('XY', ''.join( + map(lambda x: chr(x + 33), alignment2.query_qualities))) + + ps.close()	Add an option to the `PaddedSAM.queries` method to have it also return the pysam.AlignedSegment	252de3e0a17525dde6a5f4167ea1e54a70ba91ee	[ "test/test_sam.py::TestPaddedSAM::testAlsoYieldAlignments" ]	[ "test/test_sam.py::TestPaddedSAM::testAllMMatch", "test/test_sam.py::TestPaddedSAM::testAllowDuplicateIds", "test/test_sam.py::TestPaddedSAM::testDropDuplicates", "test/test_sam.py::TestPaddedSAM::testDropSecondary", "test/test_sam.py::TestPaddedSAM::testDropSupplementary", "test/test_sam.py::TestPaddedSAM::testDuplicateIdDisambiguation", "test/test_sam.py::TestPaddedSAM::testHardClipLeft", "test/test_sam.py::TestPaddedSAM::testHardClipRight", "test/test_sam.py::TestPaddedSAM::testKF414679SoftClipLeft", "test/test_sam.py::TestPaddedSAM::testKeepQualityControlFailures", "test/test_sam.py::TestPaddedSAM::testMinLength", "test/test_sam.py::TestPaddedSAM::testMinLengthWithReferenceDeletion", "test/test_sam.py::TestPaddedSAM::testMixedMatch", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReference", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReferenceButNoMatches", "test/test_sam.py::TestPaddedSAM::testNotSecondaryAndNotSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testPrimaryAndSecondaryReferenceInsertion", "test/test_sam.py::TestPaddedSAM::testQueryHardClipAndSoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesRight", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesLeftEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesRightEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipRight", "test/test_sam.py::TestPaddedSAM::testRcNeeded", "test/test_sam.py::TestPaddedSAM::testRcSuffix", "test/test_sam.py::TestPaddedSAM::testReferenceDeletion", "test/test_sam.py::TestPaddedSAM::testReferenceDeletionAlternateChar", "test/test_sam.py::TestPaddedSAM::testReferenceInsertion", "test/test_sam.py::TestPaddedSAM::testReferenceSkip", "test/test_sam.py::TestPaddedSAM::testReferenceSkipAlternateChar", "test/test_sam.py::TestPaddedSAM::testReferencesToStr", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testUnequalReferenceLengths", "test/test_sam.py::TestPaddedSAM::testUnknownReferences" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2018-07-03 11:07:54+00:00	mit	868
acorg__dark-matter-631	diff --git a/CHANGELOG.md b/CHANGELOG.md index 2468b6e..d82fc9b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +## 3.0.38 October 5, 2018 + +Fixed [#630](https://github.com/acorg/dark-matter/issues/630) to deal with +non-hard-clipped queries that have a CIGAR string that indicates they have +been clipped. + ## 3.0.37 October 1, 2018 Add a `--titlesJSONFile` option to `noninteractive-alignment-panel.py`. diff --git a/dark/__init__.py b/dark/__init__.py index 0c505ca..7513e6e 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.37' +__version__ = '3.0.38' diff --git a/dark/sam.py b/dark/sam.py index eef7854..0167fdc 100644 --- a/dark/sam.py +++ b/dark/sam.py @@ -65,6 +65,63 @@ def samReferencesToStr(filenameOrSamfile, indent=0): return _references(sam) +def _hardClip(sequence, cigartuples): + """ + Hard clip (if necessary) a sequence. + + @param sequence: A C{str} nucleotide sequence. + @param cigartuples: An iterable of (operation, length) tuples, specifying + matching as per the SAM specification. + @return: A hard-clipped C{str} sequence if hard-clipping is indicated by + the CIGAR operations and has not already been performed (as indicated + by the lengths of the sequence and the sum of the CIGAR operation + lengths). + """ + hardClipCount = cigarLength = 0 + for (operation, length) in cigartuples: + hardClipCount += operation == CHARD_CLIP + cigarLength += length + + sequenceLength = len(sequence) + clipLeft = clipRight = 0 + + if hardClipCount == 0: + pass + elif hardClipCount == 1: + # Hard clip either at the start or the end. + if cigartuples[0][0] == CHARD_CLIP: + clipLeft = cigartuples[0][1] + if sequenceLength == cigarLength: + # The LHS hard clipping has not been done. + sequence = sequence[clipLeft:] + elif cigartuples[-1][0] == CHARD_CLIP: + clipRight = cigartuples[-1][1] + if sequenceLength == cigarLength: + # The RHS hard clipping has not been done. + sequence = sequence[:-clipRight] + else: + raise ValueError( + 'Invalid CIGAR tuples (%s) contains hard-clipping operation ' + 'that is neither at the start nor the end of the sequence.' % + (cigartuples,)) + elif hardClipCount == 2: + # Hard clip at both the start and end. + assert cigartuples[0][0] == cigartuples[-1][0] == CHARD_CLIP + clipLeft, clipRight = cigartuples[0][1], cigartuples[-1][1] + if sequenceLength == cigarLength: + # The hard clipping has not been done. + sequence = sequence[clipLeft:-clipRight] + else: + raise ValueError( + 'Invalid CIGAR tuples (%s) specifies hard-clipping %d times (2 ' + 'is the maximum).' % (cigartuples, hardClipCount)) + + assert len(sequence) + clipLeft + clipRight == cigarLength, ( + '%d + %d + %d != %d' % (len(sequence), clipLeft, clipRight, + cigarLength)) + return sequence + + class SAMFilter(object): """ Filter a SAM/BAM file. @@ -378,16 +435,16 @@ class PaddedSAM(object): 'Query line %d has an empty SEQ field, but no ' 'previous alignment is present.' % lineNumber) else: - query = lastQuery + query = _hardClip(lastQuery, alignment.cigartuples) else: raise InvalidSAM( 'Query line %d has an empty SEQ field, but the ' 'alignment is not marked as secondary or ' 'supplementary.' % lineNumber) - - # Remember the last query here (before we potentially modify it - # due to it being reverse complimented for the alignment). - lastQuery = query + else: + # Remember the last query here (before we potentially modify + # it due to it being reverse complimented for the alignment). + lastQuery = query if alignment.is_reverse: if rcNeeded: @@ -495,8 +552,13 @@ class PaddedSAM(object): if operation in _CONSUMES_REFERENCE: referenceIndex += length - # Sanity check that we consumed the entire query. - assert queryIndex == len(query) + if queryIndex != len(query): + # Oops, we did not consume the entire query. + raise ValueError( + 'Query %s not fully consumed when parsing CIGAR string. ' + 'Query %s (len %d), final query index %d, CIGAR: %r' % + (alignment.query_name, query, len(query), queryIndex, + alignment.cigartuples)) # We cannot test we consumed the entire reference. The CIGAR # string applies to (and exhausts) the query but is silent	acorg/dark-matter	845ae82628e8ca00f8a1a1abbe07b07c1ca26677	diff --git a/test/test_sam.py b/test/test_sam.py index 28c640b..35acba8 100644 --- a/test/test_sam.py +++ b/test/test_sam.py @@ -4,10 +4,12 @@ from tempfile import mkstemp from os import close, unlink, write from contextlib import contextmanager +from pysam import CHARD_CLIP, CMATCH + from dark.reads import Read, ReadFilter from dark.sam import ( PaddedSAM, SAMFilter, UnequalReferenceLengthError, UnknownReference, - InvalidSAM, samReferencesToStr) + InvalidSAM, samReferencesToStr, _hardClip) # These tests actually use the filesystem to read files. That's due to the API @@ -273,6 +275,32 @@ class TestPaddedSAM(TestCase): assertRaisesRegex(self, UnequalReferenceLengthError, error, PaddedSAM, SAMFilter(filename)) + def testQueryTooLong(self): + """ + If the query sequence is longer than the total of the lengths in the + CIGAR operations, a ValueError must be raised. + """ + # This test just returns. It used to be possible to reach the + # "Query ... not fully consumed when parsing CIGAR string." + # ValueError in sam.py, prior to the fix of + # https://github.com/acorg/dark-matter/issues/630 but it is not + # possible to get a CIGAR string that has a different total length + # from the sequence length through to our code in sam.py because + # pysam catches the error. I'm leaving this test here because it + # documents that the error checked for in sam.py cannot currently + # be reached and the test may become useful. For now it just returns. + return + data = '\n'.join([ + '@SQ SN:ref1 LN:90', + 'query1 0 ref1 1 60 4M * 0 0 TCTAGG ZZZZZZ', + ]).replace(' ', '\t') + + with dataFile(data) as filename: + ps = PaddedSAM(SAMFilter(filename)) + error = ('^Query TCTAGG not fully consumed when parsing CIGAR ' + 'string\\.') + assertRaisesRegex(self, ValueError, error, list, ps.queries()) + def testAllMMatch(self): """ A simple all-'M' match must result in the expected padded sequence. @@ -866,6 +894,33 @@ class TestPaddedSAM(TestCase): self.assertEqual('XY', ''.join( map(lambda x: chr(x + 33), read2.alignment.query_qualities))) + def testHardClippingInCIGARButQueryNotHardClipped(self): + """ + As documented in https://github.com/acorg/dark-matter/issues/630 we + have to deal correctly with a case in which the CIGAR string says a + query should be hard clipped but the query sequence in the SAM file + actually isn't. This can be due to a prior alignment with a soft clip, + in which case the full query sequence has to be given before the + secondary alignment with the hard clip. + """ + data = '\n'.join([ + '@SQ SN:Chimp-D00220 LN:8', + '@SQ SN:D-AM494716 LN:8', + 'query1 0 Chimp-D00220 1 0 3S5M * 0 0 TTTTGGTT 12345678', + 'query1 256 D-AM494716 1 0 3H5M * 0 0 * ', + ]).replace(' ', '\t') + + with dataFile(data) as filename: + ps = PaddedSAM(SAMFilter(filename)) + (read1, read2) = list(ps.queries(addAlignment=True)) + + self.assertEqual(Read('query1', 'TGGTT---'), read1) + self.assertEqual('TTTTGGTT', read1.alignment.query_sequence) + + self.assertEqual(Read('query1/1', 'TGGTT---'), read2) + # pysam uses None for the query sequence on a secondary alignment. + self.assertIs(None, read2.alignment.query_sequence) + class TestSamReferencesToStr(TestCase): """ @@ -897,3 +952,104 @@ class TestSamReferencesToStr(TestCase): with dataFile(data) as filename: self.assertEqual(' id1 (length 90)\n id2 (length 91)', samReferencesToStr(filename, indent=2)) + + +class TestHardClip(TestCase): + """ + Test the _hardClip function. + """ + def testCIGARLengthTooHigh(self): + """ + If the total length of the CIGAR operations exceeds the length of the + sequence, an AssertionError must be raised. + """ + self.assertRaises(AssertionError, _hardClip, 'CGT', ((CMATCH, 5),)) + + def testCIGARLengthTooLow(self): + """ + If the total length of the CIGAR operations is less than the length of + the sequence, an AssertionError must be raised. + """ + self.assertRaises(AssertionError, _hardClip, 'CGT', ((CMATCH, 2),)) + + def testHardClipInMiddle(self): + """ + If hard clipping is given as an operation not at the beginning or end + of the sequence, a ValueError must be raised. + """ + error = ('^Invalid CIGAR tuples . contains hard-clipping operation ' + 'that is neither at the start nor the end of the sequence\.$') + self.assertRaisesRegex( + ValueError, error, + _hardClip, 'CGT', ((CMATCH, 1), (CHARD_CLIP, 1), (CMATCH, 1),)) + + def testThreeHardClips(self): + """ + If hard clipping is specified more than twice, a ValueError must be + raised. + """ + error = ('^Invalid CIGAR tuples .* specifies hard-clipping 3 times ' + '\(2 is the maximum\).$') + self.assertRaisesRegex( + ValueError, error, + _hardClip, 'CGT', + ((CHARD_CLIP, 1), (CHARD_CLIP, 1), (CHARD_CLIP, 1),)) + + def testNoClip(self): + """ + If no hard clipping is indicated, the function must return the + original sequence. + """ + self.assertEqual('CGT', _hardClip('CGT', ((CMATCH, 3),))) + + def testClipLeft(self): + """ + If hard clipping on the left is indicated, and has not been done, + the function must return the expected sequence. + """ + self.assertEqual('CGT', + _hardClip('CAACGT', ((CHARD_CLIP, 3), (CMATCH, 3),))) + + def testClipRight(self): + """ + If hard clipping on the right is indicated, and has not been done, + the function must return the expected sequence. + """ + self.assertEqual('CA', + _hardClip('CAACGT', ((CMATCH, 2), (CHARD_CLIP, 4),))) + + def testClipBoth(self): + """ + If hard clipping on the left and right is indicated, and has not been + done, the function must return the expected sequence. + """ + self.assertEqual( + 'AA', + _hardClip('CAACGT', + ((CHARD_CLIP, 1), (CMATCH, 2), (CHARD_CLIP, 3),))) + + def testClipLeftAlreadyDone(self): + """ + If hard clipping on the left is indicated, and has already been done, + the function must return the expected sequence. + """ + self.assertEqual('CGT', + _hardClip('CGT', ((CHARD_CLIP, 3), (CMATCH, 3),))) + + def testClipRightAlreadyDone(self): + """ + If hard clipping on the right is indicated, and has already been done, + the function must return the expected sequence. + """ + self.assertEqual('CA', + _hardClip('CA', ((CMATCH, 2), (CHARD_CLIP, 4),))) + + def testClipBothAlreadyDone(self): + """ + If hard clipping on the left and right is indicated, and has already + been done, the function must return the expected sequence. + """ + self.assertEqual( + 'AA', + _hardClip('AA', + ((CHARD_CLIP, 1), (CMATCH, 2), (CHARD_CLIP, 3),)))	Change SAM filtering to allow for CIGAR strings that indicate hard clipping but that have sequences that are not clipped It can happen that an aligner (`bwa mem -a` does this) can generate SAM lines like these two: ``` K00234:90:HTWVHBBXX:6:1101:1844:10493 0 Chimp-D00220 364 0 3S78M * 0 0 TTTTGGTTATCGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGCCTCATCTTATTGTTGGT AAFFFJAJJJJJFJJJ7JJJJFJFJJFJFJAFJJJJAAF<FFFAF<JJ-FF<JF-AF7F<AJF--<-F7-AA-7JFJJFJ< NM:i:1 MD:Z:69C8 AS:i:73 XS:i:73 K00234:90:HTWVHBBXX:6:1101:1844:10493 256 D-AM494716 364 0 3H78M * 0 0 * * NM:i:1 MD:Z:69C8 AS:i:73 ``` those are actually just 2 lines in the SAM file, giving alignments for the same read. The issue here is that the first alignment has a CIGAR string of `3S78M` (3 soft clipped nts, 78 matches) and because it's a soft clip the bases are still in the query string. On the next line we have `` and `` for the query and quality (because this is a secondary match (flag = 256)) and a CIGAR string of `3H78M` (3 hard clipped, 78 match). Normally with hard clipping the bases are removed from the sequence, but in this case because the query is first given with a soft clip the bases are retained. So code that assumes hard -clipped bases will be removed will break. You might think `bwa mem -a -H` would cause hard clipping to always be done (perhaps by repeating the (clipped) query sequence in secondary matches) but that's not what happens - bwa reverts to the non- `-a` option behaviour. So our code in `dark/sam.py` will need to be smarter. It should figure out in advance if the query has actually been hard clipped and use that to decide whether a hard clip indicator in the CIGAR string should consume query bases or not.	845ae82628e8ca00f8a1a1abbe07b07c1ca26677	[ "test/test_sam.py::TestSAMFilter::testAlignmentCount", "test/test_sam.py::TestSAMFilter::testDropDuplicates", "test/test_sam.py::TestSAMFilter::testDropSecondary", "test/test_sam.py::TestSAMFilter::testDropSupplementary", "test/test_sam.py::TestSAMFilter::testKeepQualityControlFailures", "test/test_sam.py::TestSAMFilter::testMaxScore", "test/test_sam.py::TestSAMFilter::testMaxScoreNoScores", "test/test_sam.py::TestSAMFilter::testMinAndMaxScore", "test/test_sam.py::TestSAMFilter::testMinLength", "test/test_sam.py::TestSAMFilter::testMinScore", "test/test_sam.py::TestSAMFilter::testMinScoreNoScores", "test/test_sam.py::TestSAMFilter::testStoreQueryIds", "test/test_sam.py::TestSAMFilter::testUnknownReferences", "test/test_sam.py::TestPaddedSAM::testAllMMatch", "test/test_sam.py::TestPaddedSAM::testAllowDuplicateIds", "test/test_sam.py::TestPaddedSAM::testAlsoYieldAlignments", "test/test_sam.py::TestPaddedSAM::testDropDuplicates", "test/test_sam.py::TestPaddedSAM::testDropSecondary", "test/test_sam.py::TestPaddedSAM::testDropSupplementary", "test/test_sam.py::TestPaddedSAM::testDuplicateIdDisambiguation", "test/test_sam.py::TestPaddedSAM::testHardClipLeft", "test/test_sam.py::TestPaddedSAM::testHardClipRight", "test/test_sam.py::TestPaddedSAM::testHardClippingInCIGARButQueryNotHardClipped", "test/test_sam.py::TestPaddedSAM::testKF414679SoftClipLeft", "test/test_sam.py::TestPaddedSAM::testKeepQualityControlFailures", "test/test_sam.py::TestPaddedSAM::testMinLength", "test/test_sam.py::TestPaddedSAM::testMixedMatch", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReference", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReferenceButNoMatches", "test/test_sam.py::TestPaddedSAM::testNotSecondaryAndNotSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testPrimaryAndSecondaryReferenceInsertion", "test/test_sam.py::TestPaddedSAM::testQueryHardClipAndSoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesRight", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesLeftEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesRightEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipRight", "test/test_sam.py::TestPaddedSAM::testQueryTooLong", "test/test_sam.py::TestPaddedSAM::testRcNeeded", "test/test_sam.py::TestPaddedSAM::testRcSuffix", "test/test_sam.py::TestPaddedSAM::testReferenceDeletion", "test/test_sam.py::TestPaddedSAM::testReferenceDeletionAlternateChar", "test/test_sam.py::TestPaddedSAM::testReferenceInsertion", "test/test_sam.py::TestPaddedSAM::testReferenceSkip", "test/test_sam.py::TestPaddedSAM::testReferenceSkipAlternateChar", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testUnequalReferenceLengths", "test/test_sam.py::TestSamReferencesToStr::testIndent", "test/test_sam.py::TestSamReferencesToStr::testSimple", "test/test_sam.py::TestHardClip::testCIGARLengthTooHigh", "test/test_sam.py::TestHardClip::testCIGARLengthTooLow", "test/test_sam.py::TestHardClip::testClipBoth", "test/test_sam.py::TestHardClip::testClipBothAlreadyDone", "test/test_sam.py::TestHardClip::testClipLeft", "test/test_sam.py::TestHardClip::testClipLeftAlreadyDone", "test/test_sam.py::TestHardClip::testClipRight", "test/test_sam.py::TestHardClip::testClipRightAlreadyDone", "test/test_sam.py::TestHardClip::testHardClipInMiddle", "test/test_sam.py::TestHardClip::testNoClip", "test/test_sam.py::TestHardClip::testThreeHardClips" ]	[]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2018-10-05 08:26:07+00:00	mit	869
acorg__dark-matter-637	diff --git a/CHANGELOG.md b/CHANGELOG.md index a68180a..77e9eb6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +## 3.0.44 Nov 1, 2018 + +Fix [636](https://github.com/acorg/dark-matter/issues/636) in which SAM file +parsing threw an exception when an unmapped sequence with no CIGAR string +occurred in a SAM file (this can happen when running `bowtie2 --all`). + ## 3.0.43 Nov 1, 2018 Fixed thinko in 3.0.42. diff --git a/dark/__init__.py b/dark/__init__.py index f10e319..e8e1c5a 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.43' +__version__ = '3.0.44' diff --git a/dark/sam.py b/dark/sam.py index a4f2c1a..f6052ca 100644 --- a/dark/sam.py +++ b/dark/sam.py @@ -332,14 +332,24 @@ class SAMFilter(object): # the previous sequence should be used. This is best # practice according to section 2.5.2 of # https://samtools.github.io/hts-specs/SAMv1.pdf So we use - # the last alignment if we get None as a query sequence. + # the last alignment query and quality strings if we get + # None as a query sequence. if alignment.query_sequence is None: if lastAlignment is None: raise InvalidSAM( 'pysam produced an alignment (number %d) with no ' 'query sequence without previously giving an ' 'alignment with a sequence.' % count) - # Use the previous query sequence and quality. + # Use the previous query sequence and quality. I'm not + # making the call to _hardClip dependent on + # alignment.cigartuples (as in the else clause below) + # because I don't think it's possible for + # alignment.cigartuples to be None in this case. If we + # have a second match on a query, then it must be + # aligned to something (i.e., it cannot be unmapped + # with no CIGAR string). The assertion will tell us if + # this is ever not the case. + assert alignment.cigartuples (alignment.query_sequence, alignment.query_qualities, _) = _hardClip( lastAlignment.query_sequence, @@ -347,11 +357,12 @@ class SAMFilter(object): alignment.cigartuples) else: lastAlignment = alignment - (alignment.query_sequence, - alignment.query_qualities, _) = _hardClip( - alignment.query_sequence, - alignment.query_qualities, - alignment.cigartuples) + if alignment.cigartuples: + (alignment.query_sequence, + alignment.query_qualities, _) = _hardClip( + alignment.query_sequence, + alignment.query_qualities, + alignment.cigartuples) if ((filterRead is None or filterRead(Read(alignment.query_name,	acorg/dark-matter	7fc47a737e687f6b0f0bfe7414c7f8947bb16bea	diff --git a/test/test_sam.py b/test/test_sam.py index 524f8a2..ab4bf4c 100644 --- a/test/test_sam.py +++ b/test/test_sam.py @@ -247,6 +247,24 @@ class TestSAMFilter(TestCase): self.assertEqual('query1', alignment1.query_name) self.assertEqual('query4', alignment2.query_name) + def testCloseButNoCIGAR(self): + """ + An unmapped query with no CIGAR string must be passed through + unchanged if dropUnmapped is not specified. + """ + data = '\n'.join([ + '@SQ SN:ref LN:10', + 'query1 4 * 0 0 * * 0 0 TCTAGG ZZZZZZ', + ]).replace(' ', '\t') + + with dataFile(data) as filename: + sf = SAMFilter(filename) + (alignment,) = list(sf.alignments()) + self.assertEqual('query1', alignment.query_name) + self.assertEqual('TCTAGG', alignment.query_sequence) + self.assertEqual('ZZZZZZ', ''.join( + map(lambda x: chr(x + 33), alignment.query_qualities))) + class TestPaddedSAM(TestCase): """	SAM parsing throws an exception Fix this: ```sh $ filter-sam.py --referenceId Sorsum_high_freq --dropSecond --dropSupp --samfile sorsum-assortedGenotypesDieter-bowtie2.sam >/dev/null Traceback (most recent call last): File "/Users/terry/.virtualenvs/lm36/bin/filter-sam.py", line 90, in <module> for kept, alignment in enumerate(samFilter.alignments(), start=1): File "/Users/terry/.virtualenvs/lm36/lib/python3.6/site-packages/dark/sam.py", line 354, in alignments alignment.cigartuples) File "/Users/terry/.virtualenvs/lm36/lib/python3.6/site-packages/dark/sam.py", line 88, in _hardClip for (operation, length) in cigartuples: TypeError: 'NoneType' object is not iterable ```	7fc47a737e687f6b0f0bfe7414c7f8947bb16bea	[ "test/test_sam.py::TestSAMFilter::testCloseButNoCIGAR" ]	[ "test/test_sam.py::TestSAMFilter::testAlignmentCount", "test/test_sam.py::TestSAMFilter::testDropDuplicates", "test/test_sam.py::TestSAMFilter::testDropSecondary", "test/test_sam.py::TestSAMFilter::testDropSupplementary", "test/test_sam.py::TestSAMFilter::testKeepQualityControlFailures", "test/test_sam.py::TestSAMFilter::testMaxScore", "test/test_sam.py::TestSAMFilter::testMaxScoreNoScores", "test/test_sam.py::TestSAMFilter::testMinAndMaxScore", "test/test_sam.py::TestSAMFilter::testMinLength", "test/test_sam.py::TestSAMFilter::testMinScore", "test/test_sam.py::TestSAMFilter::testMinScoreNoScores", "test/test_sam.py::TestSAMFilter::testStoreQueryIds", "test/test_sam.py::TestSAMFilter::testUnknownReferences", "test/test_sam.py::TestPaddedSAM::testAllMMatch", "test/test_sam.py::TestPaddedSAM::testAllowDuplicateIds", "test/test_sam.py::TestPaddedSAM::testAlsoYieldAlignments", "test/test_sam.py::TestPaddedSAM::testDropDuplicates", "test/test_sam.py::TestPaddedSAM::testDropSecondary", "test/test_sam.py::TestPaddedSAM::testDropSupplementary", "test/test_sam.py::TestPaddedSAM::testDuplicateIdDisambiguation", "test/test_sam.py::TestPaddedSAM::testHardClipLeft", "test/test_sam.py::TestPaddedSAM::testHardClipRight", "test/test_sam.py::TestPaddedSAM::testHardClippingInCIGARButQueryNotHardClipped", "test/test_sam.py::TestPaddedSAM::testKF414679SoftClipLeft", "test/test_sam.py::TestPaddedSAM::testKeepQualityControlFailures", "test/test_sam.py::TestPaddedSAM::testMinLength", "test/test_sam.py::TestPaddedSAM::testMixedMatch", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReference", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReferenceButNoMatches", "test/test_sam.py::TestPaddedSAM::testNotSecondaryAndNotSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testPrimaryAndSecondaryReferenceInsertion", "test/test_sam.py::TestPaddedSAM::testQueryHardClipAndSoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesRight", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesLeftEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesRightEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipRight", "test/test_sam.py::TestPaddedSAM::testQueryTooLong", "test/test_sam.py::TestPaddedSAM::testRcNeeded", "test/test_sam.py::TestPaddedSAM::testRcSuffix", "test/test_sam.py::TestPaddedSAM::testReferenceDeletion", "test/test_sam.py::TestPaddedSAM::testReferenceDeletionAlternateChars", "test/test_sam.py::TestPaddedSAM::testReferenceInsertion", "test/test_sam.py::TestPaddedSAM::testReferenceSkip", "test/test_sam.py::TestPaddedSAM::testReferenceSkipAlternateChars", "test/test_sam.py::TestPaddedSAM::testSecondaryAlignmentHasQuery", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryAlignmentHasQuery", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testUnequalReferenceLengths", "test/test_sam.py::TestSamReferencesToStr::testIndent", "test/test_sam.py::TestSamReferencesToStr::testSimple", "test/test_sam.py::TestHardClip::testClipBoth", "test/test_sam.py::TestHardClip::testClipBothAlreadyDone", "test/test_sam.py::TestHardClip::testClipLeft", "test/test_sam.py::TestHardClip::testClipLeftAlreadyDone", "test/test_sam.py::TestHardClip::testClipRight", "test/test_sam.py::TestHardClip::testClipRightAlreadyDone", "test/test_sam.py::TestHardClip::testHardClipInMiddle", "test/test_sam.py::TestHardClip::testNoClip", "test/test_sam.py::TestHardClip::testThreeHardClips" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2018-11-01 19:19:21+00:00	mit	870
acorg__dark-matter-647	diff --git a/CHANGELOG.md b/CHANGELOG.md index 2ce0779..3931a9b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,8 @@ +## 3.0.50 Nov 23, 2018 + +Added `bin/convert-diamond-to-sam.py` script to convert DIAMOND output +format 6 to SAM. + ## 3.0.49 Nov 22, 2018 Added `btop2cigar` to `dark.btop` to convert BTOP strings to CIGAR strings. diff --git a/bin/convert-diamond-to-sam.py b/bin/convert-diamond-to-sam.py new file mode 100755 index 0000000..38e3365 --- /dev/null +++ b/bin/convert-diamond-to-sam.py @@ -0,0 +1,145 @@ +#!/usr/bin/env python + +# See https://samtools.github.io/hts-specs/SAMv1.pdf for the SAM file +# format specification. + +from __future__ import print_function, division + +import sys +import argparse +from os.path import basename +from tempfile import TemporaryFile +from functools import partial + +from dark import __version__ as VERSION +from dark.btop import btop2cigar +from dark.diamond.conversion import diamondTabularFormatToDicts +from dark.reads import DNARead + +FIELDS = 'bitscore btop qframe qqual qseq qseqid slen sstart stitle' + +parser = argparse.ArgumentParser( + formatter_class=argparse.ArgumentDefaultsHelpFormatter, + description=('Convert DIAMOND tabular format to SAM. The DIAMOND ' + 'invocation must include --outfmt 6 %s' % FIELDS)) + +parser.add_argument( + '--printFields', default=False, action='store_true', + help=('Print the field names in the order that they must be given to ' + 'diamond --outfmt 6 to produce correct input for this script, ' + 'then exit.')) + +parser.add_argument( + '--mappingQuality', type=int, default=255, + help=('The mapping quality to use for MAPQ (field 5). The default (255) ' + 'indicates that mapping quality information is not available.')) + +parser.add_argument( + '--ram', action='store_true', default=False, + help=('Do not use a temporary file to hold the non-header SAM output. ' + 'This will run faster but use more memory since all non-header SAM ' + 'output will be stored in RAM and only written out when the full ' + 'header can be determined.')) + +parser.add_argument( + '--keepDescriptions', action='store_true', default=False, + help=('Do not discard text after the first space in query or subject ' + 'sequence ids. Note that. Note that this violates the SAM ' + 'specification, but since SAM files are TAB-separated there ' + 'is probably only a small chance this will cause any problems ' + 'downstream.')) + +args = parser.parse_args() + +if args.printFields: + print(FIELDS) + sys.exit(0) + +idOnly = not args.keepDescriptions +mappingQuality = args.mappingQuality +ram = args.ram + +if 0 > mappingQuality > 255: + raise ValueError('Mapping quality must be between 0 and 255 (inclusive)') + +referenceLengths = {} + +if ram: + nonHeaderLines = [] + emit = nonHeaderLines.append +else: + tf = TemporaryFile(mode='w+t', encoding='utf-8') + emit = partial(print, file=tf) + +for match in diamondTabularFormatToDicts(sys.stdin, FIELDS.split()): + qseqid = match['qseqid'].split()[0] if idOnly else match['qseqid'] + stitle = match['stitle'].split()[0] if idOnly else match['stitle'] + + referenceLengths[stitle] = match['slen'] + + # If the query frame is less than zero, the match was with a reverse + # complemented translation of the query. Put the reverse compliment + # into the SAM output, which seems to be standard / accepted practice + # based on my web searches. See e.g., https://www.biostars.org/p/131891/ + # for what Bowtie2 does and for some comments on this issue for SAM/BAM + # files in general. + if match['qframe'] > 0: + flag = 0 + qseq = match['qseq'] + qqual = match['qqual'] or '' + else: + flag = 16 + qseq = DNARead('id', match['qseq']).reverseComplement().sequence + qqual = match['qqual'][::-1] if match['qqual'] else '' + + emit('\t'.join(map(str, [ + # 1. QNAME + qseqid, + # 2. FLAG + flag, + # 3. RNAME + stitle, + # 4. POS + match['sstart'], + # 5. MAPQ + mappingQuality, + # 6. CIGAR + btop2cigar(match['btop']), + # 7. RNEXT + '*', + # 8. PNEXT + 0, + # 9. TLEN + 0, + # 10. SEQ + qseq, + # 11. QUAL + qqual, + # 12. Alignment score + 'AS:i:%d' % int(match['bitscore'])]))) + + +progName = basename(sys.argv[0]) + +# Print SAM headers. +print('\n'.join( + [ + '@PG\tID:DIAMOND\tPN:DIAMOND', + '@PG\tID:%s\tPN:%s (version %s)\tCL:%s %s\tPP:DIAMOND' % + (progName, progName, VERSION, progName, ' '.join(sys.argv[1:])), + '@CO\t%s is from the dark-matter package ' + '(https://github.com/acorg/dark-matter/)' % progName, + ] + + [ + '@SQ\tSN:%s\tLN:%d' % (name, referenceLengths[name]) + for name in sorted(referenceLengths) + ])) + +# Print non-header lines. +if ram: + print('\n'.join(nonHeaderLines)) +else: + tf.seek(0) + for line in tf: + print(line, end='') + tf.close() diff --git a/dark/__init__.py b/dark/__init__.py index e37701e..a768585 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.49' +__version__ = '3.0.50' diff --git a/dark/diamond/conversion.py b/dark/diamond/conversion.py index 29c2694..42c2a8d 100644 --- a/dark/diamond/conversion.py +++ b/dark/diamond/conversion.py @@ -4,6 +4,7 @@ import six import bz2 from json import dumps, loads from operator import itemgetter +from collections import Counter from Bio.File import as_handle @@ -13,6 +14,85 @@ from dark.alignments import Alignment, ReadAlignments from dark.diamond.hsp import normalizeHSP +# The keys in the following are DIAMOND format 6 field names. The values +# are one-argument functions that take a string and return an appropriately +# converted field value. +# +# The following fields are taken from the DIAMOND manual v0.9.22 2018-05-11. +# Fields whose name doesn't appear here will be left as strings. +DIAMOND_FIELD_CONVERTER = { + 'bitscore': float, + 'evalue': float, + 'frame': int, + 'gapopen': int, + 'gaps': int, + 'identicalCount': lambda nident: None if nident is None else int(nident), + 'length': int, + 'mismatch': int, + 'nident': int, + 'pident': float, + 'positive': int, + 'positiveCount': lambda pos: None if pos is None else int(pos), + 'ppos': float, + 'qcovhsp': float, + 'qend': int, + 'qframe': int, + 'qlen': int, + 'qstart': int, + 'score': float, + 'send': int, + 'slen': int, + 'sstart': int, +} + + +def diamondTabularFormatToDicts(filename, fieldNames): + """ + Read DIAMOND tabular (--outfmt 6) output and convert lines to dictionaries. + + @param filename: Either a C{str} file name or an open file pointer. + @param fieldNames: A C{list} or C{tuple} of C{str} DIAMOND field names. + Run 'diamond -help' to see the full list. + @raise ValueError: If a line of C{filename} does not have the expected + number of TAB-separated fields (i.e., len(fieldNames)). Or if + C{fieldNames} is empty or contains duplicates. + @return: A generator that yields C{dict}s with keys that are the DIAMOND + field names and values as converted by DIAMOND_FIELD_CONVERTER. + """ + nFields = len(fieldNames) + if not nFields: + raise ValueError('fieldNames cannot be empty.') + + c = Counter(fieldNames) + if c.most_common(1)[0][1] > 1: + raise ValueError( + 'fieldNames contains duplicated names: %s.' % + (', '.join(sorted(x[0] for x in c.most_common() if x[1] > 1)))) + + def identity(x): + return x + + convertFunc = DIAMOND_FIELD_CONVERTER.get + + with as_handle(filename) as fp: + for count, line in enumerate(fp, start=1): + result = {} + line = line[:-1] + values = line.split('\t') + if len(values) != nFields: + raise ValueError( + 'Line %d of %s had %d field values (expected %d). ' + 'Line was %r.' % + (count, + (filename if isinstance(filename, six.string_types) + else 'input'), + len(values), nFields, line)) + for fieldName, value in zip(fieldNames, values): + value = convertFunc(fieldName, identity)(value) + result[fieldName] = value + yield result + + class DiamondTabularFormatReader(object): """ Provide a method that yields parsed tabular records from a file. Store and diff --git a/dark/reads.py b/dark/reads.py index b2a4bcc..18171d0 100644 --- a/dark/reads.py +++ b/dark/reads.py @@ -766,7 +766,7 @@ class ReadFilter(object): only return those that have length <= 100, so your result may have less than 20 reads. The former version extracts reads of the desired length and then takes 20 reads at random from that set, so - you'll always get 20 raeds in your result, assuming there are at + you'll always get 20 reads in your result, assuming there are at least that many reads satisfying the length filter. @param trueLength: The C{int} number of reads in this C{Reads} instance. Under normal circumstances it will not be necessary to pass this diff --git a/setup.py b/setup.py index fef9e17..bc089e7 100644 --- a/setup.py +++ b/setup.py @@ -35,6 +35,7 @@ scripts = [ 'bin/compare-sequences.py', 'bin/convert-blast-xml-to-json.py', 'bin/convert-diamond-to-json.py', + 'bin/convert-diamond-to-sam.py', 'bin/convert-sam-to-fastq.sh', 'bin/dark-matter-version.py', 'bin/dna-to-aa.py',	acorg/dark-matter	b36a743b85c8a5b2b8b6d21d337deb70cff193d5	diff --git a/test/diamond/test_conversion.py b/test/diamond/test_conversion.py index 9f80670..fbc6e3f 100644 --- a/test/diamond/test_conversion.py +++ b/test/diamond/test_conversion.py @@ -3,6 +3,7 @@ from unittest import TestCase from io import BytesIO, StringIO import bz2file from bz2 import compress +from six import assertRaisesRegex try: from unittest.mock import patch @@ -13,8 +14,8 @@ from ..mocking import mockOpen from json import dumps -from dark.diamond.conversion import (JSONRecordsReader, - DiamondTabularFormatReader) +from dark.diamond.conversion import ( + JSONRecordsReader, DiamondTabularFormatReader, diamondTabularFormatToDicts) from dark.reads import Reads, AARead @@ -1137,3 +1138,113 @@ class TestJSONRecordsReader(TestCase): reader = JSONRecordsReader('file.json') alignment = list(reader.readAlignments(reads))[0] self.assertEqual('id1 1', alignment.read.id) + + +class TestDiamondTabularFormatToDicts(TestCase): + """ + Tests for the diamondTabularFormatToDicts function. + """ + + def testEmptyFieldNameList(self): + """ + If an empty field name list is passed, the function must raise a + ValueError. + """ + error = '^fieldNames cannot be empty\\.$' + assertRaisesRegex(self, ValueError, error, list, + diamondTabularFormatToDicts(None, [])) + + def testDuplicatesInFieldNameList(self): + """ + If a field name list that contains duplicates is passed, the function + must raise a ValueError. + """ + error = '^fieldNames contains duplicated names: a, b\\.$' + assertRaisesRegex( + self, ValueError, error, list, + diamondTabularFormatToDicts(None, ['a', 'b', 'a', 'c', 'b'])) + + def testTooFewFields(self): + """ + If an input line does not have enough fields, a ValueError must be + raised. + """ + data = StringIO('a\tb\n') + error = (r"^Line 1 of input had 2 field values \(expected 3\)\. " + r"Line was 'a\\tb'\.") + assertRaisesRegex( + self, ValueError, error, list, + diamondTabularFormatToDicts(data, ['a', 'b', 'c'])) + + def testTooManyFields(self): + """ + If an input line has too many fields, a ValueError must be raised. + """ + data = StringIO('a\tb\tc\n') + error = (r"^Line 1 of input had 3 field values \(expected 2\)\. " + r"Line was 'a\\tb\\tc'\.") + assertRaisesRegex( + self, ValueError, error, list, + diamondTabularFormatToDicts(data, ['a', 'b'])) + + def testUnknownField(self): + """ + An unknown field name must result in a returned field name and value + that are identical to those in the function call and its input string. + """ + data = StringIO('3.5\n') + (result,) = list(diamondTabularFormatToDicts(data, ['__blah__'])) + self.assertEqual({'__blah__': '3.5'}, result) + + def testConversions(self): + """ + The fields in input lines must be recognized and converted to their + correct types. + """ + fields = [ + 'bitscore', + 'evalue', + 'frame', + 'identicalCount', + 'positiveCount', + 'qstart', + 'qend', + 'sstart', + 'send', + 'qseq', + ] + data = StringIO( + ('3.5 1.7 1 7 4 10 12 1 2 ACGT\n' + '3.6 1.8 2 8 5 11 13 2 3 TGCA').replace(' ', '\t') + '\n' + ) + (result1, result2) = list(diamondTabularFormatToDicts(data, fields)) + + self.assertEqual( + { + 'bitscore': 3.5, + 'evalue': 1.7, + 'frame': 1, + 'identicalCount': 7, + 'positiveCount': 4, + 'qstart': 10, + 'qend': 12, + 'sstart': 1, + 'send': 2, + 'qseq': 'ACGT', + }, + result1) + + self.assertEqual( + { + 'bitscore': 3.6, + 'evalue': 1.8, + 'frame': 2, + 'identicalCount': 8, + 'positiveCount': 5, + 'qstart': 11, + 'qend': 13, + 'sstart': 2, + 'send': 3, + 'qseq': 'TGCA', + }, + result2)	Add a script to convert DIAMOND output to SAM	b36a743b85c8a5b2b8b6d21d337deb70cff193d5	[ "test/diamond/test_conversion.py::TestDiamondTabularFormatReader::testDiamondInput", "test/diamond/test_conversion.py::TestDiamondTabularFormatReader::testDiamondInputWithoutNidentOrPositives", "test/diamond/test_conversion.py::TestDiamondTabularFormatReader::testDiamondParams", "test/diamond/test_conversion.py::TestDiamondTabularFormatReader::testSaveAsJSON", "test/diamond/test_conversion.py::TestDiamondTabularFormatReader::testSaveAsJSONBzip2", "test/diamond/test_conversion.py::TestDiamondTabularFormatReader::testSpacesMustBePreserved", "test/diamond/test_conversion.py::TestJSONRecordsReader::testCorrectNumberOfAlignments", "test/diamond/test_conversion.py::TestJSONRecordsReader::testCorrectNumberOfAlignmentsMatchMissingEnd", "test/diamond/test_conversion.py::TestJSONRecordsReader::testCorrectNumberOfAlignmentsMatchMissingMiddle", "test/diamond/test_conversion.py::TestJSONRecordsReader::testCorrectNumberOfAlignmentsMatchMissingStart", "test/diamond/test_conversion.py::TestJSONRecordsReader::testCorrectNumberOfAlignmentsTwoMatchesMissingEnd", "test/diamond/test_conversion.py::TestJSONRecordsReader::testSpaceInReadIdNotInJSONRecord", "test/diamond/test_conversion.py::TestJSONRecordsReader::testSpacesMustBePreserved", "test/diamond/test_conversion.py::TestDiamondTabularFormatToDicts::testConversions", "test/diamond/test_conversion.py::TestDiamondTabularFormatToDicts::testDuplicatesInFieldNameList", "test/diamond/test_conversion.py::TestDiamondTabularFormatToDicts::testEmptyFieldNameList", "test/diamond/test_conversion.py::TestDiamondTabularFormatToDicts::testTooFewFields", "test/diamond/test_conversion.py::TestDiamondTabularFormatToDicts::testTooManyFields", "test/diamond/test_conversion.py::TestDiamondTabularFormatToDicts::testUnknownField" ]	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_added_files", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2018-11-23 14:15:52+00:00	mit	871
acorg__dark-matter-649	diff --git a/CHANGELOG.md b/CHANGELOG.md index 271f053..588c254 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,7 @@ +## 3.0.52 Nov 23, 2018 + +Added hard-clipping to CIGAR in SAM created by `convert-diamond-to-sam.py`. + ## 3.0.51 Nov 23, 2018 Use `from six import StringIO` to avoid a PY2/3 incompatibility. diff --git a/bin/convert-diamond-to-sam.py b/bin/convert-diamond-to-sam.py index 38e3365..0b3484f 100755 --- a/bin/convert-diamond-to-sam.py +++ b/bin/convert-diamond-to-sam.py @@ -16,7 +16,8 @@ from dark.btop import btop2cigar from dark.diamond.conversion import diamondTabularFormatToDicts from dark.reads import DNARead -FIELDS = 'bitscore btop qframe qqual qseq qseqid slen sstart stitle' +FIELDS = ('bitscore btop qframe qend qqual qlen qseq qseqid qstart slen ' + 'sstart stitle') parser = argparse.ArgumentParser( formatter_class=argparse.ArgumentDefaultsHelpFormatter, @@ -92,6 +93,21 @@ for match in diamondTabularFormatToDicts(sys.stdin, FIELDS.split()): qseq = DNARead('id', match['qseq']).reverseComplement().sequence qqual = match['qqual'][::-1] if match['qqual'] else '' + # Make a CIGAR string, including hard-clipped bases at the start and + # end of the query (DIAMOND outputs a hard-clipped query sequence). + startClipCount = match['qstart'] - 1 + endClipCount = match['qlen'] - match['qend'] + + assert startClipCount >= 0 + assert endClipCount >= 0, ( + 'Query sequence %s has length %d but the qend value is %d' % + (qseq, len(match['qseq']), match['qend'])) + + cigar = ( + ('%dH' % startClipCount if startClipCount else '') + + btop2cigar(match['btop'], concise=False, aa=True) + + ('%dH' % endClipCount if endClipCount else '')) + emit('\t'.join(map(str, [ # 1. QNAME qseqid, @@ -104,7 +120,7 @@ for match in diamondTabularFormatToDicts(sys.stdin, FIELDS.split()): # 5. MAPQ mappingQuality, # 6. CIGAR - btop2cigar(match['btop']), + cigar, # 7. RNEXT '', # 8. PNEXT diff --git a/dark/__init__.py b/dark/__init__.py index 3e72b1a..147b204 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.51' +__version__ = '3.0.52' diff --git a/dark/btop.py b/dark/btop.py index 9855734..aa338da 100644 --- a/dark/btop.py +++ b/dark/btop.py @@ -73,24 +73,34 @@ def countGaps(btopString): return (queryGaps, subjectGaps) -def btop2cigar(btopString, concise=False): +def btop2cigar(btopString, concise=False, aa=False): """ Convert a BTOP string to a CIGAR string. @param btopString: A C{str} BTOP sequence. @param concise: If C{True}, use 'M' for matches and mismatches instead of the more specific 'X' and '='. - - @raise ValueError: If L{parseBtop} finds an error in C{btopString}. + @param aa: If C{True}, C{btopString} will be interpreted as though it + refers to amino acids (as in the BTOP string produced by DIAMOND). + In that case, it is not possible to use the 'precise' CIGAR characters + because amino acids have multiple codons so we cannot know whether + an amino acid match is due to an exact nucleotide matches or not. + Also, the numbers in the BTOP string will be multiplied by 3 since + they refer to a number of amino acids matching. + @raise ValueError: If L{parseBtop} finds an error in C{btopString} or + if C{aa} and C{concise} are both C{True}. @return: A C{str} CIGAR string. """ + if aa and concise: + raise ValueError('aa and concise cannot both be True') + result = [] thisLength = thisOperation = currentLength = currentOperation = None for item in parseBtop(btopString): if isinstance(item, int): thisLength = item - thisOperation = CMATCH if concise else CEQUAL + thisOperation = CEQUAL if concise else CMATCH else: thisLength = 1 query, reference = item @@ -108,13 +118,16 @@ def btop2cigar(btopString, concise=False): else: # A substitution was needed. assert query != reference - thisOperation = CMATCH if concise else CDIFF + thisOperation = CDIFF if concise else CMATCH if thisOperation == currentOperation: currentLength += thisLength else: if currentOperation: - result.append('%d%s' % (currentLength, currentOperation)) + result.append( + '%d%s' % + ((3 * currentLength) if aa else currentLength, + currentOperation)) currentLength, currentOperation = thisLength, thisOperation # We reached the end of the BTOP string. If there was an operation @@ -122,6 +135,8 @@ def btop2cigar(btopString, concise=False): # case where btopString was empty. assert currentOperation or btopString == '' if currentOperation: - result.append('%d%s' % (currentLength, currentOperation)) + result.append( + '%d%s' % + ((3 * currentLength) if aa else currentLength, currentOperation)) return ''.join(result)	acorg/dark-matter	3d48d201d41d8cabaa1f31d5dd7987e882a68af3	diff --git a/test/test_btop.py b/test/test_btop.py index 9f1f22a..e019563 100644 --- a/test/test_btop.py +++ b/test/test_btop.py @@ -164,15 +164,15 @@ class TestCountGaps(TestCase): self.assertEqual((3, 2), countGaps('-GG-34-T-T39F-')) -class TestBtop2CigarConcise(TestCase): +class TestBtop2CigarPrecise(TestCase): """ - Tests for the btop2cigar function when concise is True. + Tests for the btop2cigar function when concise is False. """ def testEmpty(self): """ An empty BTOP string must result in an empty CIGAR string. """ - self.assertEqual('', btop2cigar('', concise=True)) + self.assertEqual('', btop2cigar('', concise=False)) def testMixedMatch(self): """ @@ -180,7 +180,7 @@ class TestBtop2CigarConcise(TestCase): CIGAR sense where M could be identical characters or not), the CIGAR string must be all Ms. """ - self.assertEqual('7M', btop2cigar('2GC3AT', concise=True)) + self.assertEqual('7M', btop2cigar('2GC3AT', concise=False)) def testRefenceInsertion(self): """ @@ -188,7 +188,7 @@ class TestBtop2CigarConcise(TestCase): subject (reference) does not, the CIGAR string must indicate an insertion to the reference. """ - self.assertEqual('1I', btop2cigar('A-', concise=True)) + self.assertEqual('1I', btop2cigar('A-', concise=False)) def testQueryInsertion(self): """ @@ -196,7 +196,7 @@ class TestBtop2CigarConcise(TestCase): but the query does not, the CIGAR string must indicate an deletion in the reference. """ - self.assertEqual('1D', btop2cigar('-A', concise=True)) + self.assertEqual('1D', btop2cigar('-A', concise=False)) def testAll(self): """ @@ -204,25 +204,36 @@ class TestBtop2CigarConcise(TestCase): string must be correct. """ self.assertEqual('7M2I4M2D5M', - btop2cigar('2GC3ATC-G-4-T-A5', concise=True)) + btop2cigar('2GC3ATC-G-4-T-A5', concise=False)) + def testAllAA(self): + """ + If a BTOP string specifies all possible variations, and we indicate + that the BTOP string refers to amino acids, the CIGAR string must be + correct (i.e., all counts must be tripled). + """ + self.assertEqual( + '21M6I12M6D15M', + btop2cigar('2GC3ATC-G-4-T-A5', concise=False, aa=True)) -class TestBtop2CigarPrecise(TestCase): + +class TestBtop2CigarConcise(TestCase): """ - Tests for the btop2cigar function when concise is False. + Tests for the btop2cigar function when concise is True. """ + def testEmpty(self): """ An empty BTOP string must result in an empty CIGAR string. """ - self.assertEqual('', btop2cigar('', concise=False)) + self.assertEqual('', btop2cigar('', concise=True)) def testMixedMatch(self): """ If a BTOP string specifies that some characters match and some do not, the CIGAR string must be specific about the matches / mismatches. """ - self.assertEqual('2=1X3=1X', btop2cigar('2GC3AT', concise=False)) + self.assertEqual('2=1X3=1X', btop2cigar('2GC3AT', concise=True)) def testRefenceInsertion(self): """ @@ -230,7 +241,7 @@ class TestBtop2CigarPrecise(TestCase): subject (reference) does not, the CIGAR string must indicate an insertion to the reference. """ - self.assertEqual('1I', btop2cigar('A-', concise=False)) + self.assertEqual('1I', btop2cigar('A-', concise=True)) def testQueryInsertion(self): """ @@ -238,7 +249,7 @@ class TestBtop2CigarPrecise(TestCase): but the query does not, the CIGAR string must indicate an deletion in the reference. """ - self.assertEqual('1D', btop2cigar('-A', concise=False)) + self.assertEqual('1D', btop2cigar('-A', concise=True)) def testAll(self): """ @@ -246,4 +257,12 @@ class TestBtop2CigarPrecise(TestCase): string must be correct. """ self.assertEqual('2=1X3=1X2I4=2D5=', - btop2cigar('2GC3ATC-G-4-T-A5', concise=False)) + btop2cigar('2GC3ATC-G-4-T-A5', concise=True)) + + def testWithAATrue(self): + """ + If concise and aa are both set to True, a ValueError must be raised. + """ + error = '^aa and concise cannot both be True$' + assertRaisesRegex(self, ValueError, error, btop2cigar, '', + concise=True, aa=True)	Add soft-clipping to CIGAR string in convert-diamond-to-sam.py	3d48d201d41d8cabaa1f31d5dd7987e882a68af3	[ "test/test_btop.py::TestBtop2CigarPrecise::testAll", "test/test_btop.py::TestBtop2CigarPrecise::testAllAA", "test/test_btop.py::TestBtop2CigarPrecise::testMixedMatch", "test/test_btop.py::TestBtop2CigarConcise::testAll", "test/test_btop.py::TestBtop2CigarConcise::testMixedMatch", "test/test_btop.py::TestBtop2CigarConcise::testWithAATrue" ]	[ "test/test_btop.py::TestParseBtop::testConsecutiveGaps", "test/test_btop.py::TestParseBtop::testConsecutiveIdentical", "test/test_btop.py::TestParseBtop::testEmpty", "test/test_btop.py::TestParseBtop::testOneLetter", "test/test_btop.py::TestParseBtop::testOneLetterThenANumber", "test/test_btop.py::TestParseBtop::testOneNumber", "test/test_btop.py::TestParseBtop::testOneNumberThatIsZero", "test/test_btop.py::TestParseBtop::testOneNumberWithLeadingZeroes", "test/test_btop.py::TestParseBtop::testOneNumberWithTrailingOneLetter", "test/test_btop.py::TestParseBtop::testOneQuerySubjectPair", "test/test_btop.py::TestParseBtop::testOneQuerySubjectPairAndANumber", "test/test_btop.py::TestParseBtop::testThreeLetters", "test/test_btop.py::TestParseBtop::testTwoNumbersWithOneLetterBetween", "test/test_btop.py::TestParseBtop::testTwoQuerySubjectPairs", "test/test_btop.py::TestCountGaps::testEmpty", "test/test_btop.py::TestCountGaps::testLettersButNoGaps", "test/test_btop.py::TestCountGaps::testMultipleQueryAndSubjectGaps", "test/test_btop.py::TestCountGaps::testNumberOnly", "test/test_btop.py::TestCountGaps::testOneQueryAndOneSubjectGap", "test/test_btop.py::TestCountGaps::testOneQueryGap", "test/test_btop.py::TestCountGaps::testOneSubjectGap", "test/test_btop.py::TestBtop2CigarPrecise::testEmpty", "test/test_btop.py::TestBtop2CigarPrecise::testQueryInsertion", "test/test_btop.py::TestBtop2CigarPrecise::testRefenceInsertion", "test/test_btop.py::TestBtop2CigarConcise::testEmpty", "test/test_btop.py::TestBtop2CigarConcise::testQueryInsertion", "test/test_btop.py::TestBtop2CigarConcise::testRefenceInsertion" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2018-11-23 16:46:53+00:00	mit	872
acorg__dark-matter-663	diff --git a/CHANGELOG.md b/CHANGELOG.md index fa389b6..e329501 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,10 @@ +## 3.0.60 Dec 13, 2018 + +In `reads.py`, changed the `_makeComplementTable` function so that +uppercase and lowercase bases are correctly reverse complemented into their +respective uppercase and lowercase complementary letters. Added a test to +`test/reads.py` to confirm that `reverseComplement` does this. + ## 3.0.59 Dec 11, 2018 Added `--sampleName` option to `proteins-to-pathogens`. diff --git a/dark/__init__.py b/dark/__init__.py index 278f52a..ffb465c 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -8,4 +8,4 @@ if sys.version_info < (2, 7): # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.59' +__version__ = '3.0.60' diff --git a/dark/reads.py b/dark/reads.py index 18171d0..df381e0 100644 --- a/dark/reads.py +++ b/dark/reads.py @@ -27,7 +27,8 @@ def _makeComplementTable(complementData): """ table = list(range(256)) for _from, to in complementData.items(): - table[ord(_from[0])] = ord(to[0]) + table[ord(_from[0].lower())] = ord(to[0].lower()) + table[ord(_from[0].upper())] = ord(to[0].upper()) return ''.join(map(chr, table))	acorg/dark-matter	31c6f64ccf9e55821a250a5a4324860c29782a0e	diff --git a/test/test_reads.py b/test/test_reads.py index d586ab1..4663234 100644 --- a/test/test_reads.py +++ b/test/test_reads.py @@ -652,6 +652,16 @@ class TestDNARead(TestCase): read = DNARead('id', 'ATCGMRWSVHXN') self.assertEqual('NXDBSWYKCGAT', read.reverseComplement().sequence) + def testReverseComplementLowercaseLetters(self): + """ + The reverseComplement function must correctly reverse complement + lowercase letters. The issue is described here: + https://github.com/acorg/dark-matter/issues/662 + """ + read = DNARead('id', 'CAGCAGctgcagcaccagcaccagcagcttcCACAT') + expected = ('ATGTGgaagctgctggtgctggtgctgcagCTGCTG') + self.assertEqual(expected, read.reverseComplement().sequence) + def testTranslationsOfEmptySequence(self): """ The translations function must correctly return all six (empty)	Extract-ORFs.py mistranslates lowercase letters In a sequence with mixed uppercase and lowercase letters, extract-ORFs.py output has incorrect translations only for the sites of lowercase letters. (Even though the `translations` function of `dark/reads.py` translate a sequence with mixed upper and lower case letters correctly)	31c6f64ccf9e55821a250a5a4324860c29782a0e	[ "test/test_reads.py::TestDNARead::testReverseComplementLowercaseLetters" ]	[ "test/test_reads.py::TestRead::testCasePreservation", "test/test_reads.py::TestRead::testCheckAlphabetAAReadMatchingReturnTrue", "test/test_reads.py::TestRead::testCheckAlphabetAAReadNotMatchingRaise", "test/test_reads.py::TestRead::testCheckAlphabetDNAReadMatchingReturnTrue", "test/test_reads.py::TestRead::testCheckAlphabetDNAReadNotMatchingRaise", "test/test_reads.py::TestRead::testCheckAlphabetwithReadMustBePermissive", "test/test_reads.py::TestRead::testEquality", "test/test_reads.py::TestRead::testEqualityWithDifferingIds", "test/test_reads.py::TestRead::testEqualityWithDifferingQuality", "test/test_reads.py::TestRead::testEqualityWithDifferingSequences", "test/test_reads.py::TestRead::testEqualityWithNoQuality", "test/test_reads.py::TestRead::testEqualityWithOneOmittedQuality", "test/test_reads.py::TestRead::testExpectedAttributes", "test/test_reads.py::TestRead::testFromDict", "test/test_reads.py::TestRead::testFromDictNoQuality", "test/test_reads.py::TestRead::testGetitemFullCopy", "test/test_reads.py::TestRead::testGetitemId", "test/test_reads.py::TestRead::testGetitemLength", "test/test_reads.py::TestRead::testGetitemQuality", "test/test_reads.py::TestRead::testGetitemReturnsNewRead", "test/test_reads.py::TestRead::testGetitemReversed", "test/test_reads.py::TestRead::testGetitemSequence", "test/test_reads.py::TestRead::testGetitemSingleIndex", "test/test_reads.py::TestRead::testGetitemWithStep", "test/test_reads.py::TestRead::testHashDiffersIfIdDiffers", "test/test_reads.py::TestRead::testHashDiffersIfQualityDiffers", "test/test_reads.py::TestRead::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestRead::testHashIdenticalNoQuality", "test/test_reads.py::TestRead::testHashIdenticalWithQuality", "test/test_reads.py::TestRead::testHashViaDict", "test/test_reads.py::TestRead::testHashViaSet", "test/test_reads.py::TestRead::testKeepSites", "test/test_reads.py::TestRead::testKeepSitesAllSites", "test/test_reads.py::TestRead::testKeepSitesNoSites", "test/test_reads.py::TestRead::testKeepSitesOutOfRange", "test/test_reads.py::TestRead::testKeepSitesWithQuality", "test/test_reads.py::TestRead::testLength", "test/test_reads.py::TestRead::testLowComplexityFraction", "test/test_reads.py::TestRead::testLowComplexityFractionEmptySequence", "test/test_reads.py::TestRead::testLowComplexityFractionOne", "test/test_reads.py::TestRead::testLowComplexityFractionZero", "test/test_reads.py::TestRead::testNoQuality", "test/test_reads.py::TestRead::testRemoveSites", "test/test_reads.py::TestRead::testRemoveSitesAllSites", "test/test_reads.py::TestRead::testRemoveSitesNoSites", "test/test_reads.py::TestRead::testRemoveSitesOutOfRange", "test/test_reads.py::TestRead::testRemoveSitesWithQuality", "test/test_reads.py::TestRead::testToDict", "test/test_reads.py::TestRead::testToDictNoQuality", "test/test_reads.py::TestRead::testToFASTA", "test/test_reads.py::TestRead::testToFASTAWithQuality", "test/test_reads.py::TestRead::testToFASTQ", "test/test_reads.py::TestRead::testToFASTQWithNoQuality", "test/test_reads.py::TestRead::testToUnknownFormat", "test/test_reads.py::TestRead::testUnequalLengths", "test/test_reads.py::TestRead::testWalkHSPExactMatch", "test/test_reads.py::TestRead::testWalkHSPExactMatchWithGap", "test/test_reads.py::TestRead::testWalkHSPLeftAndRightOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPLeftAndRightOverhangingMatchNoWhiskers", "test/test_reads.py::TestRead::testWalkHSPLeftOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPLeftOverhangingMatchNoWhiskers", "test/test_reads.py::TestRead::testWalkHSPRightOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPRightOverhangingMatchNoWhiskers", "test/test_reads.py::TestDNARead::testGetitemReturnsNewDNARead", "test/test_reads.py::TestDNARead::testReverseComplement", "test/test_reads.py::TestDNARead::testReverseComplementAmbiguous", "test/test_reads.py::TestDNARead::testReverseComplementReversesQuality", "test/test_reads.py::TestDNARead::testTranslationOfMultipleStopCodons", "test/test_reads.py::TestDNARead::testTranslationOfStartCodonATG", "test/test_reads.py::TestDNARead::testTranslationOfStopCodonTAG", "test/test_reads.py::TestDNARead::testTranslationOfStopCodonTGA", "test/test_reads.py::TestDNARead::testTranslations", "test/test_reads.py::TestDNARead::testTranslationsOfEmptySequence", "test/test_reads.py::TestDNARead::testTranslationsOfOneBaseSequence", "test/test_reads.py::TestDNARead::testTranslationsOfTwoBaseSequence", "test/test_reads.py::TestRNARead::testGetitemReturnsNewRNARead", "test/test_reads.py::TestRNARead::testReverseComplement", "test/test_reads.py::TestRNARead::testReverseComplementAmbiguous", "test/test_reads.py::TestRNARead::testTranslationOfStopCodonUAA", "test/test_reads.py::TestAARead::testCloseCloseORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseCloseORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseCloseORFWithJunk", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseOpenORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseOpenORFWithJunk", "test/test_reads.py::TestAARead::testCloseCloseThenCloseOpenORF", "test/test_reads.py::TestAARead::testCloseOpenORF", "test/test_reads.py::TestAARead::testCloseOpenORFWithMultipleStarts", "test/test_reads.py::TestAARead::testGetitemReturnsNewAARead", "test/test_reads.py::TestAARead::testNoStartCodon_GithubIssue239", "test/test_reads.py::TestAARead::testORFsEmptySequence", "test/test_reads.py::TestAARead::testORFsEmptySequenceWithStart", "test/test_reads.py::TestAARead::testORFsEmptySequenceWithStartStop", "test/test_reads.py::TestAARead::testORFsWithJustStartsAndStops", "test/test_reads.py::TestAARead::testORFsWithOneStopCodon", "test/test_reads.py::TestAARead::testORFsWithTwoStopCodons", "test/test_reads.py::TestAARead::testOpenCloseORF", "test/test_reads.py::TestAARead::testOpenCloseORFWithMultipleStops", "test/test_reads.py::TestAARead::testOpenCloseThenCloseCloseThenCloseOpenORF", "test/test_reads.py::TestAARead::testOpenCloseThenCloseCloseThenCloseOpenORFWithJunk", "test/test_reads.py::TestAARead::testOpenCloseThenCloseOpenORF", "test/test_reads.py::TestAARead::testOpenOpenORF", "test/test_reads.py::TestAARead::testPropertiesCorrectTranslation", "test/test_reads.py::TestAARead::testPropertyDetailsCorrectTranslation", "test/test_reads.py::TestAAReadWithX::testAlphabet", "test/test_reads.py::TestAAReadWithX::testAlphabetChecking", "test/test_reads.py::TestAAReadWithX::testGetitemReturnsNewAAReadWithX", "test/test_reads.py::TestAAReadORF::testClosedClosedId", "test/test_reads.py::TestAAReadORF::testClosedOpenId", "test/test_reads.py::TestAAReadORF::testFromDict", "test/test_reads.py::TestAAReadORF::testOpenClosedId", "test/test_reads.py::TestAAReadORF::testOpenLeft", "test/test_reads.py::TestAAReadORF::testOpenOpenId", "test/test_reads.py::TestAAReadORF::testOpenRight", "test/test_reads.py::TestAAReadORF::testSequence", "test/test_reads.py::TestAAReadORF::testStart", "test/test_reads.py::TestAAReadORF::testStartGreaterThanStop", "test/test_reads.py::TestAAReadORF::testStartNegative", "test/test_reads.py::TestAAReadORF::testStop", "test/test_reads.py::TestAAReadORF::testStopGreaterThanOriginalSequenceLength", "test/test_reads.py::TestAAReadORF::testToDict", "test/test_reads.py::TestSSAARead::testCorrectAttributes", "test/test_reads.py::TestSSAARead::testFromDict", "test/test_reads.py::TestSSAARead::testGetitemFullCopy", "test/test_reads.py::TestSSAARead::testGetitemId", "test/test_reads.py::TestSSAARead::testGetitemLength", "test/test_reads.py::TestSSAARead::testGetitemReturnsNewRead", "test/test_reads.py::TestSSAARead::testGetitemReversed", "test/test_reads.py::TestSSAARead::testGetitemSequence", "test/test_reads.py::TestSSAARead::testGetitemSingleIndex", "test/test_reads.py::TestSSAARead::testGetitemStructure", "test/test_reads.py::TestSSAARead::testGetitemWithStep", "test/test_reads.py::TestSSAARead::testHashDiffersIfIdDiffers", "test/test_reads.py::TestSSAARead::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestSSAARead::testHashDiffersIfStructureDiffers", "test/test_reads.py::TestSSAARead::testHashViaDict", "test/test_reads.py::TestSSAARead::testHashViaSet", "test/test_reads.py::TestSSAARead::testKeepSites", "test/test_reads.py::TestSSAARead::testKeepSitesAllSites", "test/test_reads.py::TestSSAARead::testKeepSitesNoSites", "test/test_reads.py::TestSSAARead::testKeepSitesOutOfRange", "test/test_reads.py::TestSSAARead::testReads", "test/test_reads.py::TestSSAARead::testRemoveSites", "test/test_reads.py::TestSSAARead::testRemoveSitesAllSites", "test/test_reads.py::TestSSAARead::testRemoveSitesNoSites", "test/test_reads.py::TestSSAARead::testRemoveSitesOutOfRange", "test/test_reads.py::TestSSAARead::testSequenceLengthMatchesStructureLength", "test/test_reads.py::TestSSAARead::testToDict", "test/test_reads.py::TestSSAARead::testToString", "test/test_reads.py::TestSSAARead::testToStringWithExplicitFastaFormat", "test/test_reads.py::TestSSAARead::testToStringWithExplicitFastaSSFormat", "test/test_reads.py::TestSSAARead::testToStringWithStructureSuffix", "test/test_reads.py::TestSSAARead::testToStringWithUnknownFormat", "test/test_reads.py::TestSSAAReadWithX::testCorrectAttributes", "test/test_reads.py::TestSSAAReadWithX::testFromDict", "test/test_reads.py::TestSSAAReadWithX::testGetitemFullCopy", "test/test_reads.py::TestSSAAReadWithX::testGetitemId", "test/test_reads.py::TestSSAAReadWithX::testGetitemLength", "test/test_reads.py::TestSSAAReadWithX::testGetitemReturnsNewRead", "test/test_reads.py::TestSSAAReadWithX::testGetitemReversed", "test/test_reads.py::TestSSAAReadWithX::testGetitemSequence", "test/test_reads.py::TestSSAAReadWithX::testGetitemSingleIndex", "test/test_reads.py::TestSSAAReadWithX::testGetitemStructure", "test/test_reads.py::TestSSAAReadWithX::testGetitemWithStep", "test/test_reads.py::TestSSAAReadWithX::testHashDiffersIfIdDiffers", "test/test_reads.py::TestSSAAReadWithX::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestSSAAReadWithX::testHashDiffersIfStructureDiffers", "test/test_reads.py::TestSSAAReadWithX::testHashViaDict", "test/test_reads.py::TestSSAAReadWithX::testHashViaSet", "test/test_reads.py::TestSSAAReadWithX::testKeepSites", "test/test_reads.py::TestSSAAReadWithX::testKeepSitesAllSites", "test/test_reads.py::TestSSAAReadWithX::testKeepSitesNoSites", "test/test_reads.py::TestSSAAReadWithX::testKeepSitesOutOfRange", "test/test_reads.py::TestSSAAReadWithX::testReads", "test/test_reads.py::TestSSAAReadWithX::testRemoveSites", "test/test_reads.py::TestSSAAReadWithX::testRemoveSitesAllSites", "test/test_reads.py::TestSSAAReadWithX::testRemoveSitesNoSites", "test/test_reads.py::TestSSAAReadWithX::testRemoveSitesOutOfRange", "test/test_reads.py::TestSSAAReadWithX::testSequenceContainingX", "test/test_reads.py::TestSSAAReadWithX::testSequenceLengthMatchesStructureLength", "test/test_reads.py::TestSSAAReadWithX::testToDict", "test/test_reads.py::TestSSAAReadWithX::testToString", "test/test_reads.py::TestSSAAReadWithX::testToStringWithExplicitFastaFormat", "test/test_reads.py::TestSSAAReadWithX::testToStringWithExplicitFastaSSFormat", "test/test_reads.py::TestSSAAReadWithX::testToStringWithStructureSuffix", "test/test_reads.py::TestSSAAReadWithX::testToStringWithUnknownFormat", "test/test_reads.py::TestTranslatedRead::testExpectedAttributes", "test/test_reads.py::TestTranslatedRead::testExpectedFrame", "test/test_reads.py::TestTranslatedRead::testFromDict", "test/test_reads.py::TestTranslatedRead::testId", "test/test_reads.py::TestTranslatedRead::testIdReverseComplemented", "test/test_reads.py::TestTranslatedRead::testMaximumORFLength", "test/test_reads.py::TestTranslatedRead::testMaximumORFLengthNoStops", "test/test_reads.py::TestTranslatedRead::testOutOfRangeFrame", "test/test_reads.py::TestTranslatedRead::testReverseComplemented", "test/test_reads.py::TestTranslatedRead::testSequence", "test/test_reads.py::TestTranslatedRead::testToDict", "test/test_reads.py::TestReadClassNameToClass::testNames", "test/test_reads.py::TestReads::testEmptyInitialReads", "test/test_reads.py::TestReads::testInitialReads", "test/test_reads.py::TestReads::testManuallyAddedReads", "test/test_reads.py::TestReads::testManuallyAddedReadsLength", 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"test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfOneFromOneRead", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfTwoFromFiveReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfZeroReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetSizeZeroNoReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetSizeZeroTwoReads", "test/test_reads.py::TestReadsFiltering::testFilterRemoveDescriptions", "test/test_reads.py::TestReadsFiltering::testFilterRemoveGaps", "test/test_reads.py::TestReadsFiltering::testFilterRemoveGapsWithQuality", "test/test_reads.py::TestReadsFiltering::testFilterRemoveSequences", "test/test_reads.py::TestReadsFiltering::testFilterRemoveSequencesNoSequences", "test/test_reads.py::TestReadsFiltering::testFilterReturnsReadInstance", "test/test_reads.py::TestReadsFiltering::testFilterTruncateTitles", "test/test_reads.py::TestReadsFiltering::testFilterWhitelist", "test/test_reads.py::TestReadsFiltering::testFilterWithMinLengthEqualToMaxLength", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatChangesIds", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatOmits", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatOmitsAndChangesIds", "test/test_reads.py::TestReadsFiltering::testFilteredReadsInstanceHasExpectedLength", "test/test_reads.py::TestReadsFiltering::testIdLambda", "test/test_reads.py::TestReadsFiltering::testIdLambdaReturningNone", "test/test_reads.py::TestReadsFiltering::testKeepSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesAllSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesNoSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesOutOfRange", "test/test_reads.py::TestReadsFiltering::testKeepSitesWithQuality", "test/test_reads.py::TestReadsFiltering::testLineNumberFile", "test/test_reads.py::TestReadsFiltering::testLineNumberFileEmpty", "test/test_reads.py::TestReadsFiltering::testLineNumberFileFirstLineTooSmall", "test/test_reads.py::TestReadsFiltering::testLineNumberFileNonAscending", "test/test_reads.py::TestReadsFiltering::testLineNumberFileRunOutOfSequences", "test/test_reads.py::TestReadsFiltering::testReadLambda", "test/test_reads.py::TestReadsFiltering::testReadLambdaReturningNone", "test/test_reads.py::TestReadsFiltering::testRemoveAndKeepSites", "test/test_reads.py::TestReadsFiltering::testRemoveSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesAllSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesNoSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesOutOfRange", "test/test_reads.py::TestReadsFiltering::testRemoveSitesWithQuality", "test/test_reads.py::TestReadsFiltering::testSampleFractionAndNoTrueLengthRaisesValueError", "test/test_reads.py::TestReadsFiltering::testSampleFractionAndRandomSubsetRaisesValueError", "test/test_reads.py::TestReadsFiltering::testSampleFractionOne", "test/test_reads.py::TestReadsFiltering::testSampleFractionPointOne", "test/test_reads.py::TestReadsFiltering::testSampleFractionZero", "test/test_reads.py::TestReadsInRAM::testAdd", "test/test_reads.py::TestReadsInRAM::testFromReads", "test/test_reads.py::TestReadsInRAM::testNoReads", "test/test_reads.py::TestReadsInRAM::testOneReadIndex", "test/test_reads.py::TestReadsInRAM::testOneReadLength", "test/test_reads.py::TestReadsInRAM::testOneReadList", "test/test_reads.py::TestReadsInRAM::testSetItem", "test/test_reads.py::TestReadsInRAM::testTwoReadsIndex", "test/test_reads.py::TestReadsInRAM::testTwoReadsLength", "test/test_reads.py::TestReadsInRAM::testTwoReadsList", "test/test_reads.py::TestSummarizePosition::testCorrectFrequencies", "test/test_reads.py::TestSummarizePosition::testExcludeShortSequences", "test/test_reads.py::TestSummarizePosition::testFrequenciesNoReads", "test/test_reads.py::TestSummarizePosition::testIndexLargerThanSequenceLength", "test/test_reads.py::TestSummarizePosition::testNumberOfExclusionsNoReads", "test/test_reads.py::TestSitesMatching::testAllMatches", "test/test_reads.py::TestSitesMatching::testIgnoreCase", "test/test_reads.py::TestSitesMatching::testMatchCase", "test/test_reads.py::TestSitesMatching::testMultipleReadsAll", "test/test_reads.py::TestSitesMatching::testMultipleReadsAllWithDifferingLengths", "test/test_reads.py::TestSitesMatching::testMultipleReadsAny", "test/test_reads.py::TestSitesMatching::testMultipleReadsAnyWithDifferingLengths", "test/test_reads.py::TestSitesMatching::testNoMatches", "test/test_reads.py::TestSitesMatching::testPartialMatch" ]	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2018-12-14 13:22:15+00:00	mit	873
acorg__dark-matter-680	diff --git a/CHANGELOG.md b/CHANGELOG.md index cf03d75..fc519cd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,16 @@ +## 3.0.70 Jul 30, 2019 + +Added `titleRegex` and `negativeTitleRegex` to `ProteinGrouper` class and +`--titleRegex` and `--negativeTitleRegex` arguments to +`proteins-to-pathogens.py`. + +## 3.0.69 Jul 30, 2019 + +Added `--title` and `--preamble` args to output from +`proteins-to-pathogens.py`. Fixed `ProteinGrouper` HTML NCBI protein link +and added genome link. Added positive and negative filtering by regex to +`TitlesAlignments` and tests. Improved NCBI link generation and tests. + ## 3.0.68 Jun 9, 2019 Refactored `SAMFilter` to allow filtering alignments in pileups. Added diff --git a/bin/proteins-to-pathogens.py b/bin/proteins-to-pathogens.py index ed0bbd8..c39670e 100755 --- a/bin/proteins-to-pathogens.py +++ b/bin/proteins-to-pathogens.py @@ -157,6 +157,14 @@ if __name__ == '__main__': '--preamble', help='Optional preamble text to show after the title.') + parser.add_argument( + '--titleRegex', default=None, + Help='A regex that pathogen names must match.') + + parser.add_argument( + '--negativeTitleRegex', default=None, + help='a regex that pathogen names must not match.') + args = parser.parse_args() if args.sampleName and args.sampleNameRegex: @@ -192,7 +200,9 @@ if __name__ == '__main__': sampleNameRegex=args.sampleNameRegex, format_=args.format, proteinFastaFilenames=proteinFastaFilenames, - saveReadLengths=args.showReadLengths) + saveReadLengths=args.showReadLengths, + titleRegex=args.titleRegex, + negativeTitleRegex=args.negativeTitleRegex) if args.filenames: filenames = args.filenames diff --git a/dark/__init__.py b/dark/__init__.py index 8df318a..50781d0 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -8,4 +8,4 @@ if sys.version_info < (2, 7): # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.69' +__version__ = '3.0.70' diff --git a/dark/proteins.py b/dark/proteins.py index 1cef243..1310abd 100644 --- a/dark/proteins.py +++ b/dark/proteins.py @@ -11,6 +11,7 @@ from textwrap import fill from dark.dimension import dimensionalIterator from dark.fasta import FastaReads from dark.fastq import FastqReads +from dark.filter import TitleFilter from dark.html import NCBISequenceLinkURL from dark.reads import Reads @@ -211,6 +212,14 @@ class ProteinGrouper(object): proteins each matched pathogen has. @param saveReadLengths: If C{True}, save the lengths of all reads matching proteins. + @param titleRegex: A regex that pathogen names must match. + Note that this matching is done on the final part of the protein title + in square brackets, according to the convention used by the NCBI viral + refseq database and RVDB. + @param negativeTitleRegex: A regex that pathogen names must not match. + Note that this matching is done on the final part of the protein title + in square brackets, according to the convention used by the NCBI viral + refseq database and RVDB. @raise ValueError: If C{format_} is unknown. """ @@ -218,7 +227,8 @@ class ProteinGrouper(object): def __init__(self, assetDir='out', sampleName=None, sampleNameRegex=None, format_='fasta', proteinFastaFilenames=None, - saveReadLengths=False): + saveReadLengths=False, titleRegex=None, + negativeTitleRegex=None): self._assetDir = assetDir self._sampleName = sampleName self._sampleNameRegex = (re.compile(sampleNameRegex) if sampleNameRegex @@ -229,6 +239,12 @@ class ProteinGrouper(object): raise ValueError("format_ must be either 'fasta' or 'fastq'.") self._saveReadLengths = saveReadLengths + if titleRegex or negativeTitleRegex: + self.titleFilter = TitleFilter( + positiveRegex=titleRegex, negativeRegex=negativeTitleRegex) + else: + self.titleFilter = None + self._pathogenProteinCount = getPathogenProteinCounts( proteinFastaFilenames) @@ -285,6 +301,11 @@ class ProteinGrouper(object): proteinName, pathogenName = splitNames(names) + # Ignore pathogens with names we don't want. + if (self.titleFilter and self.titleFilter.accept( + pathogenName) == TitleFilter.REJECT): + continue + if pathogenName not in self.pathogenNames: self.pathogenNames[pathogenName] = {}	acorg/dark-matter	e76e23cc5230e4db4742c4418b6e5b8ddb0bc8d4	diff --git a/test/test_proteins.py b/test/test_proteins.py index 3cd8d09..f68397a 100644 --- a/test/test_proteins.py +++ b/test/test_proteins.py @@ -744,6 +744,94 @@ class TestProteinGrouper(TestCase): 'GENBANK\|I44.6\|GENBANK\|J77\|VP1\n', pg.toStr()) + def testPathogenNameRegex(self): + """ + If a protein grouper is given one file with two lines from different + pathogens, and one pathogen title does not match a passed title regex, + the pathogenNames dict must be as expected. + """ + fp = StringIO( + '0.63 41.3 44.2 9 9 12 acc\|GENBANK\|I44.6\|GENBANK\|J77\|VP1 ' + '[Lausannevirus]\n' + '0.77 46.6 48.1 5 6 74 acc\|GENBANK\|I44.7\|GENBANK\|J78\|VP2 ' + '[Hepatitis B virus]\n' + ) + pg = ProteinGrouper(titleRegex='Lausannevirus') + pg.addFile('sample-filename', fp) + self.assertEqual( + { + 'Lausannevirus': { + 'sample-filename': { + 'proteins': { + 'acc\|GENBANK\|I44.6\|GENBANK\|J77\|VP1': { + 'bestScore': 44.2, + 'bluePlotFilename': 'out/0.png', + 'coverage': 0.63, + 'readsFilename': 'out/0.fasta', + 'hspCount': 9, + 'index': 0, + 'medianScore': 41.3, + 'outDir': 'out', + 'proteinLength': 12, + 'proteinName': ( + 'acc\|GENBANK\|I44.6\|GENBANK\|J77\|VP1'), + 'proteinURL': ('http://www.ncbi.nlm.nih.gov/' + 'nuccore/I44.6'), + 'genomeURL': ( + 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), + 'readCount': 9, + }, + }, + 'uniqueReadCount': None, + }, + }, + }, + pg.pathogenNames) + + def testPathogenNegativeNameRegex(self): + """ + If a protein grouper is given one file with two lines from different + pathogens, and one pathogen title does not match a passed negative + title regex, the pathogenNames dict must be as expected. + """ + fp = StringIO( + '0.63 41.3 44.2 9 9 12 acc\|GENBANK\|I44.6\|GENBANK\|J77\|VP1 ' + '[Lausannevirus]\n' + '0.77 46.6 48.1 5 6 74 acc\|GENBANK\|I44.7\|GENBANK\|J78\|VP2 ' + '[Hepatitis B virus]\n' + ) + pg = ProteinGrouper(negativeTitleRegex='Hepatitis') + pg.addFile('sample-filename', fp) + self.assertEqual( + { + 'Lausannevirus': { + 'sample-filename': { + 'proteins': { + 'acc\|GENBANK\|I44.6\|GENBANK\|J77\|VP1': { + 'bestScore': 44.2, + 'bluePlotFilename': 'out/0.png', + 'coverage': 0.63, + 'readsFilename': 'out/0.fasta', + 'hspCount': 9, + 'index': 0, + 'medianScore': 41.3, + 'outDir': 'out', + 'proteinLength': 12, + 'proteinName': ( + 'acc\|GENBANK\|I44.6\|GENBANK\|J77\|VP1'), + 'proteinURL': ('http://www.ncbi.nlm.nih.gov/' + 'nuccore/I44.6'), + 'genomeURL': ( + 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), + 'readCount': 9, + }, + }, + 'uniqueReadCount': None, + }, + }, + }, + pg.pathogenNames) + class TestPathogenSampleFiles(TestCase): """	Add title regex (positive and negative) to protein grouper	e76e23cc5230e4db4742c4418b6e5b8ddb0bc8d4	[ "test/test_proteins.py::TestProteinGrouper::testPathogenNameRegex", "test/test_proteins.py::TestProteinGrouper::testPathogenNegativeNameRegex" ]	[ "test/test_proteins.py::TestSplitNames::testNestedBrackets", "test/test_proteins.py::TestSplitNames::testNoBrackets", "test/test_proteins.py::TestSplitNames::testNormalCase", "test/test_proteins.py::TestSplitNames::testTwoSetsOfBrackets", "test/test_proteins.py::TestSplitNames::testWhitespaceStripping", "test/test_proteins.py::TestGetPathogenProteinCounts::testExpected", "test/test_proteins.py::TestGetPathogenProteinCounts::testExpectedWithTwoFiles", "test/test_proteins.py::TestGetPathogenProteinCounts::testNone", "test/test_proteins.py::TestProteinGrouper::testAssetDir", "test/test_proteins.py::TestProteinGrouper::testDuplicatePathogenProteinSample", "test/test_proteins.py::TestProteinGrouper::testNoAssetDir", "test/test_proteins.py::TestProteinGrouper::testNoFiles", "test/test_proteins.py::TestProteinGrouper::testNoFilesToStr", "test/test_proteins.py::TestProteinGrouper::testNoFilesToStrWithTitle", "test/test_proteins.py::TestProteinGrouper::testNoFilesToStrWithTitleAndPreamble", "test/test_proteins.py::TestProteinGrouper::testNoRegex", "test/test_proteins.py::TestProteinGrouper::testNoSampleName", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesDifferentPathogens", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesDifferentPathogensTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogen", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogenTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFile", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileFASTQ", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileToStr", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileWithDifferentAssetDir", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileDifferentPathogens", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileSamePathogen", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testUnknownFormat", "test/test_proteins.py::TestProteinGrouper::testUnknownPathogenType", "test/test_proteins.py::TestPathogenSampleFiles::testIdenticalReadsRemoved", "test/test_proteins.py::TestPathogenSampleFiles::testOpenNotCalledOnRepeatedCall", "test/test_proteins.py::TestPathogenSampleFiles::testProteinsSavedCorrectly", "test/test_proteins.py::TestPathogenSampleFiles::testReadLengthsAdded", "test/test_proteins.py::TestPathogenSampleFiles::testUnknownFormat", "test/test_proteins.py::TestPathogenSampleFiles::testWritePathogenIndex", "test/test_proteins.py::TestPathogenSampleFiles::testWriteSampleIndex" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2019-07-30 15:24:11+00:00	mit	874
acorg__dark-matter-686	diff --git a/CHANGELOG.md b/CHANGELOG.md index 6a08922..5f2e8a9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,12 @@ +## 3.0.79 Aug 8, 2019 + +Add `--omitVirusLinks` and `--omitSampleProteinCount` options to +`proteins-to-pathogens.py` to make HTML output less confusing when running +on RVDB or OKIAV databases. Removed highlighting of pathogens with high +protein fraction since that was done in a non-useful way. Removed index +field from HTML output and removed HSP count unless it differs from the +read count. + ## 3.0.78 Aug 2, 2019 Fixed silly import error. diff --git a/bin/proteins-to-pathogens.py b/bin/proteins-to-pathogens.py index 252d025..3daa58e 100755 --- a/bin/proteins-to-pathogens.py +++ b/bin/proteins-to-pathogens.py @@ -170,6 +170,23 @@ if __name__ == '__main__': '--negativeTitleRegex', default=None, help='a regex that pathogen names must not match.') + parser.add_argument( + '--omitVirusLinks', default=False, action='store_true', + help=('If specified, the HTML output (use --html to get this) for ' + 'viruses will not contain links to ICTV and ViralZone. ' + 'This should be used when working with viruses that do not yet ' + 'have names that can be looked up.')) + + parser.add_argument( + '--omitSampleProteinCount', default=False, action='store_true', + help=('If specified, the HTML output (use --html to get this) for ' + 'viruses will not contain counts of the number of proteins ' + 'matched by each sample for a given pathogen. This should be ' + 'used when working with RVDB where there are many sequences ' + 'for some proteins and a sample matches many of them, leading ' + 'to incorrect reporting of the number of proteins of a pathogen ' + 'that are matched by samples.')) + args = parser.parse_args() if args.sampleName and args.sampleNameRegex: @@ -186,6 +203,19 @@ if __name__ == '__main__': print('It does not make sense to use --pathogenIndexFilename ' 'without also using --html', file=sys.stderr) sys.exit(1) + if args.omitVirusLinks: + print('It does not make sense to use --omitVirusLinks ' + 'without also using --html', file=sys.stderr) + sys.exit(1) + if args.omitSampleProteinCount: + print('It does not make sense to use --omitSampleProteinCount ' + 'without also using --html', file=sys.stderr) + sys.exit(1) + + if args.omitVirusLinks and args.pathogenType != 'viral': + print('The --omitVirusLinks option only makes sense with ' + '--pathogenType viral', file=sys.stderr) + sys.exit(1) if args.proteinFastaFilename: # Flatten lists of lists that we get from using both nargs='+' and @@ -220,11 +250,14 @@ if __name__ == '__main__': grouper.addFile(filename, fp) if args.html: - print(grouper.toHTML(args.pathogenPanelFilename, - minProteinFraction=args.minProteinFraction, - pathogenType=args.pathogenType, - title=args.title, preamble=args.preamble, - sampleIndexFilename=args.sampleIndexFilename, - pathogenIndexFilename=args.pathogenIndexFilename)) + print(grouper.toHTML( + args.pathogenPanelFilename, + minProteinFraction=args.minProteinFraction, + pathogenType=args.pathogenType, + title=args.title, preamble=args.preamble, + sampleIndexFilename=args.sampleIndexFilename, + pathogenIndexFilename=args.pathogenIndexFilename, + omitVirusLinks=args.omitVirusLinks, + omitSampleProteinCount=args.omitSampleProteinCount)) else: print(grouper.toStr()) diff --git a/dark/__init__.py b/dark/__init__.py index 15c32b1..6e9c357 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -8,4 +8,4 @@ if sys.version_info < (2, 7): # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.78' +__version__ = '3.0.79' diff --git a/dark/proteins.py b/dark/proteins.py index 0449e7e..d6cefee 100644 --- a/dark/proteins.py +++ b/dark/proteins.py @@ -244,6 +244,7 @@ class ProteinGrouper(object): VIRALZONE = 'https://viralzone.expasy.org/search?query=' ICTV = 'https://talk.ictvonline.org/search-124283882/?q=' READCOUNT_MARKER = 'READ-COUNT' + READ_AND_HSP_COUNT_STR_SEP = '/' def __init__(self, assetDir='out', sampleName=None, sampleNameRegex=None, format_='fasta', proteinFastaFilenames=None, @@ -362,7 +363,7 @@ class ProteinGrouper(object): proteinURL = NCBISequenceLinkURL(proteinName, field=2) genomeURL = NCBISequenceLinkURL(proteinName, field=4) - proteins[proteinName] = { + proteinInfo = proteins[proteinName] = { 'bestScore': float(bestScore), 'bluePlotFilename': join(outDir, '%d.png' % index), 'coverage': float(coverage), @@ -378,6 +379,12 @@ class ProteinGrouper(object): 'readCount': int(readCount), } + if proteinInfo['readCount'] == proteinInfo['hspCount']: + proteinInfo['readAndHspCountStr'] = readCount + else: + proteinInfo['readAndHspCountStr'] = '%s%s%s' % ( + readCount, self.READ_AND_HSP_COUNT_STR_SEP, hspCount) + if self._saveReadLengths: readsClass = (FastaReads if self._format == 'fasta' else FastqReads) @@ -435,8 +442,8 @@ class ProteinGrouper(object): for proteinName in sorted(proteins): append( ' %(coverage).2f\t%(medianScore).2f\t' - '%(bestScore).2f\t%(readCount)4d\t%(hspCount)4d\t' - '%(index)3d\t%(proteinName)s' + '%(bestScore).2f\t%(readAndHspCountStr)11s\t' + '%(proteinName)s' % proteins[proteinName]) append('') @@ -445,7 +452,8 @@ class ProteinGrouper(object): def toHTML(self, pathogenPanelFilename=None, minProteinFraction=0.0, pathogenType='viral', title='Summary of pathogens', preamble=None, sampleIndexFilename=None, - pathogenIndexFilename=None): + pathogenIndexFilename=None, omitVirusLinks=False, + omitSampleProteinCount=False): """ Produce an HTML string representation of the pathogen summary. @@ -465,6 +473,13 @@ class ProteinGrouper(object): @param pathogenIndexFilename: A C{str} filename to write a pathogen index file to. Lines in the file will have an integer index, a space, and then the pathogen name. + @param omitVirusLinks: If C{True}, links to ICTV and ViralZone will be + omitted in output. + @param omitSampleProteinCount: If C{True}, do not display a number of + matched pathogen proteins for a sample. This should be used when + those numbers are inaccurate (e.g., when using the unclustered RVDB + protein database and there are many sequences for the same + protein). @return: An HTML C{str} suitable for printing. """ if pathogenType not in ('bacterial', 'viral'): @@ -475,7 +490,6 @@ class ProteinGrouper(object): if not exists(self._pathogenDataDir): os.mkdir(self._pathogenDataDir) - highlightSymbol = '&starf;' self._computeUniqueReadCounts() if pathogenPanelFilename: @@ -548,10 +562,6 @@ class ProteinGrouper(object): margin-top: 10px; margin-bottom: 3px; } - .significant { - color: red; - margin-right: 2px; - } .sample { margin-top: 5px; margin-bottom: 2px; @@ -599,10 +609,10 @@ class ProteinGrouper(object): '<li>Coverage fraction.</li>', '<li>Median bit score.</li>', '<li>Best bit score.</li>', - '<li>Read count.</li>', - '<li>HSP count (a read can match a protein more than once).</li>', - '<li>Protein length (in AAs).</li>', - '<li>Index (just ignore this).</li>', + '<li>Read count (if the HSP count differs, read and HSP ', + ('counts are both given, separated by "%s").</li>' % + self.READ_AND_HSP_COUNT_STR_SEP), + '<li>Protein length (in amino acids).</li>', ] if self._saveReadLengths: @@ -644,11 +654,6 @@ class ProteinGrouper(object): 'but all pathogens have at least %.2f%% of their ' 'proteins matched by at least one sample.' % percent) - append('Samples that match a pathogen (and pathogens with a ' - 'matching sample) with at least this protein fraction are ' - 'highlighted using <span class="significant">%s</span>.' % - highlightSymbol) - append('</p>') if pathogenPanelFilename: @@ -692,7 +697,7 @@ class ProteinGrouper(object): samples = self.pathogenNames[pathogenName] sampleCount = len(samples) pathogenProteinCount = self._pathogenProteinCount[pathogenName] - if pathogenType == 'viral': + if pathogenType == 'viral' and not omitVirusLinks: quoted = quote(pathogenName) pathogenLinksHTML = ( ' (<a href="%s%s">ICTV</a>, <a href="%s%s">ViralZone</a>)' @@ -755,21 +760,19 @@ class ProteinGrouper(object): uniqueReadCount = samples[sampleName]['uniqueReadCount'] pathogenReadCount += uniqueReadCount - if pathogenProteinCount and ( - proteinCount / pathogenProteinCount >= - minProteinFraction): - highlight = ('<span class="significant">%s</span>' % - highlightSymbol) + if omitSampleProteinCount: + proteinCountHTML = '' else: - highlight = '' + proteinCountHTML = '%d protein%s, ' % ( + proteinCount, '' if proteinCount == 1 else 's') append( '<p class="sample indented">' - '%sSample <a href="#sample-%s">%s</a> ' - '(%d protein%s, <a href="%s">%d de-duplicated (by id) ' + 'Sample <a href="#sample-%s">%s</a> ' + '(%s<a href="%s">%d de-duplicated (by id) ' 'read%s</a>, <a href="%s">panel</a>):</p>' % - (highlight, sampleName, sampleName, - proteinCount, '' if proteinCount == 1 else 's', + (sampleName, sampleName, + proteinCountHTML, readsFileName, uniqueReadCount, '' if uniqueReadCount == 1 else 's', self.sampleNames[sampleName])) @@ -780,8 +783,7 @@ class ProteinGrouper(object): '<li>' '<span class="stats">' '%(coverage).2f %(medianScore)6.2f %(bestScore)6.2f ' - '%(readCount)5d %(hspCount)5d %(proteinLength)4d ' - '%(index)3d ' + '%(readAndHspCountStr)11s %(proteinLength)4d ' % proteinMatch ) @@ -861,7 +863,7 @@ class ProteinGrouper(object): '<a id="sample-%s"></a>' '<p class="sample">Sample ' '<span class="sample-name">%s</span> ' - 'matched proteins from 0 pathogens.</p>' % + 'did not match anything.</p>' % (sampleName, sampleName)) continue @@ -875,24 +877,19 @@ class ProteinGrouper(object): proteinCount = len(proteins) pathogenProteinCount = self._pathogenProteinCount[pathogenName] - highlight = '' if pathogenProteinCount: proteinCountStr = '%d/%d protein%s' % ( proteinCount, pathogenProteinCount, '' if pathogenProteinCount == 1 else 's') - if (proteinCount / pathogenProteinCount >= - minProteinFraction): - highlight = ('<span class="significant">%s</span>' % - highlightSymbol) else: proteinCountStr = '%d protein%s' % ( proteinCount, '' if proteinCount == 1 else 's') append( '<p class="sample indented">' - '%s<a href="#pathogen-%s">%s</a> %s, ' + '<a href="#pathogen-%s">%s</a> %s, ' '<a href="%s">%d de-duplicated (by id) read%s</a>:</p>' % - (highlight, pathogenName, pathogenName, + (pathogenName, pathogenName, proteinCountStr, readsFileName, uniqueReadCount, '' if uniqueReadCount == 1 else 's')) append('<ul class="protein-list indented">') @@ -902,8 +899,7 @@ class ProteinGrouper(object): '<li>' '<span class="stats">' '%(coverage).2f %(medianScore)6.2f %(bestScore)6.2f ' - '%(readCount)5d %(hspCount)5d %(proteinLength)4d ' - '%(index)3d ' + '%(readAndHspCountStr)11s %(proteinLength)4d ' '</span> ' '<span class="protein-name">' '%(proteinName)s'	acorg/dark-matter	3398b2f5af3d2fa4dcce840ad04ff605a5221fb9	diff --git a/test/test_proteins.py b/test/test_proteins.py index ba46f58..cf00b38 100644 --- a/test/test_proteins.py +++ b/test/test_proteins.py @@ -259,6 +259,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': None, @@ -298,6 +299,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': None, @@ -337,6 +339,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': None, @@ -411,6 +414,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 9, + 'readAndHspCountStr': '9', }, 'acc\|GENBANK\|I44.7\|GENBANK\|J78\|VP2': { 'bestScore': 48.1, @@ -429,6 +433,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J78'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': None, @@ -472,6 +477,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 9, + 'readAndHspCountStr': '9', }, }, 'uniqueReadCount': None, @@ -497,6 +503,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J78'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': None, @@ -543,6 +550,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 9, + 'readAndHspCountStr': '9', }, }, 'uniqueReadCount': None, @@ -566,6 +574,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J78'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': None, @@ -633,6 +642,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 9, + 'readAndHspCountStr': '9', }, }, 'uniqueReadCount': None, @@ -658,6 +668,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J78'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': None, @@ -740,7 +751,7 @@ class TestProteinGrouper(TestCase): '\n' 'Lausannevirus (in 1 sample)\n' ' sample-filename (1 protein, 5 reads)\n' - ' 0.77\t46.60\t48.10\t 5\t 6\t 0\tacc\|' + ' 0.77\t46.60\t48.10\t 5/6\tacc\|' 'GENBANK\|I44.6\|GENBANK\|J77\|VP1\n', pg.toStr()) @@ -780,6 +791,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 9, + 'readAndHspCountStr': '9', }, }, 'uniqueReadCount': None, @@ -824,6 +836,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 9, + 'readAndHspCountStr': '9', }, }, 'uniqueReadCount': None, @@ -1076,6 +1089,7 @@ class TestPathogenSampleFiles(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 9, + 'readAndHspCountStr': '9', }, 'acc\|GENBANK\|I44.7\|GENBANK\|J78\|VP2': { 'bestScore': 48.1, @@ -1094,6 +1108,7 @@ class TestPathogenSampleFiles(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J78'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': 3,	Add options to proteins-to-pathogens.py to omit virus links and incorrect virus protein counts	3398b2f5af3d2fa4dcce840ad04ff605a5221fb9	[ "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesDifferentPathogens", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogen", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFile", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileFASTQ", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileToStr", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileWithDifferentAssetDir", "test/test_proteins.py::TestProteinGrouper::testPathogenNameRegex", "test/test_proteins.py::TestProteinGrouper::testPathogenNegativeNameRegex", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileDifferentPathogens", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileSamePathogen", "test/test_proteins.py::TestPathogenSampleFiles::testProteinsSavedCorrectly" ]	[ "test/test_proteins.py::TestSplitNames::testNestedBrackets", "test/test_proteins.py::TestSplitNames::testNoBrackets", "test/test_proteins.py::TestSplitNames::testNormalCase", "test/test_proteins.py::TestSplitNames::testTwoSetsOfBrackets", "test/test_proteins.py::TestSplitNames::testWhitespaceStripping", "test/test_proteins.py::TestGetPathogenProteinCounts::testExpected", "test/test_proteins.py::TestGetPathogenProteinCounts::testExpectedWithTwoFiles", "test/test_proteins.py::TestGetPathogenProteinCounts::testNone", "test/test_proteins.py::TestProteinGrouper::testAssetDir", "test/test_proteins.py::TestProteinGrouper::testDuplicatePathogenProteinSample", "test/test_proteins.py::TestProteinGrouper::testNoAssetDir", "test/test_proteins.py::TestProteinGrouper::testNoFiles", "test/test_proteins.py::TestProteinGrouper::testNoFilesToStr", "test/test_proteins.py::TestProteinGrouper::testNoFilesToStrWithTitle", "test/test_proteins.py::TestProteinGrouper::testNoFilesToStrWithTitleAndPreamble", "test/test_proteins.py::TestProteinGrouper::testNoRegex", "test/test_proteins.py::TestProteinGrouper::testNoSampleName", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesDifferentPathogensTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogenTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testUnknownFormat", "test/test_proteins.py::TestProteinGrouper::testUnknownPathogenType", "test/test_proteins.py::TestPathogenSampleFiles::testIdenticalReadsRemoved", "test/test_proteins.py::TestPathogenSampleFiles::testOpenNotCalledOnRepeatedCall", "test/test_proteins.py::TestPathogenSampleFiles::testPathogenIndex", "test/test_proteins.py::TestPathogenSampleFiles::testReadLengthsAdded", "test/test_proteins.py::TestPathogenSampleFiles::testUnknownFormat", "test/test_proteins.py::TestPathogenSampleFiles::testWritePathogenIndex", "test/test_proteins.py::TestPathogenSampleFiles::testWriteSampleIndex" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2019-08-08 13:18:14+00:00	mit	875
acorg__dark-matter-704	diff --git a/CHANGELOG.md b/CHANGELOG.md index ee662c9..9212725 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,7 @@ +## 3.1.31 Jan 13, 2020 + +Added `sam-coverage-depth.py`. + ## 3.1.30 Jan 13, 2020 Added `--minGenomeLength` to `make-protein-database.py`. diff --git a/bin/sam-coverage-depth.py b/bin/sam-coverage-depth.py new file mode 100755 index 0000000..7516f61 --- /dev/null +++ b/bin/sam-coverage-depth.py @@ -0,0 +1,122 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import sys +import argparse +from collections import Counter +from numpy import std + +from dark.filter import ( + addFASTAFilteringCommandLineOptions, parseFASTAFilteringCommandLineOptions) +from dark.reads import Reads +from dark.sam import samfile, SAMFilter, samReferences, UnknownReference +from dark.utils import pct + + +def baseCountsToStr(counts): + """ + Convert base counts to a string. + + @param counts: A C{Counter} instance. + @return: A C{str} representation of nucleotide counts. + """ + return ' '.join([ + ('%s:%d' % (base, counts[base])) for base in sorted(counts)]) + + +parser = argparse.ArgumentParser( + formatter_class=argparse.ArgumentDefaultsHelpFormatter, + description=('Print SAM/BAM file coverage statistics by offset. ' + 'Output lines show the offset.')) + +addFASTAFilteringCommandLineOptions(parser) +SAMFilter.addFilteringOptions(parser, samfileIsPositional=True) + +parser.add_argument( + '--noOffsets', default=False, action='store_true', + help='Do not print per-offset details of base counts.') + +parser.add_argument( + '--noStats', default=False, action='store_true', + help='Do not print final average and standard deviation statistics.') + +args = parser.parse_args() + +if args.noOffsets and args.noStats: + print('You have used both --noOffsets and --noStats, so there is no ' + 'output!', file=sys.stderr) + sys.exit(1) + +# We don't have a file of reads, we just want a read filter that we +# can use to filter the SAM file query sequences. +reads = parseFASTAFilteringCommandLineOptions(args, Reads()) +samFilter = SAMFilter.parseFilteringOptions(args, reads.filterRead) + +printOffsets = not args.noOffsets +printStats = not args.noStats + +if samFilter.referenceIds and len(samFilter.referenceIds) > 1: + print('Only one reference id can be given. To calculate coverage for more ' + 'than one reference, run this script multiple times.', + file=sys.stderr) + sys.exit(1) + +try: + referenceLengths = samFilter.referenceLengths() +except UnknownReference: + referenceId = samFilter.referenceIds.pop() + referenceIds = samReferences(args.samfile) + print('Reference %r does not appear in SAM file %s. Known ' + 'references are: %s.' % ( + referenceId, args.samfile, ', '.join(sorted(referenceIds))), + file=sys.stderr) + sys.exit(1) + +if printStats: + counts = [] + +with samfile(args.samfile) as sam: + + if samFilter.referenceIds: + # No need to check if the given reference id is in referenceLengths + # because the samFilter.referenceLengths call above catched that. + referenceId = samFilter.referenceIds.pop() + else: + if len(referenceLengths) == 1: + referenceId = list(referenceLengths)[0] + else: + print('SAM file %r contains %d references (%s). Only one ' + 'reference id can be analyzed at a time. Please use ' + '--referenceId to specify the one you want examined.' % ( + args.samfile, len(referenceLengths), + ', '.join(sorted(referenceLengths))), file=sys.stderr) + sys.exit(1) + + for column in sam.pileup(reference=referenceId): + bases = Counter() + for read in column.pileups: + if (not read.is_del and not read.is_refskip and + samFilter.filterAlignment(read.alignment)): + base = read.alignment.query_sequence[read.query_position] + bases[base] += 1 + + baseCount = sum(bases.values()) + + if printStats: + counts.append(baseCount) + + if printOffsets: + print('%d: %d %s' % (column.reference_pos + 1, baseCount, + baseCountsToStr(bases))) + +if printStats: + referenceLength = referenceLengths[referenceId] + print('Reference id: %s' % referenceId) + print('Reference length: %d' % referenceLength) + print('Bases covered: %s' % pct(len(counts), referenceLength)) + print('Min coverage depth: %d' % ( + 0 if len(counts) < referenceLength else min(counts))) + print('Max coverage depth: %d' % max(counts)) + print('Mean coverage depth: %.3f' % (sum(counts) / referenceLength)) + print('Coverage depth s.d.: %.3f' % std(counts)) diff --git a/dark/__init__.py b/dark/__init__.py index 324a302..da9777a 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.1.30' +__version__ = '3.1.31' diff --git a/dark/sam.py b/dark/sam.py index b668b4f..07a5e08 100644 --- a/dark/sam.py +++ b/dark/sam.py @@ -334,13 +334,10 @@ class SAMFilter(object): SAM/BAM file is read. @return: A C{SAMFilter} instance. """ - referenceIds = (set(chain.from_iterable(args.referenceId)) - if args.referenceId else None) - return cls( args.samfile, filterRead=filterRead, - referenceIds=referenceIds, + referenceIds=set(args.referenceId) if args.referenceId else None, storeQueryIds=storeQueryIds, dropUnmapped=args.dropUnmapped, dropSecondary=args.dropSecondary, diff --git a/dark/utils.py b/dark/utils.py index 0059330..1ffa57f 100644 --- a/dark/utils.py +++ b/dark/utils.py @@ -259,6 +259,22 @@ def countPrint(mesg, count, len1, len2=None): count, len2, percentage(count, len2))) +def pct(a, b): + """ + Format a string showing two integers and what percentage the first + is of the second. + + @param a: An C{int}, the numerator. + @param b: An C{int}, the denominator. + """ + assert 0 <= a <= b + if b: + return ('%d/%d (%.3f%%)' % + (a, b, (a / b if b else 0.0) * 100.0)) + else: + return '0/0 (0.000%)' + + @contextmanager def cd(newdir): """	acorg/dark-matter	5d785403629c4bd5c2e848219ed0fc4fc896c3cf	diff --git a/test/test_utils.py b/test/test_utils.py index f7d7ed6..5656906 100644 --- a/test/test_utils.py +++ b/test/test_utils.py @@ -14,8 +14,8 @@ except ImportError: from .mocking import mockOpen from dark.utils import ( - numericallySortFilenames, median, asHandle, parseRangeString, StringIO, - baseCountsToStr, nucleotidesToStr, countPrint) + numericallySortFilenames, median, asHandle, parseRangeString, pct, + StringIO, baseCountsToStr, nucleotidesToStr, countPrint) class TestNumericallySortFilenames(TestCase): @@ -382,3 +382,36 @@ class TestCountPrint(TestCase): ' 2/8 (25.00%) of sequence 2', countPrint('Count is', count, len1, len2) ) + + +class TestPct(TestCase): + """ + Test the pct function. + """ + def testZeroNumerator(self): + """ + The pct function must produce the correct result if the numerator is + zero. + """ + self.assertEqual('0/10 (0.000%)', pct(0, 10)) + + def testZeroDenominator(self): + """ + The pct function must produce the correct result if the denominator is + zero. + """ + self.assertEqual('0/0 (0.000%)', pct(0, 0)) + + def testOneHalf(self): + """ + The pct function must produce the correct result if the numerator is + one half of the denominator. + """ + self.assertEqual('5/10 (50.000%)', pct(5, 10)) + + def testOneSeventh(self): + """ + The pct function must produce the correct result if the numerator is + one seventh of the denominator. + """ + self.assertEqual('2/14 (14.286%)', pct(2, 14))	Add a script to print per-offset coverage and overall coverage stats from a SAM/BAM file	5d785403629c4bd5c2e848219ed0fc4fc896c3cf	[ "test/test_utils.py::TestNumericallySortFilenames::testBasename", "test/test_utils.py::TestNumericallySortFilenames::testNoNames", "test/test_utils.py::TestNumericallySortFilenames::testOneNonNumericName", "test/test_utils.py::TestNumericallySortFilenames::testOneNumericName", "test/test_utils.py::TestNumericallySortFilenames::testSeveralNames", "test/test_utils.py::TestNumericallySortFilenames::testSeveralNamesWithUnequalPrefixLengths", "test/test_utils.py::TestMedian::testEmptyArgRaises", "test/test_utils.py::TestMedian::testMedianOfFive", "test/test_utils.py::TestMedian::testMedianOfFour", "test/test_utils.py::TestMedian::testMedianOfOne", "test/test_utils.py::TestMedian::testMedianOfThree", "test/test_utils.py::TestMedian::testMedianOfTwo", "test/test_utils.py::TestAsHandle::testOpenFile", "test/test_utils.py::TestAsHandle::testStr", "test/test_utils.py::TestParseRangeString::testEmptyString", "test/test_utils.py::TestParseRangeString::testSingleNumber", "test/test_utils.py::TestParseRangeString::testSingleNumberSpaceAfter", "test/test_utils.py::TestParseRangeString::testSingleNumberSpaceBefore", "test/test_utils.py::TestParseRangeString::testSingleNumberSpaceBeforeAndAfter", "test/test_utils.py::TestParseRangeString::testSingleRange", "test/test_utils.py::TestParseRangeString::testSingleRangeWithSpaceAfterHyphen", "test/test_utils.py::TestParseRangeString::testSingleRangeWithSpaceBeforeAfterHyphen", "test/test_utils.py::TestParseRangeString::testSingleRangeWithSpaceBeforeHyphen", "test/test_utils.py::TestParseRangeString::testTwoOverlappingRanges", "test/test_utils.py::TestParseRangeString::testTwoRanges", "test/test_utils.py::TestParseRangeString::testTwoRangesAndANumber", "test/test_utils.py::TestParseRangeString::testTwoRangesAndTwoNumbers", "test/test_utils.py::TestParseRangeString::testZeroConversion", "test/test_utils.py::TestStringIO::testContextManager", "test/test_utils.py::TestStringIO::testInitializedRead", "test/test_utils.py::TestStringIO::testInitiallyEmpty", "test/test_utils.py::TestStringIO::testWriteRead", "test/test_utils.py::TestBaseCountsToStr::testSimple", "test/test_utils.py::TestNucleotidesToStr::testSimple", "test/test_utils.py::TestCountPrint::testSimple", "test/test_utils.py::TestCountPrint::testTwoSequences", "test/test_utils.py::TestPct::testOneHalf", "test/test_utils.py::TestPct::testOneSeventh", "test/test_utils.py::TestPct::testZeroDenominator", "test/test_utils.py::TestPct::testZeroNumerator" ]	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-01-13 01:04:10+00:00	mit	876
acorg__dark-matter-705	diff --git a/CHANGELOG.md b/CHANGELOG.md index 18dbb93..5a22e5b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,7 @@ +## 3.1.37 Jan 13, 2020 + +Add final `genome-protein-summary.py` script. + ## 3.1.35 Jan 13, 2020 Drop Python 3.8 from Travis and tox checking. diff --git a/bin/genome-protein-summary.py b/bin/genome-protein-summary.py index cb0608d..71ce8b4 100755 --- a/bin/genome-protein-summary.py +++ b/bin/genome-protein-summary.py @@ -14,22 +14,19 @@ from dark.genbank import GenomeRanges from dark.genomes import GenomeProteinInfo from dark.reads import Reads from dark.sam import SAMFilter, samReferences +from dark.utils import pct -def pct(a, b): - assert a <= b - if b: - return ('%d/%d (%.3f%%)' % - (a, b, (a / b if b else 0.0) * 100.0)) - else: - return '0/0 (0.00%)' - - -def summarize(gpi, sortOn): +def summarize(gpi, sortOn, minReadOffsetCount): """ Print a summary of the genome proteins. @param gpi: A C{GenomeProteinInfo} instance. + @param sortOn: How to sort proteins for output. One of 'coverage', + 'depth', 'name', 'offset', or 'readCount'. + @param minReadOffsetCount: The minimum number of reads offsets that must + overlap a protein for the read to be considered as sufficiently + intersecting the protein. """ genome = gpi.genome @@ -48,9 +45,9 @@ def summarize(gpi, sortOn): print(' Whole genome coverage (not just proteins):') print(' Reads matching genome: %d' % len(gpi.readIdsMatchingGenome)) - print(' Covered offsets: %s' % ( + print(' Covered genome offsets: %s' % ( pct(len(gpi.coveredOffsetCount), genome['length']))) - print(' Average depth: %.3f' % ( + print(' Average depth across genome: %.3f' % ( sum(gpi.coveredOffsetCount.values()) / genome['length'])) coveredProteinOffsetCount = coveredProteinBasesCount = 0 @@ -58,16 +55,15 @@ def summarize(gpi, sortOn): coveredProteinOffsetCount += bool(gpi.coveredOffsetCount[offset]) coveredProteinBasesCount += gpi.coveredOffsetCount[offset] - print(' Total protein coverage:') + print(' Total protein coverage (irrespective of minReadOffsetCount):') print(' Reads matching proteins: %d' % len(gpi.readIdsForAllProteins())) - print(' Covered offsets: %s' % ( + print(' Proteins with any coverage: %s' % + pct(len(gpi.coveredProteins), genome['proteinCount'])) + print(' Covered protein offsets: %s' % ( pct(coveredProteinOffsetCount, len(gpi.offsets)))) - print(' Average depth: %.3f' % ( + print(' Average depth across proteins: %.3f' % ( coveredProteinBasesCount / len(gpi.offsets))) - print(' Proteins matched: %s (sorted by %s):' % ( - pct(len(gpi.coveredProteins), genome['proteinCount']), sortOn)) - if sortOn == 'name': def key(proteinAccession): return gpi.proteins[proteinAccession]['name'] @@ -93,25 +89,41 @@ def summarize(gpi, sortOn): return coverage['totalBases'] / coverage['ntLength'] reverse = True - for i, proteinAccession in enumerate( - sorted(gpi.coveredProteins, key=key, reverse=reverse), - start=1): + if minReadOffsetCount is None: + print(' Proteins covered (no minReadOffsetCount):') + else: + print(' Proteins covered (minReadOffsetCount=%d):' % + minReadOffsetCount) + + proteinCount = 0 + for proteinAccession in sorted(gpi.coveredProteins, key=key, + reverse=reverse): protein = gpi.proteins[proteinAccession] - print(' %d: %s (%d AA, %d nt with stop codon, %s)' % - (i, protein['product'], protein['length'], - protein['length'] * 3 + 3, protein['accession'])) - coverage = gpi.proteinCoverageInfo(proteinAccession) + coverage = gpi.proteinCoverageInfo(proteinAccession, + minReadOffsetCount) + + readCount = len(coverage['readIds']) - print(' Read count: %d' % len(coverage['readIds'])) + if readCount: + proteinCount += 1 - print(' Covered offsets: %s' % ( - pct(coverage['coveredOffsets'], coverage['ntLength']))) + print(' %d: %s (%d AA, %d nt with stop codon, %s)' % + (proteinCount, protein['product'], protein['length'], + protein['length'] * 3 + 3, protein['accession'])) - print(' Average depth: %.3f' % ( - coverage['totalBases'] / coverage['ntLength'])) + print(' Read count: %d' % readCount) - print(' Offsets: %s' % protein['offsets']) + print(' Covered offsets: %s' % ( + pct(coverage['coveredOffsets'], coverage['ntLength']))) + + print(' Average depth: %.3f' % ( + coverage['totalBases'] / coverage['ntLength'])) + + print(' Offsets: %s' % protein['offsets']) + + print(' Proteins matched: %s (sorted by %s):' % ( + pct(proteinCount, genome['proteinCount']), sortOn)) if __name__ == '__main__': @@ -124,11 +136,23 @@ if __name__ == '__main__': help=('The filename of an Sqlite3 database holding protein and ' 'genome information, as built by make-protein-database.py')) + parser.add_argument( + '--progress', default=False, action='store_true', + help='Print progress info to standard error.') + parser.add_argument( '--sortOn', default='readCount', choices=('coverage', 'depth', 'name', 'offset', 'readCount'), help='How to sort proteins for output.') + parser.add_argument( + '--minReadOffsetCount', type=int, + help=('The minimum number of reads offsets that must overlap a ' + 'protein for the read to be considered as sufficiently ' + 'intersecting the protein. Use this to prevent reads that ' + 'just overlap the protein in a very small number offsets ' + 'from being counted.')) + parser.add_argument( '--skipTranslationChecks', dest='checkTranslations', action='store_false', default=True, @@ -184,11 +208,13 @@ if __name__ == '__main__': referenceId, file=sys.stderr) else: if samfiles: - print('Processing %d SAM file%s for matches with %r:' % - (len(samfiles), '' if len(samfiles) == 1 else 's', - referenceId), file=sys.stderr) + if args.progress: + print('Processing %d SAM file%s for matches with %r:' % + (len(samfiles), '' if len(samfiles) == 1 else 's', + referenceId), file=sys.stderr) for i, filename in enumerate(samfiles, start=1): - print(' %d: %s' % (i, filename), file=sys.stderr) + if args.progress: + print(' %d: %s' % (i, filename), file=sys.stderr) gpInfo.addSAM(filename, filterAlignment) - summarize(gpInfo, args.sortOn) + summarize(gpInfo, args.sortOn, args.minReadOffsetCount) diff --git a/dark/__init__.py b/dark/__init__.py index 7336433..8aacdfa 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.1.36' +__version__ = '3.1.37' diff --git a/dark/genomes.py b/dark/genomes.py index 63b642b..e920d56 100644 --- a/dark/genomes.py +++ b/dark/genomes.py @@ -24,10 +24,11 @@ class GenomeProteinInfo(object): # self.proteins is keyed by protein accession number. self.proteins = {} self.coveredProteins = set() - # self.offsets is keyed by offset, values are dicts that contain a list - # of protein accession numbers that overlap that offset and a set of - # read ids (if any) that match at that offset. The offsets keys are - # only those that correspond to a protein. + # self.offsets is keyed by genome offset, values are dicts that + # contain a list of protein accession numbers that overlap that + # offset and a set of read ids (if any) that match at that offset. + # The offsets keys are only those that correspond to one or more + # proteins in the genome. self.offsets = {} # self.coveredOffsetCount holds the read counts for all offsets covered # by reads, regardless of whether the offsets correspond to proteins or @@ -123,11 +124,17 @@ class GenomeProteinInfo(object): offsetInfo['proteinAccessions']) offsetInfo['readIds'].add(readId) - def proteinCoverageInfo(self, proteinAccession): + def proteinCoverageInfo(self, proteinAccession, minReadOffsetCount=None): """ Calculate coverage information for a protein. @param proteinAccession: A C{str} accession number. + @param minReadOffsetCount: An C{int}, specifying the minimum number of + reads offsets that must overlap the protein for the read to be + considered as sufficiently intersecting the protein. Use this to + prevent reads that just overlap the protein in a very small number + offsets from being counted. Or C{None} to indicate that no such + filtering should be applied. @raises KeyError: If C{proteinAccession} is not known. @return: A C{dict} containing * the number of covered offsets, @@ -143,6 +150,13 @@ class GenomeProteinInfo(object): offsetsSeen = set() proteinLength = 0 + if minReadOffsetCount is not None and minReadOffsetCount < 2: + # Zero or one is equivalent to not giving a value. + minReadOffsetCount = None + + if minReadOffsetCount: + readOffsetCounts = Counter() + for (start, stop, forward) in GenomeRanges(protein['offsets']).ranges: proteinLength += stop - start for offset in range(start, stop): @@ -153,10 +167,15 @@ class GenomeProteinInfo(object): coveredOffsets += 1 totalBases += len(readIds) allReadIds.update(readIds) - - # The +3 in the following is because the database holds the AA length, - # not including the stop codon. But the database range covers the stop - # codon. + if minReadOffsetCount: + readOffsetCounts.update(readIds) + + # Sanity check that the sum of the range lengths is the same as the + # overall length given in the database. + # + # The +3 in the following is because the database holds the AA + # length, not including the stop codon. But the database range + # covers the stop codon. dbProteinLength = self.proteins[proteinAccession]['length'] * 3 + 3 if proteinLength != dbProteinLength: raise ValueError( @@ -164,6 +183,12 @@ class GenomeProteinInfo(object): 'database protein length (%d) for protein %s!' % (proteinLength, dbProteinLength, proteinAccession)) + # Do not report on reads whose overlapping offset count is too low. + if minReadOffsetCount: + unwanted = set(readId for readId in readOffsetCounts + if readOffsetCounts[readId] < minReadOffsetCount) + allReadIds.symmetric_difference_update(unwanted) + return { 'coveredOffsets': coveredOffsets, 'totalBases': totalBases,	acorg/dark-matter	7e8ca419ef2d6d10287c020e194587a400052ad6	diff --git a/test/test_genomes.py b/test/test_genomes.py index 4819f31..c221136 100644 --- a/test/test_genomes.py +++ b/test/test_genomes.py @@ -172,3 +172,32 @@ class TestGenomeProteinInfo(TestCase): self.assertEqual(750, info['totalBases']) self.assertEqual((3221 - 2306) + (1623 - 0), info['ntLength']) self.assertEqual({'query1', 'query2', 'query3'}, info['readIds']) + + def testTooFewReadOffsetsBAM1(self): + """ + Test that a read is not returned as overlapping a protein unless it + meets the minimum number of required overlapping offsets. + """ + gpi = GenomeProteinInfo('KJ586809.1', DB, True) + gpi.addSAM(BAM1) + + # Look at protein AJF20804.1 coverage (its ranges are 2306-3221 and + # 0-1623). There should be no matching reads because the query + # (query1) is only 200 nt long and so cannot match with at least + # 500 nucleotides. + info = gpi.proteinCoverageInfo('AJF20804.1', 500) + self.assertEqual(set(), info['readIds']) + + def testSufficientReadOffsetsBAM1(self): + """ + Test that a read is returned as overlapping a protein when it meets + the minimum number of required overlapping offsets. + """ + gpi = GenomeProteinInfo('KJ586809.1', DB, True) + gpi.addSAM(BAM1) + + # Look at protein AJF20804.1 coverage (its ranges are 2306-3221 and + # 0-1623). The query (query1) must be returned as it has 200 + # matching nucleotides. + info = gpi.proteinCoverageInfo('AJF20804.1', 199) + self.assertEqual({'query1'}, info['readIds'])	Add tool to summarize protein hits in a SAM/BAM file	7e8ca419ef2d6d10287c020e194587a400052ad6	[ "test/test_genomes.py::TestGenomeProteinInfo::testSufficientReadOffsetsBAM1", "test/test_genomes.py::TestGenomeProteinInfo::testTooFewReadOffsetsBAM1" ]	[ "test/test_genomes.py::TestGenomeProteinInfo::testLoadBAM1", "test/test_genomes.py::TestGenomeProteinInfo::testLoadBAM12", "test/test_genomes.py::TestGenomeProteinInfo::testLoadBAM123", "test/test_genomes.py::TestGenomeProteinInfo::testLoadReference" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-01-13 10:35:47+00:00	mit	877
acorg__dark-matter-726	diff --git a/CHANGELOG.md b/CHANGELOG.md index 66b60e7..17a90c5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,7 @@ +## 3.1.70 March 24, 2020 + +Added `--maxNFraction` arg to `filter-fasta.py`. + ## 3.1.69 March 23, 2020 Added `--md5` arg to `fasta-sequences.py`. @@ -429,9 +433,9 @@ Removed bone-headed use of full path to `fasta-join.sh` from ## 3.0.63 Jan 14, 2019 -Added `compareAaReads` and `matchToString` to `aa.py`. Wrote tests in +Added `compareAaReads` and `matchToString` to `aa.py`. Wrote tests in `test_aa.py` for both. Moved `countPrint` to utils, used by `matchToString` -in `dna.py` and `aa.py`. Added `compare-aa-sequences.py` to the bin. +in `dna.py` and `aa.py`. Added `compare-aa-sequences.py` to the bin. ## 3.0.62 Dec 30, 2018 @@ -444,9 +448,9 @@ and the underlying `ReadFilter` class. ## 3.0.60 Dec 13, 2018 -In `reads.py`, changed the `_makeComplementTable` function so that +In `reads.py`, changed the `_makeComplementTable` function so that uppercase and lowercase bases are correctly reverse complemented into their -respective uppercase and lowercase complementary letters. Added a test to +respective uppercase and lowercase complementary letters. Added a test to `test/reads.py` to confirm that `reverseComplement` does this. ## 3.0.59 Dec 11, 2018 diff --git a/dark/__init__.py b/dark/__init__.py index 52bc094..01d72bb 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.1.69' +__version__ = '3.1.70' diff --git a/dark/filter.py b/dark/filter.py index 07e00d7..216db82 100644 --- a/dark/filter.py +++ b/dark/filter.py @@ -1,3 +1,5 @@ +from __future__ import division + import re from math import ceil from collections import OrderedDict @@ -187,6 +189,10 @@ def addFASTAFilteringCommandLineOptions(parser): '--maxLength', type=int, metavar='N', help='The maximum sequence length') + parser.add_argument( + '--maxNFraction', type=float, metavar='N', + help='The maximum fraction of Ns that can be present in the sequence') + parser.add_argument( '--whitelist', action='append', metavar='SEQUENCE-ID', help='Sequence titles (ids) that should be whitelisted') @@ -297,6 +303,7 @@ def parseFASTAFilteringCommandLineOptions(args, reads): return reads.filter( minLength=args.minLength, maxLength=args.maxLength, + maxNFraction=args.maxNFraction, whitelist=set(args.whitelist) if args.whitelist else None, blacklist=set(args.blacklist) if args.blacklist else None, whitelistFile=args.whitelistFile, blacklistFile=args.blacklistFile, diff --git a/dark/reads.py b/dark/reads.py index 8da2fef..113ffdd 100644 --- a/dark/reads.py +++ b/dark/reads.py @@ -817,6 +817,8 @@ class ReadFilter(object): @param minLength: The minimum acceptable length. @param maxLength: The maximum acceptable length. + @param maxNFraction: The maximum fraction of Ns that can be present in the + sequence. @param removeGaps: If C{True} remove all gaps ('-' characters) from the read sequences. @param whitelist: If not C{None}, a set of exact read ids that are @@ -935,8 +937,8 @@ class ReadFilter(object): # save and restore the state of the RNG and/or to optionally add # 'seed=XXX' to the end of the id of the first read, etc. - def __init__(self, minLength=None, maxLength=None, removeGaps=False, - whitelist=None, blacklist=None, + def __init__(self, minLength=None, maxLength=None, maxNFraction=None, + removeGaps=False, whitelist=None, blacklist=None, whitelistFile=None, blacklistFile=None, titleRegex=None, negativeTitleRegex=None, truncateTitlesAfter=None, keepSequences=None, @@ -960,6 +962,7 @@ class ReadFilter(object): self.minLength = minLength self.maxLength = maxLength + self.maxNFraction = maxNFraction self.removeGaps = removeGaps self.head = head self.removeDuplicates = removeDuplicates @@ -1126,6 +1129,11 @@ class ReadFilter(object): (self.maxLength is not None and readLen > self.maxLength)): return False + if self.maxNFraction is not None: + nFraction = read.sequence.count('N') / readLen + if self.maxNFraction < nFraction: + return False + if self.removeGaps: if read.quality is None: read = read.__class__(read.id, read.sequence.replace('-', ''))	acorg/dark-matter	4c3115b2c5e585068988dfec0a7330b2d4f2ba37	diff --git a/test/test_reads.py b/test/test_reads.py index 273b87d..ea53b3f 100644 --- a/test/test_reads.py +++ b/test/test_reads.py @@ -2550,6 +2550,46 @@ class TestReads(TestCase): self.assertEqual(sorted([read2, read3]), sorted(reads)) self.assertEqual(3, reads.unfilteredLength()) + def testMaxNFractionAllPassNoNs(self): + """ + Test filtering by maximum fraction of Ns. If there are no Ns in the + sequences, all must pass the filtering. + """ + read1 = Read('id1', 'ATTA') + read2 = Read('id2', 'ATTAAC') + initialReads = Reads([read1, read2]) + initialReads.filter(maxNFraction=0.9) + + reads = Reads(initialReads) + self.assertEqual([read1, read2], list(reads)) + + def testMaxNFractionOnePasses(self): + """ + Test filtering by maximum fraction of Ns. If there are too many Ns in + one of the sequences, only one must pass the filtering. + """ + read1 = Read('id1', 'ATTA') + read2 = Read('id2', 'ATTNNN') + initialReads = Reads([read1, read2]) + initialReads.filter(maxNFraction=0.4) + + reads = Reads(initialReads) + self.assertEqual([read1], list(reads)) + + def testMaxNFractionAllPassNs(self): + """ + Test filtering by maximum fraction of Ns. If there are Ns in the + sequence, but below the threshold, all sequences must pass the + filtering. + """ + read1 = Read('id1', 'ATTA') + read2 = Read('id2', 'ATTNNN') + initialReads = Reads([read1, read2]) + initialReads.filter(maxNFraction=0.6) + + reads = Reads(initialReads) + self.assertEqual([read1, read2], list(reads)) + def testNoVariableSitesConfirm(self): """ If two Reads have no bases that are variable, nothing should be	Add filtering options for maximum number of Ns in a sequence	4c3115b2c5e585068988dfec0a7330b2d4f2ba37	[ "test/test_reads.py::TestReads::testMaxNFractionAllPassNoNs", "test/test_reads.py::TestReads::testMaxNFractionAllPassNs", "test/test_reads.py::TestReads::testMaxNFractionOnePasses" ]	[ "test/test_reads.py::TestRead::testCasePreservation", "test/test_reads.py::TestRead::testCheckAlphabetAAReadMatchingReturnTrue", "test/test_reads.py::TestRead::testCheckAlphabetAAReadNotMatchingRaise", "test/test_reads.py::TestRead::testCheckAlphabetDNAReadMatchingReturnTrue", "test/test_reads.py::TestRead::testCheckAlphabetDNAReadNotMatchingRaise", "test/test_reads.py::TestRead::testCheckAlphabetwithReadMustBePermissive", "test/test_reads.py::TestRead::testEquality", "test/test_reads.py::TestRead::testEqualityWithDifferingIds", "test/test_reads.py::TestRead::testEqualityWithDifferingQuality", "test/test_reads.py::TestRead::testEqualityWithDifferingSequences", "test/test_reads.py::TestRead::testEqualityWithNoQuality", "test/test_reads.py::TestRead::testEqualityWithOneOmittedQuality", "test/test_reads.py::TestRead::testExpectedAttributes", "test/test_reads.py::TestRead::testFromDict", "test/test_reads.py::TestRead::testFromDictNoQuality", "test/test_reads.py::TestRead::testGetitemFullCopy", "test/test_reads.py::TestRead::testGetitemId", "test/test_reads.py::TestRead::testGetitemLength", "test/test_reads.py::TestRead::testGetitemQuality", "test/test_reads.py::TestRead::testGetitemReturnsNewRead", "test/test_reads.py::TestRead::testGetitemReversed", "test/test_reads.py::TestRead::testGetitemSequence", "test/test_reads.py::TestRead::testGetitemSingleIndex", "test/test_reads.py::TestRead::testGetitemWithStep", "test/test_reads.py::TestRead::testHashDiffersIfIdDiffers", "test/test_reads.py::TestRead::testHashDiffersIfQualityDiffers", "test/test_reads.py::TestRead::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestRead::testHashIdenticalNoQuality", "test/test_reads.py::TestRead::testHashIdenticalWithQuality", "test/test_reads.py::TestRead::testHashViaDict", "test/test_reads.py::TestRead::testHashViaSet", "test/test_reads.py::TestRead::testKeepSites", "test/test_reads.py::TestRead::testKeepSitesAllSites", "test/test_reads.py::TestRead::testKeepSitesNoSites", "test/test_reads.py::TestRead::testKeepSitesOutOfRange", "test/test_reads.py::TestRead::testKeepSitesWithQuality", "test/test_reads.py::TestRead::testLength", "test/test_reads.py::TestRead::testLowComplexityFraction", "test/test_reads.py::TestRead::testLowComplexityFractionEmptySequence", "test/test_reads.py::TestRead::testLowComplexityFractionOne", "test/test_reads.py::TestRead::testLowComplexityFractionZero", "test/test_reads.py::TestRead::testNoQuality", "test/test_reads.py::TestRead::testRemoveSites", "test/test_reads.py::TestRead::testRemoveSitesAllSites", "test/test_reads.py::TestRead::testRemoveSitesNoSites", "test/test_reads.py::TestRead::testRemoveSitesOutOfRange", "test/test_reads.py::TestRead::testRemoveSitesWithQuality", "test/test_reads.py::TestRead::testReverseNoQuality", "test/test_reads.py::TestRead::testReverseWithQuality", "test/test_reads.py::TestRead::testToDict", "test/test_reads.py::TestRead::testToDictNoQuality", "test/test_reads.py::TestRead::testToFASTA", "test/test_reads.py::TestRead::testToFASTAWithQuality", "test/test_reads.py::TestRead::testToFASTQ", "test/test_reads.py::TestRead::testToFASTQWithNoQuality", "test/test_reads.py::TestRead::testToUnknownFormat", "test/test_reads.py::TestRead::testUnequalLengths", "test/test_reads.py::TestRead::testWalkHSPExactMatch", "test/test_reads.py::TestRead::testWalkHSPExactMatchWithGap", "test/test_reads.py::TestRead::testWalkHSPLeftAndRightOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPLeftAndRightOverhangingMatchNoWhiskers", "test/test_reads.py::TestRead::testWalkHSPLeftOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPLeftOverhangingMatchNoWhiskers", "test/test_reads.py::TestRead::testWalkHSPRightOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPRightOverhangingMatchNoWhiskers", "test/test_reads.py::TestDNARead::testGetitemReturnsNewDNARead", "test/test_reads.py::TestDNARead::testReverseComplement", "test/test_reads.py::TestDNARead::testReverseComplementAmbiguous", "test/test_reads.py::TestDNARead::testReverseComplementLowercaseLetters", "test/test_reads.py::TestDNARead::testReverseComplementReversesQuality", "test/test_reads.py::TestDNARead::testTranslationOfMultipleStopCodons", "test/test_reads.py::TestDNARead::testTranslationOfStartCodonATG", "test/test_reads.py::TestDNARead::testTranslationOfStopCodonTAG", "test/test_reads.py::TestDNARead::testTranslationOfStopCodonTGA", "test/test_reads.py::TestDNARead::testTranslations", "test/test_reads.py::TestDNARead::testTranslationsOfEmptySequence", "test/test_reads.py::TestDNARead::testTranslationsOfOneBaseSequence", "test/test_reads.py::TestDNARead::testTranslationsOfTwoBaseSequence", "test/test_reads.py::TestRNARead::testGetitemReturnsNewRNARead", "test/test_reads.py::TestRNARead::testReverseComplement", "test/test_reads.py::TestRNARead::testReverseComplementAmbiguous", "test/test_reads.py::TestRNARead::testTranslationOfStopCodonUAA", "test/test_reads.py::TestDNAKozakRead::testEqualFunction", "test/test_reads.py::TestDNAKozakRead::testEqualFunctionDifferentKozakSequence", "test/test_reads.py::TestDNAKozakRead::testEqualFunctionDifferentOriginalSequence", "test/test_reads.py::TestDNAKozakRead::testSequence", "test/test_reads.py::TestDNAKozakRead::testStart", "test/test_reads.py::TestDNAKozakRead::testStartGreaterThanStop", "test/test_reads.py::TestDNAKozakRead::testStartNegative", "test/test_reads.py::TestDNAKozakRead::testStop", "test/test_reads.py::TestDNAKozakRead::testStopGreaterThanOriginalSequenceLength", "test/test_reads.py::TestAARead::testCloseCloseORF", "test/test_reads.py::TestAARead::testCloseCloseORFWithJunk", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseCloseORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseCloseORFWithJunk", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseOpenORFWithJunk", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenNothingORF", 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"test/test_reads.py::TestTranslatedRead::testIdReverseComplemented", "test/test_reads.py::TestTranslatedRead::testMaximumORFLength", "test/test_reads.py::TestTranslatedRead::testMaximumORFLengthNoOpenORF", "test/test_reads.py::TestTranslatedRead::testMaximumORFLengthNoStops", "test/test_reads.py::TestTranslatedRead::testOutOfRangeFrame", "test/test_reads.py::TestTranslatedRead::testReverseComplemented", "test/test_reads.py::TestTranslatedRead::testSequence", "test/test_reads.py::TestTranslatedRead::testToDict", "test/test_reads.py::TestReadClassNameToClass::testNames", "test/test_reads.py::TestReads::testEmptyInitialReads", "test/test_reads.py::TestReads::testInitialReads", "test/test_reads.py::TestReads::testManuallyAddedReads", "test/test_reads.py::TestReads::testManuallyAddedReadsLength", "test/test_reads.py::TestReads::testNoReads", "test/test_reads.py::TestReads::testNoReadsLength", "test/test_reads.py::TestReads::testNoVariableSitesConfirm", "test/test_reads.py::TestReads::testNoVariableSitesUnconfirm", "test/test_reads.py::TestReads::testOneAmbiguousCompatibleVariableSitesConfirm", "test/test_reads.py::TestReads::testOneAmbiguousCompatibleVariableSitesUnconfirm", "test/test_reads.py::TestReads::testOneAmbiguousIncompatibleVariableSitesConfirm", "test/test_reads.py::TestReads::testOneAmbiguousIncompatibleVariableSitesUnconfirm", "test/test_reads.py::TestReads::testOneVariableSitesConfirm", "test/test_reads.py::TestReads::testOneVariableSitesUnconfirm", "test/test_reads.py::TestReads::testRepeatedIter", "test/test_reads.py::TestReads::testSaveAsFASTA", "test/test_reads.py::TestReads::testSaveAsFASTQ", "test/test_reads.py::TestReads::testSaveAsFASTQFailsOnReadWithNoQuality", "test/test_reads.py::TestReads::testSaveFASTAIsDefault", "test/test_reads.py::TestReads::testSaveReturnsReadCount", "test/test_reads.py::TestReads::testSaveToFileDescriptor", "test/test_reads.py::TestReads::testSaveWithUnknownFormat", "test/test_reads.py::TestReads::testSaveWithUppercaseFormat", "test/test_reads.py::TestReads::testSubclass", "test/test_reads.py::TestReads::testSubclassLength", "test/test_reads.py::TestReads::testSubclassWithAdditionalReads", "test/test_reads.py::TestReads::testUnfilteredLengthAdditionalReads", "test/test_reads.py::TestReads::testUnfilteredLengthAdditionalReadsAfterFiltering", "test/test_reads.py::TestReads::testUnfilteredLengthBeforeIterating", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReads", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReadsAfterFiltering", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReadsIsReads", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReadsIsReadsWithAdditional", "test/test_reads.py::TestReads::testUnfilteredLengthInitialSubclassThenFiltered", "test/test_reads.py::TestReads::testUnfilteredLengthInitialSubclassWithAdditionalThenFiltered", "test/test_reads.py::TestReads::testUnfilteredLengthInitialSubclassWithNoLen", "test/test_reads.py::TestReads::testUnfilteredLengthNoReads", "test/test_reads.py::TestReads::testVariableSitesHeterogeneous", "test/test_reads.py::TestReads::testVariableSitesHeterogeneousCounts", "test/test_reads.py::TestReads::testVariableSitesTooHomogeneous", "test/test_reads.py::TestReads::testVariableSitesUnequalLengths", "test/test_reads.py::TestReadsFiltering::testAddFiltersThenClearFilters", "test/test_reads.py::TestReadsFiltering::testFilterBlacklist", "test/test_reads.py::TestReadsFiltering::testFilterDoNotRemoveDescriptions", "test/test_reads.py::TestReadsFiltering::testFilterDuplicates", "test/test_reads.py::TestReadsFiltering::testFilterDuplicatesById", "test/test_reads.py::TestReadsFiltering::testFilterDuplicatesByIdMD5", "test/test_reads.py::TestReadsFiltering::testFilterDuplicatesUseMD5", "test/test_reads.py::TestReadsFiltering::testFilterHead", "test/test_reads.py::TestReadsFiltering::testFilterHeadZero", "test/test_reads.py::TestReadsFiltering::testFilterKeepSequences", "test/test_reads.py::TestReadsFiltering::testFilterKeepSequencesNoSequences", "test/test_reads.py::TestReadsFiltering::testFilterNegativeRegex", "test/test_reads.py::TestReadsFiltering::testFilterNoArgs", "test/test_reads.py::TestReadsFiltering::testFilterOnLengthEverythingMatches", "test/test_reads.py::TestReadsFiltering::testFilterOnLengthNothingMatches", "test/test_reads.py::TestReadsFiltering::testFilterOnMaxLength", "test/test_reads.py::TestReadsFiltering::testFilterOnMinLength", "test/test_reads.py::TestReadsFiltering::testFilterPositiveRegex", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfFiveFromFiveReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfFiveFromOneRead", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfOneFromOneRead", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfTwoFromFiveReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfZeroReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetSizeZeroNoReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetSizeZeroTwoReads", "test/test_reads.py::TestReadsFiltering::testFilterRemoveDescriptions", "test/test_reads.py::TestReadsFiltering::testFilterRemoveGaps", "test/test_reads.py::TestReadsFiltering::testFilterRemoveGapsWithQuality", "test/test_reads.py::TestReadsFiltering::testFilterRemoveSequences", "test/test_reads.py::TestReadsFiltering::testFilterRemoveSequencesNoSequences", "test/test_reads.py::TestReadsFiltering::testFilterReturnsReadInstance", "test/test_reads.py::TestReadsFiltering::testFilterTruncateTitles", "test/test_reads.py::TestReadsFiltering::testFilterWhitelist", "test/test_reads.py::TestReadsFiltering::testFilterWithMinLengthEqualToMaxLength", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatChangesIds", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatOmits", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatOmitsAndChangesIds", "test/test_reads.py::TestReadsFiltering::testFilteredReadsInstanceHasExpectedLength", "test/test_reads.py::TestReadsFiltering::testIdLambda", "test/test_reads.py::TestReadsFiltering::testIdLambdaReturningNone", "test/test_reads.py::TestReadsFiltering::testKeepSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesAllSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesNoSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesOutOfRange", "test/test_reads.py::TestReadsFiltering::testKeepSitesWithQuality", "test/test_reads.py::TestReadsFiltering::testLineNumberFile", "test/test_reads.py::TestReadsFiltering::testLineNumberFileEmpty", "test/test_reads.py::TestReadsFiltering::testLineNumberFileFirstLineTooSmall", "test/test_reads.py::TestReadsFiltering::testLineNumberFileNonAscending", "test/test_reads.py::TestReadsFiltering::testLineNumberFileRunOutOfSequences", "test/test_reads.py::TestReadsFiltering::testReadLambda", "test/test_reads.py::TestReadsFiltering::testReadLambdaReturningNone", "test/test_reads.py::TestReadsFiltering::testRemoveAndKeepSites", "test/test_reads.py::TestReadsFiltering::testRemoveSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesAllSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesNoSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesOutOfRange", "test/test_reads.py::TestReadsFiltering::testRemoveSitesWithQuality", "test/test_reads.py::TestReadsFiltering::testReverse", "test/test_reads.py::TestReadsFiltering::testReverseAndReverseComplement", "test/test_reads.py::TestReadsFiltering::testReverseComplement", "test/test_reads.py::TestReadsFiltering::testReverseComplementAARead", "test/test_reads.py::TestReadsFiltering::testReverseComplementNonDNA", "test/test_reads.py::TestReadsFiltering::testSampleFractionAndNoTrueLengthRaisesValueError", "test/test_reads.py::TestReadsFiltering::testSampleFractionAndRandomSubsetRaisesValueError", "test/test_reads.py::TestReadsFiltering::testSampleFractionOne", "test/test_reads.py::TestReadsFiltering::testSampleFractionPointOne", "test/test_reads.py::TestReadsFiltering::testSampleFractionZero", "test/test_reads.py::TestReadsInRAM::testAdd", "test/test_reads.py::TestReadsInRAM::testFastaFile", "test/test_reads.py::TestReadsInRAM::testFromReads", "test/test_reads.py::TestReadsInRAM::testNoReads", "test/test_reads.py::TestReadsInRAM::testOneReadIndex", "test/test_reads.py::TestReadsInRAM::testOneReadLength", "test/test_reads.py::TestReadsInRAM::testOneReadList", "test/test_reads.py::TestReadsInRAM::testSetItem", "test/test_reads.py::TestReadsInRAM::testTwoReadsIndex", "test/test_reads.py::TestReadsInRAM::testTwoReadsLength", "test/test_reads.py::TestReadsInRAM::testTwoReadsList", "test/test_reads.py::TestSummarizePosition::testCorrectFrequencies", "test/test_reads.py::TestSummarizePosition::testExcludeShortSequences", "test/test_reads.py::TestSummarizePosition::testFrequenciesNoReads", "test/test_reads.py::TestSummarizePosition::testIndexLargerThanSequenceLength", "test/test_reads.py::TestSummarizePosition::testNumberOfExclusionsNoReads", "test/test_reads.py::TestSitesMatching::testAllMatches", "test/test_reads.py::TestSitesMatching::testIgnoreCase", "test/test_reads.py::TestSitesMatching::testMatchCase", "test/test_reads.py::TestSitesMatching::testMultipleReadsAll", "test/test_reads.py::TestSitesMatching::testMultipleReadsAllWithDifferingLengths", "test/test_reads.py::TestSitesMatching::testMultipleReadsAny", "test/test_reads.py::TestSitesMatching::testMultipleReadsAnyWithDifferingLengths", "test/test_reads.py::TestSitesMatching::testNoMatches", "test/test_reads.py::TestSitesMatching::testPartialMatch" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-03-24 11:35:19+00:00	mit	878
adafruit__Adafruit_CircuitPython_GPS-76	diff --git a/adafruit_gps.py b/adafruit_gps.py index 10bc89c..a28a065 100644 --- a/adafruit_gps.py +++ b/adafruit_gps.py @@ -50,11 +50,11 @@ _ST_MAX = _RMC_4_1 _SENTENCE_PARAMS = ( # 0 - _GLL - "dcdcfcC", + "dcdcscC", # 1 - _RMC - "fcdcdcffiDCC", + "scdcdcffsDCC", # 2 - _GGA - "fdcdciiffsfsIS", + "sdcdciiffsfsIS", # 3 - _GSA "ciIIIIIIIIIIIIfff", # 4 - _GSA_4_11 @@ -68,7 +68,7 @@ _SENTENCE_PARAMS = ( # 8 - _GSV19 "iiiiiiIiiiIiiiIiiiI", # 9 - _RMC_4_1 - "fcdcdcffiDCCC", + "scdcdcffsDCCC", ) @@ -394,9 +394,9 @@ class GPS: return (data_type, sentence[delimiter + 1 :]) def _update_timestamp_utc(self, time_utc, date=None): - hours = time_utc // 10000 - mins = (time_utc // 100) % 100 - secs = time_utc % 100 + hours = int(time_utc[0:2]) + mins = int(time_utc[2:4]) + secs = int(time_utc[4:6]) if date is None: if self.timestamp_utc is None: day, month, year = 0, 0, 0 @@ -405,9 +405,9 @@ class GPS: month = self.timestamp_utc.tm_mon year = self.timestamp_utc.tm_year else: - day = date // 10000 - month = (date // 100) % 100 - year = 2000 + date % 100 + day = int(date[0:2]) + month = int(date[2:4]) + year = 2000 + int(date[4:6]) self.timestamp_utc = time.struct_time( (year, month, day, hours, mins, secs, 0, 0, -1) @@ -429,7 +429,7 @@ class GPS: self.longitude = _read_degrees(data, 2, "w") # UTC time of position - self._update_timestamp_utc(int(data[4])) + self._update_timestamp_utc(data[4]) # Status Valid(A) or Invalid(V) self.isactivedata = data[5] @@ -450,7 +450,7 @@ class GPS: return False # Params didn't parse # UTC time of position and date - self._update_timestamp_utc(int(data[0]), data[8]) + self._update_timestamp_utc(data[0], data[8]) # Status Valid(A) or Invalid(V) self.isactivedata = data[1] @@ -494,7 +494,7 @@ class GPS: return False # Params didn't parse # UTC time of position - self._update_timestamp_utc(int(data[0])) + self._update_timestamp_utc(data[0]) # Latitude self.latitude = _read_degrees(data, 1, "s")	adafruit/Adafruit_CircuitPython_GPS	b9e06e93f258ef3251b8104e19c9cfd435d12d60	diff --git a/tests/adafruit_gps_test.py b/tests/adafruit_gps_test.py index 9e09c85..8a956f3 100644 --- a/tests/adafruit_gps_test.py +++ b/tests/adafruit_gps_test.py @@ -140,14 +140,14 @@ def test_GPS_update_timestamp_UTC_date_None(): assert gps.datetime is None assert gps.timestamp_utc is None exp_struct = time.struct_time((0, 0, 0, 22, 14, 11, 0, 0, -1)) - gps._update_timestamp_utc(time_utc=221411) + gps._update_timestamp_utc(time_utc="221411") assert gps.timestamp_utc == exp_struct def test_GPS_update_timestamp_UTC_date_not_None(): gps = GPS(uart=UartMock()) exp_struct = time.struct_time((2021, 10, 2, 22, 14, 11, 0, 0, -1)) - gps._update_timestamp_utc(time_utc=221411, date=21021) + gps._update_timestamp_utc(time_utc="221411", date="021021") assert gps.timestamp_utc == exp_struct @@ -157,7 +157,7 @@ def test_GPS_update_timestamp_timestamp_utc_was_not_none_new_date_none(): gps.timestamp_utc = time.struct_time((2021, 10, 2, 22, 10, 11, 0, 0, -1)) exp_struct = time.struct_time((2021, 10, 2, 22, 14, 11, 0, 0, -1)) # update the timestamp - gps._update_timestamp_utc(time_utc=221411) + gps._update_timestamp_utc(time_utc="221411") assert gps.timestamp_utc == exp_struct	Usage of float causes timestamp_utc to be imprecise NMEA timestamp is written as HHMMSS.sss, which is stored as float in the module. Later it is converted to int which is inaccurate: See example: ``` >> int(184105.000) 184104 ``` This is then math'ed into the fields in time_struct. Propose storing the NMEA sentence as string instead, and grabbing the sections of the sting directly.	b9e06e93f258ef3251b8104e19c9cfd435d12d60	[ "tests/adafruit_gps_test.py::test_GPS_update_timestamp_timestamp_utc_was_not_none_new_date_none", "tests/adafruit_gps_test.py::test_GPS_update_timestamp_UTC_date_None", "tests/adafruit_gps_test.py::test_GPS_update_timestamp_UTC_date_not_None" ]	[ "tests/adafruit_gps_test.py::test_parse_talker_regular", "tests/adafruit_gps_test.py::test_GPS_update_empty_sentence", "tests/adafruit_gps_test.py::test_read_degrees[west", "tests/adafruit_gps_test.py::test_GPS_update_from_GSA[greater", "tests/adafruit_gps_test.py::test_parse_float_invalid[None]", "tests/adafruit_gps_test.py::test_parse_degrees[long", "tests/adafruit_gps_test.py::test_parse_float", "tests/adafruit_gps_test.py::test_GPS_update_rmc_has_magnetic_variation[E]", "tests/adafruit_gps_test.py::test_parse_data_unknown_sentence_type[10]", "tests/adafruit_gps_test.py::test_GPS_update_from_GSV_both_parts_sats_are_removed", "tests/adafruit_gps_test.py::test_parse_str_invalid[]", "tests/adafruit_gps_test.py::test_read_sentence_too_few_in_waiting", "tests/adafruit_gps_test.py::test_GPS_update_rmc_fix_is_set", "tests/adafruit_gps_test.py::test_GPS_update_data_type_too_short", "tests/adafruit_gps_test.py::test_GPS_update_sentence_is_None", "tests/adafruit_gps_test.py::test_read_degrees[south", "tests/adafruit_gps_test.py::test_GPS_send_command_without_checksum", "tests/adafruit_gps_test.py::test_parse_degrees[leading", "tests/adafruit_gps_test.py::test_parse_int_invalid[None]", "tests/adafruit_gps_test.py::test_parse_str_invalid[None]", "tests/adafruit_gps_test.py::test_parse_degrees[regular", "tests/adafruit_gps_test.py::test_parse_str_valid", "tests/adafruit_gps_test.py::test_GPS_update_from_GLL", "tests/adafruit_gps_test.py::test_parse_int_invalid[]", "tests/adafruit_gps_test.py::test_GPS_update_with_unknown_talker", "tests/adafruit_gps_test.py::test_read_degrees[north", "tests/adafruit_gps_test.py::test_GPS_update_from_GSV_first_part", "tests/adafruit_gps_test.py::test_GPS_update_rmc_debug_shows_sentence", "tests/adafruit_gps_test.py::test_GPS_update_rmc_no_magnetic_variation", "tests/adafruit_gps_test.py::test_parse_degrees_too_short", "tests/adafruit_gps_test.py::test_GPS_update_from_GSA[smaller", "tests/adafruit_gps_test.py::test_GPS_update_rmc_invalid_checksum", "tests/adafruit_gps_test.py::test_GPS_update_from_GGA", "tests/adafruit_gps_test.py::test_parse_data_unexpected_parameter_type", "tests/adafruit_gps_test.py::test_GPS_update_rmc_has_magnetic_variation[W]", "tests/adafruit_gps_test.py::test_parse_data_unknown_sentence_type[-1]", "tests/adafruit_gps_test.py::test_parse_talker_prop_code", "tests/adafruit_gps_test.py::test_read_degrees[east", "tests/adafruit_gps_test.py::test_GPS_update_rmc_fix_is_set_new", "tests/adafruit_gps_test.py::test_parse_float_invalid[]", "tests/adafruit_gps_test.py::test_GPS_send_command_with_checksum", "tests/adafruit_gps_test.py::test_GPS_update_from_RMC", "tests/adafruit_gps_test.py::test_param_types_does_not_match_data_items", "tests/adafruit_gps_test.py::test_parse_int", "tests/adafruit_gps_test.py::test_parse_sentence_invalid_delimiter" ]	{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-12-08 21:02:48+00:00	mit	879
adafruit__circup-21	diff --git a/circup.py b/circup.py index da2acab..5e9aef8 100644 --- a/circup.py +++ b/circup.py @@ -502,9 +502,21 @@ def ensure_latest_bundle(): logger.exception(ex) if tag > old_tag: logger.info("New version available ({}).".format(tag)) - get_bundle(tag) - with open(BUNDLE_DATA, "w", encoding="utf-8") as data: - json.dump({"tag": tag}, data) + try: + get_bundle(tag) + with open(BUNDLE_DATA, "w", encoding="utf-8") as data: + json.dump({"tag": tag}, data) + except requests.exceptions.HTTPError as ex: + # See #20 for reason this this + click.secho( + ( + "There was a problem downloading the bundle. " + "Please try again in a moment." + ), + fg="red", + ) + logger.exception(ex) + sys.exit(1) else: logger.info("Current library bundle up to date ({}).".format(tag)) @@ -761,10 +773,14 @@ def install(name, py): # pragma: no cover shutil.copyfile(source_path, target_path) else: # Use pre-compiled mpy modules. - module_name = os.path.basename(metadata["path"]).replace(".py", ".mpy") + module_name = os.path.basename(metadata["path"]).replace( + ".py", ".mpy" + ) if not module_name: # Must be a directory based module. - module_name = os.path.basename(os.path.dirname(metadata["path"])) + module_name = os.path.basename( + os.path.dirname(metadata["path"]) + ) major_version = CPY_VERSION.split(".")[0] bundle_platform = "{}mpy".format(major_version) bundle_path = ""	adafruit/circup	024a8bc0cb4555cb122aadd567bd991222fd630a	diff --git a/tests/test_circup.py b/tests/test_circup.py index 32e8ae8..40b87ee 100644 --- a/tests/test_circup.py +++ b/tests/test_circup.py @@ -26,6 +26,7 @@ import circup import ctypes import pytest import json +import requests from unittest import mock @@ -545,8 +546,8 @@ def test_ensure_latest_bundle_bad_bundle_data(): def test_ensure_latest_bundle_to_update(): """ - If the version found in the BUNDLE_DATA is out of date, the cause an update - to the bundle. + If the version found in the BUNDLE_DATA is out of date, then cause an + update to the bundle. """ with mock.patch("circup.get_latest_tag", return_value="54321"), mock.patch( "circup.os.path.isfile", return_value=True @@ -561,6 +562,30 @@ def test_ensure_latest_bundle_to_update(): assert mock_json.dump.call_count == 1 # Current version saved to file. +def test_ensure_latest_bundle_to_update_http_error(): + """ + If an HTTP error happens during a bundle update, print a friendly + error message and exit 1. + """ + with mock.patch("circup.get_latest_tag", return_value="54321"), mock.patch( + "circup.os.path.isfile", return_value=True + ), mock.patch("circup.open"), mock.patch( + "circup.get_bundle", side_effect=requests.exceptions.HTTPError("404") + ) as mock_gb, mock.patch( + "circup.json" + ) as mock_json, mock.patch( + "circup.click.secho" + ) as mock_click, mock.patch( + "circup.sys.exit" + ) as mock_exit: + mock_json.load.return_value = {"tag": "12345"} + circup.ensure_latest_bundle() + mock_gb.assert_called_once_with("54321") + assert mock_json.dump.call_count == 0 # not saved. + mock_click.call_count == 1 # friendly message. + mock_exit.assert_called_once_with(1) # exit 1. + + def test_ensure_latest_bundle_no_update(): """ If the version found in the BUNDLE_DATA is NOT out of date, just log the	Error while running CircUp Show during bundle release I kind of got lucky finding this one. At the time I ran it, the release had been created, but the bundle asset hadn't been finished being generated. ``` bash-3.2$ circup show Found device at /Volumes/CIRCUITPY, running CircuitPython 5.0.0-alpha.4. Downloading latest version information. Traceback (most recent call last): File "/usr/local/bin/circup", line 10, in <module> sys.exit(main()) File "/usr/local/lib/python3.7/site-packages/click/core.py", line 764, in __call__ return self.main(args, kwargs) File "/usr/local/lib/python3.7/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/usr/local/lib/python3.7/site-packages/click/core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/usr/local/lib/python3.7/site-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, ctx.params) File "/usr/local/lib/python3.7/site-packages/click/core.py", line 555, in invoke return callback(args, **kwargs) File "/usr/local/lib/python3.7/site-packages/circup.py", line 719, in show available_modules = get_bundle_versions() File "/usr/local/lib/python3.7/site-packages/circup.py", line 403, in get_bundle_versions ensure_latest_bundle() File "/usr/local/lib/python3.7/site-packages/circup.py", line 505, in ensure_latest_bundle get_bundle(tag) File "/usr/local/lib/python3.7/site-packages/circup.py", line 547, in get_bundle r.raise_for_status() File "/usr/local/lib/python3.7/site-packages/requests/models.py", line 940, in raise_for_status raise HTTPError(http_error_msg, response=self) requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://github.com/adafruit/Adafruit_CircuitPython_Bundle/releases/download/20191029/adafruit-circuitpython-bundle-py-20191029.zip ```	024a8bc0cb4555cb122aadd567bd991222fd630a	[ "tests/test_circup.py::test_ensure_latest_bundle_to_update_http_error" ]	[ "tests/test_circup.py::test_Module_init_file_module", "tests/test_circup.py::test_Module_init_directory_module", "tests/test_circup.py::test_Module_outofdate", "tests/test_circup.py::test_Module_outofdate_bad_versions", "tests/test_circup.py::test_Module_row", "tests/test_circup.py::test_Module_update_dir", "tests/test_circup.py::test_Module_update_file", "tests/test_circup.py::test_Module_repr", "tests/test_circup.py::test_find_device_posix_exists", "tests/test_circup.py::test_find_device_posix_no_mount_command", "tests/test_circup.py::test_find_device_posix_missing", "tests/test_circup.py::test_find_device_nt_exists", "tests/test_circup.py::test_find_device_nt_missing", "tests/test_circup.py::test_find_device_unknown_os", "tests/test_circup.py::test_get_latest_tag", "tests/test_circup.py::test_extract_metadata_python", "tests/test_circup.py::test_extract_metadata_byte_code", "tests/test_circup.py::test_find_modules", "tests/test_circup.py::test_find_modules_goes_bang", "tests/test_circup.py::test_get_bundle_versions", "tests/test_circup.py::test_get_circuitpython_version", "tests/test_circup.py::test_get_device_versions", "tests/test_circup.py::test_get_modules_empty_path", "tests/test_circup.py::test_get_modules_that_are_files", "tests/test_circup.py::test_get_modules_that_are_directories", "tests/test_circup.py::test_get_modules_that_are_directories_with_no_metadata", "tests/test_circup.py::test_ensure_latest_bundle_no_bundle_data", "tests/test_circup.py::test_ensure_latest_bundle_bad_bundle_data", "tests/test_circup.py::test_ensure_latest_bundle_to_update", "tests/test_circup.py::test_ensure_latest_bundle_no_update", "tests/test_circup.py::test_get_bundle", "tests/test_circup.py::test_get_bundle_network_error" ]	{ "failed_lite_validators": [ "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }	2019-10-30 08:45:28+00:00	mit	880
adamboche__python-marshmallow-union-29	diff --git a/src/marshmallow_union/__init__.py b/src/marshmallow_union/__init__.py index 69e3099..b3b86e1 100644 --- a/src/marshmallow_union/__init__.py +++ b/src/marshmallow_union/__init__.py @@ -59,9 +59,22 @@ class Union(marshmallow.fields.Field): for candidate_field in fields: try: - return candidate_field.serialize( - attr, obj, error_store=error_store, kwargs - ) + try: + return candidate_field.serialize( + attr, obj, error_store=error_store, kwargs + ) + except TypeError: + # When serialising a mapping (eg dict) value item, 'attr' and 'obj' + # is none (as a dict value is not an attribute of anything). This + # causes issues with the attribute-get methods within + # 'marshmallow', but can be bypassed by passing the known 'value' + # directly to '_serialize' + if attr is obj is None: + # pylint: disable=protected-access + return candidate_field._serialize( + value, attr, obj, **kwargs + ) + raise # pylint: disable=broad-except except Exception as exc: pass	adamboche/python-marshmallow-union	49f82a94403b686e56c4509cf75bca40a9dfe23a	diff --git a/tests/test_union.py b/tests/test_union.py index 10e6066..c4ffd4f 100644 --- a/tests/test_union.py +++ b/tests/test_union.py @@ -32,6 +32,19 @@ class OtherSchema(marshmallow.Schema): ) +class MappingSchema(marshmallow.Schema): + """Schema with union inside mapping.""" + items = marshmallow.fields.Dict( + marshmallow.fields.String(), + marshmallow_union.Union( + [ + marshmallow.fields.Integer(), + marshmallow.fields.List(marshmallow.fields.Integer()), + ], + ), + ) + + class StrIntSchema(marshmallow.Schema): """Schema with str and int candidates.""" @@ -46,6 +59,7 @@ class StrIntSchema(marshmallow.Schema): ({"name": "Alice", "number_or_numbers": [25, 50]}, OtherSchema()), ({"x": 5}, StrIntSchema()), ({"x": "hello"}, StrIntSchema()), + ({"items": {"a": 42, "b": [17]}}, MappingSchema()), ], ) def test_round_trip(data, schema): @@ -60,6 +74,7 @@ def test_round_trip(data, schema): [ ({"name": "Alice", "number_or_numbers": "twenty-five"}, PersonSchema()), ({"name": "Alice", "number_or_numbers": {"x": 14}}, PersonSchema()), + ({"items": {"a": 42, "b": "spam"}}, MappingSchema()), ], ) def test_raises(data, schema):	Support union for mapping value When using a union for a mapping value-type, marshmallow-union raises `ExceptionGroup` during serialisation. All candidate fields raise as marshmallow-union calls `schema.serialise(attr, obj, ...)`. However, inside a mapping value-type, marshmallow calls `schema._serialise(value, None, None)`, as the mapping values are not part of the serialised object. ### Reproduction ```python import typing as t import dataclasses import marshmallow import marshmallow_dataclass @marshmallow_dataclass.dataclass class Foo: bar: t.Dict[str, t.Union[int, str]] = dataclasses.field(default_factory=dict) obj = Foo(bar={"spam": "eggs", "ham": 42}) schema = Foo.Schema() schema.dump(obj) ``` ### Expected ```python {'bar': {'spam': 'eggs', 'ham': 42}} ``` ### Actual ```python Traceback (most recent call last): File "<stdin>", line 1, in <module> File "~/env-tmp/lib/python3.7/site-packages/marshmallow/schema.py", line 553, in dump result = self._serialize(processed_obj, many=many) File "~/env-tmp/lib/python3.7/site-packages/marshmallow/schema.py", line 517, in _serialize value = field_obj.serialize(attr_name, obj, accessor=self.get_attribute) File "~/env-tmp/lib/python3.7/site-packages/marshmallow/fields.py", line 325, in serialize return self._serialize(value, attr, obj, kwargs) File "`/env-tmp/lib/python3.7/site-packages/marshmallow/fields.py", line 1510, in _serialize result[keys[k]] = self.value_field._serialize(v, None, None, kwargs) File "~/env-tmp/lib/python3.7/site-packages/marshmallow_union/__init__.py", line 69, in _serialize raise ExceptionGroup("All serializers raised exceptions.\n", error_store.errors) marshmallow_union.ExceptionGroup: ('All serializers raised exceptions.\n', {}) ``` ### Environment * OS: Ubuntu 19:10 * Python: 3.7.5 * marshmallow: 3.2.2 * marshmallow-union: 0.1.12 * marshmallow-dataclass: 7.1	49f82a94403b686e56c4509cf75bca40a9dfe23a	[ "tests/test_union.py::test_round_trip[data5-schema5]" ]	[ "tests/test_union.py::test_round_trip[data0-schema0]", "tests/test_union.py::test_round_trip[data1-schema1]", "tests/test_union.py::test_round_trip[data2-schema2]", "tests/test_union.py::test_round_trip[data3-schema3]", "tests/test_union.py::test_round_trip[data4-schema4]", "tests/test_union.py::test_raises[data0-schema0]", "tests/test_union.py::test_raises[data1-schema1]", "tests/test_union.py::test_raises[data2-schema2]" ]	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2019-12-27 12:40:46+00:00	mit	881
adamboche__python-marshmallow-union-33	diff --git a/src/marshmallow_union/__init__.py b/src/marshmallow_union/__init__.py index 22d5ef4..ee47920 100644 --- a/src/marshmallow_union/__init__.py +++ b/src/marshmallow_union/__init__.py @@ -13,6 +13,7 @@ class MarshmallowUnionException(Exception): class ExceptionGroup(MarshmallowUnionException): """Collection of possibly multiple exceptions.""" + def __init__(self, msg: str, errors): self.msg = msg self.errors = errors @@ -63,8 +64,8 @@ class Union(marshmallow.fields.Field): for candidate_field in fields: try: - return candidate_field.serialize( - attr, obj, error_store=error_store, kwargs + return candidate_field._serialize( + value, attr, obj, error_store=error_store, kwargs ) except ValueError as e: error_store.store_error({attr: e})	adamboche/python-marshmallow-union	58bfc9fb069e00478afba87da3e003464cbdaebe	diff --git a/tests/test_union.py b/tests/test_union.py index 6377c06..c93f004 100644 --- a/tests/test_union.py +++ b/tests/test_union.py @@ -52,6 +52,14 @@ class IntStrSchema(marshmallow.Schema): x = marshmallow_union.Union([marshmallow.fields.Int(), marshmallow.fields.String()]) +class ListUnionSchema(marshmallow.Schema): + """Schema with a list of unions.""" + + l = marshmallow.fields.List( + marshmallow_union.Union([marshmallow.fields.Int(), marshmallow.fields.String()]) + ) + + @pytest.mark.parametrize( "data, schema", [ @@ -59,6 +67,7 @@ class IntStrSchema(marshmallow.Schema): ({"name": "Alice", "number_or_numbers": [25, 50]}, PersonSchema()), ({"name": "Alice", "number_or_numbers": [25, 50]}, OtherSchema()), ({"x": 5}, IntStrSchema()), + ({"l": ["h", 5, "n", 1]}, ListUnionSchema()), ({"x": "hello"}, IntStrSchema()), ({"items": {"a": 42, "b": [17]}}, MappingSchema()), ],	_serialize ignores the given value The `_serialize` method of `Union` calls the `serialize` method (instead of `_serialize`) on the underlying fields. This means that it ignores the given `value` parameter, and may try to serialize a completely different value. See: https://github.com/adamboche/python-marshmallow-union/blob/master/src/marshmallow_union/__init__.py#L66-L68 Initially reported in: https://github.com/lovasoa/marshmallow_dataclass/issues/67	58bfc9fb069e00478afba87da3e003464cbdaebe	[ "tests/test_union.py::test_round_trip[data4-schema4]" ]	[ "tests/test_union.py::test_round_trip[data0-schema0]", "tests/test_union.py::test_round_trip[data1-schema1]", "tests/test_union.py::test_round_trip[data2-schema2]", "tests/test_union.py::test_round_trip[data3-schema3]", "tests/test_union.py::test_round_trip[data5-schema5]", "tests/test_union.py::test_round_trip[data6-schema6]", "tests/test_union.py::test_load_raises[data0-schema0]", "tests/test_union.py::test_load_raises[data1-schema1]", "tests/test_union.py::test_load_raises[data2-schema2]", "tests/test_union.py::test_dump_raises[data0-schema0]", "tests/test_union.py::test_dump_raises[data1-schema1]", "tests/test_union.py::test_dump_raises[data2-schema2]" ]	{ "failed_lite_validators": [ "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }	2020-05-23 13:45:41+00:00	mit	882
adamchainz__apig-wsgi-118	diff --git a/src/apig_wsgi.py b/src/apig_wsgi.py index efb01d2..d5ea0f0 100644 --- a/src/apig_wsgi.py +++ b/src/apig_wsgi.py @@ -94,10 +94,8 @@ def get_environ(event, binary_support): if key == "CONTENT_TYPE": environ["CONTENT_TYPE"] = values[-1] - continue elif key == "HOST": environ["SERVER_NAME"] = values[-1] - continue elif key == "X_FORWARDED_FOR": environ["REMOTE_ADDR"] = values[-1].split(", ")[0] elif key == "X_FORWARDED_PROTO":	adamchainz/apig-wsgi	4f3b043beb5067379a7d1459aea751eb74a27e5e	diff --git a/tests/test_apig_wsgi.py b/tests/test_apig_wsgi.py index 736d859..fff9c37 100644 --- a/tests/test_apig_wsgi.py +++ b/tests/test_apig_wsgi.py @@ -343,10 +343,60 @@ def test_special_headers(simple_app): simple_app.handler(event, None) assert simple_app.environ["CONTENT_TYPE"] == "text/plain" + assert simple_app.environ["HTTP_CONTENT_TYPE"] == "text/plain" assert simple_app.environ["SERVER_NAME"] == "example.com" + assert simple_app.environ["HTTP_HOST"] == "example.com" assert simple_app.environ["REMOTE_ADDR"] == "1.2.3.4" + assert simple_app.environ["HTTP_X_FORWARDED_FOR"] == "1.2.3.4, 5.6.7.8" assert simple_app.environ["wsgi.url_scheme"] == "https" + assert simple_app.environ["HTTP_X_FORWARDED_PROTO"] == "https" assert simple_app.environ["SERVER_PORT"] == "123" + assert simple_app.environ["HTTP_X_FORWARDED_PORT"] == "123" + + +def test_special_content_type(simple_app): + event = make_event(headers={"Content-Type": ["text/plain"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["CONTENT_TYPE"] == "text/plain" + assert simple_app.environ["HTTP_CONTENT_TYPE"] == "text/plain" + + +def test_special_host(simple_app): + event = make_event(headers={"Host": ["example.com"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["SERVER_NAME"] == "example.com" + assert simple_app.environ["HTTP_HOST"] == "example.com" + + +def test_special_x_forwarded_for(simple_app): + event = make_event(headers={"X-Forwarded-For": ["1.2.3.4, 5.6.7.8"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["REMOTE_ADDR"] == "1.2.3.4" + assert simple_app.environ["HTTP_X_FORWARDED_FOR"] == "1.2.3.4, 5.6.7.8" + + +def test_x_forwarded_proto(simple_app): + event = make_event(headers={"X-Forwarded-Proto": ["https"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["wsgi.url_scheme"] == "https" + assert simple_app.environ["HTTP_X_FORWARDED_PROTO"] == "https" + + +def test_x_forwarded_port(simple_app): + event = make_event(headers={"X-Forwarded-Port": ["123"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["SERVER_PORT"] == "123" + assert simple_app.environ["HTTP_X_FORWARDED_PORT"] == "123" def test_no_headers(simple_app):	2.5.0 Multivalue support breaks Host Header support The new update for 2.5.0 broke for us, because we're trying to access the HTTP Host header directly, rather than accessing via the `SERVER_NAME` WSGI variable. Was this intentional, or just a byproduct of trying to also set `SERVER_NAME` for WSGI spec compliance?	4f3b043beb5067379a7d1459aea751eb74a27e5e	[ "tests/test_apig_wsgi.py::test_special_headers", "tests/test_apig_wsgi.py::test_special_content_type", "tests/test_apig_wsgi.py::test_special_host" ]	[ "tests/test_apig_wsgi.py::test_get", "tests/test_apig_wsgi.py::test_get_missing_content_type", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::test_get_binary_support_binary", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]", "tests/test_apig_wsgi.py::test_get_binary_support_no_content_type", "tests/test_apig_wsgi.py::test_post", "tests/test_apig_wsgi.py::test_post_binary_support", "tests/test_apig_wsgi.py::test_querystring_none", "tests/test_apig_wsgi.py::test_querystring_none_single", "tests/test_apig_wsgi.py::test_querystring_empty", "tests/test_apig_wsgi.py::test_querystring_empty_single", "tests/test_apig_wsgi.py::test_querystring_one", "tests/test_apig_wsgi.py::test_querystring_one_single", "tests/test_apig_wsgi.py::test_querystring_encoding_value", "tests/test_apig_wsgi.py::test_querystring_encoding_key", "tests/test_apig_wsgi.py::test_querystring_multi", "tests/test_apig_wsgi.py::test_plain_header", "tests/test_apig_wsgi.py::test_plain_header_single", "tests/test_apig_wsgi.py::test_plain_header_multi", "tests/test_apig_wsgi.py::test_special_x_forwarded_for", "tests/test_apig_wsgi.py::test_x_forwarded_proto", "tests/test_apig_wsgi.py::test_x_forwarded_port", "tests/test_apig_wsgi.py::test_no_headers", "tests/test_apig_wsgi.py::test_headers_None", "tests/test_apig_wsgi.py::test_exc_info", "tests/test_apig_wsgi.py::test_request_context", "tests/test_apig_wsgi.py::test_full_event" ]	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2020-02-26 12:33:27+00:00	isc	883
adamchainz__apig-wsgi-156	diff --git a/HISTORY.rst b/HISTORY.rst index 048a4ab..8eb3af1 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -1,6 +1,12 @@ History ======= +* Add defaults for ``SERVER_HOST``, ``SERVER_PORT`` and ``wsgi.url_scheme``. + This enables responding to `ELB health check events + <https://docs.aws.amazon.com/elasticloadbalancing/latest/application/lambda-functions.html#enable-health-checks-lambda>`__, + which don't contain the relevant headers + (`Issue #155 <https://github.com/adamchainz/apig-wsgi/pull/155>`__). + 2.6.0 (2020-03-07) ------------------ diff --git a/src/apig_wsgi.py b/src/apig_wsgi.py index 4c7a17a..c12b638 100644 --- a/src/apig_wsgi.py +++ b/src/apig_wsgi.py @@ -62,12 +62,15 @@ def get_environ(event, context, binary_support): "REQUEST_METHOD": method, "SCRIPT_NAME": "", "SERVER_PROTOCOL": "HTTP/1.1", + "SERVER_NAME": "", + "SERVER_PORT": "", "wsgi.errors": sys.stderr, "wsgi.input": BytesIO(body), "wsgi.multiprocess": False, "wsgi.multithread": False, "wsgi.run_once": False, "wsgi.version": (1, 0), + "wsgi.url_scheme": "http", } # Multi-value query strings need explicit activation on ALB	adamchainz/apig-wsgi	d42e72a00409c1ce51011db1d46ecd9a1667984a	diff --git a/tests/test_apig_wsgi.py b/tests/test_apig_wsgi.py index 2e091a8..8339a89 100644 --- a/tests/test_apig_wsgi.py +++ b/tests/test_apig_wsgi.py @@ -472,6 +472,29 @@ def test_full_event(simple_app): assert simple_app.environ["apig_wsgi.full_event"] == event +def test_elb_health_check(simple_app): + """ + Check compatibility with health check events as per: + https://docs.aws.amazon.com/elasticloadbalancing/latest/application/lambda-functions.html#enable-health-checks-lambda # noqa: B950 + """ + event = { + "requestContext": {"elb": {"targetGroupArn": "..."}}, + "httpMethod": "GET", + "path": "/", + "queryStringParameters": {}, + "headers": {"user-agent": "ELB-HealthChecker/2.0"}, + "body": "", + "isBase64Encoded": False, + } + + simple_app.handler(event, None) + + environ = simple_app.environ + assert environ["SERVER_NAME"] == "" + assert environ["SERVER_PORT"] == "" + assert environ["wsgi.url_scheme"] == "http" + + def test_context(simple_app): context = ContextStub(aws_request_id="test-request-id")	ELB Health Checks not handled Hello! Thank you for your tool it's great. We have a little issue when using a lambda as an ELB target when we turn on health check because the event looks like this: ``` { "requestContext": { "elb": { "targetGroupArn": "arn:aws:elasticloadbalancing:region:123456789012:targetgroup/my-target-group/6d0ecf831eec9f09" } }, "httpMethod": "GET", "path": "/", "queryStringParameters": {}, "headers": { "user-agent": "ELB-HealthChecker/2.0" }, "body": "", "isBase64Encoded": false } ``` source: https://docs.aws.amazon.com/elasticloadbalancing/latest/application/lambda-functions.html#enable-health-checks-lambda This has almost no headers leading to this error ``` File "/var/task/flask/app.py", line 2306, in wsgi_app ctx = self.request_context(environ) File "/var/task/flask/app.py", line 2223, in request_context return RequestContext(self, environ) File "/var/task/flask/ctx.py", line 284, in __init__ self.url_adapter = app.create_url_adapter(self.request) File "/var/task/flask/app.py", line 2040, in create_url_adapter subdomain=subdomain) File "/var/task/werkzeug/routing.py", line 1502, in bind_to_environ wsgi_server_name = get_host(environ).lower() File "/var/task/werkzeug/wsgi.py", line 168, in get_host rv = environ["SERVER_NAME"] ``` i found with some testing that i can patch the event like this to make it work: ``` def elb_health_check_patcher(handler): @wraps(handler) def wrapper(event, context): user_agent = event.get('headers', {}).get('user-agent') if user_agent == "ELB-HealthChecker/2.0": event['headers']['x-forwarded-proto'] = 'http' event['headers']['host'] = 'elb-health-check' return handler(event, context) return wrapper handler = elb_health_check_patcher(make_lambda_handler(my_app)) ``` I may propose a PR soon if you're open to :)	d42e72a00409c1ce51011db1d46ecd9a1667984a	[ "tests/test_apig_wsgi.py::test_elb_health_check" ]	[ "tests/test_apig_wsgi.py::test_get", "tests/test_apig_wsgi.py::test_get_missing_content_type", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::test_get_binary_support_binary", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]", "tests/test_apig_wsgi.py::test_get_binary_support_no_content_type", "tests/test_apig_wsgi.py::test_post", "tests/test_apig_wsgi.py::test_post_binary_support", "tests/test_apig_wsgi.py::test_querystring_none", "tests/test_apig_wsgi.py::test_querystring_none_single", "tests/test_apig_wsgi.py::test_querystring_empty", "tests/test_apig_wsgi.py::test_querystring_empty_single", "tests/test_apig_wsgi.py::test_querystring_one", "tests/test_apig_wsgi.py::test_querystring_one_single", "tests/test_apig_wsgi.py::test_querystring_encoding_value", "tests/test_apig_wsgi.py::test_querystring_encoding_key", "tests/test_apig_wsgi.py::test_querystring_multi", "tests/test_apig_wsgi.py::test_plain_header", "tests/test_apig_wsgi.py::test_plain_header_single", "tests/test_apig_wsgi.py::test_plain_header_multi", "tests/test_apig_wsgi.py::test_special_headers", "tests/test_apig_wsgi.py::test_special_content_type", "tests/test_apig_wsgi.py::test_special_host", "tests/test_apig_wsgi.py::test_special_x_forwarded_for", "tests/test_apig_wsgi.py::test_x_forwarded_proto", "tests/test_apig_wsgi.py::test_x_forwarded_port", "tests/test_apig_wsgi.py::test_no_headers", "tests/test_apig_wsgi.py::test_headers_None", "tests/test_apig_wsgi.py::test_exc_info", "tests/test_apig_wsgi.py::test_request_context", "tests/test_apig_wsgi.py::test_full_event", "tests/test_apig_wsgi.py::test_context" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2020-07-10 18:59:38+00:00	isc	884
adamchainz__apig-wsgi-187	diff --git a/HISTORY.rst b/HISTORY.rst index 724abe9..f4bc806 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -3,6 +3,9 @@ History ======= * Support Python 3.9. +* Fix query string parameter encoding so that symbols are correctly re-encoded + for WSGI, for API Gateway format version 1 + (`Issue #186 <https://github.com/adamchainz/apig-wsgi/pull/186>`__). 2.9.0 (2020-10-12) ------------------ @@ -11,7 +14,8 @@ History * Always send ``isBase64Encoded`` in responses, as per the AWS documentation. * Support `format version 2 <https://docs.aws.amazon.com/apigateway/latest/developerguide/http-api-develop-integrations-lambda.html>`, - which was introduced by API Gateway for “HTTP API's”. + which was introduced by API Gateway for “HTTP API's” + (`Issue #124 <https://github.com/adamchainz/apig-wsgi/pull/124>`__).. * ``binary_support`` now defaults to ``None``, which means that it will automatically enable binary support for format version 2 events. diff --git a/src/apig_wsgi.py b/src/apig_wsgi.py index a261c38..424d008 100644 --- a/src/apig_wsgi.py +++ b/src/apig_wsgi.py @@ -2,6 +2,7 @@ import sys from base64 import b64decode, b64encode from collections import defaultdict from io import BytesIO +from urllib.parse import urlencode __all__ = ("make_lambda_handler",) @@ -87,14 +88,13 @@ def get_environ_v1(event, context, binary_support): # Multi-value query strings need explicit activation on ALB if "multiValueQueryStringParameters" in event: - # may be None when testing on console - multi_params = event["multiValueQueryStringParameters"] or {} + environ["QUERY_STRING"] = urlencode( + # may be None when testing on console + event["multiValueQueryStringParameters"] or (), + doseq=True, + ) else: - single_params = event.get("queryStringParameters") or {} - multi_params = {key: [value] for key, value in single_params.items()} - environ["QUERY_STRING"] = "&".join( - "{}={}".format(key, val) for (key, vals) in multi_params.items() for val in vals - ) + environ["QUERY_STRING"] = urlencode(event.get("queryStringParameters") or ()) # Multi-value headers need explicit activation on ALB if "multiValueHeaders" in event:	adamchainz/apig-wsgi	afaf2e5ae3279b15657431b24dcc01105ec2a5ce	diff --git a/tests/test_apig_wsgi.py b/tests/test_apig_wsgi.py index 6eca17c..2c98ab4 100644 --- a/tests/test_apig_wsgi.py +++ b/tests/test_apig_wsgi.py @@ -328,19 +328,19 @@ class TestV1Events: assert simple_app.environ["QUERY_STRING"] == "foo=bar" - def test_querystring_encoding_value(self, simple_app): - event = make_v1_event(qs_params={"foo": ["a%20bar"]}) + def test_querystring_encoding_plus_value(self, simple_app): + event = make_v1_event(qs_params={"a": ["b+c"]}, qs_params_multi=False) simple_app.handler(event, None) - assert simple_app.environ["QUERY_STRING"] == "foo=a%20bar" + assert simple_app.environ["QUERY_STRING"] == "a=b%2Bc" - def test_querystring_encoding_key(self, simple_app): - event = make_v1_event(qs_params={"a%20foo": ["bar"]}) + def test_querystring_encoding_plus_key(self, simple_app): + event = make_v1_event(qs_params={"a+b": ["c"]}, qs_params_multi=False) simple_app.handler(event, None) - assert simple_app.environ["QUERY_STRING"] == "a%20foo=bar" + assert simple_app.environ["QUERY_STRING"] == "a%2Bb=c" def test_querystring_multi(self, simple_app): event = make_v1_event(qs_params={"foo": ["bar", "baz"]}) @@ -349,6 +349,20 @@ class TestV1Events: assert simple_app.environ["QUERY_STRING"] == "foo=bar&foo=baz" + def test_querystring_multi_encoding_plus_value(self, simple_app): + event = make_v1_event(qs_params={"a": ["b+c", "d"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a=b%2Bc&a=d" + + def test_querystring_multi_encoding_plus_key(self, simple_app): + event = make_v1_event(qs_params={"a+b": ["c"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a%2Bb=c" + def test_plain_header(self, simple_app): event = make_v1_event(headers={"Test-Header": ["foobar"]})	QueryStringParameters encoding issue Hi, I suspect an issue while providing queryParameters. When performing a query to my API using <API_ROOT>/logs?start_time=2020-10-12T14:00:00%2B02:00&end_time=2020-10-12T15:00:00%2B02:00 I get my query string values in Flask endpoint as: start_time = "2020-10-12T14:00:00 02:00" end_time = "2020-10-12T15:00:00 02:00" and it should be : start_time = "2020-10-12T14:00:00+02:00" end_time = "2020-10-12T15:00:00+02:00" Note: The "+" has been removed I think this is because API Gateway is providing queryStringParameters decoded and your are not encoding them back to store them in environ["QUERY_STRING"]. If we look to what other WSGI adapters (like Zappa) are doing: ``` if 'multiValueQueryStringParameters' in event_info: query = event_info['multiValueQueryStringParameters'] query_string = urlencode(query, doseq=True) if query else '' else: query = event_info.get('queryStringParameters', {}) query_string = urlencode(query) if query else '' ``` Hope it helps.	afaf2e5ae3279b15657431b24dcc01105ec2a5ce	[ "tests/test_apig_wsgi.py::TestV1Events::test_querystring_encoding_plus_value", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_encoding_plus_key", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_multi_encoding_plus_value", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_multi_encoding_plus_key" ]	[ "tests/test_apig_wsgi.py::TestV1Events::test_get", "tests/test_apig_wsgi.py::TestV1Events::test_get_missing_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_get_single_header", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_no_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_post", "tests/test_apig_wsgi.py::TestV1Events::test_post_binary_support", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_none", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_none_single", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_empty", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_empty_single", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_one", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_one_single", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_multi", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header_single", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header_multi", "tests/test_apig_wsgi.py::TestV1Events::test_special_headers", "tests/test_apig_wsgi.py::TestV1Events::test_special_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_special_host", "tests/test_apig_wsgi.py::TestV1Events::test_special_x_forwarded_for", "tests/test_apig_wsgi.py::TestV1Events::test_x_forwarded_proto", "tests/test_apig_wsgi.py::TestV1Events::test_x_forwarded_port", "tests/test_apig_wsgi.py::TestV1Events::test_no_headers", "tests/test_apig_wsgi.py::TestV1Events::test_headers_None", "tests/test_apig_wsgi.py::TestV1Events::test_exc_info", "tests/test_apig_wsgi.py::TestV1Events::test_request_context", "tests/test_apig_wsgi.py::TestV1Events::test_full_event", "tests/test_apig_wsgi.py::TestV1Events::test_elb_health_check", "tests/test_apig_wsgi.py::TestV1Events::test_context", "tests/test_apig_wsgi.py::TestV2Events::test_get", "tests/test_apig_wsgi.py::TestV2Events::test_get_missing_content_type", "tests/test_apig_wsgi.py::TestV2Events::test_cookie", "tests/test_apig_wsgi.py::TestV2Events::test_two_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_mixed_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_set_one_cookie", "tests/test_apig_wsgi.py::TestV2Events::test_set_two_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV2Events::test_special_headers", "tests/test_apig_wsgi.py::TestUnknownVersionEvents::test_errors" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-10-12 22:45:22+00:00	mit	885
adamchainz__apig-wsgi-272	diff --git a/HISTORY.rst b/HISTORY.rst index 6b356b4..cd7d803 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,6 +2,8 @@ History ======= +* Fix handling of query string encoding in ALB deployments. + 2.11.0 (2021-05-10) ------------------- diff --git a/example/README.rst b/example/README.rst index b0d17a3..c00ff7b 100644 --- a/example/README.rst +++ b/example/README.rst @@ -47,7 +47,13 @@ other requirements into it, and run the deployment playbook: source venv/bin/activate python -m pip install -U pip wheel python -m pip install -r requirements.txt - ansible-playbook playbook.yml + +To run the playbook, you'll need to specify a VPC ID and two subnet IDs in order +to create an ALB. + +.. code-block:: sh + + ansible-playbook playbook.yml -e "vpc_id=vpc-12345678" -e "subnet_id_1=subnet-12345678" -e "subnet_id_2=subnet-12345678" Ansible should complete with a ``PLAY RECAP`` at the end like: diff --git a/example/deployment/files/cloudformation_site.yml b/example/deployment/files/cloudformation_site.yml index ac2fcfa..72f4716 100644 --- a/example/deployment/files/cloudformation_site.yml +++ b/example/deployment/files/cloudformation_site.yml @@ -16,6 +16,15 @@ Parameters: LambdaIAMRoleArn: Type: String + VpcId: + Type: String + + SubnetId1: + Type: String + + SubnetId2: + Type: String + Resources: # Lambda @@ -33,13 +42,20 @@ Resources: Runtime: python3.8 Timeout: 20 - LambdaPermission: + LambdaPermissionAPIGW: Type: AWS::Lambda::Permission Properties: Action: lambda:InvokeFunction FunctionName: !GetAtt LambdaFunction.Arn Principal: apigateway.amazonaws.com + LambdaPermissionALB: + Type: AWS::Lambda::Permission + Properties: + Action: lambda:InvokeFunction + FunctionName: !GetAtt LambdaFunction.Arn + Principal: elasticloadbalancing.amazonaws.com + # new style HTTP API HttpApi: @@ -110,6 +126,49 @@ Resources: DeploymentId: !Ref Deployment StageName: prod + # ALB + + LoadBalancer: + Type: AWS::ElasticLoadBalancingV2::LoadBalancer + Properties: + Scheme: internet-facing + Subnets: + - !Ref SubnetId1 + - !Ref SubnetId2 + SecurityGroups: [!Ref SecurityGroup] + + TargetGroup: + Type: AWS::ElasticLoadBalancingV2::TargetGroup + DependsOn: LambdaPermissionALB + Properties: + TargetType: lambda + Targets: + - Id: !GetAtt LambdaFunction.Arn + TargetGroupAttributes: + - Key: lambda.multi_value_headers.enabled + Value: True + + HttpListener: + Type: AWS::ElasticLoadBalancingV2::Listener + Properties: + LoadBalancerArn: !Ref LoadBalancer + Port: 80 + Protocol: HTTP + DefaultActions: + - TargetGroupArn: !Ref TargetGroup + Type: forward + + SecurityGroup: + Type: AWS::EC2::SecurityGroup + Properties: + GroupDescription: Allow http on port 80 + VpcId: !Ref VpcId + SecurityGroupIngress: + - IpProtocol: tcp + FromPort: 80 + ToPort: 80 + CidrIp: 0.0.0.0/0 + Outputs: HttpApiUrl: @@ -117,3 +176,6 @@ Outputs: RestApiUrl: Value: !Sub https://${RestApi}.execute-api.${AWS::Region}.amazonaws.com/${StageApi}/ + + AlbUrl: + Value: !GetAtt LoadBalancer.DNSName diff --git a/example/deployment/playbook.yml b/example/deployment/playbook.yml index 1eae34c..728919a 100755 --- a/example/deployment/playbook.yml +++ b/example/deployment/playbook.yml @@ -95,6 +95,9 @@ PackageS3Key: '{{ zip_name }}' PackageS3ObjectVersion: '{{ (s3_result.stdout\|from_json).VersionId }}' LambdaIAMRoleArn: '{{ base_stack_result.stack_outputs.LambdaIAMRoleArn }}' + VpcId: '{{ vpc_id }}' + SubnetId1: '{{ subnet_id_1 }}' + SubnetId2: '{{ subnet_id_2 }}' register: site_stack_result - name: debug @@ -102,3 +105,4 @@ msg: \| New style "HTTP API" using v2 events at {{ site_stack_result.stack_outputs.HttpApiUrl }} Old style REST API using v1 events at {{ site_stack_result.stack_outputs.RestApiUrl }} + ALB at {{ site_stack_result.stack_outputs.AlbUrl }} diff --git a/src/apig_wsgi.py b/src/apig_wsgi.py index a8f41b5..814cab3 100644 --- a/src/apig_wsgi.py +++ b/src/apig_wsgi.py @@ -13,6 +13,8 @@ DEFAULT_NON_BINARY_CONTENT_TYPE_PREFIXES = ( "application/vnd.api+json", ) +RESERVED_URI_CHARACTERS = r"!#$&'()*+,/:;=?@[]%" + def make_lambda_handler( wsgi_app, binary_support=None, non_binary_content_type_prefixes=None @@ -37,13 +39,19 @@ def make_lambda_handler( non_binary_content_type_prefixes = tuple(non_binary_content_type_prefixes) def handler(event, context): - # Assume version 1 since ALB isn't documented as sending a version. - version = event.get("version", "1.0") - if version == "1.0": + # ALB doesn't send a version, but requestContext will contain a key named 'elb'. + if "requestContext" in event and "elb" in event["requestContext"]: + version = "alb" + else: + version = event.get("version", "1.0") + + if version in ("1.0", "alb"): # Binary support deafults 'off' on version 1 event_binary_support = binary_support or False environ = get_environ_v1( - event, context, binary_support=event_binary_support + event, + context, + encode_query_params=(version == "1.0"), ) response = V1Response( binary_support=event_binary_support, @@ -65,7 +73,7 @@ def make_lambda_handler( return handler -def get_environ_v1(event, context, binary_support): +def get_environ_v1(event, context, encode_query_params): body = get_body(event) environ = { "CONTENT_LENGTH": str(len(body)), @@ -87,15 +95,24 @@ def get_environ_v1(event, context, binary_support): "apig_wsgi.multi_value_headers": False, } + if encode_query_params: + safe_chars = "" + else: + safe_chars = RESERVED_URI_CHARACTERS + # Multi-value query strings need explicit activation on ALB if "multiValueQueryStringParameters" in event: environ["QUERY_STRING"] = urlencode( # may be None when testing on console event["multiValueQueryStringParameters"] or (), doseq=True, + safe=safe_chars, ) else: - environ["QUERY_STRING"] = urlencode(event.get("queryStringParameters") or ()) + environ["QUERY_STRING"] = urlencode( + event.get("queryStringParameters") or (), + safe=safe_chars, + ) # Multi-value headers need explicit activation on ALB if "multiValueHeaders" in event:	adamchainz/apig-wsgi	066f0b7c1e81e81dd4991c388f46ddfc4ddaf94e	diff --git a/tests/test_apig_wsgi.py b/tests/test_apig_wsgi.py index 71c1fbf..e107817 100644 --- a/tests/test_apig_wsgi.py +++ b/tests/test_apig_wsgi.py @@ -106,6 +106,7 @@ def make_v1_event( event["isBase64Encoded"] = True else: event["body"] = body + event["isBase64Encoded"] = False if request_context is not None: event["requestContext"] = request_context @@ -538,6 +539,81 @@ class TestV1Events: assert response["body"] == "Hi there!" +# ALB tests + + +def make_alb_event(args, request_context=None, kwargs): + if request_context is None: + request_context = {} + request_context["elb"] = { + "targetGroupArn": "arn:aws:elasticloadbalancing:::targetgroup/etc" + } + + event = make_v1_event(args, request_context=request_context, **kwargs) + + del event["version"] + if "isBase64Encoded" not in event: + event["isBase64Encoded"] = False + + return event + + +class TestAlbEvents: + # Query string params from ALB are the same as rawQueryStringParameters + # in API GW V2... that is they don't need to be encoded. + def test_querystring_encoding_plus_value(self, simple_app): + event = make_alb_event(qs_params={"a": ["b+c"]}, qs_params_multi=False) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a=b+c" + + def test_querystring_encoding_plus_key(self, simple_app): + event = make_alb_event(qs_params={"a+b": ["c"]}, qs_params_multi=False) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a+b=c" + + def test_querystring_multi(self, simple_app): + event = make_alb_event(qs_params={"foo": ["bar", "baz"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "foo=bar&foo=baz" + + def test_querystring_multi_encoding_plus_value(self, simple_app): + event = make_alb_event(qs_params={"a": ["b+c", "d"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a=b+c&a=d" + + def test_querystring_multi_encoding_plus_key(self, simple_app): + event = make_alb_event(qs_params={"a+b": ["c"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a+b=c" + + def test_querystring_contains_encoded_value(self, simple_app): + event = make_alb_event(qs_params={"a": ["foo%3Dbar"]}, qs_params_multi=False) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a=foo%3Dbar" + + def test_querystring_multi_contains_encoded_value(self, simple_app): + # a = ['foo=bar', '$20', '100%'] + event = make_alb_event( + qs_params={"a": ["foo%3Dbar", "%2420", "100%25"]}, qs_params_multi=True + ) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a=foo%3Dbar&a=%2420&a=100%25" + + # v2 tests	Query Params - difference between API GW and ALB I noticed if I go to a URL with a query string like this: `?x=foo%3Dbar` The event sent to a lambda from ALB contains: ```json "queryStringParameters": { "x": "foo%3Dbar" } ``` And the event sent from API Gateway contains: ```json "queryStringParameters": { "x": "foo=bar" } ``` For the ALB, the QUERY_STRING in the WSGI environment is set to: ``` x=foo%253Dbar ``` And for API Gateway, it is set to: ``` x=foo%3Dbar ``` So I think the processing of query params for ALB needs to not urlencode the data. I am working on a PR for this and will hopefully submit later today.	066f0b7c1e81e81dd4991c388f46ddfc4ddaf94e	[ "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_encoding_plus_value", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_encoding_plus_key", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi_encoding_plus_value", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi_encoding_plus_key", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_contains_encoded_value", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi_contains_encoded_value" ]	[ "tests/test_apig_wsgi.py::TestV1Events::test_get", "tests/test_apig_wsgi.py::TestV1Events::test_get_missing_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_get_single_header", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_no_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_post", "tests/test_apig_wsgi.py::TestV1Events::test_post_binary_support", "tests/test_apig_wsgi.py::TestV1Events::test_path_unquoting", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_none", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_none_single", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_empty", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_empty_single", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_one", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_one_single", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_encoding_plus_value", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_encoding_plus_key", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_multi", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_multi_encoding_plus_value", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_multi_encoding_plus_key", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header_single", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header_multi", "tests/test_apig_wsgi.py::TestV1Events::test_special_headers", "tests/test_apig_wsgi.py::TestV1Events::test_special_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_special_host", "tests/test_apig_wsgi.py::TestV1Events::test_special_x_forwarded_for", "tests/test_apig_wsgi.py::TestV1Events::test_x_forwarded_proto", "tests/test_apig_wsgi.py::TestV1Events::test_x_forwarded_port", "tests/test_apig_wsgi.py::TestV1Events::test_no_headers", "tests/test_apig_wsgi.py::TestV1Events::test_headers_None", "tests/test_apig_wsgi.py::TestV1Events::test_exc_info", "tests/test_apig_wsgi.py::TestV1Events::test_request_context", "tests/test_apig_wsgi.py::TestV1Events::test_full_event", "tests/test_apig_wsgi.py::TestV1Events::test_elb_health_check", "tests/test_apig_wsgi.py::TestV1Events::test_context", "tests/test_apig_wsgi.py::TestV1Events::test_empty_and_uncloseable_content", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi", "tests/test_apig_wsgi.py::TestV2Events::test_get", "tests/test_apig_wsgi.py::TestV2Events::test_get_missing_content_type", "tests/test_apig_wsgi.py::TestV2Events::test_cookie", "tests/test_apig_wsgi.py::TestV2Events::test_two_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_mixed_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_set_one_cookie", "tests/test_apig_wsgi.py::TestV2Events::test_set_two_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV2Events::test_plain_header", "tests/test_apig_wsgi.py::TestV2Events::test_special_headers", "tests/test_apig_wsgi.py::TestV2Events::test_path_unquoting", "tests/test_apig_wsgi.py::TestV2Events::test_empty_and_uncloseable_content", "tests/test_apig_wsgi.py::TestUnknownVersionEvents::test_errors" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-08-24 10:00:38+00:00	mit	886
adamchainz__apig-wsgi-290	diff --git a/HISTORY.rst b/HISTORY.rst index b2d240b..c1e65a8 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,6 +2,10 @@ History ======= +* Handle ``requestContext`` being ``None``, as can happen from Lambda invoke. + + Thanks to scottmn for the report in `Issue #289 <https://github.com/adamchainz/apig-wsgi/issues/289>`__. + 2.12.0 (2021-08-24) ------------------- diff --git a/src/apig_wsgi/__init__.py b/src/apig_wsgi/__init__.py index 2d1389d..0217ad6 100644 --- a/src/apig_wsgi/__init__.py +++ b/src/apig_wsgi/__init__.py @@ -58,7 +58,11 @@ def make_lambda_handler( def handler(event: Dict[str, Any], context: Any) -> Dict[str, Any]: # ALB doesn't send a version, but requestContext will contain a key named 'elb'. - if "requestContext" in event and "elb" in event["requestContext"]: + if ( + "requestContext" in event + and isinstance(event["requestContext"], dict) + and "elb" in event["requestContext"] + ): version = "alb" else: version = event.get("version", "1.0")	adamchainz/apig-wsgi	87e53add20433c5a8b8550b1958d4160e95ab49c	diff --git a/tests/test_apig_wsgi.py b/tests/test_apig_wsgi.py index 7697d40..528ae91 100644 --- a/tests/test_apig_wsgi.py +++ b/tests/test_apig_wsgi.py @@ -1,7 +1,17 @@ import sys from base64 import b64encode from io import BytesIO -from typing import Any, Callable, Dict, Generator, Iterable, List, Optional, Tuple +from typing import ( + Any, + Callable, + Dict, + Generator, + Iterable, + List, + Optional, + Tuple, + Union, +) import pytest @@ -82,6 +92,13 @@ class ContextStub: # v1 tests +class Sentinel: + pass + + +SENTINEL = Sentinel() + + def make_v1_event( *, method: str = "GET", @@ -92,7 +109,7 @@ def make_v1_event( headers_multi: bool = True, body: str = "", binary: bool = False, - request_context: Optional[Dict[str, Any]] = None, + request_context: Union[Dict[str, Any], None, Sentinel] = SENTINEL, ) -> Dict[str, Any]: if headers is None: headers = {"Host": ["example.com"]} @@ -125,7 +142,7 @@ def make_v1_event( event["body"] = body event["isBase64Encoded"] = False - if request_context is not None: + if request_context is not SENTINEL: event["requestContext"] = request_context return event @@ -507,6 +524,14 @@ class TestV1Events: assert simple_app.environ["apig_wsgi.request_context"] == context + def test_request_context_none(self, simple_app: App) -> None: + # Invoking lambdas can lead to requestContext being JSON null + event = make_v1_event(request_context=None) + + simple_app.handler(event, None) + + # Simply don't crash + def test_full_event(self, simple_app: App) -> None: event = make_v1_event()	Error when requestContext is None ### Python Version 3.8 ### Package Version 2.12.0 ### Description I have a lambda that is called through API Gateway, but can also be invoked directly via a lambda client. Upgrading to 2.12.0 started causing this error when invoked via client. ``` [ERROR] TypeError: argument of type 'NoneType' is not iterable Traceback (most recent call last): File "/var/task/apig_wsgi/__init__.py", line 61, in handler if "requestContext" in event and "elb" in event["requestContext"]: ``` This is being done from Kotlin code, using `com.amazonaws.services.lambda.AWSLambda` client. When an `AwsProxyRequest` object is constructed, it has `requestContext=null` by default. This results in the error above. I can update my invoke code to set a dummy requestContext, but I do believe it is valid to be None in the direct lambda invocation use case. Does it make sense to add a `not None` check here for requestContext? Thanks.	87e53add20433c5a8b8550b1958d4160e95ab49c	[ "tests/test_apig_wsgi.py::TestV1Events::test_request_context_none" ]	[ "tests/test_apig_wsgi.py::TestV1Events::test_get", "tests/test_apig_wsgi.py::TestV1Events::test_get_missing_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_get_single_header", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_custom_text_content_types[application/vnd.custom]", 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"tests/test_apig_wsgi.py::TestV1Events::test_plain_header_single", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header_multi", "tests/test_apig_wsgi.py::TestV1Events::test_special_headers", "tests/test_apig_wsgi.py::TestV1Events::test_special_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_special_host", "tests/test_apig_wsgi.py::TestV1Events::test_special_x_forwarded_for", "tests/test_apig_wsgi.py::TestV1Events::test_x_forwarded_proto", "tests/test_apig_wsgi.py::TestV1Events::test_x_forwarded_port", "tests/test_apig_wsgi.py::TestV1Events::test_no_headers", "tests/test_apig_wsgi.py::TestV1Events::test_headers_None", "tests/test_apig_wsgi.py::TestV1Events::test_exc_info", "tests/test_apig_wsgi.py::TestV1Events::test_request_context", "tests/test_apig_wsgi.py::TestV1Events::test_full_event", "tests/test_apig_wsgi.py::TestV1Events::test_elb_health_check", "tests/test_apig_wsgi.py::TestV1Events::test_context", "tests/test_apig_wsgi.py::TestV1Events::test_empty_and_uncloseable_content", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_encoding_plus_value", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_encoding_plus_key", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi_encoding_plus_value", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi_encoding_plus_key", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_contains_encoded_value", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi_contains_encoded_value", "tests/test_apig_wsgi.py::TestV2Events::test_get", "tests/test_apig_wsgi.py::TestV2Events::test_get_missing_content_type", "tests/test_apig_wsgi.py::TestV2Events::test_cookie", "tests/test_apig_wsgi.py::TestV2Events::test_two_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_mixed_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_set_one_cookie", "tests/test_apig_wsgi.py::TestV2Events::test_set_two_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV2Events::test_plain_header", "tests/test_apig_wsgi.py::TestV2Events::test_special_headers", "tests/test_apig_wsgi.py::TestV2Events::test_path_unquoting", "tests/test_apig_wsgi.py::TestV2Events::test_empty_and_uncloseable_content", "tests/test_apig_wsgi.py::TestUnknownVersionEvents::test_errors" ]	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2021-09-23 20:25:57+00:00	mit	887
adamchainz__apig-wsgi-80	diff --git a/HISTORY.rst b/HISTORY.rst index c6365ca..3669cc5 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -7,6 +7,7 @@ Pending Release .. Insert new release notes below this line * Update Python support to 3.5-3.7, as 3.4 has reached its end of life. +* Return binary content for gzipped responses with text or JSON content types. 2.2.0 (2019-04-15) ------------------ diff --git a/apig_wsgi.py b/apig_wsgi.py index aa36d78..be2930f 100644 --- a/apig_wsgi.py +++ b/apig_wsgi.py @@ -101,14 +101,7 @@ class Response(object): def as_apig_response(self): response = {"statusCode": self.status_code, "headers": dict(self.headers)} - - content_type = self._get_content_type() - should_send_binary = self.binary_support and ( - content_type is None - or not content_type.startswith(("text/", "application/json")) - ) - - if should_send_binary: + if self._should_send_binary(): response["isBase64Encoded"] = True response["body"] = b64encode(self.body.getvalue()).decode("utf-8") else: @@ -116,10 +109,31 @@ class Response(object): return response + def _should_send_binary(self): + """ + Determines if binary response should be sent to API Gateway + """ + if not self.binary_support: + return False + + content_type = self._get_content_type() + non_binary_content_types = ("text/", "application/json") + if not content_type.startswith(non_binary_content_types): + return True + + content_encoding = self._get_content_encoding() + # Content type is non-binary but the content encoding might be. + return "gzip" in content_encoding.lower() + def _get_content_type(self): - content_type_headers = [ - v for k, v in self.headers if k.lower() == "content-type" - ] - if len(content_type_headers): - return content_type_headers[-1] + return self._get_header("content-type") or "" + + def _get_content_encoding(self): + return self._get_header("content-encoding") or "" + + def _get_header(self, header_name): + header_name = header_name.lower() + matching_headers = [v for k, v in self.headers if k.lower() == header_name] + if len(matching_headers): + return matching_headers[-1] return None	adamchainz/apig-wsgi	80868a1a740711fe1fdf3c523d0e400c788a1b14	diff --git a/test_apig_wsgi.py b/test_apig_wsgi.py index 6a921ea..72531fd 100644 --- a/test_apig_wsgi.py +++ b/test_apig_wsgi.py @@ -21,6 +21,11 @@ def simple_app(): yield app +parametrize_text_content_type = pytest.mark.parametrize( + "text_content_type", ["text/plain", "text/html", "application/json"] +) + + def make_event( method="GET", qs_params=None, @@ -69,14 +74,15 @@ def test_get_missing_content_type(simple_app): assert response == {"statusCode": 200, "headers": {}, "body": "Hello World\n"} -def test_get_binary_support_text(simple_app): +@parametrize_text_content_type +def test_get_binary_support_text(simple_app, text_content_type): simple_app.handler = make_lambda_handler(simple_app, binary_support=True) + simple_app.headers = [("Content-Type", text_content_type)] response = simple_app.handler(make_event(), None) - assert response == { "statusCode": 200, - "headers": {"Content-Type": "text/plain"}, + "headers": {"Content-Type": text_content_type}, "body": "Hello World\n", } @@ -96,6 +102,27 @@ def test_get_binary_support_binary(simple_app): } +@parametrize_text_content_type +def test_get_binary_support_binary_text_with_gzip_content_encoding( + simple_app, text_content_type +): + simple_app.handler = make_lambda_handler(simple_app, binary_support=True) + simple_app.headers = [ + ("Content-Type", text_content_type), + ("Content-Encoding", "gzip"), + ] + simple_app.response = b"\x13\x37" + + response = simple_app.handler(make_event(), None) + + assert response == { + "statusCode": 200, + "headers": {"Content-Type": text_content_type, "Content-Encoding": "gzip"}, + "body": b64encode(b"\x13\x37").decode("utf-8"), + "isBase64Encoded": True, + } + + def test_get_binary_support_no_content_type(simple_app): simple_app.handler = make_lambda_handler(simple_app, binary_support=True) simple_app.headers = []	Ability to send binary response with `text/` or `application/json` content type Problem -------- `Response.as_apig_response` is hardcoded to not return binary response when the content-type of the response is either `text/` or `application/json`. https://github.com/adamchainz/apig-wsgi/blob/b0ce56cbb3ff67586c398f57bc13590bf0961940/apig_wsgi.py#L105-L109 This becomes a problem for use cases like returning a gzip response from the application with the above content types. Possible Solution ----------------- Check if the `Content-Encoding` header has `gzip` in it or not, and return the binary response based on that.* This fix would keep the hardcoded values, something like this should work: ```python def _should_send_binary(self): """Determines if binary response should be sent to API Gateway """ non_binary_content_types = ("text/", "application/json") content_type = self._get_content_type() or '' content_encoding = self._get_content_encoding() or '' supports_binary = self.binary_support is_binary_content_type = not content_type.startswith(non_binary_content_types) if supports_binary and is_binary_content_type: return True # Content type is non-binary but the content encoding is. elif supports_binary and not is_binary_content_type: return 'gzip' in content_encoding.lower() return False ``` Allow `Response` class to be extended so that users can handle this logic on their own. This can be done by introducing the same `Response._should_send_binary` method which defaults to the current behaviour. The `make_lambda_handler` function can then be allowed to have an argument like `response_class` to facilitate this. I can create a PR for either of the fixes which seem more appropriate to you. What do you think about this?	80868a1a740711fe1fdf3c523d0e400c788a1b14	[ "test_apig_wsgi.py::test_get_binary_support_binary_text_with_gzip_content_encoding[text/plain]", "test_apig_wsgi.py::test_get_binary_support_binary_text_with_gzip_content_encoding[text/html]", "test_apig_wsgi.py::test_get_binary_support_binary_text_with_gzip_content_encoding[application/json]" ]	[ "test_apig_wsgi.py::test_get", "test_apig_wsgi.py::test_get_missing_content_type", "test_apig_wsgi.py::test_get_binary_support_text[text/plain]", "test_apig_wsgi.py::test_get_binary_support_text[text/html]", "test_apig_wsgi.py::test_get_binary_support_text[application/json]", "test_apig_wsgi.py::test_get_binary_support_binary", "test_apig_wsgi.py::test_get_binary_support_no_content_type", "test_apig_wsgi.py::test_post", "test_apig_wsgi.py::test_post_binary_support", "test_apig_wsgi.py::test_querystring_none", "test_apig_wsgi.py::test_querystring_empty", "test_apig_wsgi.py::test_querystring_one", "test_apig_wsgi.py::test_plain_header", "test_apig_wsgi.py::test_special_headers", "test_apig_wsgi.py::test_no_headers", "test_apig_wsgi.py::test_headers_None", "test_apig_wsgi.py::test_exc_info", "test_apig_wsgi.py::test_request_context" ]	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2019-08-18 23:01:41+00:00	isc	888
adamchainz__apig-wsgi-93	diff --git a/HISTORY.rst b/HISTORY.rst index 4b65c01..1ed117d 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -13,6 +13,9 @@ Pending Release (`docs <https://docs.python.org/3.8/library/importlib.metadata.html#distribution-versions>`__ / `backport <https://pypi.org/project/importlib-metadata/>`__). * Update Python support to 3.5-3.8. +* Add `application/vnd.api+json` to default non-binary content type prefixes. +* Add support for custom non-binary content type prefixes. This lets you control + which content types should be treated as plain text when binary support is enabled. 2.3.0 (2019-08-19) ------------------ diff --git a/README.rst b/README.rst index 8f54234..3404304 100644 --- a/README.rst +++ b/README.rst @@ -39,8 +39,8 @@ Python 3.5-3.8 supported. Usage ===== -``make_lambda_handler(app, binary_support=False)`` --------------------------------------------------- +``make_lambda_handler(app, binary_support=False, non_binary_content_type_prefixes=None)`` +----------------------------------------------------------------------------------------- ``app`` should be a WSGI app, for example from Django's ``wsgi.py`` or Flask's ``Flask()`` object. @@ -53,8 +53,10 @@ using ``'/'`` is the best way to do it, since it is used to match the request 'Accept' header as well, which WSGI applications are likely to ignore). Note that binary responses aren't sent if your response has a 'Content-Type' -starting 'text/html' or 'application/json' - this is to support sending larger -text responses. +starting 'text/', 'application/json' or 'application/vnd.api+json' - this +is to support sending larger text responses. To support other content types +than the ones specified above, you can set `non_binary_content_type_prefixes` +to a list of content type prefixes of your choice. If the event from API Gateway contains the ``requestContext`` key, for example from custom request authorizers, this will be available in the WSGI environ diff --git a/src/apig_wsgi.py b/src/apig_wsgi.py index e804a20..f6bd5ee 100644 --- a/src/apig_wsgi.py +++ b/src/apig_wsgi.py @@ -5,16 +5,41 @@ from urllib.parse import urlencode __all__ = ("make_lambda_handler",) +DEFAULT_NON_BINARY_CONTENT_TYPE_PREFIXES = ( + "text/", + "application/json", + "application/vnd.api+json", +) -def make_lambda_handler(wsgi_app, binary_support=False): + +def make_lambda_handler( + wsgi_app, binary_support=False, non_binary_content_type_prefixes=None +): """ Turn a WSGI app callable into a Lambda handler function suitable for running on API Gateway. + + Parameters + ---------- + wsgi_app : function + WSGI Application callable + binary_support : bool + Whether to support returning APIG-compatible binary responses + non_binary_content_type_prefixes : tuple of str + Tuple of content type prefixes which should be considered "Non-Binary" when + `binray_support` is True. This prevents apig_wsgi from unexpectedly encoding + non-binary responses as binary. """ + if non_binary_content_type_prefixes is None: + non_binary_content_type_prefixes = DEFAULT_NON_BINARY_CONTENT_TYPE_PREFIXES + non_binary_content_type_prefixes = tuple(non_binary_content_type_prefixes) def handler(event, context): environ = get_environ(event, binary_support=binary_support) - response = Response(binary_support=binary_support) + response = Response( + binary_support=binary_support, + non_binary_content_type_prefixes=non_binary_content_type_prefixes, + ) result = wsgi_app(environ, response.start_response) response.consume(result) return response.as_apig_response() @@ -73,11 +98,12 @@ def get_environ(event, binary_support): class Response(object): - def __init__(self, binary_support): + def __init__(self, binary_support, non_binary_content_type_prefixes): self.status_code = 500 self.headers = [] self.body = BytesIO() self.binary_support = binary_support + self.non_binary_content_type_prefixes = non_binary_content_type_prefixes def start_response(self, status, response_headers, exc_info=None): if exc_info is not None: @@ -113,8 +139,7 @@ class Response(object): return False content_type = self._get_content_type() - non_binary_content_types = ("text/", "application/json") - if not content_type.startswith(non_binary_content_types): + if not content_type.startswith(self.non_binary_content_type_prefixes): return True content_encoding = self._get_content_encoding()	adamchainz/apig-wsgi	af9d96d0ac950f9b04e6d365acf0b3a4f5e8e690	diff --git a/tests/test_apig_wsgi.py b/tests/test_apig_wsgi.py index 72531fd..f6b77e9 100644 --- a/tests/test_apig_wsgi.py +++ b/tests/test_apig_wsgi.py @@ -6,6 +6,8 @@ import pytest from apig_wsgi import make_lambda_handler +CUSTOM_NON_BINARY_CONTENT_TYPE_PREFIXES = ["test/custom", "application/vnd.custom"] + @pytest.fixture() def simple_app(): @@ -21,8 +23,14 @@ def simple_app(): yield app -parametrize_text_content_type = pytest.mark.parametrize( - "text_content_type", ["text/plain", "text/html", "application/json"] +parametrize_default_text_content_type = pytest.mark.parametrize( + "text_content_type", + ["text/plain", "text/html", "application/json", "application/vnd.api+json"], +) + + +parametrize_custom_text_content_type = pytest.mark.parametrize( + "text_content_type", CUSTOM_NON_BINARY_CONTENT_TYPE_PREFIXES ) @@ -74,8 +82,8 @@ def test_get_missing_content_type(simple_app): assert response == {"statusCode": 200, "headers": {}, "body": "Hello World\n"} -@parametrize_text_content_type -def test_get_binary_support_text(simple_app, text_content_type): +@parametrize_default_text_content_type +def test_get_binary_support_default_text_content_types(simple_app, text_content_type): simple_app.handler = make_lambda_handler(simple_app, binary_support=True) simple_app.headers = [("Content-Type", text_content_type)] @@ -87,6 +95,23 @@ def test_get_binary_support_text(simple_app, text_content_type): } +@parametrize_custom_text_content_type +def test_get_binary_support_custom_text_content_types(simple_app, text_content_type): + simple_app.handler = make_lambda_handler( + simple_app, + binary_support=True, + non_binary_content_type_prefixes=CUSTOM_NON_BINARY_CONTENT_TYPE_PREFIXES, + ) + simple_app.headers = [("Content-Type", text_content_type)] + + response = simple_app.handler(make_event(), None) + assert response == { + "statusCode": 200, + "headers": {"Content-Type": text_content_type}, + "body": "Hello World\n", + } + + def test_get_binary_support_binary(simple_app): simple_app.handler = make_lambda_handler(simple_app, binary_support=True) simple_app.headers = [("Content-Type", "application/octet-stream")] @@ -102,8 +127,8 @@ def test_get_binary_support_binary(simple_app): } -@parametrize_text_content_type -def test_get_binary_support_binary_text_with_gzip_content_encoding( +@parametrize_default_text_content_type +def test_get_binary_support_binary_default_text_with_gzip_content_encoding( simple_app, text_content_type ): simple_app.handler = make_lambda_handler(simple_app, binary_support=True) @@ -123,6 +148,31 @@ def test_get_binary_support_binary_text_with_gzip_content_encoding( } +@parametrize_custom_text_content_type +def test_get_binary_support_binary_custom_text_with_gzip_content_encoding( + simple_app, text_content_type +): + simple_app.handler = make_lambda_handler( + simple_app, + binary_support=True, + non_binary_content_type_prefixes=CUSTOM_NON_BINARY_CONTENT_TYPE_PREFIXES, + ) + simple_app.headers = [ + ("Content-Type", text_content_type), + ("Content-Encoding", "gzip"), + ] + simple_app.response = b"\x13\x37" + + response = simple_app.handler(make_event(), None) + + assert response == { + "statusCode": 200, + "headers": {"Content-Type": text_content_type, "Content-Encoding": "gzip"}, + "body": b64encode(b"\x13\x37").decode("utf-8"), + "isBase64Encoded": True, + } + + def test_get_binary_support_no_content_type(simple_app): simple_app.handler = make_lambda_handler(simple_app, binary_support=True) simple_app.headers = []	Ability to have custom white list for non binary content types ## Problem The `Response` class has a whitelist of "non binary content types" which includes: - `text/*` - `application/json` https://github.com/adamchainz/apig-wsgi/blob/f24dd8df21a4ab693992ababf4cfb9735af27b57/src/apig_wsgi.py#L116 All other response types are assumed to be binary if `binary_support` is True. This becomes a problem if you want to return text content for other content types. For example, [JSON:API](https://jsonapi.org/) APIs have `application/vnd.api+json` content type. ## Possible solution The library should provide ability to either extend the `Response` class or pass the `non_binary_content_types` directly to `make_lambda_handler` call. ```python wsgi_handler = make_lambda_handler(application, binary_support=True, response_class=MyResponse) wsgi_handler = make_lambda_handler(application, binary_support=True, non_binary_content_types=my_content_type_list) ``` I can create PR for either of these approaches. What do you think?	af9d96d0ac950f9b04e6d365acf0b3a4f5e8e690	[ "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]" ]	[ "tests/test_apig_wsgi.py::test_get", "tests/test_apig_wsgi.py::test_get_missing_content_type", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::test_get_binary_support_binary", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::test_get_binary_support_no_content_type", "tests/test_apig_wsgi.py::test_post", "tests/test_apig_wsgi.py::test_post_binary_support", "tests/test_apig_wsgi.py::test_querystring_none", "tests/test_apig_wsgi.py::test_querystring_empty", "tests/test_apig_wsgi.py::test_querystring_one", "tests/test_apig_wsgi.py::test_plain_header", "tests/test_apig_wsgi.py::test_special_headers", "tests/test_apig_wsgi.py::test_no_headers", "tests/test_apig_wsgi.py::test_headers_None", "tests/test_apig_wsgi.py::test_exc_info", "tests/test_apig_wsgi.py::test_request_context" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2019-11-13 19:03:20+00:00	isc	889
adamchainz__ec2-metadata-166	diff --git a/src/ec2_metadata.py b/src/ec2_metadata.py index ec3e695..a03813d 100644 --- a/src/ec2_metadata.py +++ b/src/ec2_metadata.py @@ -1,3 +1,5 @@ +import time + import requests from cached_property import cached_property @@ -10,6 +12,7 @@ SERVICE_URL = "http://169.254.169.254/2016-09-02/" DYNAMIC_URL = SERVICE_URL + "dynamic/" METADATA_URL = SERVICE_URL + "meta-data/" USERDATA_URL = SERVICE_URL + "user-data/" +TOKEN_TTL_SECONDS = 21600 class BaseLazyObject(object): @@ -24,8 +27,26 @@ class EC2Metadata(BaseLazyObject): if session is None: session = requests.Session() self._session = session + self._token_updated_at = 0 + + def _ensure_fresh_token(self): + """ Update the metadata token if needed. + + Tokens are rotated 1 minute before they would expire. + """ + now = time.time() + if now - self._token_updated_at > (TOKEN_TTL_SECONDS - 60): + token = self._session.put( + "http://169.254.169.254/latest/api/token", + headers={ + "X-aws-ec2-metadata-token-ttl-seconds": str(TOKEN_TTL_SECONDS) + }, + ).text + self._session.headers.update({"X-aws-ec2-metadata-token": token}) + self._token_updated_at = now def _get_url(self, url, allow_404=False): + self._ensure_fresh_token() resp = self._session.get(url, timeout=1.0) if resp.status_code != 404 or not allow_404: resp.raise_for_status()	adamchainz/ec2-metadata	2607b63c8ecb07c82b8716d6738814000fc3437d	diff --git a/tests/test_ec2_metadata.py b/tests/test_ec2_metadata.py index 0e4b43d..e71ccf1 100644 --- a/tests/test_ec2_metadata.py +++ b/tests/test_ec2_metadata.py @@ -4,6 +4,7 @@ import requests from ec2_metadata import ( DYNAMIC_URL, METADATA_URL, + TOKEN_TTL_SECONDS, USERDATA_URL, NetworkInterface, ec2_metadata, @@ -16,11 +17,20 @@ def clear_it(): example_mac = "00:11:22:33:44:55" +example_token = "AABBCC" # EC2Metadata tests +def _mock_token_request(requests_mock): + requests_mock.put( + "http://169.254.169.254/latest/api/token", + headers={"X-aws-ec2-metadata-token-ttl-seconds": str(TOKEN_TTL_SECONDS)}, + text=example_token, + ) + + def add_identity_doc_response(requests_mock, overrides=None): identity_doc = { "accountId": "123456789012", @@ -35,6 +45,7 @@ def add_identity_doc_response(requests_mock, overrides=None): } if overrides: identity_doc.update(overrides) + _mock_token_request(requests_mock) requests_mock.get(DYNAMIC_URL + "instance-identity/document", json=identity_doc) return identity_doc @@ -45,17 +56,20 @@ def test_account_id(requests_mock): def test_account_id_error(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(DYNAMIC_URL + "instance-identity/document", status_code=500) with pytest.raises(requests.exceptions.HTTPError): ec2_metadata.account_id def test_ami_id(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "ami-id", text="ami-12345678") assert ec2_metadata.ami_id == "ami-12345678" def test_ami_id_cached(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "ami-id", text="ami-12345678") ec2_metadata.ami_id requests_mock.get(METADATA_URL + "ami-id", status_code=500) @@ -63,6 +77,7 @@ def test_ami_id_cached(requests_mock): def test_ami_id_cached_cleared(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "ami-id", text="ami-12345678") ec2_metadata.ami_id @@ -74,42 +89,50 @@ def test_ami_id_cached_cleared(requests_mock): def test_ami_launch_index(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "ami-launch-index", text="0") assert ec2_metadata.ami_launch_index == 0 def test_ami_manifest_path(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "ami-manifest-path", text="(unknown)") assert ec2_metadata.ami_manifest_path == "(unknown)" def test_availability_zone(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "placement/availability-zone", text="eu-west-1a") assert ec2_metadata.availability_zone == "eu-west-1a" def test_iam_info(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "iam/info", text="{}") assert ec2_metadata.iam_info == {} def test_iam_info_none(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "iam/info", status_code=404) assert ec2_metadata.iam_info is None def test_iam_info_unexpected(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "iam/info", status_code=500) with pytest.raises(requests.exceptions.HTTPError): ec2_metadata.iam_info def test_instance_action(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "instance-action", text="none") assert ec2_metadata.instance_action == "none" def test_instance_id(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "instance-id", text="i-12345678") assert ec2_metadata.instance_id == "i-12345678" @@ -120,6 +143,7 @@ def test_instance_identity(requests_mock): def test_instance_profile_arn(requests_mock): + _mock_token_request(requests_mock) requests_mock.get( METADATA_URL + "iam/info", text='{"InstanceProfileArn": "arn:foobar"}' ) @@ -127,11 +151,13 @@ def test_instance_profile_arn(requests_mock): def test_instance_profile_arn_none(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "iam/info", status_code=404) assert ec2_metadata.instance_profile_arn is None def test_instance_profile_id(requests_mock): + _mock_token_request(requests_mock) requests_mock.get( METADATA_URL + "iam/info", text='{"InstanceProfileId": "some-id"}' ) @@ -139,31 +165,37 @@ def test_instance_profile_id(requests_mock): def test_instance_profile_id_none(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "iam/info", status_code=404) assert ec2_metadata.instance_profile_id is None def test_instance_type(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "instance-type", text="t2.nano") assert ec2_metadata.instance_type == "t2.nano" def test_kernel_id(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "kernel-id", text="aki-dc9ed9af") assert ec2_metadata.kernel_id == "aki-dc9ed9af" def test_kernel_id_none(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "kernel-id", status_code=404) assert ec2_metadata.kernel_id is None def test_mac(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "mac", text=example_mac) assert ec2_metadata.mac == example_mac def test_network_interfaces(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "network/interfaces/macs/", text=example_mac + "/") assert ec2_metadata.network_interfaces == { example_mac: NetworkInterface(example_mac, ec2_metadata) @@ -171,6 +203,7 @@ def test_network_interfaces(requests_mock): def test_private_hostname(requests_mock): + _mock_token_request(requests_mock) requests_mock.get( METADATA_URL + "local-hostname", text="ip-172-30-0-0.eu-west-1.compute.internal" ) @@ -178,11 +211,13 @@ def test_private_hostname(requests_mock): def test_private_ipv4(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "local-ipv4", text="172.30.0.0") assert ec2_metadata.private_ipv4 == "172.30.0.0" def test_public_hostname(requests_mock): + _mock_token_request(requests_mock) requests_mock.get( METADATA_URL + "public-hostname", text="ec2-1-2-3-4.compute-1.amazonaws.com" ) @@ -190,16 +225,19 @@ def test_public_hostname(requests_mock): def test_public_hostname_none(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "public-hostname", status_code=404) assert ec2_metadata.public_hostname is None def test_public_ipv4(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "public-ipv4", text="1.2.3.4") assert ec2_metadata.public_ipv4 == "1.2.3.4" def test_public_ipv4_none(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "public-ipv4", status_code=404) assert ec2_metadata.public_ipv4 is None @@ -210,18 +248,21 @@ def test_region(requests_mock): def test_reservation_id(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "reservation-id", text="r-12345678901234567") assert ec2_metadata.reservation_id == "r-12345678901234567" def test_security_groups_single(requests_mock): # most common case: a single SG + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "security-groups", text="security-group-one") assert ec2_metadata.security_groups == ["security-group-one"] def test_security_groups_two(requests_mock): # another common case: multiple SGs + _mock_token_request(requests_mock) requests_mock.get( METADATA_URL + "security-groups", text="security-group-one\nsecurity-group-2" ) @@ -231,16 +272,19 @@ def test_security_groups_two(requests_mock): def test_security_groups_emptystring(requests_mock): # Check '' too. Can't create an instance without a SG on EC2 but we should # safely handle it, perhaps it's possible in e.g. OpenStack. + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "security-groups", text="") assert ec2_metadata.security_groups == [] def test_user_data_none(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(USERDATA_URL, status_code=404) assert ec2_metadata.user_data is None def test_user_data_something(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(USERDATA_URL, content=b"foobar") assert ec2_metadata.user_data == b"foobar" @@ -250,6 +294,7 @@ def test_user_data_something(requests_mock): def add_interface_response(requests_mock, url, text="", kwargs): full_url = METADATA_URL + "network/interfaces/macs/" + example_mac + url + _mock_token_request(requests_mock) requests_mock.get(full_url, text=text, kwargs)	Update to version 2.0 https://aws.amazon.com/blogs/security/defense-in-depth-open-firewalls-reverse-proxies-ssrf-vulnerabilities-ec2-instance-metadata-service/ This requires a new "knock" PUT request to get a session token before accessing any bits of data.	2607b63c8ecb07c82b8716d6738814000fc3437d	[ "tests/test_ec2_metadata.py::test_network_interface_equal", "tests/test_ec2_metadata.py::test_network_interface_not_equal", "tests/test_ec2_metadata.py::test_network_interface_not_equal_class", "tests/test_ec2_metadata.py::test_network_interface_repr" ]	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }	2020-03-06 02:57:13+00:00	isc	890
adamchainz__ec2-metadata-350	diff --git a/HISTORY.rst b/HISTORY.rst index 9a6d9e6..23dbfa2 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,6 +2,10 @@ History ======= +* Return ``None`` for ``availability_zone_id`` when the underlying endpoint returns HTTP 404. + + Thanks to Amir Rossert in `PR #350 <https://github.com/adamchainz/ec2-metadata/pull/350>`__. + 2.9.0 (2022-03-25) ------------------ diff --git a/README.rst b/README.rst index 1671b48..f435b1f 100644 --- a/README.rst +++ b/README.rst @@ -133,8 +133,8 @@ See AWS docs page `Retrieve the target lifecycle state through instance metadata The name of the current AZ e.g. ``'eu-west-1a'``. -``availability_zone_id: str`` -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +``availability_zone_id: str \| None`` +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The unique, cross-account ID of the current AZ e.g. ``'use1-az6'``. See AWS docs page `AZ IDs for your AWS resources diff --git a/src/ec2_metadata/__init__.py b/src/ec2_metadata/__init__.py index 0db8376..520d9aa 100644 --- a/src/ec2_metadata/__init__.py +++ b/src/ec2_metadata/__init__.py @@ -98,8 +98,13 @@ class EC2Metadata(BaseLazyObject): return self._get_url(f"{self.metadata_url}placement/availability-zone").text @cached_property - def availability_zone_id(self) -> str: - return self._get_url(f"{self.metadata_url}placement/availability-zone-id").text + def availability_zone_id(self) -> str \| None: + resp = self._get_url( + f"{self.metadata_url}placement/availability-zone-id", allow_404=True + ) + if resp.status_code == 404: + return None + return resp.text @cached_property def ami_launch_index(self) -> int:	adamchainz/ec2-metadata	d72b0da489514e46519f49bd080860afb9fd3189	diff --git a/tests/test_ec2_metadata.py b/tests/test_ec2_metadata.py index 24f6af1..55f701b 100644 --- a/tests/test_ec2_metadata.py +++ b/tests/test_ec2_metadata.py @@ -161,6 +161,14 @@ def test_availability_zone_id(em_requests_mock): assert ec2_metadata.availability_zone_id == "use1-az6" +def test_availability_zone_id_none(em_requests_mock): + em_requests_mock.get( + "http://169.254.169.254/latest/meta-data/placement/availability-zone-id", + status_code=404, + ) + assert ec2_metadata.availability_zone_id is None + + def test_domain(em_requests_mock): em_requests_mock.get( "http://169.254.169.254/latest/meta-data/services/domain",	availability_zone_id may return 404 ### Python Version 3.8.10 ### Package Version 2.7.0 ### Description In some cases `ec2_metadata.availability_zone_id` returns 404 ``` ----> 1 ec2_metadata.availability_zone_id File functools.py:967, in __get__(self, instance, owner) File ec2_metadata/__init__.py:87, in availability_zone_id(self) File ec2_metadata/__init__.py:65, in _get_url(self, url, allow_404) File requests/models.py:960, in raise_for_status(self) HTTPError: 404 Client Error: Not Found for url: http://169.254.169.254/latest/meta-data/placement/availability-zone-id ``` I assume that all that is needed is to use `allow_404` in `_get_url`	d72b0da489514e46519f49bd080860afb9fd3189	[ "tests/test_ec2_metadata.py::test_availability_zone_id_none" ]	[ "tests/test_ec2_metadata.py::test_instance_profile_name", "tests/test_ec2_metadata.py::test_network_interface_repr", "tests/test_ec2_metadata.py::test_public_hostname_none", "tests/test_ec2_metadata.py::test_tags_one", "tests/test_ec2_metadata.py::test_kernel_id", "tests/test_ec2_metadata.py::test_network_interface_owner_id", "tests/test_ec2_metadata.py::test_instance_profile_id", "tests/test_ec2_metadata.py::test_instance_type", "tests/test_ec2_metadata.py::test_iam_info_none", "tests/test_ec2_metadata.py::test_network_interface_device_number", "tests/test_ec2_metadata.py::test_instance_profile_arn_none", "tests/test_ec2_metadata.py::test_network_interface_subnet_ipv4_cidr_block", "tests/test_ec2_metadata.py::test_region", "tests/test_ec2_metadata.py::test_network_interface_subnet_id", "tests/test_ec2_metadata.py::test_autoscaling_target_lifecycle_state_none", "tests/test_ec2_metadata.py::test_network_interface_vpc_ipv4_cidr_block", "tests/test_ec2_metadata.py::test_network_interface_ipv6s", "tests/test_ec2_metadata.py::test_tags_multiple", "tests/test_ec2_metadata.py::test_ami_id_cached", "tests/test_ec2_metadata.py::test_spot_instance_action_none", "tests/test_ec2_metadata.py::test_account_id_token_error", "tests/test_ec2_metadata.py::test_security_groups_emptystring", "tests/test_ec2_metadata.py::test_instance_profile_arn", "tests/test_ec2_metadata.py::test_network_interface_vpc_ipv6_cidr_blocks_none", "tests/test_ec2_metadata.py::test_instance_identity", "tests/test_ec2_metadata.py::test_network_interface_private_ipv4s", "tests/test_ec2_metadata.py::test_tags_len", "tests/test_ec2_metadata.py::test_network_interface_public_ipv4s_empty", "tests/test_ec2_metadata.py::test_domain", "tests/test_ec2_metadata.py::test_ami_id_cached_cleared", "tests/test_ec2_metadata.py::test_public_ipv4_none", "tests/test_ec2_metadata.py::test_network_interfaces", "tests/test_ec2_metadata.py::test_tags_empty", "tests/test_ec2_metadata.py::test_ami_manifest_path", "tests/test_ec2_metadata.py::test_network_interface_ipv4_associations", "tests/test_ec2_metadata.py::test_network_interface_vpc_ipv6_cidr_blocks", "tests/test_ec2_metadata.py::test_availability_zone", "tests/test_ec2_metadata.py::test_network_interface_vpc_id", "tests/test_ec2_metadata.py::test_network_interface_not_equal", "tests/test_ec2_metadata.py::test_kernel_id_none", "tests/test_ec2_metadata.py::test_private_hostname", "tests/test_ec2_metadata.py::test_network_interface_public_ipv4s", "tests/test_ec2_metadata.py::test_iam_security_credentials_none", "tests/test_ec2_metadata.py::test_account_id_error", "tests/test_ec2_metadata.py::test_iam_security_credentials", "tests/test_ec2_metadata.py::test_instance_profile_id_none", "tests/test_ec2_metadata.py::test_tags_repeat_access", "tests/test_ec2_metadata.py::test_network_interface_subnet_ipv6_cidr_blocks_none", "tests/test_ec2_metadata.py::test_instance_action", "tests/test_ec2_metadata.py::test_network_interface_vpc_ipv4_cidr_blocks_none", "tests/test_ec2_metadata.py::test_autoscaling_target_lifecycle_state_in_service", "tests/test_ec2_metadata.py::test_account_id", "tests/test_ec2_metadata.py::test_tags_not_enabled", "tests/test_ec2_metadata.py::test_network_interface_public_hostname_none", "tests/test_ec2_metadata.py::test_network_interface_interface_id", "tests/test_ec2_metadata.py::test_availability_zone_id", "tests/test_ec2_metadata.py::test_user_data_none", "tests/test_ec2_metadata.py::test_reservation_id", "tests/test_ec2_metadata.py::test_network_interface_public_hostname", "tests/test_ec2_metadata.py::test_network_interface_not_equal_class", "tests/test_ec2_metadata.py::test_network_interface_ipv6s_none", "tests/test_ec2_metadata.py::test_iam_info_unexpected", "tests/test_ec2_metadata.py::test_security_groups_two", "tests/test_ec2_metadata.py::test_spot_instance_action", "tests/test_ec2_metadata.py::test_network_interface_private_hostname", "tests/test_ec2_metadata.py::test_custom_session", "tests/test_ec2_metadata.py::test_network_interface_equal", "tests/test_ec2_metadata.py::test_user_data_something", "tests/test_ec2_metadata.py::test_network_interface_vpc_ipv4_cidr_blocks", "tests/test_ec2_metadata.py::test_security_groups_single", "tests/test_ec2_metadata.py::test_partition", "tests/test_ec2_metadata.py::test_instance_id", "tests/test_ec2_metadata.py::test_network_interface_subnet_ipv4_cidr_block_none", "tests/test_ec2_metadata.py::test_mac", "tests/test_ec2_metadata.py::test_private_ipv4", "tests/test_ec2_metadata.py::test_ami_launch_index", "tests/test_ec2_metadata.py::test_public_hostname", "tests/test_ec2_metadata.py::test_tags_iter", "tests/test_ec2_metadata.py::test_public_ipv4", "tests/test_ec2_metadata.py::test_network_interface_subnet_ipv6_cidr_blocks", "tests/test_ec2_metadata.py::test_ami_id", "tests/test_ec2_metadata.py::test_network_interface_vpc_ipv4_cidr_block_none", "tests/test_ec2_metadata.py::test_network_interface_security_group_ids", "tests/test_ec2_metadata.py::test_iam_info", "tests/test_ec2_metadata.py::test_network_interface_security_groups" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2022-03-06 15:47:09+00:00	mit	891
adamchainz__pip-lock-121	diff --git a/HISTORY.rst b/HISTORY.rst index 9f9cc5b..568f9d1 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -12,6 +12,7 @@ History ``importlib.metadata.version("pip-lock")`` (`docs <https://docs.python.org/3.8/library/importlib.metadata.html#distribution-versions>`__ / `backport <https://pypi.org/project/importlib-metadata/>`__). +* Fix parsing of package names featuring extras e.g. ``package[extra1,extra2]``. 2.0.0 (2019-02-28) ------------------ diff --git a/src/pip_lock.py b/src/pip_lock.py index 9d93bfa..3c1e7a0 100644 --- a/src/pip_lock.py +++ b/src/pip_lock.py @@ -40,8 +40,11 @@ def get_package_versions(lines, ignore_external=False): if ignore_external and line.startswith("-e"): continue - name, version_plus = line.split("==", 1) - versions[name.lower()] = version_plus.split(" ", 1)[0] + full_name, version_and_extras = line.split("==", 1) + # Strip extras + name = full_name.split("[", 1)[0].lower() + version = version_and_extras.split(" ", 1)[0] + versions[name] = version return versions	adamchainz/pip-lock	4a0e0106254aeceb13f7ff068ce295424b1d44a2	diff --git a/tests/test_pip_lock.py b/tests/test_pip_lock.py index da3f02a..c4a3881 100644 --- a/tests/test_pip_lock.py +++ b/tests/test_pip_lock.py @@ -17,7 +17,7 @@ def create_file(tmpdir, name, text): return str(t) -class TestReadPip(object): +class TestReadPip: def test_read(self, tmpdir): path = create_file(tmpdir, "requirements.txt", "package1==1.0\npackage2==1.1") assert read_pip(path) == ["package1==1.0", "package2==1.1"] @@ -33,7 +33,7 @@ class TestReadPip(object): assert read_pip(path) == [""] -class TestGetPackageVersion(object): +class TestGetPackageVersion: def test_version(self): assert get_package_versions(["package1==1.0", "package2==1.1"]) == { "package1": "1.0", @@ -53,7 +53,7 @@ class TestGetPackageVersion(object): assert get_package_versions(["https://www.google.com"]) == {} -class TestGetMismatches(object): +class TestGetMismatches: def setUp(self, tmpdir): super(TestGetMismatches, self).setUp() self.requirements_path = create_file( @@ -115,8 +115,17 @@ class TestGetMismatches(object): assert get_mismatches(requirements_path) == {} + @mock.patch("pip_lock.pip_freeze") + def test_package_with_extra(self, pip_freeze, tmpdir): + pip_freeze.return_value = ["package==1.1"] + requirements_path = create_file( + tmpdir, "requirements.txt", "package[anextra]==1.1" + ) + + assert get_mismatches(requirements_path) == {} + -class TestPrintErrors(object): +class TestPrintErrors: def test_errors(self, capsys): print_errors(["error message 1", "error message 2"]) _, err = capsys.readouterr() @@ -131,7 +140,7 @@ class TestPrintErrors(object): assert "post text" in err -class TestCheckRequirements(object): +class TestCheckRequirements: @mock.patch("pip_lock.get_mismatches") def test_no_mismatches(self, get_mismatches): get_mismatches.return_value = {}	pip-lock does detect dependencies with setup extras There are requirement mismatches with requirements.txt * Package django-storages[boto3] is in requirements.txt but not in virtualenv	4a0e0106254aeceb13f7ff068ce295424b1d44a2	[ "tests/test_pip_lock.py::TestGetMismatches::test_package_with_extra" ]	[ "tests/test_pip_lock.py::TestReadPip::test_read", "tests/test_pip_lock.py::TestReadPip::test_include", "tests/test_pip_lock.py::TestReadPip::test_empty", "tests/test_pip_lock.py::TestGetPackageVersion::test_version", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_empty", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_comments", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_includes", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_urls", "tests/test_pip_lock.py::TestGetMismatches::test_relative_requirements_file", "tests/test_pip_lock.py::TestGetMismatches::test_version_mismatch", "tests/test_pip_lock.py::TestGetMismatches::test_missing", "tests/test_pip_lock.py::TestGetMismatches::test_no_mismatches", "tests/test_pip_lock.py::TestGetMismatches::test_no_mismatches_case_insensitive", "tests/test_pip_lock.py::TestGetMismatches::test_empty", "tests/test_pip_lock.py::TestGetMismatches::test_editable_packages", "tests/test_pip_lock.py::TestPrintErrors::test_errors", "tests/test_pip_lock.py::TestPrintErrors::test_pre_post_text", "tests/test_pip_lock.py::TestCheckRequirements::test_no_mismatches", "tests/test_pip_lock.py::TestCheckRequirements::test_mismatches", "tests/test_pip_lock.py::TestCheckRequirements::test_relative_requirements_file" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2019-12-19 11:50:52+00:00	isc	892
adamchainz__pip-lock-208	diff --git a/HISTORY.rst b/HISTORY.rst index ed86591..e15c981 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,6 +2,9 @@ History ======= +* Fix to ignore lines that represent arguments to pip, such as + ``--find-links``. + 2.2.0 (2020-12-13) ------------------ diff --git a/src/pip_lock.py b/src/pip_lock.py index 38edddf..a050b3f 100644 --- a/src/pip_lock.py +++ b/src/pip_lock.py @@ -27,7 +27,7 @@ def get_package_versions(lines, ignore_external_and_at=False): for line in lines: line = line.strip() - if len(line) == 0 or line.startswith("#") or line.startswith("-r "): + if len(line) == 0 or line.startswith(("#", "-")): continue if line.startswith("https://"):	adamchainz/pip-lock	a70ab3c56a094044a1de38f9c66c29d9f022b274	diff --git a/tests/test_pip_lock.py b/tests/test_pip_lock.py index cca27a5..7dde0c4 100644 --- a/tests/test_pip_lock.py +++ b/tests/test_pip_lock.py @@ -49,6 +49,9 @@ class TestGetPackageVersion: def test_ignore_includes(self): assert get_package_versions(["-r example.txt"]) == {} + def test_ignore_arguments(self): + assert get_package_versions(["--find-links file:./wheels"]) == {} + def test_ignore_urls(self): assert get_package_versions(["https://www.google.com"]) == {}	Crashes on lines providing arguments to pip For example `--find-links`	a70ab3c56a094044a1de38f9c66c29d9f022b274	[ "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_arguments" ]	[ "tests/test_pip_lock.py::TestReadPip::test_read", "tests/test_pip_lock.py::TestReadPip::test_include", "tests/test_pip_lock.py::TestReadPip::test_empty", "tests/test_pip_lock.py::TestGetPackageVersion::test_version", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_empty", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_comments", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_includes", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_urls", "tests/test_pip_lock.py::TestGetMismatches::test_relative_requirements_file", "tests/test_pip_lock.py::TestGetMismatches::test_version_mismatch", "tests/test_pip_lock.py::TestGetMismatches::test_missing", "tests/test_pip_lock.py::TestGetMismatches::test_no_mismatches", "tests/test_pip_lock.py::TestGetMismatches::test_no_mismatches_case_insensitive", "tests/test_pip_lock.py::TestGetMismatches::test_empty", "tests/test_pip_lock.py::TestGetMismatches::test_editable_packages_ignored", "tests/test_pip_lock.py::TestGetMismatches::test_at_packages_ignored", "tests/test_pip_lock.py::TestGetMismatches::test_package_with_extra", "tests/test_pip_lock.py::TestPrintErrors::test_errors", "tests/test_pip_lock.py::TestPrintErrors::test_pre_post_text", "tests/test_pip_lock.py::TestCheckRequirements::test_no_mismatches", "tests/test_pip_lock.py::TestCheckRequirements::test_mismatches", "tests/test_pip_lock.py::TestCheckRequirements::test_relative_requirements_file" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2021-01-22 11:34:16+00:00	mit	893
adamchainz__time-machine-101	diff --git a/HISTORY.rst b/HISTORY.rst index 0178c5f..3548383 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,6 +2,8 @@ History ======= +* Prevent ``ImportError`` on Windows where ``time.tzset()`` is unavailable. + 2.0.0 (2021-01-17) ------------------ diff --git a/src/time_machine.py b/src/time_machine.py index ed2cfb2..9b4de81 100644 --- a/src/time_machine.py +++ b/src/time_machine.py @@ -5,7 +5,6 @@ import os import sys import uuid from time import gmtime as orig_gmtime -from time import tzset from types import GeneratorType from typing import Optional from unittest import TestCase, mock @@ -21,6 +20,12 @@ except ImportError: # Dummy value that won't compare equal to any value CLOCK_REALTIME = float("inf") +try: + from time import tzset +except ImportError: # pragma: no cover + # Windows + tzset = None + try: # Python 3.8+ or have installed backports.zoneinfo from zoneinfo import ZoneInfo @@ -137,13 +142,13 @@ class Coordinates: self._start() def _start(self): - if self._destination_tzname is not None: + if tzset is not None and self._destination_tzname is not None: self._orig_tz = os.environ.get("TZ") os.environ["TZ"] = self._destination_tzname tzset() def _stop(self): - if self._destination_tzname is not None: + if tzset is not None and self._destination_tzname is not None: if self._orig_tz is None: del os.environ["TZ"] else:	adamchainz/time-machine	5b2536a1bfb47dc0619d7d03302cf1edc5a51112	diff --git a/tests/test_time_machine.py b/tests/test_time_machine.py index 8f6aa5f..ce7695b 100644 --- a/tests/test_time_machine.py +++ b/tests/test_time_machine.py @@ -379,6 +379,17 @@ def test_destination_datetime_tzinfo_zoneinfo_nested(): assert time.tzname == orig_tzname [email protected](ZoneInfo is None, reason="Requires ZoneInfo") +def test_destination_datetime_tzinfo_zoneinfo_windows(): + orig_timezone = time.timezone + + pretend_windows_no_tzset = mock.patch.object(time_machine, "tzset", new=None) + + dest = LIBRARY_EPOCH_DATETIME.replace(tzinfo=ZoneInfo("Africa/Addis_Ababa")) + with pretend_windows_no_tzset, time_machine.travel(dest): + assert time.timezone == orig_timezone + + @time_machine.travel(EPOCH_DATETIME.replace(tzinfo=None) + dt.timedelta(seconds=120)) def test_destination_datetime_naive(): assert time.time() == EPOCH + 120.0	[v2] ImportError for tzset on Windows In one of my project, I received an automatic update to update time-machine to the newly published v2 and my CI crashes on Windows (Python 3.7, 3.8 and 3.9) with the following error: ``` ImportError: cannot import name 'tzset' from 'time' (unknown location) ``` I don't own a Windows machine, but one can check the logs here: https://github.com/browniebroke/netlify-builds/pull/27/checks?check_run_id=1716666697#step:6:52 Not really urgent or anything, but I thought I report the problem. Is it a missing dependency or something different with the stdlib?	5b2536a1bfb47dc0619d7d03302cf1edc5a51112	[ "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_windows", "tests/test_time_machine.py::test_traveller_object", "tests/test_time_machine.py::test_move_to_datetime_with_tzinfo_zoneinfo", "tests/test_time_machine.py::test_fixture_unused" ]	[ "tests/test_time_machine.py::test_import_without_clock_realtime", "tests/test_time_machine.py::test_datetime_now_no_args", "tests/test_time_machine.py::test_datetime_now_no_args_no_tick", "tests/test_time_machine.py::test_datetime_now_arg", "tests/test_time_machine.py::test_datetime_utcnow", "tests/test_time_machine.py::test_datetime_utcnow_no_tick", "tests/test_time_machine.py::test_date_today", "tests/test_time_machine.py::test_time_clock_gettime_realtime", "tests/test_time_machine.py::test_time_clock_gettime_monotonic_unaffected", "tests/test_time_machine.py::test_time_clock_gettime_ns_realtime", "tests/test_time_machine.py::test_time_clock_gettime_ns_monotonic_unaffected", "tests/test_time_machine.py::test_time_gmtime_no_args", "tests/test_time_machine.py::test_time_gmtime_no_args_no_tick", "tests/test_time_machine.py::test_time_gmtime_arg", "tests/test_time_machine.py::test_time_localtime", "tests/test_time_machine.py::test_time_localtime_no_tick", "tests/test_time_machine.py::test_time_localtime_arg", "tests/test_time_machine.py::test_time_strftime_no_args", "tests/test_time_machine.py::test_time_strftime_no_args_no_tick", "tests/test_time_machine.py::test_time_strftime_arg", "tests/test_time_machine.py::test_time_time", "tests/test_time_machine.py::test_time_time_windows", "tests/test_time_machine.py::test_time_time_no_tick", "tests/test_time_machine.py::test_time_time_ns", "tests/test_time_machine.py::test_time_time_ns_no_tick", "tests/test_time_machine.py::test_nestable", "tests/test_time_machine.py::test_unsupported_type", "tests/test_time_machine.py::test_exceptions_dont_break_it", "tests/test_time_machine.py::test_destination_datetime", "tests/test_time_machine.py::test_destination_datetime_tzinfo_non_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_nested", "tests/test_time_machine.py::test_destination_datetime_naive", "tests/test_time_machine.py::test_destination_date", "tests/test_time_machine.py::test_destination_string", "tests/test_time_machine.py::test_destination_callable_lambda_float", "tests/test_time_machine.py::test_destination_callable_lambda_string", "tests/test_time_machine.py::test_destination_generator", "tests/test_time_machine.py::test_function_decorator", "tests/test_time_machine.py::test_coroutine_decorator", "tests/test_time_machine.py::test_class_decorator_fails_non_testcase", "tests/test_time_machine.py::UnitTestMethodTests::test_method_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_class_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_stacked_method_decorator", "tests/test_time_machine.py::UnitTestClassCustomSetUpClassTests::test_class_decorator", "tests/test_time_machine.py::test_shift_with_timedelta", "tests/test_time_machine.py::test_shift_integer_delta", "tests/test_time_machine.py::test_shift_negative_delta", "tests/test_time_machine.py::test_shift_wrong_delta", "tests/test_time_machine.py::test_shift_when_tick", "tests/test_time_machine.py::test_move_to_datetime", "tests/test_time_machine.py::test_move_to_datetime_no_tick", "tests/test_time_machine.py::test_move_to_past_datetime", "tests/test_time_machine.py::test_uuid1", "tests/test_time_machine.py::test_fixture_used", "tests/test_time_machine.py::test_fixture_used_twice" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-01-18 10:34:15+00:00	mit	894
adamchainz__time-machine-152	diff --git a/HISTORY.rst b/HISTORY.rst index 3265158..5390cf4 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,6 +2,10 @@ History ======= +* Allow passing ``tick`` to ``Coordinates.move_to()`` and the pytest fixture’s + ``time_machine.move_to()``. This allows freezing or unfreezing of time when + travelling. + 2.2.0 (2021-07-02) ------------------ diff --git a/README.rst b/README.rst index c4dc27b..d95ff70 100644 --- a/README.rst +++ b/README.rst @@ -235,12 +235,14 @@ Here’s a worked example changing the current timezone: The ``start()`` method and entry of the context manager both return a ``Coordinates`` object that corresponds to the given "trip" in time. This has a couple methods that can be used to travel to other times. -``move_to(destination)`` -^^^^^^^^^^^^^^^^^^^^^^^^ +``move_to(destination, tick=None)`` +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ``move_to()`` moves the current time to a new destination. ``destination`` may be any of the types supported by ``travel``. +``tick`` may be set to a boolean, to change the ``tick`` flag of ``travel``. + For example: .. code-block:: python diff --git a/src/time_machine/__init__.py b/src/time_machine/__init__.py index 7f297a9..a8302b8 100644 --- a/src/time_machine/__init__.py +++ b/src/time_machine/__init__.py @@ -163,12 +163,18 @@ class Coordinates: self._destination_timestamp_ns += int(total_seconds * NANOSECONDS_PER_SECOND) - def move_to(self, destination: DestinationType) -> None: + def move_to( + self, + destination: DestinationType, + tick: Optional[bool] = None, + ) -> None: self._stop() timestamp, self._destination_tzname = extract_timestamp_tzname(destination) self._destination_timestamp_ns = int(timestamp * NANOSECONDS_PER_SECOND) self._requested = False self._start() + if tick is not None: + self._tick = tick def _start(self) -> None: if HAVE_TZSET and self._destination_tzname is not None: @@ -421,13 +427,19 @@ if pytest is not None: # pragma: no branch self.traveller = None self.coordinates = None - def move_to(self, destination: DestinationType) -> None: + def move_to( + self, + destination: DestinationType, + tick: Optional[bool] = None, + ) -> None: if self.traveller is None: - self.traveller = travel(destination) + if tick is None: + tick = True + self.traveller = travel(destination, tick=tick) self.coordinates = self.traveller.start() else: assert self.coordinates is not None - self.coordinates.move_to(destination) + self.coordinates.move_to(destination, tick=tick) def stop(self) -> None: if self.traveller is not None:	adamchainz/time-machine	665670beddc1f330ce182984bfd1fddeda0587a1	diff --git a/tests/test_time_machine.py b/tests/test_time_machine.py index ccf3862..175a7d5 100644 --- a/tests/test_time_machine.py +++ b/tests/test_time_machine.py @@ -633,6 +633,20 @@ def test_move_to_datetime_with_tzinfo_zoneinfo(): assert time.daylight == orig_daylight +def test_move_to_datetime_change_tick_on(): + with time_machine.travel(EPOCH, tick=False) as traveller: + traveller.move_to(EPOCH_PLUS_ONE_YEAR_DATETIME, tick=True) + assert time.time() == EPOCH_PLUS_ONE_YEAR + assert time.time() > EPOCH_PLUS_ONE_YEAR + + +def test_move_to_datetime_change_tick_off(): + with time_machine.travel(EPOCH, tick=True) as traveller: + traveller.move_to(EPOCH_PLUS_ONE_YEAR_DATETIME, tick=False) + assert time.time() == EPOCH_PLUS_ONE_YEAR + assert time.time() == EPOCH_PLUS_ONE_YEAR + + # uuid tests @@ -664,6 +678,19 @@ def test_fixture_used(time_machine): assert time.time() == EPOCH +def test_fixture_used_tick_false(time_machine): + time_machine.move_to(EPOCH, tick=False) + assert time.time() == EPOCH + assert time.time() == EPOCH + + +def test_fixture_used_tick_true(time_machine): + time_machine.move_to(EPOCH, tick=True) + original = time.time() + assert original == EPOCH + assert original < time.time() < EPOCH + 10.0 + + def test_fixture_used_twice(time_machine): time_machine.move_to(EPOCH) assert time.time() == EPOCH	Freeze time instead of just shifting it Hi! This library looks very cool, even more with the added support for pytest. I have a question which might be more related with me not understanding the use cases or purpose than the tool itself. I thought I would be able to tell the library: everytime I call now I want you to return this. Instead what I found is that when I call the `move_to` method in the time_machine fixture, time goes back to that time but the starts moving forward accurately. What I wanted to be able to do is to always get the same value when utcnow is called so I can test the value of queries that I am generating on the fly. Is this possible? Thanks!	665670beddc1f330ce182984bfd1fddeda0587a1	[ "tests/test_time_machine.py::test_move_to_datetime_change_tick_on", "tests/test_time_machine.py::test_move_to_datetime_change_tick_off", "tests/test_time_machine.py::test_fixture_used_tick_false", "tests/test_time_machine.py::test_fixture_used_tick_true" ]	[ "tests/test_time_machine.py::test_import_without_clock_realtime", "tests/test_time_machine.py::test_datetime_now_no_args", "tests/test_time_machine.py::test_datetime_now_no_args_no_tick", "tests/test_time_machine.py::test_datetime_now_arg", "tests/test_time_machine.py::test_datetime_utcnow", "tests/test_time_machine.py::test_datetime_utcnow_no_tick", "tests/test_time_machine.py::test_date_today", "tests/test_time_machine.py::test_time_clock_gettime_realtime", "tests/test_time_machine.py::test_time_clock_gettime_monotonic_unaffected", "tests/test_time_machine.py::test_time_clock_gettime_ns_realtime", "tests/test_time_machine.py::test_time_clock_gettime_ns_monotonic_unaffected", "tests/test_time_machine.py::test_time_gmtime_no_args", "tests/test_time_machine.py::test_time_gmtime_no_args_no_tick", "tests/test_time_machine.py::test_time_gmtime_arg", "tests/test_time_machine.py::test_time_localtime", "tests/test_time_machine.py::test_time_localtime_no_tick", "tests/test_time_machine.py::test_time_localtime_arg", "tests/test_time_machine.py::test_time_strftime_no_args", "tests/test_time_machine.py::test_time_strftime_no_args_no_tick", "tests/test_time_machine.py::test_time_strftime_arg", "tests/test_time_machine.py::test_time_time", "tests/test_time_machine.py::test_time_time_windows", "tests/test_time_machine.py::test_time_time_no_tick", "tests/test_time_machine.py::test_time_time_ns", "tests/test_time_machine.py::test_time_time_ns_no_tick", "tests/test_time_machine.py::test_nestable", "tests/test_time_machine.py::test_unsupported_type", "tests/test_time_machine.py::test_exceptions_dont_break_it", "tests/test_time_machine.py::test_destination_datetime", "tests/test_time_machine.py::test_destination_datetime_tzinfo_non_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_nested", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_windows", "tests/test_time_machine.py::test_destination_int", "tests/test_time_machine.py::test_destination_datetime_naive", "tests/test_time_machine.py::test_destination_date", "tests/test_time_machine.py::test_destination_string", "tests/test_time_machine.py::test_destination_callable_lambda_float", "tests/test_time_machine.py::test_destination_callable_lambda_string", "tests/test_time_machine.py::test_destination_generator", "tests/test_time_machine.py::test_traveller_object", "tests/test_time_machine.py::test_function_decorator", "tests/test_time_machine.py::test_coroutine_decorator", "tests/test_time_machine.py::test_class_decorator_fails_non_testcase", "tests/test_time_machine.py::UnitTestMethodTests::test_method_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_class_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_stacked_method_decorator", "tests/test_time_machine.py::UnitTestClassCustomSetUpClassTests::test_class_decorator", "tests/test_time_machine.py::test_shift_with_timedelta", "tests/test_time_machine.py::test_shift_integer_delta", "tests/test_time_machine.py::test_shift_negative_delta", "tests/test_time_machine.py::test_shift_wrong_delta", "tests/test_time_machine.py::test_shift_when_tick", "tests/test_time_machine.py::test_move_to_datetime", "tests/test_time_machine.py::test_move_to_datetime_no_tick", "tests/test_time_machine.py::test_move_to_past_datetime", "tests/test_time_machine.py::test_move_to_datetime_with_tzinfo_zoneinfo", "tests/test_time_machine.py::test_uuid1", "tests/test_time_machine.py::test_fixture_unused", "tests/test_time_machine.py::test_fixture_used", "tests/test_time_machine.py::test_fixture_used_twice" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-07-05 15:02:34+00:00	mit	895
adamchainz__time-machine-207	diff --git a/HISTORY.rst b/HISTORY.rst index 78e067b..7af039e 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,6 +2,10 @@ History ======= +* Add ``time_machine.escape_hatch``, which provides functions to bypass time-machine. + + Thanks to Matt Pegler for the feature request in `Issue #206 <https://github.com/adamchainz/time-machine/issues/206>`__. + 2.4.1 (2021-11-27) ------------------ diff --git a/README.rst b/README.rst index 4532090..f23ce06 100644 --- a/README.rst +++ b/README.rst @@ -310,6 +310,52 @@ For example: assert dt.date.today().isoformat() == "2015-10-21" +``escape_hatch`` +---------------- + +The ``escape_hatch`` object provides functions to bypass time-machine. +These allow you to call the real datetime functions, without any mocking. +It also provides a way to check if time-machine is currently time travelling. + +These capabilities are useful in rare circumstances. +For example, if you need to authenticate with an external service during time travel, you may need the real value of ``datetime.now()``. + +The functions are: + +* ``escape_hatch.is_travelling() -> bool`` - returns ``True`` if ``time_machine.travel()`` is active, ``False`` otherwise. + +* ``escape_hatch.datetime.datetime.now()`` - wraps the real ``datetime.datetime.now()``. + +* ``escape_hatch.datetime.datetime.utcnow()`` - wraps the real ``datetime.datetime.utcnow()``. + +* ``escape_hatch.time.clock_gettime()`` - wraps the real ``time.clock_gettime()``. + +* ``escape_hatch.time.clock_gettime_ns()`` - wraps the real ``time.clock_gettime_ns()``. + +* ``escape_hatch.time.gmtime()`` - wraps the real ``time.gmtime()``. + +* ``escape_hatch.time.localtime()`` - wraps the real ``time.localtime()``. + +* ``escape_hatch.time.strftime()`` - wraps the real ``time.strftime()``. + +* ``escape_hatch.time.time()`` - wraps the real ``time.time()``. + +* ``escape_hatch.time.time_ns()`` - wraps the real ``time.time_ns()``. + +For example: + +.. code-block:: python + + import time_machine + + + with time_machine.travel(...): + if time_machine.escape_hatch.is_travelling(): + print("We need to go back to the future!") + + real_now = time_machine.escape_hatch.datetime.datetime.now() + external_authenticate(now=real_now) + Caveats ======= diff --git a/src/time_machine/__init__.py b/src/time_machine/__init__.py index 0e67b1b..4c57870 100644 --- a/src/time_machine/__init__.py +++ b/src/time_machine/__init__.py @@ -77,6 +77,9 @@ DestinationType = Union[ TypingGenerator[DestinationBaseType, None, None], ] +# copied from typeshed: +_TimeTuple = Tuple[int, int, int, int, int, int, int, int, int] + def extract_timestamp_tzname( destination: DestinationType, @@ -389,10 +392,6 @@ def localtime(secs: Optional[float] = None) -> struct_time: return _time_machine.original_localtime(coordinates_stack[-1].time()) -# copied from typeshed: -_TimeTuple = Tuple[int, int, int, int, int, int, int, int, int] - - def strftime(format: str, t: Union[_TimeTuple, struct_time, None] = None) -> str: if t is not None: return _time_machine.original_strftime(format, t) @@ -453,3 +452,63 @@ if pytest is not None: # pragma: no branch yield fixture finally: fixture.stop() + + +# escape hatch + + +class _EscapeHatchDatetimeDatetime: + def now(self, tz: Optional[dt.tzinfo] = None) -> dt.datetime: + return _time_machine.original_now(tz) + + def utcnow(self) -> dt.datetime: + return _time_machine.original_utcnow() + + +class _EscapeHatchDatetime: + def __init__(self) -> None: + self.datetime = _EscapeHatchDatetimeDatetime() + + +class _EscapeHatchTime: + def clock_gettime(self, clk_id: int) -> float: + return _time_machine.original_clock_gettime(clk_id) + + if sys.version_info >= (3, 7): + + def clock_gettime_ns(self, clk_id: int) -> int: + return _time_machine.original_clock_gettime_ns(clk_id) + + def gmtime(self, secs: Optional[float] = None) -> struct_time: + return _time_machine.original_gmtime(secs) + + def localtime(self, secs: Optional[float] = None) -> struct_time: + return _time_machine.original_localtime(secs) + + def strftime( + self, format: str, t: Union[_TimeTuple, struct_time, None] = None + ) -> str: + if t is not None: + return _time_machine.original_strftime(format, t) + else: + return _time_machine.original_strftime(format) + + def time(self) -> float: + return _time_machine.original_time() + + if sys.version_info >= (3, 7): + + def time_ns(self) -> int: + return _time_machine.original_time_ns() + + +class _EscapeHatch: + def __init__(self) -> None: + self.datetime = _EscapeHatchDatetime() + self.time = _EscapeHatchTime() + + def is_travelling(self) -> bool: + return bool(coordinates_stack) + + +escape_hatch = _EscapeHatch()	adamchainz/time-machine	29a9f0aa44204c9bf236f350fdc5015fd10e8e2c	diff --git a/tests/test_time_machine.py b/tests/test_time_machine.py index a23a99e..8cb4f63 100644 --- a/tests/test_time_machine.py +++ b/tests/test_time_machine.py @@ -222,18 +222,18 @@ def test_time_localtime_arg(): assert local_time.tm_mday == 1 -def test_time_strftime_no_args(): +def test_time_strftime_format(): with time_machine.travel(EPOCH): assert time.strftime("%Y-%m-%d") == "1970-01-01" assert int(time.strftime("%Y")) >= 2020 -def test_time_strftime_no_args_no_tick(): +def test_time_strftime_format_no_tick(): with time_machine.travel(EPOCH, tick=False): assert time.strftime("%S") == "00" -def test_time_strftime_arg(): +def test_time_strftime_format_t(): with time_machine.travel(EPOCH): assert ( time.strftime("%Y-%m-%d", time.localtime(EPOCH_PLUS_ONE_YEAR)) @@ -718,3 +718,100 @@ def test_fixture_used_twice(time_machine): time_machine.move_to(EPOCH_PLUS_ONE_YEAR) assert time.time() == EPOCH_PLUS_ONE_YEAR + + +# escape hatch tests + + +class TestEscapeHatch: + def test_is_travelling_false(self): + assert time_machine.escape_hatch.is_travelling() is False + + def test_is_travelling_true(self): + with time_machine.travel(EPOCH): + assert time_machine.escape_hatch.is_travelling() is True + + def test_datetime_now(self): + real_now = dt.datetime.now() + + with time_machine.travel(EPOCH): + eh_now = time_machine.escape_hatch.datetime.datetime.now() + assert eh_now >= real_now + + def test_datetime_now_tz(self): + real_now = dt.datetime.now(tz=dt.timezone.utc) + + with time_machine.travel(EPOCH): + eh_now = time_machine.escape_hatch.datetime.datetime.now(tz=dt.timezone.utc) + assert eh_now >= real_now + + def test_datetime_utcnow(self): + real_now = dt.datetime.utcnow() + + with time_machine.travel(EPOCH): + eh_now = time_machine.escape_hatch.datetime.datetime.utcnow() + assert eh_now >= real_now + + @py_have_clock_gettime + def test_time_clock_gettime(self): + now = time.clock_gettime(time.CLOCK_REALTIME) + + with time_machine.travel(EPOCH + 180.0): + eh_now = time_machine.escape_hatch.time.clock_gettime(time.CLOCK_REALTIME) + assert eh_now >= now + + @py_3_7_plus + @py_have_clock_gettime + def test_time_clock_gettime_ns(self): + now = time.clock_gettime_ns(time.CLOCK_REALTIME) + + with time_machine.travel(EPOCH + 190.0): + eh_now = time_machine.escape_hatch.time.clock_gettime_ns( + time.CLOCK_REALTIME + ) + assert eh_now >= now + + def test_time_gmtime(self): + now = time.gmtime() + + with time_machine.travel(EPOCH): + eh_now = time_machine.escape_hatch.time.gmtime() + assert eh_now >= now + + def test_time_localtime(self): + now = time.localtime() + + with time_machine.travel(EPOCH): + eh_now = time_machine.escape_hatch.time.localtime() + assert eh_now >= now + + def test_time_strftime_no_arg(self): + today = dt.date.today() + + with time_machine.travel(EPOCH): + eh_formatted = time_machine.escape_hatch.time.strftime("%Y-%m-%d") + eh_today = dt.datetime.strptime(eh_formatted, "%Y-%m-%d").date() + assert eh_today >= today + + def test_time_strftime_arg(self): + with time_machine.travel(EPOCH): + formatted = time_machine.escape_hatch.time.strftime( + "%Y-%m-%d", + time.localtime(EPOCH_PLUS_ONE_YEAR), + ) + assert formatted == "1971-01-01" + + def test_time_time(self): + now = time.time() + + with time_machine.travel(EPOCH): + eh_now = time_machine.escape_hatch.time.time() + assert eh_now >= now + + @py_3_7_plus + def test_time_time_ns(self): + now = time.time_ns() + + with time_machine.travel(EPOCH): + eh_now = time_machine.escape_hatch.time.time_ns() + assert eh_now >= now	Flag that we're time traveling, with access to true datetime ### Description In some of our integration tests we make API calls to external services. Some of these require a timestamp for use in authentication. I know that excluding some modules from time-machine isn't possible due to the implementation, but having some signal that we're time traveling would suffice, along with access to the unpatched datetime module.	29a9f0aa44204c9bf236f350fdc5015fd10e8e2c	[ "tests/test_time_machine.py::TestEscapeHatch::test_is_travelling_false", "tests/test_time_machine.py::TestEscapeHatch::test_is_travelling_true", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_now", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_now_tz", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_utcnow", "tests/test_time_machine.py::TestEscapeHatch::test_time_clock_gettime", "tests/test_time_machine.py::TestEscapeHatch::test_time_clock_gettime_ns", "tests/test_time_machine.py::TestEscapeHatch::test_time_gmtime", "tests/test_time_machine.py::TestEscapeHatch::test_time_localtime", "tests/test_time_machine.py::TestEscapeHatch::test_time_strftime_no_arg", "tests/test_time_machine.py::TestEscapeHatch::test_time_strftime_arg", "tests/test_time_machine.py::TestEscapeHatch::test_time_time", "tests/test_time_machine.py::TestEscapeHatch::test_time_time_ns" ]	[ "tests/test_time_machine.py::test_import_without_clock_realtime", "tests/test_time_machine.py::test_datetime_now_no_args", "tests/test_time_machine.py::test_datetime_now_no_args_no_tick", "tests/test_time_machine.py::test_datetime_now_arg", "tests/test_time_machine.py::test_datetime_utcnow", "tests/test_time_machine.py::test_datetime_utcnow_no_tick", "tests/test_time_machine.py::test_date_today", "tests/test_time_machine.py::test_time_clock_gettime_realtime", "tests/test_time_machine.py::test_time_clock_gettime_monotonic_unaffected", "tests/test_time_machine.py::test_time_clock_gettime_ns_realtime", "tests/test_time_machine.py::test_time_clock_gettime_ns_monotonic_unaffected", "tests/test_time_machine.py::test_time_gmtime_no_args", "tests/test_time_machine.py::test_time_gmtime_no_args_no_tick", "tests/test_time_machine.py::test_time_gmtime_arg", "tests/test_time_machine.py::test_time_localtime", "tests/test_time_machine.py::test_time_localtime_no_tick", "tests/test_time_machine.py::test_time_localtime_arg", "tests/test_time_machine.py::test_time_strftime_format", "tests/test_time_machine.py::test_time_strftime_format_no_tick", "tests/test_time_machine.py::test_time_strftime_format_t", "tests/test_time_machine.py::test_time_time", "tests/test_time_machine.py::test_time_time_windows", "tests/test_time_machine.py::test_time_time_no_tick", "tests/test_time_machine.py::test_time_time_ns", "tests/test_time_machine.py::test_time_time_ns_no_tick", "tests/test_time_machine.py::test_nestable", "tests/test_time_machine.py::test_unsupported_type", "tests/test_time_machine.py::test_exceptions_dont_break_it", "tests/test_time_machine.py::test_destination_datetime", "tests/test_time_machine.py::test_destination_datetime_tzinfo_non_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_nested", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_no_orig_tz", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_windows", "tests/test_time_machine.py::test_destination_int", "tests/test_time_machine.py::test_destination_datetime_naive", "tests/test_time_machine.py::test_destination_date", "tests/test_time_machine.py::test_destination_string", "tests/test_time_machine.py::test_destination_callable_lambda_float", "tests/test_time_machine.py::test_destination_callable_lambda_string", "tests/test_time_machine.py::test_destination_generator", "tests/test_time_machine.py::test_traveller_object", "tests/test_time_machine.py::test_function_decorator", "tests/test_time_machine.py::test_coroutine_decorator", "tests/test_time_machine.py::test_class_decorator_fails_non_testcase", "tests/test_time_machine.py::UnitTestMethodTests::test_method_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_class_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_stacked_method_decorator", "tests/test_time_machine.py::UnitTestClassCustomSetUpClassTests::test_class_decorator", "tests/test_time_machine.py::test_shift_with_timedelta", "tests/test_time_machine.py::test_shift_integer_delta", "tests/test_time_machine.py::test_shift_negative_delta", "tests/test_time_machine.py::test_shift_wrong_delta", "tests/test_time_machine.py::test_shift_when_tick", "tests/test_time_machine.py::test_move_to_datetime", "tests/test_time_machine.py::test_move_to_datetime_no_tick", "tests/test_time_machine.py::test_move_to_past_datetime", "tests/test_time_machine.py::test_move_to_datetime_with_tzinfo_zoneinfo", "tests/test_time_machine.py::test_move_to_datetime_change_tick_on", "tests/test_time_machine.py::test_move_to_datetime_change_tick_off", "tests/test_time_machine.py::test_uuid1", "tests/test_time_machine.py::test_fixture_unused", "tests/test_time_machine.py::test_fixture_used", "tests/test_time_machine.py::test_fixture_used_tick_false", "tests/test_time_machine.py::test_fixture_used_tick_true", "tests/test_time_machine.py::test_fixture_used_twice" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-12-14 07:56:53+00:00	mit	896
adamchainz__time-machine-298	diff --git a/CHANGELOG.rst b/CHANGELOG.rst index c524071..71b1598 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -2,6 +2,10 @@ Changelog ========= +* Add support for ``datetime.timedelta`` to ``time_machine.travel()``. + + Thanks to Nate Dudenhoeffer in `PR #298 <https://github.com/adamchainz/time-machine/pull/298>`__. + * Add ``shift()`` method to the ``time_machine`` pytest fixture. Thanks to Stefaan Lippens in `PR #312 <https://github.com/adamchainz/time-machine/pull/312>`__. diff --git a/README.rst b/README.rst index 755325c..88db11f 100644 --- a/README.rst +++ b/README.rst @@ -77,6 +77,9 @@ It may be: If it has ``tzinfo`` set to a \|zoneinfo-instance\|_, the current timezone will also be mocked. * A ``datetime.date``. This will be converted to a UTC datetime with the time 00:00:00. +* A ``datetime.timedelta``. + This will be interpreted relative to the current time. + If already within a ``travel()`` block, the ``shift()`` method is easier to use (documented below). * A ``float`` or ``int`` specifying a `Unix timestamp <https://en.m.wikipedia.org/wiki/Unix_time>`__ * A string, which will be parsed with `dateutil.parse <https://dateutil.readthedocs.io/en/stable/parser.html>`__ and converted to a timestamp. Again, if the result is naive, it will be assumed to have the UTC time zone. diff --git a/src/time_machine/__init__.py b/src/time_machine/__init__.py index c0d6bda..4fa2142 100644 --- a/src/time_machine/__init__.py +++ b/src/time_machine/__init__.py @@ -84,6 +84,7 @@ DestinationBaseType = Union[ int, float, dt.datetime, + dt.timedelta, dt.date, str, ] @@ -124,6 +125,8 @@ def extract_timestamp_tzname( if dest.tzinfo is None: dest = dest.replace(tzinfo=dt.timezone.utc) timestamp = dest.timestamp() + elif isinstance(dest, dt.timedelta): + timestamp = time() + dest.total_seconds() elif isinstance(dest, dt.date): timestamp = dt.datetime.combine( dest, dt.time(0, 0), tzinfo=dt.timezone.utc	adamchainz/time-machine	ac337ab7dc568675de7f90c8fb387160e3f08496	diff --git a/tests/test_time_machine.py b/tests/test_time_machine.py index 9736be4..0f086bf 100644 --- a/tests/test_time_machine.py +++ b/tests/test_time_machine.py @@ -444,6 +444,24 @@ def test_destination_date(): assert time.time() == EPOCH +def test_destination_timedelta(): + now = time.time() + with time_machine.travel(dt.timedelta(seconds=3600)): + assert now + 3600 <= time.time() <= now + 3601 + + +def test_destination_timedelta_negative(): + now = time.time() + with time_machine.travel(dt.timedelta(seconds=-3600)): + assert now - 3600 <= time.time() <= now - 3599 + + +def test_destination_timedelta_nested(): + with time_machine.travel(EPOCH): + with time_machine.travel(dt.timedelta(seconds=10)): + assert time.time() == EPOCH + 10.0 + + @time_machine.travel("1970-01-01 00:01 +0000") def test_destination_string(): assert time.time() == EPOCH + 60.0	Allow passing dt.timedelta objects to travel() It would offset the current time by the given amount, which would be pretty useful for some tests that check "X is true until N minutes in the future"	ac337ab7dc568675de7f90c8fb387160e3f08496	[ "tests/test_time_machine.py::test_destination_timedelta", "tests/test_time_machine.py::test_destination_timedelta_negative", "tests/test_time_machine.py::test_destination_timedelta_nested" ]	[ "tests/test_time_machine.py::test_import_without_clock_realtime", "tests/test_time_machine.py::test_datetime_now_no_args", "tests/test_time_machine.py::test_datetime_now_no_args_no_tick", "tests/test_time_machine.py::test_datetime_now_arg", "tests/test_time_machine.py::test_datetime_utcnow", "tests/test_time_machine.py::test_datetime_utcnow_no_tick", "tests/test_time_machine.py::test_date_today", "tests/test_time_machine.py::test_time_clock_gettime_realtime", "tests/test_time_machine.py::test_time_clock_gettime_monotonic_unaffected", "tests/test_time_machine.py::test_time_clock_gettime_ns_realtime", "tests/test_time_machine.py::test_time_clock_gettime_ns_monotonic_unaffected", "tests/test_time_machine.py::test_time_gmtime_no_args", "tests/test_time_machine.py::test_time_gmtime_no_args_no_tick", "tests/test_time_machine.py::test_time_gmtime_arg", "tests/test_time_machine.py::test_time_localtime", "tests/test_time_machine.py::test_time_localtime_no_tick", "tests/test_time_machine.py::test_time_localtime_arg", "tests/test_time_machine.py::test_time_montonic", "tests/test_time_machine.py::test_time_monotonic_ns", "tests/test_time_machine.py::test_time_strftime_format", "tests/test_time_machine.py::test_time_strftime_format_no_tick", "tests/test_time_machine.py::test_time_strftime_format_t", "tests/test_time_machine.py::test_time_time", "tests/test_time_machine.py::test_time_time_windows", "tests/test_time_machine.py::test_time_time_no_tick", "tests/test_time_machine.py::test_time_time_ns", "tests/test_time_machine.py::test_time_time_ns_no_tick", "tests/test_time_machine.py::test_nestable", "tests/test_time_machine.py::test_unsupported_type", "tests/test_time_machine.py::test_exceptions_dont_break_it", "tests/test_time_machine.py::test_destination_datetime", "tests/test_time_machine.py::test_destination_datetime_tzinfo_non_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_nested", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_no_orig_tz", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_windows", "tests/test_time_machine.py::test_destination_int", "tests/test_time_machine.py::test_destination_datetime_naive", "tests/test_time_machine.py::test_destination_date", "tests/test_time_machine.py::test_destination_string", "tests/test_time_machine.py::test_destination_callable_lambda_float", "tests/test_time_machine.py::test_destination_callable_lambda_string", "tests/test_time_machine.py::test_destination_generator", "tests/test_time_machine.py::test_traveller_object", "tests/test_time_machine.py::test_function_decorator", "tests/test_time_machine.py::test_coroutine_decorator", "tests/test_time_machine.py::test_class_decorator_fails_non_testcase", "tests/test_time_machine.py::TestMethodDecorator::test_method_decorator", "tests/test_time_machine.py::UnitTestMethodTests::test_method_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_class_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_stacked_method_decorator", "tests/test_time_machine.py::UnitTestClassCustomSetUpClassTests::test_class_decorator", "tests/test_time_machine.py::test_shift_with_timedelta", "tests/test_time_machine.py::test_shift_integer_delta", "tests/test_time_machine.py::test_shift_negative_delta", "tests/test_time_machine.py::test_shift_wrong_delta", "tests/test_time_machine.py::test_shift_when_tick", "tests/test_time_machine.py::test_move_to_datetime", "tests/test_time_machine.py::test_move_to_datetime_no_tick", "tests/test_time_machine.py::test_move_to_past_datetime", "tests/test_time_machine.py::test_move_to_datetime_with_tzinfo_zoneinfo", "tests/test_time_machine.py::test_move_to_datetime_change_tick_on", "tests/test_time_machine.py::test_move_to_datetime_change_tick_off", "tests/test_time_machine.py::test_uuid1", "tests/test_time_machine.py::test_fixture_unused", "tests/test_time_machine.py::test_fixture_used", "tests/test_time_machine.py::test_fixture_used_tick_false", "tests/test_time_machine.py::test_fixture_used_tick_true", "tests/test_time_machine.py::test_fixture_move_to_twice", "tests/test_time_machine.py::test_fixture_move_to_and_shift", "tests/test_time_machine.py::test_fixture_shift_without_move_to", "tests/test_time_machine.py::TestEscapeHatch::test_is_travelling_false", "tests/test_time_machine.py::TestEscapeHatch::test_is_travelling_true", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_now", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_now_tz", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_utcnow", "tests/test_time_machine.py::TestEscapeHatch::test_time_clock_gettime", "tests/test_time_machine.py::TestEscapeHatch::test_time_clock_gettime_ns", "tests/test_time_machine.py::TestEscapeHatch::test_time_gmtime", "tests/test_time_machine.py::TestEscapeHatch::test_time_localtime", "tests/test_time_machine.py::TestEscapeHatch::test_time_monotonic", "tests/test_time_machine.py::TestEscapeHatch::test_time_monotonic_ns", "tests/test_time_machine.py::TestEscapeHatch::test_time_strftime_no_arg", "tests/test_time_machine.py::TestEscapeHatch::test_time_strftime_arg", "tests/test_time_machine.py::TestEscapeHatch::test_time_time", "tests/test_time_machine.py::TestEscapeHatch::test_time_time_ns" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-11-03 01:33:14+00:00	mit	897
adamchainz__time-machine-433	diff --git a/CHANGELOG.rst b/CHANGELOG.rst index d83e48d..5984577 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -2,6 +2,10 @@ Changelog ========= +* Fix segmentation fault when the first ``travel()`` call in a process uses a ``timedelta``. + + Thanks to Marcin Sulikowski for the report in `Issue #431 <https://github.com/adamchainz/time-machine/issues/431>`__. + 2.14.0 (2024-03-03) ------------------- diff --git a/src/time_machine/__init__.py b/src/time_machine/__init__.py index 877b325..2553b3d 100644 --- a/src/time_machine/__init__.py +++ b/src/time_machine/__init__.py @@ -5,6 +5,7 @@ import functools import inspect import os import sys +import time as time_module import uuid from collections.abc import Generator from time import gmtime as orig_gmtime @@ -126,7 +127,7 @@ def extract_timestamp_tzname( dest = dest.replace(tzinfo=dt.timezone.utc) timestamp = dest.timestamp() elif isinstance(dest, dt.timedelta): - timestamp = time() + dest.total_seconds() + timestamp = time_module.time() + dest.total_seconds() elif isinstance(dest, dt.date): timestamp = dt.datetime.combine( dest, dt.time(0, 0), tzinfo=dt.timezone.utc	adamchainz/time-machine	8e28b9e74c3d6a50b7d6ec09a9e50903d4dc8bdd	diff --git a/tests/test_time_machine.py b/tests/test_time_machine.py index 11dc433..5557148 100644 --- a/tests/test_time_machine.py +++ b/tests/test_time_machine.py @@ -3,6 +3,7 @@ from __future__ import annotations import asyncio import datetime as dt import os +import subprocess import sys import time import typing @@ -10,6 +11,7 @@ import uuid from contextlib import contextmanager from importlib.util import module_from_spec from importlib.util import spec_from_file_location +from textwrap import dedent from unittest import SkipTest from unittest import TestCase from unittest import mock @@ -472,6 +474,25 @@ def test_destination_timedelta(): assert now + 3600 <= time.time() <= now + 3601 +def test_destination_timedelta_first_travel_in_process(): + # Would previously segfault + subprocess.run( + [ + sys.executable, + "-c", + dedent( + """ + from datetime import timedelta + import time_machine + with time_machine.travel(timedelta()): + pass + """ + ), + ], + check=True, + ) + + def test_destination_timedelta_negative(): now = time.time() with time_machine.travel(dt.timedelta(seconds=-3600)):	Segmentation fault in `time_machine_travel(timedelta())` ### Python Version 3.12 ### pytest Version _No response_ ### Package Version 2.14.0 ### Description The following Python script: ```py from datetime import timedelta import time_machine with time_machine.travel(timedelta()): pass ``` crashes due to a segmentation fault in the constructor of the `travel` class. The crash happens when the constructor tries to determine the destination timestamp like this: ```py timestamp = time() + dest.total_seconds() ``` where `time()` calls `result = _time_machine.original_time()` which crashes if time_machine's patches are not applied yet and thus the `original_time` function pointer is still `NULL`.	8e28b9e74c3d6a50b7d6ec09a9e50903d4dc8bdd	[ "tests/test_time_machine.py::test_destination_timedelta_first_travel_in_process" ]	[ "tests/test_time_machine.py::test_import_without_clock_realtime", "tests/test_time_machine.py::test_datetime_now_no_args", "tests/test_time_machine.py::test_datetime_now_no_args_no_tick", "tests/test_time_machine.py::test_datetime_now_arg", "tests/test_time_machine.py::test_datetime_utcnow", "tests/test_time_machine.py::test_datetime_utcnow_no_tick", "tests/test_time_machine.py::test_date_today", "tests/test_time_machine.py::test_time_clock_gettime_realtime", "tests/test_time_machine.py::test_time_clock_gettime_monotonic_unaffected", "tests/test_time_machine.py::test_time_clock_gettime_ns_realtime", "tests/test_time_machine.py::test_time_clock_gettime_ns_monotonic_unaffected", "tests/test_time_machine.py::test_time_gmtime_no_args", "tests/test_time_machine.py::test_time_gmtime_no_args_no_tick", "tests/test_time_machine.py::test_time_gmtime_arg", "tests/test_time_machine.py::test_time_localtime", "tests/test_time_machine.py::test_time_localtime_no_tick", "tests/test_time_machine.py::test_time_localtime_arg", "tests/test_time_machine.py::test_time_montonic", "tests/test_time_machine.py::test_time_monotonic_ns", "tests/test_time_machine.py::test_time_strftime_format", "tests/test_time_machine.py::test_time_strftime_format_no_tick", "tests/test_time_machine.py::test_time_strftime_format_t", "tests/test_time_machine.py::test_time_time", "tests/test_time_machine.py::test_time_time_windows", "tests/test_time_machine.py::test_time_time_no_tick", "tests/test_time_machine.py::test_time_time_ns", "tests/test_time_machine.py::test_time_time_ns_no_tick", "tests/test_time_machine.py::test_nestable", "tests/test_time_machine.py::test_unsupported_type", "tests/test_time_machine.py::test_exceptions_dont_break_it", "tests/test_time_machine.py::test_destination_datetime", "tests/test_time_machine.py::test_destination_datetime_tzinfo_non_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_nested", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_no_orig_tz", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_windows", "tests/test_time_machine.py::test_destination_int", "tests/test_time_machine.py::test_destination_datetime_naive", "tests/test_time_machine.py::test_destination_date", "tests/test_time_machine.py::test_destination_timedelta", "tests/test_time_machine.py::test_destination_timedelta_negative", "tests/test_time_machine.py::test_destination_timedelta_nested", "tests/test_time_machine.py::test_destination_string", "tests/test_time_machine.py::test_destination_string_naive[1970-01-01", "tests/test_time_machine.py::test_destination_string_naive[1970-01-01-UTC-0]", "tests/test_time_machine.py::test_destination_string_naive[1970-01-01-Europe/Amsterdam--3600]", "tests/test_time_machine.py::test_destination_string_naive[1970-01-01-US/Eastern-18000]", "tests/test_time_machine.py::test_destination_callable_lambda_float", "tests/test_time_machine.py::test_destination_callable_lambda_string", "tests/test_time_machine.py::test_destination_generator", "tests/test_time_machine.py::test_traveller_object", "tests/test_time_machine.py::test_function_decorator", "tests/test_time_machine.py::test_coroutine_decorator", "tests/test_time_machine.py::test_class_decorator_fails_non_testcase", "tests/test_time_machine.py::ClassDecoratorInheritanceTests::test_ineheritance_correctly_rebound", "tests/test_time_machine.py::TestMethodDecorator::test_method_decorator", "tests/test_time_machine.py::UnitTestMethodTests::test_method_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_class_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_stacked_method_decorator", "tests/test_time_machine.py::UnitTestClassCustomSetUpClassTests::test_class_decorator", "tests/test_time_machine.py::test_shift_with_timedelta", "tests/test_time_machine.py::test_shift_integer_delta", "tests/test_time_machine.py::test_shift_negative_delta", "tests/test_time_machine.py::test_shift_wrong_delta", "tests/test_time_machine.py::test_shift_when_tick", "tests/test_time_machine.py::test_move_to_datetime", "tests/test_time_machine.py::test_move_to_datetime_no_tick", "tests/test_time_machine.py::test_move_to_past_datetime", "tests/test_time_machine.py::test_move_to_datetime_with_tzinfo_zoneinfo", "tests/test_time_machine.py::test_move_to_datetime_change_tick_on", "tests/test_time_machine.py::test_move_to_datetime_change_tick_off", "tests/test_time_machine.py::test_uuid1", "tests/test_time_machine.py::test_fixture_unused", "tests/test_time_machine.py::test_fixture_used", "tests/test_time_machine.py::test_fixture_used_tick_false", "tests/test_time_machine.py::test_fixture_used_tick_true", "tests/test_time_machine.py::test_fixture_move_to_twice", "tests/test_time_machine.py::test_fixture_move_to_and_shift", "tests/test_time_machine.py::test_fixture_shift_without_move_to", "tests/test_time_machine.py::TestEscapeHatch::test_is_travelling_false", "tests/test_time_machine.py::TestEscapeHatch::test_is_travelling_true", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_now", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_now_tz", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_utcnow", "tests/test_time_machine.py::TestEscapeHatch::test_time_clock_gettime", "tests/test_time_machine.py::TestEscapeHatch::test_time_clock_gettime_ns", "tests/test_time_machine.py::TestEscapeHatch::test_time_gmtime", "tests/test_time_machine.py::TestEscapeHatch::test_time_localtime", "tests/test_time_machine.py::TestEscapeHatch::test_time_monotonic", "tests/test_time_machine.py::TestEscapeHatch::test_time_monotonic_ns", "tests/test_time_machine.py::TestEscapeHatch::test_time_strftime_no_arg", "tests/test_time_machine.py::TestEscapeHatch::test_time_strftime_arg", "tests/test_time_machine.py::TestEscapeHatch::test_time_time", "tests/test_time_machine.py::TestEscapeHatch::test_time_time_ns" ]	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2024-03-22 23:03:40+00:00	mit	898
adamchainz__time-machine-54	diff --git a/HISTORY.rst b/HISTORY.rst index 485c825..f5a2f8c 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -1,6 +1,12 @@ History ======= +* Correctly return naive datetimes from ``datetime.utcnow()`` whilst time + travelling. + + Thanks to Søren Pilgård and Bart Van Loon for the report in + `Issue #52 <https://github.com/adamchainz/time-machine/issues/52>`__. + 1.2.0 (2020-07-08) ------------------ diff --git a/src/time_machine.py b/src/time_machine.py index 0832f6a..d0ed6ff 100644 --- a/src/time_machine.py +++ b/src/time_machine.py @@ -206,7 +206,7 @@ def utcnow(): if not coordinates_stack: return _time_machine.original_utcnow() else: - return dt.datetime.fromtimestamp(time(), dt.timezone.utc) + return dt.datetime.utcfromtimestamp(time()) # time module	adamchainz/time-machine	48a2a4df24ba188533fdf03f6cfc4b78db33f17a	diff --git a/tests/test_time_machine.py b/tests/test_time_machine.py index bf85da5..4eacde2 100644 --- a/tests/test_time_machine.py +++ b/tests/test_time_machine.py @@ -88,6 +88,7 @@ def test_datetime_utcnow(): assert now.minute == 0 assert now.second == 0 assert now.microsecond == 0 + assert now.tzinfo is None assert dt.datetime.utcnow() >= LIBRARY_EPOCH_DATETIME	datetime.datetime.utcnow() should not have tzinfo Hi, I find this library very neat and have started using it in multiple tests. But there is one issue: ```python In [1]: import datetime In [2]: import time_machine In [3]: @time_machine.travel("2020-07-28 13:15:30.478705") ...: def foo(): ...: return datetime.datetime.utcnow() ...: In [4]: datetime.datetime.utcnow() Out[4]: datetime.datetime(2020, 7, 31, 13, 46, 25, 828701) In [5]: foo() Out[5]: datetime.datetime(2020, 7, 28, 13, 15, 30, 478705, tzinfo=datetime.timezone.utc) ``` time_machine adds a timezone on datetime instances created via `.utcnow()` but this is wrong according to python. It even specifies it directly in the documentation https://docs.python.org/3/library/datetime.html#datetime.datetime.utcnow > Return the current UTC date and time, with tzinfo None. This change in the behaviour of the datetime library can cause changes in behaviour of the tested code. Eg. when serialized to a string it adds "+00:00"	48a2a4df24ba188533fdf03f6cfc4b78db33f17a	[ "tests/test_time_machine.py::test_datetime_utcnow" ]	[ "tests/test_time_machine.py::test_import_without_clock_realtime", "tests/test_time_machine.py::test_datetime_now_no_args", "tests/test_time_machine.py::test_datetime_now_no_args_no_tick", "tests/test_time_machine.py::test_datetime_now_arg", "tests/test_time_machine.py::test_datetime_utcnow_no_tick", "tests/test_time_machine.py::test_date_today", "tests/test_time_machine.py::test_time_clock_gettime_realtime", "tests/test_time_machine.py::test_time_clock_gettime_monotonic_unaffected", "tests/test_time_machine.py::test_time_clock_gettime_ns_realtime", "tests/test_time_machine.py::test_time_clock_gettime_ns_monotonic_unaffected", "tests/test_time_machine.py::test_time_gmtime_no_args", "tests/test_time_machine.py::test_time_gmtime_no_args_no_tick", "tests/test_time_machine.py::test_time_gmtime_arg", "tests/test_time_machine.py::test_time_localtime", "tests/test_time_machine.py::test_time_localtime_no_tick", "tests/test_time_machine.py::test_time_localtime_arg", "tests/test_time_machine.py::test_time_strftime_no_args", "tests/test_time_machine.py::test_time_strftime_no_args_no_tick", "tests/test_time_machine.py::test_time_strftime_arg", "tests/test_time_machine.py::test_time_time", "tests/test_time_machine.py::test_time_time_no_tick", "tests/test_time_machine.py::test_time_time_ns", "tests/test_time_machine.py::test_time_time_ns_no_tick", "tests/test_time_machine.py::test_nestable", "tests/test_time_machine.py::test_unsupported_type", "tests/test_time_machine.py::test_exceptions_dont_break_it", "tests/test_time_machine.py::test_destination_datetime", "tests/test_time_machine.py::test_destination_datetime_timezone", "tests/test_time_machine.py::test_destination_datetime_naive", "tests/test_time_machine.py::test_destination_date", "tests/test_time_machine.py::test_destination_string", "tests/test_time_machine.py::test_destination_callable_lambda_float", "tests/test_time_machine.py::test_destination_callable_lambda_string", "tests/test_time_machine.py::test_destination_generator", "tests/test_time_machine.py::test_traveller_object", "tests/test_time_machine.py::test_function_decorator", "tests/test_time_machine.py::test_coroutine_decorator", "tests/test_time_machine.py::test_class_decorator_fails_non_testcase", "tests/test_time_machine.py::UnitTestMethodTests::test_method_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_class_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_stacked_method_decorator", "tests/test_time_machine.py::UnitTestClassCustomSetUpClassTests::test_class_decorator", "tests/test_time_machine.py::test_tz_offset_float", "tests/test_time_machine.py::test_tz_offset_timedelta", "tests/test_time_machine.py::test_tz_offset_unsupported_type", "tests/test_time_machine.py::test_shift_with_timedelta", "tests/test_time_machine.py::test_shift_integer_delta", "tests/test_time_machine.py::test_shift_negative_delta", "tests/test_time_machine.py::test_shift_wrong_delta", "tests/test_time_machine.py::test_shift_when_tick", "tests/test_time_machine.py::test_move_to_datetime", "tests/test_time_machine.py::test_move_to_datetime_when_tick", "tests/test_time_machine.py::test_move_to_past_datetime", "tests/test_time_machine.py::test_move_to_past_datetime_when_tick", "tests/test_time_machine.py::test_uuid1" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2020-08-29 21:48:07+00:00	isc	899
adamgilman__furlong-5	diff --git a/.gitignore b/.gitignore index 894a44c..06f9e54 100644 --- a/.gitignore +++ b/.gitignore @@ -5,7 +5,11 @@ __pycache__/ # C extensions .so - +bin/ +include/* +lib/* +man/* +pip-selfcheck.json # Distribution / packaging .Python build/ diff --git a/README.md b/README.md new file mode 100644 index 0000000..12231f7 --- /dev/null +++ b/README.md @@ -0,0 +1,34 @@ +# Hello Furlong +Furlong aims to make units conversions easy and pythonic with a simple to understand and magical interface. Simply declare the unit and value and convert to anything you can think of. If we don't support a unit conversion, open a pull request to add it for everyone! + +## How it works +Bring Furlong into your project with a simple name, f is recommended but, not required + +`from furlong import Furlong as f` + +Declare the unit and value of the base measurement + +`length_of_wall = f(inches=300)` + +Then convert to any unit you'd like! + +``` +length_of_wall.asCentimeters() +30.48 +``` + +Done! + +## Error handling + +* [TODO] + +## Units supported + +* ### Length + * inches + * centimeters + +* ### Volume + +* ### Weight diff --git a/furlong/__init__.py b/furlong/__init__.py new file mode 100644 index 0000000..10cb1e8 --- /dev/null +++ b/furlong/__init__.py @@ -0,0 +1,1 @@ +from .furlong import Furlong \ No newline at end of file diff --git a/furlong/furlong.py b/furlong/furlong.py new file mode 100644 index 0000000..b23faeb --- /dev/null +++ b/furlong/furlong.py @@ -0,0 +1,19 @@ +class Furlong(object): + conversion_table = { + 'inches' : ('centimeters', 2.54), + } + def __init__(self, *kwargs): + for key, value in kwargs.items(): + self.unit = key + self.value = value + + for base, conv in Furlong.conversion_table.items(): + func_name, conv_value = Furlong.conversion_table[base] + func_name = "as" + func_name.title() + setattr(self, func_name, self._make_convertor( conv_value )) + + def _make_convertor(self, conv_value): + def _convertor(): + return self.value conv_value + + return _convertor \ No newline at end of file	adamgilman/furlong	42e6917523242f349a9b825bf0a91f1643856645	diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/tests_fobject.py b/tests/tests_fobject.py new file mode 100644 index 0000000..4196907 --- /dev/null +++ b/tests/tests_fobject.py @@ -0,0 +1,17 @@ +import unittest +from furlong import Furlong as f + +class TestSimpleConversionTests(unittest.TestCase): + def test_fixed_conversion_test(self): + self.assertEqual( f(inches=12).asCentimeters(), 30.48 ) + + +class TestDyanmicFunctionNaming(unittest.TestCase): + def test_dyanmic_function_exists(self): + test_conv = { + 'testbase' : ('testconv', -1111), + } + f.conversion_table.update( test_conv ) + self.assertIsInstance( f(testbase=1), f ) + self.assertTrue( callable( f(testbase=1).asTestconv ) ) + self.assertEqual( f(testbase=2).asTestconv(), -2222 ) \ No newline at end of file	Provide a simple interface for unit conversions Declare a unit type ``` length = f(inches=12) length.asCentimeters() 30.48 ``` Simple and extensible	42e6917523242f349a9b825bf0a91f1643856645	[ "tests/tests_fobject.py::TestSimpleConversionTests::test_fixed_conversion_test", "tests/tests_fobject.py::TestDyanmicFunctionNaming::test_dyanmic_function_exists" ]	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_added_files" ], "has_test_patch": true, "is_lite": false }	2018-07-14 09:55:52+00:00	mit	900
adamjstewart__fiscalyear-5	diff --git a/.travis.yml b/.travis.yml index f829e95..416d131 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,13 +1,15 @@ language: python +dist: xenial + python: - - 2.6 - 2.7 - - 3.3 - 3.4 - 3.5 - 3.6 + - 3.7 + - 3.8-dev -script: py.test --cov=fiscalyear +script: pytest --cov=fiscalyear after_success: codecov diff --git a/LICENSE b/LICENSE index 247c0b8..f2c31c2 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2017 Adam J. Stewart +Copyright (c) 2017-2019 Adam J. Stewart Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.rst b/README.rst index b7d0874..30cf856 100644 --- a/README.rst +++ b/README.rst @@ -7,6 +7,12 @@ .. image:: https://readthedocs.org/projects/fiscalyear/badge/?version=latest :target: https://fiscalyear.readthedocs.io +.. image:: https://badge.fury.io/py/fiscalyear.svg + :target: https://pypi.org/project/fiscalyear/ + +.. image:: https://anaconda.org/conda-forge/fiscalyear/badges/version.svg + :target: https://anaconda.org/conda-forge/fiscalyear + Overview ======== diff --git a/docs/installation.rst b/docs/installation.rst index 8355ecf..41a9b4c 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -17,6 +17,16 @@ The recommended way to install ``fiscalyear`` is with ``pip``. The fiscalyear module will now appear with your base Python installation. +Anaconda +-------- + +You can also install ``fiscalyear`` with the ``conda`` package manager. + +.. code-block:: console + + $ conda install -c conda-forge fiscalyear + + Spack ----- diff --git a/fiscalyear.py b/fiscalyear.py index c6f8ddc..f3a7640 100644 --- a/fiscalyear.py +++ b/fiscalyear.py @@ -24,10 +24,41 @@ START_MONTH = 10 START_DAY = 1 +def _validate_fiscal_calendar_params(start_year, start_month, start_day): + """Raise an Exception if the calendar parameters are invalid. + + :param start_year: Relationship between the start of the fiscal year and + the calendar year. Possible values: ``'previous'`` or ``'same'``. + :type start_year: str + :param start_month: The first month of the fiscal year + :type start_month: int or str + :param start_day: The first day of the first month of the fiscal year + :type start_day: int or str + :raises TypeError: If ``start_year`` is not a ``str``. + :raises ValueError: If ``start_year`` is not ``'previous'`` or ``'same'`` + :raises ValueError: If ``start_month`` or ``start_day`` is not an int or + int-like string + :raises ValueError: If ``start_month`` or ``start_day`` is out of range + """ + if not isinstance(start_year, str): + raise TypeError("'start_year' must be a 'str', not: '%s'" % type(str)) + if start_year not in ('previous', 'same'): + msg = "'start_year' must be either 'previous' or 'same', not: '%s'" + raise ValueError(msg % start_year) + _check_day(start_month, start_day) + + +def setup_fiscal_calendar(start_year, start_month, start_day): + """Change the global calendar settings.""" + _validate_fiscal_calendar_params(start_year, start_month, start_day) + global START_YEAR, START_MONTH, START_DAY + START_YEAR = start_year + START_MONTH = start_month + START_DAY = start_day + + @contextlib.contextmanager -def fiscal_calendar(start_year=None, - start_month=None, - start_day=None): +def fiscal_calendar(start_year=None, start_month=None, start_day=None): """A context manager that lets you modify the start of the fiscal calendar inside the scope of a with-statement. @@ -38,43 +69,22 @@ def fiscal_calendar(start_year=None, :type start_month: int or str :param start_day: The first day of the first month of the fiscal year :type start_day: int or str - :raises AssertionError: If ``start_year`` is not ``'previous'`` or ``'same'`` - :raises TypeError: If ``start_month`` or ``start_day`` is not an int or int-like string + :raises ValueError: If ``start_year`` is not ``'previous'`` or ``'same'`` + :raises TypeError: If ``start_month`` or ``start_day`` is not an int or + int-like string :raises ValueError: If ``start_month`` or ``start_day`` is out of range """ - global START_YEAR - global START_MONTH - global START_DAY - - # Use default values if not changed - if start_year is None: - start_year = START_YEAR - if start_month is None: - start_month = START_MONTH - if start_day is None: - start_day = START_DAY - - assert isinstance(start_year, str) - assert start_year == 'previous' or start_year == 'same' - start_month = _check_month(start_month) - start_day = _check_day(start_month, start_day) - - # Backup previous values - old_start_year = START_YEAR - old_start_month = START_MONTH - old_start_day = START_DAY + # If arguments are omitted, use the currently active values. + start_year = START_YEAR if start_year is None else start_year + start_month = START_MONTH if start_month is None else start_month + start_day = START_DAY if start_day is None else start_day # Temporarily change global variables - START_YEAR = start_year - START_MONTH = start_month - START_DAY = start_day - + previous_values = (START_YEAR, START_MONTH, START_DAY) + setup_fiscal_calendar(start_year, start_month, start_day) yield - # Restore previous values - START_YEAR = old_start_year - START_MONTH = old_start_month - START_DAY = old_start_day + setup_fiscal_calendar(*previous_values) def _check_int(value): @@ -225,11 +235,9 @@ class FiscalYear(object): return self == item elif isinstance(item, FiscalQuarter): return self._fiscal_year == item.fiscal_year - elif (isinstance(item, FiscalDateTime) or - isinstance(item, datetime.datetime)): + elif isinstance(item, datetime.datetime): return self.start <= item <= self.end - elif (isinstance(item, FiscalDate) or - isinstance(item, datetime.date)): + elif isinstance(item, datetime.date): return self.start.date() <= item <= self.end.date() else: raise TypeError("can't compare '%s' to '%s'" % ( @@ -405,11 +413,9 @@ class FiscalQuarter(object): """ if isinstance(item, FiscalQuarter): return self == item - elif (isinstance(item, FiscalDateTime) or - isinstance(item, datetime.datetime)): + elif isinstance(item, datetime.datetime): return self.start <= item <= self.end - elif (isinstance(item, FiscalDate) or - isinstance(item, datetime.date)): + elif isinstance(item, datetime.date): return self.start.date() <= item <= self.end.date() else: raise TypeError("can't compare '%s' to '%s'" % ( diff --git a/setup.cfg b/setup.cfg index 4bca33d..d928416 100644 --- a/setup.cfg +++ b/setup.cfg @@ -4,3 +4,6 @@ test=pytest [build_sphinx] source-dir=docs build-dir=docs/_build + +[metadata] +license-file = LICENSE diff --git a/setup.py b/setup.py index 7939d81..05153b5 100755 --- a/setup.py +++ b/setup.py @@ -42,6 +42,8 @@ setuptools.setup( 'Programming Language :: Python :: 3.4', 'Programming Language :: Python :: 3.5', 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', + 'Programming Language :: Python :: 3.8', # Type of package 'Topic :: Office/Business :: Financial :: Accounting',	adamjstewart/fiscalyear	77c5c0c82a62de36e77284e924f744bb1e770a31	diff --git a/test_fiscalyear.py b/test_fiscalyear.py index 690835f..5b2779f 100644 --- a/test_fiscalyear.py +++ b/test_fiscalyear.py @@ -9,8 +9,143 @@ import pytest US_FEDERAL = ('previous', 10, 1) UK_PERSONAL = ('same', 4, 6) -# Default to U.S. -fiscalyear.START_YEAR, fiscalyear.START_MONTH, fiscalyear.START_DAY = US_FEDERAL + +class TestCheckInt(object): + @pytest.mark.parametrize("value, exception", [ + ('asdf', TypeError), + ("-999", TypeError), + # Technically speaking, _check_int should accept negative integers + # but this isn't a public function + datetime doesn't handle them + # anyway. + (float(), TypeError), + (object(), TypeError), + ]) + def test_invalid_input(self, value, exception): + with pytest.raises(exception): + fiscalyear._check_int(value) + + @pytest.mark.parametrize("value", [1, 2, 0, -1, -2, "1", "0", "999"]) + def test_valid_input(self, value): + assert int(value) == fiscalyear._check_int(value) + + +class TestCheckYear(object): + @pytest.mark.parametrize("value, exception", [ + ('asdf', TypeError), + (float(), TypeError), + (object(), TypeError), + ("-1", TypeError), + (-1, ValueError), + (0, ValueError), + ("0", ValueError), + (10000, ValueError), + ("10000", ValueError), + ]) + def test_invalid_input(self, value, exception): + with pytest.raises(exception): + fiscalyear._check_year(value) + + @pytest.mark.parametrize("value", [1, 2, "1", "999"]) + def test_valid_input(self, value): + assert int(value) == fiscalyear._check_year(value) + + +class TestCheckDay(object): + @pytest.mark.parametrize("month, day, exception", [ + (1, 'asdf', TypeError), + (1, "-999", TypeError), + (1, float(), TypeError), + (1, object(), TypeError), + (1, -1, ValueError), + (1, "-1", TypeError), + (1, 0, ValueError), + (1, "0", ValueError), + (1, 32, ValueError), + (1, 32, ValueError), + ]) + def test_invalid_input(self, month, day, exception): + with pytest.raises(exception): + fiscalyear._check_day(month, day) + + @pytest.mark.parametrize("month, day", [(1, 1), (1, 2), (1, "1"), (1, 31), (1, "31")]) + def test_valid_input(self, month, day): + assert int(day) == fiscalyear._check_day(month, day) + + +class TestCheckQuarter(object): + @pytest.mark.parametrize("value, exception", [ + ('asdf', TypeError), + (float(), TypeError), + (object(), TypeError), + ("-1", TypeError), + (-1, ValueError), + (0, ValueError), + ("0", ValueError), + (5, ValueError), + ("5", ValueError), + ]) + def test_invalid_input(self, value, exception): + with pytest.raises(exception): + fiscalyear._check_quarter(value) + + @pytest.mark.parametrize("value", [1, 2, "1", "4"]) + def test_valid_input(self, value): + assert int(value) == fiscalyear._check_quarter(value) + + +class TestCalendarSettingsValidator(object): + @pytest.mark.parametrize("arguments, exception", [ + (dict(start_year='asdf', start_month=12, start_day=1), ValueError), + (dict(start_year=float(1999), start_month=12, start_day=1), TypeError), + (dict(start_year=object(), start_month=12, start_day=1), TypeError), + + (dict(start_year='same', start_month='asdf', start_day=1), TypeError), + (dict(start_year='same', start_month=float(12), start_day=1), TypeError), + (dict(start_year='same', start_month=object(), start_day=1), TypeError), + (dict(start_year='same', start_month=-1, start_day=1), ValueError), + (dict(start_year='same', start_month=0, start_day=1), ValueError), + (dict(start_year='same', start_month=13, start_day=1), ValueError), + + (dict(start_year='same', start_month=12, start_day='asdf'), TypeError), + (dict(start_year='same', start_month=12, start_day=float(1)), TypeError), + (dict(start_year='same', start_month=12, start_day=object()), TypeError), + (dict(start_year='same', start_month=12, start_day=0), ValueError), + (dict(start_year='same', start_month=12, start_day=-1), ValueError), + (dict(start_year='same', start_month=12, start_day=32), ValueError), + ]) + def test_invalid_input(self, arguments, exception): + with pytest.raises(exception): + fiscalyear._validate_fiscal_calendar_params(arguments) + + @pytest.mark.parametrize("arguments", [ + dict(start_year='same', start_month=1, start_day=1), + dict(start_year='same', start_month=1, start_day=31), + dict(start_year='same', start_month=12, start_day=1), + dict(start_year='previous', start_month=1, start_day=1), + dict(start_year='previous', start_month=1, start_day=31), + dict(start_year='previous', start_month=12, start_day=1), + ]) + def test_valid_input(self, arguments): + fiscalyear._validate_fiscal_calendar_params(arguments) + + +class TestSetupFiscalCalendar(object): + + def test_setup_fiscal_calendar(self): + # Test defaults + day = fiscalyear.FiscalDate(2017, 12, 1) + assert day.fiscal_year == 2018 + assert day.quarter == 1 + + # Change fiscal year settings + fiscalyear.setup_fiscal_calendar("same", 1, 1) + assert day.fiscal_year == 2017 + assert day.quarter == 4 + + # Restore defaults and re-test + fiscalyear.setup_fiscal_calendar("previous", 10, 1) + assert day.fiscal_year == 2018 + assert day.quarter == 1 class TestFiscalCalendar: @@ -86,6 +221,10 @@ class TestFiscalCalendar: assert fiscalyear.START_DAY == 1 def test_wrong_type(self): + with pytest.raises(TypeError): + with fiscalyear.fiscal_calendar(start_year=6.5): + pass + with pytest.raises(TypeError): with fiscalyear.fiscal_calendar(start_month=6.5): pass	Add a function for easily changing the global "START_*" parameters I think it would make sense to have a function that would make changing the global parameters easier. E.g. ``` python def setup_fiscal_year(start_year, start_month, start_day): global START_YEAR, START_MONTH, START_DAY START_YEAR = start_year START_MONTH = start_month START_DAY = start_day def test_setup_fiscal_year(): # test defaults day = fiscalyear.FiscalDate(2017, 12, 1) assert day.fiscal_year == 2018 assert day.quarter == 1 # change fiscal year settings fiscalyear.setup_fiscal_year("same", 1, 1) assert day.fiscal_year == 2017 assert day.quarter == 4 # restore defaults and re-test fiscalyear.setup_fiscal_year("previous", 10, 1) assert day.fiscal_year == 2018 assert day.quarter == 1 ``` This could also make it possible to change the Fiscal Year settings even if you don't import the whole module. E.g. ``` python In [4]: from fiscalyear import FiscalQuarter, setup_fiscal_year In [5]: quarter = FiscalQuarter(2018, 1) In [6]: quarter.start Out[6]: FiscalDateTime(2017, 10, 1, 0, 0) In [7]: setup_fiscal_year('same', 1, 1) In [8]: quarter.start Out[8]: FiscalDateTime(2018, 1, 1, 0, 0) ```	77c5c0c82a62de36e77284e924f744bb1e770a31	[ "test_fiscalyear.py::TestCalendarSettingsValidator::test_invalid_input[arguments0-ValueError]", "test_fiscalyear.py::TestCalendarSettingsValidator::test_invalid_input[arguments1-TypeError]", "test_fiscalyear.py::TestCalendarSettingsValidator::test_invalid_input[arguments2-TypeError]", "test_fiscalyear.py::TestCalendarSettingsValidator::test_invalid_input[arguments3-TypeError]", "test_fiscalyear.py::TestCalendarSettingsValidator::test_invalid_input[arguments4-TypeError]", "test_fiscalyear.py::TestCalendarSettingsValidator::test_invalid_input[arguments5-TypeError]", "test_fiscalyear.py::TestCalendarSettingsValidator::test_invalid_input[arguments6-ValueError]", "test_fiscalyear.py::TestCalendarSettingsValidator::test_invalid_input[arguments7-ValueError]", "test_fiscalyear.py::TestCalendarSettingsValidator::test_invalid_input[arguments8-ValueError]", "test_fiscalyear.py::TestCalendarSettingsValidator::test_invalid_input[arguments9-TypeError]", "test_fiscalyear.py::TestCalendarSettingsValidator::test_invalid_input[arguments10-TypeError]", "test_fiscalyear.py::TestCalendarSettingsValidator::test_invalid_input[arguments11-TypeError]", "test_fiscalyear.py::TestCalendarSettingsValidator::test_invalid_input[arguments12-ValueError]", "test_fiscalyear.py::TestCalendarSettingsValidator::test_invalid_input[arguments13-ValueError]", "test_fiscalyear.py::TestCalendarSettingsValidator::test_invalid_input[arguments14-ValueError]", "test_fiscalyear.py::TestCalendarSettingsValidator::test_valid_input[arguments0]", 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"test_fiscalyear.py::TestFiscalQuarter::test_less_than", "test_fiscalyear.py::TestFiscalQuarter::test_less_than_equals", "test_fiscalyear.py::TestFiscalQuarter::test_equals", "test_fiscalyear.py::TestFiscalQuarter::test_not_equals", "test_fiscalyear.py::TestFiscalQuarter::test_greater_than", "test_fiscalyear.py::TestFiscalQuarter::test_greater_than_equals", "test_fiscalyear.py::TestFiscalDate::test_basic", "test_fiscalyear.py::TestFiscalDate::test_fiscal_year", "test_fiscalyear.py::TestFiscalDate::test_prev_fiscal_year", "test_fiscalyear.py::TestFiscalDate::test_next_fiscal_year", "test_fiscalyear.py::TestFiscalDate::test_prev_quarter", "test_fiscalyear.py::TestFiscalDate::test_next_quarter", "test_fiscalyear.py::TestFiscalDateTime::test_basic", "test_fiscalyear.py::TestFiscalDateTime::test_fiscal_year", "test_fiscalyear.py::TestFiscalDateTime::test_prev_fiscal_year", "test_fiscalyear.py::TestFiscalDateTime::test_next_fiscal_year", "test_fiscalyear.py::TestFiscalDateTime::test_prev_quarter", "test_fiscalyear.py::TestFiscalDateTime::test_next_quarter" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2018-02-08 16:57:16+00:00	mit	901
adamjstewart__fiscalyear-9	diff --git a/fiscalyear.py b/fiscalyear.py index 661c703..d4a569f 100644 --- a/fiscalyear.py +++ b/fiscalyear.py @@ -530,7 +530,12 @@ class FiscalQuarter(object): if month < START_MONTH: year += 1 - return FiscalDateTime(year, month, START_DAY, 0, 0, 0) + # Find the last day of the month + # If START_DAY is later, choose last day of month instead + max_day = calendar.monthrange(year, month)[1] + day = min(START_DAY, max_day) + + return FiscalDateTime(year, month, day, 0, 0, 0) @property def end(self):	adamjstewart/fiscalyear	a59cde7a881a85c5a65e523623e23668c2cb991c	diff --git a/test_fiscalyear.py b/test_fiscalyear.py index 2395737..f80953c 100644 --- a/test_fiscalyear.py +++ b/test_fiscalyear.py @@ -275,6 +275,35 @@ class TestFiscalCalendar: with fiscalyear.fiscal_calendar(start_month=2, start_day=29): pass + def test_corner_cases(self): + # start_day does not exist in all months + with fiscalyear.fiscal_calendar(start_month=5, start_day=31): + # Non-leap year + assert fiscalyear.FiscalQuarter(2019, 1).start.day == 31 + assert fiscalyear.FiscalQuarter(2019, 1).end.day == 30 + + assert fiscalyear.FiscalQuarter(2019, 2).start.day == 31 + assert fiscalyear.FiscalQuarter(2019, 2).end.day == 29 + + assert fiscalyear.FiscalQuarter(2019, 3).start.day == 30 + assert fiscalyear.FiscalQuarter(2019, 3).end.day == 27 + + assert fiscalyear.FiscalQuarter(2019, 4).start.day == 28 + assert fiscalyear.FiscalQuarter(2019, 4).end.day == 30 + + # Leap year + assert fiscalyear.FiscalQuarter(2020, 1).start.day == 31 + assert fiscalyear.FiscalQuarter(2020, 1).end.day == 30 + + assert fiscalyear.FiscalQuarter(2020, 2).start.day == 31 + assert fiscalyear.FiscalQuarter(2020, 2).end.day == 29 + + assert fiscalyear.FiscalQuarter(2020, 3).start.day == 30 + assert fiscalyear.FiscalQuarter(2020, 3).end.day == 28 + + assert fiscalyear.FiscalQuarter(2020, 4).start.day == 29 + assert fiscalyear.FiscalQuarter(2020, 4).end.day == 30 + class TestFiscalYear:	FiscalCalendar starting on 31st day of the month throws ValueError If the `FiscalCalendar` starts on the 31st of any month with 31 days, then `FiscalDate().quarter` throws a `ValueError`. Example code: ```python from fiscalyear import FiscalDate, FiscalYear, fiscal_calendar with fiscal_calendar(start_month=12, start_day=31): fiscal_date = FiscalDate(2019, 10, 22) fiscal_date.quarter ``` Traceback: ``` Traceback (most recent call last): File "<input>", line 3, in <module> File "/site-packages/fiscalyear.py", line 594, in quarter if self in q: File "/site-packages/fiscalyear.py", line 413, in __contains__ return self.start.date() <= item <= self.end.date() File "/site-packages/fiscalyear.py", line 493, in end next_start = self.next_quarter.start File "/site-packages/fiscalyear.py", line 485, in start return FiscalDateTime(year, month, START_DAY, 0, 0, 0) ValueError: day is out of range for month ``` The quarters generated are: * December 31st * March 31st * June 31st ← Not a valid day, so it breaks.	a59cde7a881a85c5a65e523623e23668c2cb991c	[ "test_fiscalyear.py::TestFiscalCalendar::test_corner_cases", "test_fiscalyear.py::TestFiscalQuarter::test_current", 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"test_fiscalyear.py::TestFiscalCalendar::test_complex", "test_fiscalyear.py::TestFiscalCalendar::test_nested", "test_fiscalyear.py::TestFiscalCalendar::test_wrong_type", "test_fiscalyear.py::TestFiscalCalendar::test_out_of_range", "test_fiscalyear.py::TestFiscalYear::test_basic", "test_fiscalyear.py::TestFiscalYear::test_current", "test_fiscalyear.py::TestFiscalYear::test_repr", "test_fiscalyear.py::TestFiscalYear::test_str", "test_fiscalyear.py::TestFiscalYear::test_from_string", "test_fiscalyear.py::TestFiscalYear::test_wrong_type", "test_fiscalyear.py::TestFiscalYear::test_out_of_range", "test_fiscalyear.py::TestFiscalYear::test_prev_fiscal_year", "test_fiscalyear.py::TestFiscalYear::test_next_fiscal_year", "test_fiscalyear.py::TestFiscalYear::test_start", "test_fiscalyear.py::TestFiscalYear::test_end", "test_fiscalyear.py::TestFiscalYear::test_q1", "test_fiscalyear.py::TestFiscalYear::test_q2", "test_fiscalyear.py::TestFiscalYear::test_q3", "test_fiscalyear.py::TestFiscalYear::test_q4", "test_fiscalyear.py::TestFiscalYear::test_contains", "test_fiscalyear.py::TestFiscalYear::test_less_than", "test_fiscalyear.py::TestFiscalYear::test_less_than_equals", "test_fiscalyear.py::TestFiscalYear::test_equals", "test_fiscalyear.py::TestFiscalYear::test_not_equals", "test_fiscalyear.py::TestFiscalYear::test_greater_than", "test_fiscalyear.py::TestFiscalYear::test_greater_than_equals", "test_fiscalyear.py::TestFiscalQuarter::test_basic", "test_fiscalyear.py::TestFiscalQuarter::test_repr", "test_fiscalyear.py::TestFiscalQuarter::test_str", "test_fiscalyear.py::TestFiscalQuarter::test_from_string", "test_fiscalyear.py::TestFiscalQuarter::test_wrong_type", "test_fiscalyear.py::TestFiscalQuarter::test_out_of_range", "test_fiscalyear.py::TestFiscalQuarter::test_prev_quarter", "test_fiscalyear.py::TestFiscalQuarter::test_next_quarter", "test_fiscalyear.py::TestFiscalQuarter::test_bad_start_year", "test_fiscalyear.py::TestFiscalQuarter::test_q1_start", "test_fiscalyear.py::TestFiscalQuarter::test_q1_end", "test_fiscalyear.py::TestFiscalQuarter::test_q2_start", "test_fiscalyear.py::TestFiscalQuarter::test_q2_end", "test_fiscalyear.py::TestFiscalQuarter::test_q3_start", "test_fiscalyear.py::TestFiscalQuarter::test_q3_end", "test_fiscalyear.py::TestFiscalQuarter::test_q4_start", "test_fiscalyear.py::TestFiscalQuarter::test_q4_end", "test_fiscalyear.py::TestFiscalQuarter::test_less_than", "test_fiscalyear.py::TestFiscalQuarter::test_less_than_equals", "test_fiscalyear.py::TestFiscalQuarter::test_equals", "test_fiscalyear.py::TestFiscalQuarter::test_not_equals", "test_fiscalyear.py::TestFiscalQuarter::test_greater_than", "test_fiscalyear.py::TestFiscalQuarter::test_greater_than_equals", "test_fiscalyear.py::TestFiscalDate::test_fiscal_year", "test_fiscalyear.py::TestFiscalDateTime::test_fiscal_year" ]	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2019-10-23 01:02:35+00:00	mit	902
adamlwgriffiths__Pyrr-88	diff --git a/CHANGELOG.md b/CHANGELOG.md index 9215a38..624dd4e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](http://keepachangelog.com/) and this project adheres to [Semantic Versioning](http://semver.org/). +## [0.10.3] - 2019-04-19 + +- Fix some of the plane.create_(xz,xy,yz) not inverting correctly. +- Fix incorrect distance in point_height_above_plane. + ## [0.10.2] - 2019-03-13 - Add MANIFEST.in and add /tests and /docs to source dist (#90) diff --git a/pyrr/plane.py b/pyrr/plane.py index 97e5b98..12d06e0 100755 --- a/pyrr/plane.py +++ b/pyrr/plane.py @@ -5,7 +5,8 @@ Planes are represented using a numpy.array of shape (4,). The values represent the plane equation using the values A,B,C,D. The first three values are the normal vector. -The fourth value is the distance of the plane from the origin, down the normal. +The fourth value is the distance of the origin from the plane, down the normal. +A negative value indicates the origin is behind the plane, relative to the normal. .. seealso: http://en.wikipedia.org/wiki/Plane_(geometry) .. seealso: http://mathworld.wolfram.com/Plane.html @@ -17,12 +18,15 @@ from .utils import all_parameters_as_numpy_arrays, parameters_as_numpy_arrays def create(normal=None, distance=0.0, dtype=None): - """Creates a plane that runs along the X,Y plane. + """Creates a plane oriented toward the normal, at distance below the origin. + If no normal is provided, the plane will by created at the origin with a normal + of [0, 0, 1]. - It crosses the origin with a normal of 0,0,1 (+Z). + Negative distance indicates the plane is facing toward the origin. :rtype: numpy.array - :return: A plane that runs along the X,Y plane. + :return: A plane with the specified normal at a distance from the origin of + -distance. """ if normal is None: normal = [0.0, 0.0, 1.0] @@ -75,37 +79,43 @@ def create_from_position(position, normal, dtype=None): normal. """ dtype = dtype or position.dtype - # -d = a * px + b * py + c * pz + # -d = a * x + b * y + c * z n = vector.normalize(normal) d = -np.sum(n * position) - return create(n, d, dtype) + return create(n, -d, dtype) def create_xy(invert=False, distance=0., dtype=None): """Create a plane on the XY plane, starting at the origin with +Z being the up vector. - The distance is the distance along the normal (-Z if inverted, otherwise +Z). + The plane is distance units along the Z axis. -Z if inverted. """ - invert = -1. if invert else 1. - return np.array([0., 0., 1. * invert, distance]) + pl = np.array([0., 0., 1., distance]) + if invert: + pl = invert_normal(pl) + return pl def create_xz(invert=False, distance=0., dtype=None): """Create a plane on the XZ plane, starting at the origin with +Y being the up vector. - The distance is the distance along the normal (-Y if inverted, otherwise +Y). + The plane is distance units along the Y axis. -Y if inverted. """ - invert = -1. if invert else 1. - return np.array([0., 1. * invert, 0., distance]) + pl = np.array([0., 1., 0., distance]) + if invert: + pl = invert_normal(pl) + return pl def create_yz(invert=False, distance=0., dtype=None): """Create a plane on the YZ plane, starting at the origin with +X being the up vector. - The distance is the distance along the normal (-X if inverted, otherwise +X). + The plane is distance units along the X axis. -X if inverted. """ - invert = -1. if invert else 1. - return np.array([1. * invert, 0., 0., distance]) + pl = np.array([1., 0., 0., distance]) + if invert: + pl = invert_normal(pl) + return pl def invert_normal(plane): """Flips the normal of the plane. @@ -127,7 +137,7 @@ def position(plane): :rtype: numpy.array :return: A valid position that lies on the plane. """ - return plane[:3] * plane[3] + return normal(plane) * distance(plane) def normal(plane): """Extracts the normal vector from a plane. @@ -137,3 +147,10 @@ def normal(plane): :return: The normal vector of the plane. """ return plane[:3].copy() + +def distance(plane): + """Distance the plane is from the origin along its the normal. + + Negative value indicates the plane is facing the origin. + """ + return plane[3] diff --git a/pyrr/version.py b/pyrr/version.py index cb94a70..a76b028 100755 --- a/pyrr/version.py +++ b/pyrr/version.py @@ -1,4 +1,5 @@ # -- coding: utf-8 -- # the version of software # this is used by the setup.py script -__version__ = '0.10.2' +__version__ = '0.10.3' +	adamlwgriffiths/Pyrr	530820191954abcb9c7c54602fe13ba16912ba48	diff --git a/pyrr/geometric_tests.py b/pyrr/geometric_tests.py index 2f60c2e..601e8f6 100755 --- a/pyrr/geometric_tests.py +++ b/pyrr/geometric_tests.py @@ -5,7 +5,7 @@ various forms data types. from __future__ import absolute_import, division, print_function import math import numpy as np -from . import rectangle, vector, vector3 +from . import rectangle, vector, vector3, plane from .utils import all_parameters_as_numpy_arrays, parameters_as_numpy_arrays, solve_quadratic_equation """ @@ -75,12 +75,12 @@ def point_intersect_rectangle(point, rect): return None return point -@parameters_as_numpy_arrays('ray', 'plane') -def ray_intersect_plane(ray, plane, front_only=False): +@parameters_as_numpy_arrays('ray', 'pl') +def ray_intersect_plane(ray, pl, front_only=False): """Calculates the intersection point of a ray and a plane. :param numpy.array ray: The ray to test for intersection. - :param numpy.array plane: The ray to test for intersection. + :param numpy.array pl: The plane to test for intersection. :param boolean front_only: Specifies if the ray should only hit the front of the plane. Collisions from the rear of the plane will be @@ -103,8 +103,8 @@ def ray_intersect_plane(ray, plane, front_only=False): if rd.n == 0, the ray is parallel to the plane. """ - p = plane[:3] * plane[3] - n = plane[:3] + p = plane.position(pl) + n = plane.normal(pl) rd_n = vector.dot(ray[1], n) if rd_n == 0.0: @@ -306,7 +306,7 @@ def ray_intersect_aabb(ray, aabb): return point @all_parameters_as_numpy_arrays -def point_height_above_plane(point, plane): +def point_height_above_plane(point, pl): """Calculates how high a point is above a plane. :param numpy.array point: The point to check. @@ -316,17 +316,17 @@ def point_height_above_plane(point, plane): negative if the point is behind the plane. """ """ - http://www.vitutor.com/geometry/distance/point_plane.html - d(P) = (AX + BY + CZ + D) / sqrt(A^2 + B^2 + C^2) - - Normal is unit length, so it's length is 1.0. - Therefore, we can ignore the division all together. - Just perform Pn . [XYZ1] + Because we store normalised normal, we can simply + use: n . (p - p0) + where: + n is the plane normal + p is the plane position + p0 is the point """ - return np.dot(plane, [point[0], point[1], point[2], 1.0]) + return vector.dot(plane.normal(pl), point - plane.position(pl)) @all_parameters_as_numpy_arrays -def point_closest_point_on_plane(point, plane): +def point_closest_point_on_plane(point, pl): """Calculates the point on a plane that is closest to a point. :param numpy.array point: The point to check with. @@ -343,8 +343,8 @@ def point_closest_point_on_plane(point, plane): d is the value of normal dot position n is the plane normal """ - n = plane[:3] - p = n * plane[3] + n = plane.normal(pl) + p = n * plane.distance(pl) d = np.dot(p, n) qn = np.dot(point, n) return point + (n * (d - qn)) diff --git a/tests/test_geometric_tests.py b/tests/test_geometric_tests.py index c982b12..0d52e3e 100644 --- a/tests/test_geometric_tests.py +++ b/tests/test_geometric_tests.py @@ -204,6 +204,15 @@ class test_geometric_tests(unittest.TestCase): self.assertEqual(result, None) def test_point_height_above_plane(self): + pl = plane.create([0., 1., 0.], 1.) + p = np.array([0., 1., 0.]) + result = gt.point_height_above_plane(p, pl) + self.assertEqual(result, 0.) + + p = np.array([0., 0., 0.]) + result = gt.point_height_above_plane(p, pl) + self.assertEqual(result, -1.) + v1 = np.array([ 0.0, 0.0, 1.0]) v2 = np.array([ 1.0, 0.0, 1.0]) v3 = np.array([ 0.0, 1.0, 1.0]) @@ -215,6 +224,11 @@ class test_geometric_tests(unittest.TestCase): result = gt.point_height_above_plane(p, pl) self.assertEqual(result, 19.) + pl = plane.create_xz(distance=5.) + p = np.array([0., 5., 0.]) + h = gt.point_height_above_plane(p, pl) + self.assertEqual(h, 0.) + def test_point_closest_point_on_plane(self): pl = np.array([ 0.0, 1.0, 0.0, 0.0]) p = np.array([ 5.0, 20.0, 5.0]) @@ -300,4 +314,3 @@ class test_geometric_tests(unittest.TestCase): if __name__ == '__main__': unittest.main() - diff --git a/tests/test_plane.py b/tests/test_plane.py index 79fa8b8..0cb7ba6 100644 --- a/tests/test_plane.py +++ b/tests/test_plane.py @@ -3,7 +3,7 @@ try: except: import unittest import numpy as np -from pyrr import plane +from pyrr import plane, vector class test_plane(unittest.TestCase): def test_import(self): @@ -15,18 +15,26 @@ class test_plane(unittest.TestCase): result = plane.create() self.assertTrue(np.allclose(result, [0,0,1,0])) - def test_create_2(self): result = plane.create([1.,0.,0.], 5.) self.assertTrue(np.allclose(result, [1.,0.,0.,5.])) def test_create_from_points(self): - vecs = np.array([ - [ 1.0, 0.0, 0.0 ], - [ 0.0, 1.0, 0.0 ], - [ 1.0, 1.0, 0.0 ] - ]) - result = plane.create_from_points(vecs) + result = plane.create_from_points( + [1., 0., 0.], + [0., 1., 0.], + [1., 1., 0.], + ) self.assertTrue(np.allclose(result, [0.,0.,1.,0.])) + self.assertTrue(np.allclose(plane.position(result), [0., 0., 0.])) + + result = plane.create_from_points( + [1., 1., 0.], + [1., 1., 1.], + [0., 1., 1.], + ) + expected = plane.create([0.,1.,0.], 1.) + self.assertTrue(np.allclose(result, expected)) + self.assertTrue(np.allclose(plane.position(result), [0., 1., 0.])) def test_create_from_position(self): position = np.array([1.0, 0.0, 0.0]) @@ -34,29 +42,42 @@ class test_plane(unittest.TestCase): result = plane.create_from_position(position, normal) self.assertTrue(np.allclose(result, [0., 1., 0., 0.])) + p0 = position + [1., 0., 0.] + p = position + n = vector.normalise(normal) + coplanar = p - p0 + self.assertEqual(np.sum(n coplanar), 0.) + def test_create_xy(self): result = plane.create_xy() self.assertTrue(np.allclose(result, [0., 0., 1., 0.])) - def test_create_xy_invert_distance(self): + result = plane.create_xy(distance=2.) + self.assertTrue(np.allclose(result, [0., 0., 1., 2.])) + result = plane.create_xy(invert=True, distance=2.) - self.assertTrue(np.allclose(result, [0., 0., -1., 2.])) + self.assertTrue(np.allclose(result, [0., 0., -1., -2.])) def test_create_xz(self): result = plane.create_xz() self.assertTrue(np.allclose(result, [0., 1., 0., 0.])) - def test_create_xz_invert_distance(self): + result = plane.create_xz(distance=2.) + self.assertTrue(np.allclose(result, [0., 1., 0., 2.])) + result = plane.create_xz(invert=True, distance=2.) - self.assertTrue(np.allclose(result, [0., -1., 0., 2.])) + self.assertTrue(np.allclose(result, [0., -1., 0., -2.])) def test_create_yz(self): result = plane.create_yz() self.assertTrue(np.allclose(result, [1., 0., 0., 0.])) - def test_create_yz_invert_distance(self): + result = plane.create_yz(distance=2.) + self.assertTrue(np.allclose(result, [1., 0., 0., 2.])) + result = plane.create_yz(invert=True, distance=2.) - self.assertTrue(np.allclose(result, [-1., 0., 0., 2.])) + print(result) + self.assertTrue(np.allclose(result, [-1., 0., 0., -2.])) def test_invert_normal(self): p = np.array([1.0, 0.0, 0.0, 1.0]) @@ -64,9 +85,12 @@ class test_plane(unittest.TestCase): self.assertTrue(np.allclose(result, [-1.0, 0.0, 0.0, -1.0])) def test_position(self): - p = plane.create_xz(distance=5.) + p = plane.create_xz(distance=-5.) result = plane.position(p) - self.assertTrue(np.allclose(result, [0.,5.,0.])) + self.assertTrue(np.allclose(result, [0.,-5.,0.])) + + p = plane.create_from_position(position=[0., 0., 1.], normal=[0., 0., 1.]) + self.assertTrue(np.allclose(plane.position(p), [0., 0., 1.])) def test_normal(self): p = plane.create_xz(distance=5.) @@ -75,4 +99,3 @@ class test_plane(unittest.TestCase): if __name__ == '__main__': unittest.main() -	Inconsitent Position / Distance to plane Thank you for this useful Library. There is some unexpected behavior for planes concerning the sign of the distance: Take for example the following Plane: ``` plane = pyrr.plane.create_from_position(position=[0, 0, 1], normal=[0, 0, 1]) ``` which returns the expected plane: `array([ 0, 0, 1, -1])`. However `pyrr.plane.position(plane)` returns `array([ 0, 0, -1])`, instead of `[0, 0, 1]` A related issue can be observed when calculating the distance of a point calculated to lie on the plane, which should therefore be 0: ```pyrr.geometric_tests.point_height_above_plane(pyrr.geometric_tests.point_closest_point_on_plane([0, 0, 1], plane), plane)``` but returns -2	530820191954abcb9c7c54602fe13ba16912ba48	[ "tests/test_geometric_tests.py::test_geometric_tests::test_point_closest_point_on_plane", "tests/test_geometric_tests.py::test_geometric_tests::test_point_height_above_plane", "tests/test_plane.py::test_plane::test_create_from_points", "tests/test_plane.py::test_plane::test_create_xy", "tests/test_plane.py::test_plane::test_create_xz", "tests/test_plane.py::test_plane::test_create_yz", "tests/test_plane.py::test_plane::test_position" ]	[ "tests/test_geometric_tests.py::test_geometric_tests::test_import", "tests/test_geometric_tests.py::test_geometric_tests::test_point_closest_point_on_line", "tests/test_geometric_tests.py::test_geometric_tests::test_point_closest_point_on_line_2", "tests/test_geometric_tests.py::test_geometric_tests::test_point_closest_point_on_line_segment", "tests/test_geometric_tests.py::test_geometric_tests::test_point_closest_point_on_ray", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_line", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_line_invalid", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_line_segment", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_line_segment_invalid", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_rectangle_invalid_intersections_1", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_rectangle_invalid_intersections_2", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_rectangle_invalid_intersections_3", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_rectangle_valid_intersections_1", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_rectangle_valid_intersections_2", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_rectangle_valid_intersections_3", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_coincident_ray", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_coincident_ray_2", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_coincident_ray_3", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_aabb_invalid_1", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_aabb_valid_1", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_aabb_valid_2", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_aabb_valid_3", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_plane", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_plane_front_only", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_plane_invalid", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_sphere_no_solution_1", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_sphere_no_solution_2", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_parallel_ray", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_parallel_ray_2", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_parallel_ray_3", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_does_intersect_sphere_1", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_does_intersect_sphere_2", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_does_intersect_sphere_3", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_does_intersect_sphere_4", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_penetration_sphere_1", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_penetration_sphere_2", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_penetration_sphere_3", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_penetration_sphere_4", "tests/test_geometric_tests.py::test_geometric_tests::test_vector_parallel_vector", "tests/test_geometric_tests.py::test_geometric_tests::test_vector_parallel_vector_invalid", "tests/test_plane.py::test_plane::test_create", "tests/test_plane.py::test_plane::test_create_from_position", "tests/test_plane.py::test_plane::test_import", "tests/test_plane.py::test_plane::test_invert_normal", "tests/test_plane.py::test_plane::test_normal" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2019-02-06 12:26:02+00:00	bsd-3-clause	903
adbar__simplemma-114	diff --git a/simplemma/language_detector.py b/simplemma/language_detector.py index 52369a6..f6fab14 100644 --- a/simplemma/language_detector.py +++ b/simplemma/language_detector.py @@ -198,14 +198,18 @@ class LanguageDetector: Returns: float: The proportion of text in the target language(s). """ - return sum( - percentage - for ( - lang_code, - percentage, - ) in self.proportion_in_each_language(text).items() - if lang_code != "unk" - ) + tokens = self._token_sampler.sample_text(text) + if len(tokens) == 0: + return 0 + + in_target = 0 + for token in tokens: + for lang_code in self._lang: + candidate = self._lemmatization_strategy.get_lemma(token, lang_code) + if candidate is not None: + in_target += 1 + break + return in_target / len(tokens) def main_language( self,	adbar/simplemma	fa1d96469ca601b5249b8d5cbb42c1474cfd83bb	diff --git a/tests/test_language_detector.py b/tests/test_language_detector.py index 4affdd1..ad68f0c 100644 --- a/tests/test_language_detector.py +++ b/tests/test_language_detector.py @@ -108,6 +108,15 @@ def test_in_target_language() -> None: == 1.0 ) + langs = ("en", "de") + text = "It was a true gift" + assert ( + LanguageDetector(lang=langs).proportion_in_target_languages(text) + == in_target_language(text, lang=langs) + == 1.0 + ) + in_target_language("It was a true gift", lang=("en", "de")) + def test_main_language(): text = "Dieser Satz ist auf Deutsch."	in_target_language can count words twice and return ratios above 1.0 I noticed that in current `main` version, the `in_target_language` function can return ratios above 1.0 when given more than one language and the words in the input are matching several languages. Example: >>> in_target_language('It was a true gift', lang='en') 1.0 >>> in_target_language('It was a true gift', lang='de') 0.6666666666666666 >>> in_target_language('It was a true gift', lang=('en','de')) 1.6666666666666665 Simplemma 0.9.1 doesn't have this problem: >>> in_target_language('It was a true gift', lang='en') 1.0 >>> in_target_language('It was a true gift', lang='de') 0.6666666666666666 >>> in_target_language('It was a true gift', lang=('en','de')) 1.0 It's not just a question of capping the scores at 1.0. The problem is that a single word can count more than once if it happens to match multiple languages. Below is an example that demonstrates the problem. I added nonsense words that don't match any language, but their presence is compensated by words that are counted twice. Current `main` version: >>> in_target_language('It was a true gift xxx yyy', lang=('en','de')) 1.0 Simplemma 0.9.1: >>> in_target_language('It was a true gift xxx yyy', lang=('en','de')) 0.6	fa1d96469ca601b5249b8d5cbb42c1474cfd83bb	[ "tests/test_language_detector.py::test_in_target_language" ]	[ "tests/test_language_detector.py::test_proportion_in_each_language", "tests/test_language_detector.py::test_main_language" ]	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2023-09-12 17:03:16+00:00	mit	904
adbar__simplemma-85	diff --git a/simplemma/__init__.py b/simplemma/__init__.py index 74510e6..6a553e8 100644 --- a/simplemma/__init__.py +++ b/simplemma/__init__.py @@ -7,6 +7,7 @@ __license__ = "MIT" __version__ = "0.9.1" +from .dictionary_factory import DictionaryFactory, DefaultDictionaryFactory from .language_detector import LanguageDetector, in_target_language, langdetect from .lemmatizer import Lemmatizer, lemmatize, lemma_iterator, text_lemmatizer, is_known from .tokenizer import Tokenizer, RegexTokenizer, simple_tokenizer @@ -16,5 +17,3 @@ from .token_sampler import ( MostCommonTokenSampler, RelaxedMostCommonTokenSampler, ) -from .dictionary_factory import DictionaryFactory, DefaultDictionaryFactory -from .dictionary_pickler import * diff --git a/simplemma/dictionary_pickler.py b/training/dictionary_pickler.py similarity index 90% rename from simplemma/dictionary_pickler.py rename to training/dictionary_pickler.py index 5f400ee..f0b92e0 100644 --- a/simplemma/dictionary_pickler.py +++ b/training/dictionary_pickler.py @@ -7,15 +7,11 @@ from operator import itemgetter from pathlib import Path from typing import Dict, List, Optional -try: - from .dictionary_factory import SUPPORTED_LANGUAGES - from .strategies.defaultrules import DEFAULT_RULES - from .utils import levenshtein_dist -# local error, also ModuleNotFoundError for Python >= 3.6 -except ImportError: # pragma: no cover - from dictionary_factory import SUPPORTED_LANGUAGES # type: ignore - from strategies.defaultrules import DEFAULT_RULES # type: ignore - from utils import levenshtein_dist # type: ignore +import simplemma +from simplemma.dictionary_factory import SUPPORTED_LANGUAGES +from simplemma.strategies.defaultrules import DEFAULT_RULES +from simplemma.utils import levenshtein_dist + LOGGER = logging.getLogger(__name__) @@ -138,7 +134,7 @@ def _pickle_dict( mydict = dict(sorted(mydict.items(), key=itemgetter(1))) if filepath is None: filename = f"data/{langcode}.plzma" - filepath = str(Path(__file__).parent / filename) + filepath = str(Path(simplemma.__file__).parent / filename) with lzma.open(filepath, "wb") as filehandle: # , filters=my_filters, preset=9 pickle.dump(mydict, filehandle, protocol=4) LOGGER.debug("%s %s", langcode, len(mydict)) diff --git a/eval/eval-requirements.txt b/training/eval/eval-requirements.txt similarity index 100% rename from eval/eval-requirements.txt rename to training/eval/eval-requirements.txt diff --git a/eval/udscore.py b/training/eval/udscore.py similarity index 84% rename from eval/udscore.py rename to training/eval/udscore.py index 34e3a9c..e6bd507 100644 --- a/eval/udscore.py +++ b/training/eval/udscore.py @@ -5,7 +5,8 @@ from collections import Counter from os import makedirs, path from conllu import parse_incr # type: ignore -from simplemma import lemmatize +from simplemma import Lemmatizer, DefaultDictionaryFactory +from simplemma.strategies.default import DefaultStrategy if not path.exists("csv"): makedirs("csv") @@ -66,6 +67,16 @@ for filedata in data_files: with open(filename, "r", encoding="utf-8") as myfile: data_file = myfile.read() start = time.time() + dictionary_factory = DefaultDictionaryFactory() + strategies = DefaultStrategy(greedy=False) + lemmatizer = Lemmatizer( + dictionary_factory=dictionary_factory, + lemmatization_strategy=DefaultStrategy(greedy=False), + ) + greedy_lemmatizer = Lemmatizer( + dictionary_factory=dictionary_factory, + lemmatization_strategy=DefaultStrategy(greedy=True), + ) print("==", filedata, "==") for tokenlist in parse_incr(data_file): for token in tokenlist: @@ -75,13 +86,10 @@ for filedata in data_files: continue initial = bool(token["id"] == 1) + token_form = token["form"].lower() if initial else token["form"] - greedy_candidate = lemmatize( - token["form"], lang=language, greedy=True, initial=initial - ) - candidate = lemmatize( - token["form"], lang=language, greedy=False, initial=initial - ) + candidate = lemmatizer.lemmatize(token_form, lang=language) + greedy_candidate = greedy_lemmatizer.lemmatize(token_form, lang=language) if token["upos"] in ("ADJ", "NOUN"): focus_total += 1	adbar/simplemma	b575330e558851c728af74bb62208af445d6a283	diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 4ebd08b..c73b552 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -86,11 +86,11 @@ jobs: flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - name: Code format with black - run: black --check --diff simplemma tests + run: black --check --diff simplemma training tests - name: Type checking with mypy if: matrix.python-version != '3.6' - run: mypy -p simplemma -p tests + run: mypy -p simplemma -p training -p tests - name: Test with pytest run: pytest --cov=./ --cov-report=xml diff --git a/tests/test_dictionary_pickler.py b/tests/test_dictionary_pickler.py index 1dad1fa..95dd1bb 100644 --- a/tests/test_dictionary_pickler.py +++ b/tests/test_dictionary_pickler.py @@ -1,7 +1,7 @@ import os import tempfile -from simplemma import dictionary_pickler +from training import dictionary_pickler TEST_DIR = os.path.abspath(os.path.dirname(__file__))	Separate scripts used to create the dictionaries from actual src & tests `tests/udscore.py` and `src/dictionary_pickler.py` seem to be scripts used to create the dictionaries and validate their quality. I suggest that they are moved to a separate folder `training` or whatever you want	b575330e558851c728af74bb62208af445d6a283	[ "tests/test_dictionary_pickler.py::test_logic" ]	[]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2023-05-10 17:08:31+00:00	mit	905
aequitas__python-rflink-39	diff --git a/.travis.yml b/.travis.yml index 30fa75f..e52730d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,11 +7,13 @@ python: - 3.8 - 2.7 - pypy3 -install: pip install tox-travis python-coveralls codeclimate-test-reporter +# python-coveralls 5.0 no longer supports python34 +install: pip install tox-travis codeclimate-test-reporter script: tox matrix: allow_failures: - python: 2.7 + - python: 3.4 - python: pypy3 include: - python: 3.7 diff --git a/rflink/parser.py b/rflink/parser.py index 05e7ea0..8a74a52 100644 --- a/rflink/parser.py +++ b/rflink/parser.py @@ -305,7 +305,7 @@ def decode_packet(packet: str) -> PacketType: # convert key=value pairs where needed for attr in filter(None, attrs.strip(DELIM).split(DELIM)): - key, value = attr.lower().split("=") + key, value = attr.lower().split("=", 1) if key in VALUE_TRANSLATION: value = VALUE_TRANSLATION[key](value) name = PACKET_FIELDS.get(key, key) diff --git a/rflink/protocol.py b/rflink/protocol.py index a3c54da..9922910 100644 --- a/rflink/protocol.py +++ b/rflink/protocol.py @@ -151,7 +151,7 @@ class PacketHandling(ProtocolBase): try: packet = decode_packet(raw_packet) except BaseException: - log.exception("failed to parse packet: %s", packet) + log.exception("failed to parse packet data: %s", raw_packet) log.debug("decoded packet: %s", packet)	aequitas/python-rflink	1b2ea3d82e4138fb5b35c763df94aa0a63d24acf	diff --git a/tests/test_parse.py b/tests/test_parse.py index 3f55831..274e0ae 100644 --- a/tests/test_parse.py +++ b/tests/test_parse.py @@ -80,6 +80,10 @@ PROTOCOL_SAMPLES = os.path.join(os.path.dirname(__file__), "protocol_samples.txt "20;00;Internal Pullup on RF-in disabled;", {"message": "Internal Pullup on RF-in disabled"}, ], + [ + "20;9A;FA500;ID=0000db9e;SWITCH=01;CMD=SET_LEVEL=2;", + {"command": "set_level=2"}, + ], ], ) def test_packet_parsing(packet, expect):	decode_packet: too many values to unpack (expected 2) I use rflink integration in my HA setup and often get this in HA log: > 2020-01-22 07:49:56 ERROR (MainThread) [rflink.protocol] failed to parse packet: None > Traceback (most recent call last): > File "/usr/local/lib/python3.7/site-packages/rflink/protocol.py", line 152, in handle_raw_packet > packet = decode_packet(raw_packet) > File "/usr/local/lib/python3.7/site-packages/rflink/parser.py", line 308, in decode_packet > key, value = attr.lower().split("=") > ValueError: too many values to unpack (expected 2) Obvoiusly there is no impact on the functionality, but the messages flood the log. I hope it's possible to rewrite the code so it account for situations like this.	1b2ea3d82e4138fb5b35c763df94aa0a63d24acf	[ "tests/test_parse.py::test_packet_parsing[20;9A;FA500;ID=0000db9e;SWITCH=01;CMD=SET_LEVEL=2;-expect15]" ]	[ "tests/test_parse.py::test_packet_parsing[20;2D;UPM/Esic;ID=0001;TEMP=00cf;HUM=16;BAT=OK;-expect0]", "tests/test_parse.py::test_packet_parsing[20;36;Alecto", "tests/test_parse.py::test_packet_parsing[20;08;UPM/Esic;ID=1003;RAIN=0010;BAT=OK;-expect2]", "tests/test_parse.py::test_packet_parsing[20;46;Kaku;ID=44;SWITCH=4;CMD=OFF;-expect3]", "tests/test_parse.py::test_packet_parsing[20;E0;NewKaku;ID=cac142;SWITCH=1;CMD=ALLOFF;-expect4]", "tests/test_parse.py::test_packet_parsing[20;00;Nodo", "tests/test_parse.py::test_packet_parsing[20;01;VER=1.1;REV=45;BUILD=04;-expect6]", "tests/test_parse.py::test_packet_parsing[20;01;PONG;-expect7]", 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"tests/test_parse.py::test_packet_valiation[10;UNITEC;7796;01;ON;]", "tests/test_parse.py::test_packet_valiation[10;UNITEC;7796;01;PAIR;]", "tests/test_parse.py::test_packet_valiation[10;REBOOT;]", "tests/test_parse.py::test_packet_valiation[10;PING;]", "tests/test_parse.py::test_packet_valiation[10;VERSION;]", "tests/test_parse.py::test_packet_valiation[10;RFDEBUG=ON;]", "tests/test_parse.py::test_packet_valiation[10;RFUDEBUG=ON;]", "tests/test_parse.py::test_packet_valiation[10;QRFDEBUG=ON;]", "tests/test_parse.py::test_packet_valiation[10;TRISTATEINVERT;]", "tests/test_parse.py::test_packet_valiation[10;RTSCLEAN;]", "tests/test_parse.py::test_packet_valiation[10;RTSRECCLEAN=9;]", "tests/test_parse.py::test_packet_valiation[10;RTSSHOW;]", "tests/test_parse.py::test_packet_valiation[10;RTSINVERT;]", "tests/test_parse.py::test_packet_valiation[10;RTSLONGTX;]", "tests/test_parse.py::test_packet_valiation[11;20;0B;NewKaku;ID=000005;SWITCH=2;CMD=ON;]", "tests/test_parse.py::test_packet_valiation[20;D3;OK;]", "tests/test_parse.py::test_packet_valiation[20;D4;NewKaku;ID=000005;SWITCH=2;CMD=ON;]" ]	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2020-01-25 20:01:16+00:00	mit	906
aesara-devs__aesara-465	diff --git a/aesara/tensor/math_opt.py b/aesara/tensor/math_opt.py index e90d6b425..ad0eeb92b 100644 --- a/aesara/tensor/math_opt.py +++ b/aesara/tensor/math_opt.py @@ -11,7 +11,6 @@ from functools import reduce import numpy as np import aesara.scalar.basic as aes -from aesara import compile from aesara.assert_op import assert_op from aesara.configdefaults import config from aesara.graph.basic import Constant, Variable @@ -74,6 +73,7 @@ from aesara.tensor.math import ( expm1, ge, int_div, + isinf, log, log1p, makeKeepDims, @@ -2286,34 +2286,33 @@ def local_log1p(fgraph, node): @register_stabilize @register_specialize @local_optimizer([log]) -def local_log_add(fgraph, node): - # log(exp(x)+exp(y)) - # - # Suppose x >= y - # log(exp(x) + exp(y)) - # log(exp(x) * (1 + exp(y)/exp(x))) - # x + log(1 + exp(y)/exp(x)) - # x + log1p(exp(y)/exp(x)) - # x + log1p(exp(y-x)) +def local_log_add_exp(fgraph, node): + # log(exp(x)+exp(y)+exp(z)) = max + log(x-max, y-max, z-max) + if node.op == log: z = node.inputs[0] if z.owner and z.owner.op == add: zi = z.owner.inputs - if len(zi) != 2: - # -- upgrading Maximum to handle multiple inputs wasn't trivial - # TODO - # raise NotImplementedError() - return pre_exp = [x.owner.inputs[0] for x in zi if x.owner and x.owner.op == exp] + # all arguments to add are exp(<something>) if len(pre_exp) == len(zi): - # all arguments to add are exp(<something>) - max_pre = maximum(pre_exp) - - ret = max_pre + log1p(exp(add([p - max_pre for p in pre_exp]))) - ret.tag.values_eq_approx = values_eq_approx_remove_inf + # Do not offset when max_pre = -np.inf, to avoid nan in the output + # Switch statement is placed directly inside add to break the self-symmetry + # of the returned output (otherwise the optimization would not stabilize) + max_pre = reduce(maximum, pre_exp) + ret = max_pre + log( + add( + *[ + switch(isinf(max_pre), exp(max_pre), exp(p - max_pre)) + for p in pre_exp + ] + ) + ) return [ret] +@register_stabilize +@register_specialize @local_optimizer([log]) def local_log_sum_exp(fgraph, node): # log(sum_i(exp(x_i))) = x_max + log(sum_i(exp(x_i - x_max))) @@ -2342,7 +2341,19 @@ def local_log_sum_exp(fgraph, node): max_pre_exp = aet_max(pre_exp, axis=axis) max_pre_exp_keepdims = makeKeepDims(pre_exp, max_pre_exp, axis) - ret = max_pre_exp + log(aet_sum(exp(pre_exp - max_pre_exp_keepdims), axis=axis)) + # Do not offset when max_pre = -np.inf, to avoid nan in the output + # Switch statement is placed directly inside sum to break the self-symmetry + # of the returned output (otherwise the optimization would not stabilize) + ret = max_pre_exp + log( + aet_sum( + switch( + isinf(max_pre_exp_keepdims), + exp(max_pre_exp_keepdims), + exp(pre_exp - max_pre_exp_keepdims), + ), + axis=axis, + ), + ) # Restore the dimshuffle op, if any. if dimshuffle_op: @@ -2351,14 +2362,6 @@ def local_log_sum_exp(fgraph, node): return [ret] -compile.optdb.register( - "local_log_sum_exp", - in2out(local_log_sum_exp, ignore_newtrees=True), - 1.6, - "fast_run", -) - - def add_calculate(num, denum, aslist=False, out_type=None): # TODO: make sure that this function and mul_calculate are similar if out_type is None:	aesara-devs/aesara	b84ac43a8dd23c888131e9b3f5654f81402da76c	diff --git a/tests/tensor/test_math_opt.py b/tests/tensor/test_math_opt.py index 98a1d8a80..55dfbae0b 100644 --- a/tests/tensor/test_math_opt.py +++ b/tests/tensor/test_math_opt.py @@ -1840,10 +1840,7 @@ def test_log1p(): assert [node.op for node in f.maker.fgraph.toposort()] == [log1p] [email protected]( - reason="log(add(exp)) is not stabilized when adding more than 2 elements, see #623" -) -def test_log_add(): +def test_local_log_add_exp(): m = config.mode if m == "FAST_COMPILE": m = "FAST_RUN" @@ -1858,26 +1855,28 @@ def test_log_add(): y = dvector() f = function([x, y], log(exp(x) + exp(y)), mode=m) - f([10000], [10000]) # causes overflow if handled incorrectly - assert np.isfinite(f([10000], [10000])) + # test that it gives the correct result when it doesn't overflow + f([10], [10]) # doesn't causes overflow + utt.assert_allclose(f([10], [10]), 10 + np.log1p(1)) + + assert np.isfinite(f([10000], [10000])) # causes overflow if handled incorrectly utt.assert_allclose(f([10000], [10000]), 10000 + np.log1p(1)) - # test that it give the same result when it don't overflow - f([10], [10]) # don't causes overflow - utt.assert_allclose(f([10], [10]), 10 + np.log1p(1)) + # test that when max = +-inf, optimized output still works correctly + assert f([-np.inf], [-np.inf]) == -np.inf + assert f([np.inf], [np.inf]) == np.inf + assert f([np.inf], [-np.inf]) == np.inf - # test that it also works with more than two args, (this currently fails) + # test that it also works with more than two args x = dvector() y = dvector() f = function([x, y], log(exp(x) + exp(y) + exp(x - y) + exp(x + y)), mode=m) - f([10000], [10000]) # causes overflow if handled incorrectly + assert np.isfinite(f([10000], [10000])) # causes overflow if handled incorrectly utt.assert_allclose(f([10000], [10000]), 20000) # TODO: test that the optimization works in the presence of broadcasting. - # TODO: (write and) test that the optimization works with Sum in addition to working with Add. - def test_local_subtensor_of_dot(): m1 = matrix() @@ -4001,6 +4000,16 @@ def test_local_log_sum_exp3(): assert np.allclose(optimised_ret, 100.0) +def test_local_log_sum_exp_inf(): + # Test that when max = +-inf, optimized output still works correctly + x = vector("x") + f = compile_graph_log_sum_exp(x, axis=0) + + assert f([-np.inf, -np.inf]) == -np.inf + assert f([np.inf, np.inf]) == np.inf + assert f([-np.inf, np.inf]) == np.inf + + def test_local_reciprocal_1_plus_exp(): x = vector("x") y = aet.reciprocal(1 + exp(x))	LogSumExp of `-inf` returns `nan` instead of `-inf` ```python x = at.vector('x') res1 = at.log(at.sum(at.exp(x))) # nan with sum res2 = at.log(at.prod(at.exp(x))) # but not with prod fun = aesara.function([x], [res1, res2]) print(fun(np.array([-np.inf, -np.inf]))) # [array(nan), array(-inf)] ``` for reference in numpy we get `-inf`, together with a divide by zero encountered in log ```python print(np.log(np.sum(np.exp([-np.inf, -np.inf])))) # -inf ``` This showed up in the pymc3 `logsumexp` function which returns `nan` with this input: ```python from pymc3.math import logsumexp x = at.vector('x') res = logsumexp(x) fun = aesara.function([x], res) print(fun(np.array([-np.inf, -np.inf]))) # [nan] ``` Whereas the scipy reference works fine ```python print(scipy.special.logsumexp([-np.inf, -np.inf])) # -inf ``` Weirdly it happens with addition, but not subtraction or multiplication, so maybe the problem is not the sum but the addition? ```python x = at.vector('x') res1 = at.log(at.exp(x[0]) + at.exp(x[1])) res2 = at.log(at.exp(x[0]) - at.exp(x[1])) fun = aesara.function([x], [res1, res2]) print(fun(np.array([-np.inf, -np.inf]))) # [array(nan), array(-inf)]	b84ac43a8dd23c888131e9b3f5654f81402da76c	[ "tests/tensor/test_math_opt.py::test_local_log_add_exp" ]	[ "tests/tensor/test_math_opt.py::TestGreedyDistribute::test_main", "tests/tensor/test_math_opt.py::TestAlgebraicCanonize::test_muldiv", "tests/tensor/test_math_opt.py::TestAlgebraicCanonize::test_abs_mul_div", "tests/tensor/test_math_opt.py::test_mixeddiv", "tests/tensor/test_math_opt.py::TestFusion::test_add_mul_fusion_inplace", "tests/tensor/test_math_opt.py::TestLocalUselessElemwiseComparison::test_inequality_with_self", "tests/tensor/test_math_opt.py::TestLocalUselessElemwiseComparison::test_shape_add_inequality", "tests/tensor/test_math_opt.py::TestLocalUselessElemwiseComparison::test_and", "tests/tensor/test_math_opt.py::TestLocalUselessElemwiseComparison::test_and_int", "tests/tensor/test_math_opt.py::TestLocalUselessElemwiseComparison::test_or", "tests/tensor/test_math_opt.py::TestLocalUselessElemwiseComparison::test_or_int", "tests/tensor/test_math_opt.py::TestLocalUselessElemwiseComparison::test_xor", "tests/tensor/test_math_opt.py::TestExpLog::test_log_exp", "tests/tensor/test_math_opt.py::TestLocalMergeSwitchSameCond::test_elemwise", "tests/tensor/test_math_opt.py::TestLocalSumProd::test_local_sum_prod_all_to_none", "tests/tensor/test_math_opt.py::TestLocalSumProd::test_local_sum_sum_prod_prod", "tests/tensor/test_math_opt.py::TestLocalSumProd::test_local_sum_sum_int8", "tests/tensor/test_math_opt.py::TestLocalSumProd::test_local_sum_sum_dtype", "tests/tensor/test_math_opt.py::test_local_add_specialize", "tests/tensor/test_math_opt.py::TestIntDivByOne::test1", "tests/tensor/test_math_opt.py::TestIntDivByOne::test3", "tests/tensor/test_math_opt.py::test_local_sumsqr2dot", "tests/tensor/test_math_opt.py::TestSigmoidOpts::test_1msigmoid", "tests/tensor/test_math_opt.py::TestSigmoidOpts::test_perform_sigm_times_exp", "tests/tensor/test_math_opt.py::TestSoftplusOpts::test_logsigm_to_softplus", "tests/tensor/test_math_opt.py::TestSigmoidUtils::test_compute_mul", "tests/tensor/test_math_opt.py::TestSigmoidUtils::test_parse_mul_tree", "tests/tensor/test_math_opt.py::TestSigmoidUtils::test_is_1pexp" ]	{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-06-06 13:15:11+00:00	bsd-3-clause	907
aesara-devs__aesara-779	diff --git a/aesara/tensor/__init__.py b/aesara/tensor/__init__.py index af894fa98..787bd4871 100644 --- a/aesara/tensor/__init__.py +++ b/aesara/tensor/__init__.py @@ -134,6 +134,9 @@ from aesara.tensor.extra_ops import ( # noqa squeeze, unique, unravel_index, + linspace, + logspace, + geomspace, ) from aesara.tensor.shape import ( # noqa reshape, diff --git a/aesara/tensor/extra_ops.py b/aesara/tensor/extra_ops.py index 9db12b045..d054f5d46 100644 --- a/aesara/tensor/extra_ops.py +++ b/aesara/tensor/extra_ops.py @@ -1636,6 +1636,29 @@ class BroadcastTo(Op): broadcast_to_ = BroadcastTo() +def geomspace(start, end, steps, base=10.0): + from aesara.tensor.math import log + + start = at.as_tensor_variable(start) + end = at.as_tensor_variable(end) + return base linspace(log(start) / log(base), log(end) / log(base), steps) + + +def logspace(start, end, steps, base=10.0): + start = at.as_tensor_variable(start) + end = at.as_tensor_variable(end) + return base linspace(start, end, steps) + + +def linspace(start, end, steps): + start = at.as_tensor_variable(start) + end = at.as_tensor_variable(end) + arr = at.arange(steps) + arr = at.shape_padright(arr, max(start.ndim, end.ndim)) + multiplier = (end - start) / (steps - 1) + return start + arr * multiplier + + def broadcast_to( x: TensorVariable, shape: Union[TensorVariable, Tuple[Variable]] ) -> TensorVariable:	aesara-devs/aesara	980c4c2c72b9c8b51d8627cc75fb655a9fd600ed	diff --git a/tests/tensor/test_extra_ops.py b/tests/tensor/test_extra_ops.py index a6aa85cb0..ce57ae6ae 100644 --- a/tests/tensor/test_extra_ops.py +++ b/tests/tensor/test_extra_ops.py @@ -36,6 +36,9 @@ from aesara.tensor.extra_ops import ( diff, fill_diagonal, fill_diagonal_offset, + geomspace, + linspace, + logspace, ravel_multi_index, repeat, searchsorted, @@ -65,6 +68,11 @@ from aesara.utils import LOCAL_BITWIDTH, PYTHON_INT_BITWIDTH from tests import unittest_tools as utt +def set_test_value(x, v): + x.tag.test_value = v + return x + + def test_cpu_contiguous(): a = fmatrix("a") i = iscalar("i") @@ -1222,3 +1230,28 @@ def test_broadcast_arrays(): assert np.array_equal(x_bcast_val, x_bcast_exp) assert np.array_equal(y_bcast_val, y_bcast_exp) + + [email protected]( + "start, stop, num_samples", + [ + (1, 10, 50), + (np.array([5, 6]), np.array([[10, 10], [10, 10]]), 25), + (1, np.array([5, 6]), 30), + ], +) +def test_space_ops(start, stop, num_samples): + z = linspace(start, stop, num_samples) + aesara_res = function(inputs=[], outputs=z)() + numpy_res = np.linspace(start, stop, num=num_samples) + assert np.allclose(aesara_res, numpy_res) + + z = logspace(start, stop, num_samples) + aesara_res = function(inputs=[], outputs=z)() + numpy_res = np.logspace(start, stop, num=num_samples) + assert np.allclose(aesara_res, numpy_res) + + z = geomspace(start, stop, num_samples) + aesara_res = function(inputs=[], outputs=z)() + numpy_res = np.geomspace(start, stop, num=num_samples) + assert np.allclose(aesara_res, numpy_res)	Implement Op for `linspace` and similar numpy functions The following numpy functions don't have to counterpart in Aesara: * [linspace](https://numpy.org/doc/stable/reference/generated/numpy.linspace.html) * [logspace](https://numpy.org/doc/stable/reference/generated/numpy.logspace.html) * [geomspace](https://numpy.org/doc/stable/reference/generated/numpy.geomspace.html) I am not familiar with all of them, so some might not make sense, or they might be low priority. `linspace` would definitely be nice to have.	980c4c2c72b9c8b51d8627cc75fb655a9fd600ed	[ "tests/tensor/test_extra_ops.py::test_cpu_contiguous", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_searchsortedOp_on_sorted_input", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_searchsortedOp_wrong_side_kwd", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_searchsortedOp_on_no_1d_inp", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_searchsortedOp_on_float_sorter", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_searchsortedOp_on_int_sorter", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_searchsortedOp_on_right_side", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_infer_shape", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_grad", "tests/tensor/test_extra_ops.py::TestDiffOp::test_diffOp", "tests/tensor/test_extra_ops.py::TestDiffOp::test_output_type[x_type0]", "tests/tensor/test_extra_ops.py::TestDiffOp::test_output_type[x_type1]", "tests/tensor/test_extra_ops.py::TestDiffOp::test_output_type[x_type2]", "tests/tensor/test_extra_ops.py::TestDiffOp::test_output_type[x_type3]", "tests/tensor/test_extra_ops.py::TestDiffOp::test_infer_shape", "tests/tensor/test_extra_ops.py::TestDiffOp::test_grad", "tests/tensor/test_extra_ops.py::TestDiffOp::test_grad_not_implemented", "tests/tensor/test_extra_ops.py::TestSqueeze::test_op", "tests/tensor/test_extra_ops.py::TestSqueeze::test_infer_shape", "tests/tensor/test_extra_ops.py::TestSqueeze::test_grad", "tests/tensor/test_extra_ops.py::TestSqueeze::test_var_interface", "tests/tensor/test_extra_ops.py::TestSqueeze::test_axis", "tests/tensor/test_extra_ops.py::TestCompress::test_op", "tests/tensor/test_extra_ops.py::TestRepeat::test_basic", "tests/tensor/test_extra_ops.py::TestRepeat::test_grad", "tests/tensor/test_extra_ops.py::TestRepeat::test_broadcastable", "tests/tensor/test_extra_ops.py::TestBartlett::test_perform", "tests/tensor/test_extra_ops.py::TestBartlett::test_infer_shape", "tests/tensor/test_extra_ops.py::TestFillDiagonal::test_infer_shape", "tests/tensor/test_extra_ops.py::TestFillDiagonalOffset::test_gradient", "tests/tensor/test_extra_ops.py::TestFillDiagonalOffset::test_infer_shape", "tests/tensor/test_extra_ops.py::test_to_one_hot", "tests/tensor/test_extra_ops.py::TestUnique::test_basic_vector[x0-inp0-None]", "tests/tensor/test_extra_ops.py::TestUnique::test_basic_vector[x1-inp1-None]", "tests/tensor/test_extra_ops.py::TestUnique::test_basic_vector[x2-inp2-0]", "tests/tensor/test_extra_ops.py::TestUnique::test_basic_vector[x3-inp3-0]", "tests/tensor/test_extra_ops.py::TestUnique::test_basic_vector[x4-inp4--1]", "tests/tensor/test_extra_ops.py::TestUnique::test_basic_vector[x5-inp5--1]", "tests/tensor/test_extra_ops.py::TestUnique::test_infer_shape[x0-inp0-None]", "tests/tensor/test_extra_ops.py::TestUnique::test_infer_shape[x2-inp2-0]", "tests/tensor/test_extra_ops.py::TestUnique::test_infer_shape[x3-inp3-0]", "tests/tensor/test_extra_ops.py::TestUnique::test_infer_shape[x4-inp4--1]", "tests/tensor/test_extra_ops.py::TestUnique::test_infer_shape[x5-inp5--1]", "tests/tensor/test_extra_ops.py::test_broadcast_shape_symbolic[s1_vals0-s2_vals0-exp_res0]", "tests/tensor/test_extra_ops.py::test_broadcast_shape_symbolic[s1_vals1-s2_vals1-exp_res1]", "tests/tensor/test_extra_ops.py::test_broadcast_shape_symbolic[s1_vals2-s2_vals2-exp_res2]", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_avoid_useless_scalars", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_avoid_useless_subtensors", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_perform", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_gradient[<lambda>-input_dims0]", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_gradient[<lambda>-input_dims1]", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_gradient[<lambda>-input_dims2]", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_gradient[<lambda>-input_dims3]", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_infer_shape", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_inplace", "tests/tensor/test_extra_ops.py::test_broadcast_arrays", "tests/tensor/test_extra_ops.py::test_space_ops[1-10-50]", "tests/tensor/test_extra_ops.py::test_space_ops[start1-stop1-25]", "tests/tensor/test_extra_ops.py::test_space_ops[1-stop2-30]" ]	[]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2022-01-22 11:36:31+00:00	bsd-3-clause	908
aesara-devs__aesara-854	diff --git a/aesara/tensor/c_code/dimshuffle.c b/aesara/tensor/c_code/dimshuffle.c index d97df5254..6c67bd1bf 100644 --- a/aesara/tensor/c_code/dimshuffle.c +++ b/aesara/tensor/c_code/dimshuffle.c @@ -31,6 +31,8 @@ int APPLY_SPECIFIC(cpu_dimshuffle)(PyArrayObject input, PyArrayObject res, PyArrayObject transposed_input = (PyArrayObject )PyArray_Transpose(_input, &permute); + Py_DECREF(_input); + PyDimMem_FREE(permute.ptr); npy_intp res_shape = PyArray_DIMS(transposed_input); @@ -68,7 +70,7 @@ int APPLY_SPECIFIC(cpu_dimshuffle)(PyArrayObject input, PyArrayObject res, res = (PyArrayObject )PyArray_Newshape(transposed_input, &reshape_shape, NPY_CORDER); - / Py_XDECREF(transposed_input); */ + Py_DECREF(transposed_input); PyDimMem_FREE(reshape_shape.ptr);	aesara-devs/aesara	3d8553f7b56caed8686e3db9bfbe5ffea110b70a	diff --git a/tests/tensor/test_elemwise.py b/tests/tensor/test_elemwise.py index 0ad4a76a6..1ad8ca9b2 100644 --- a/tests/tensor/test_elemwise.py +++ b/tests/tensor/test_elemwise.py @@ -1,4 +1,5 @@ import math +import tracemalloc from copy import copy import numpy as np @@ -141,6 +142,41 @@ class TestDimShuffle(unittest_tools.InferShapeTester): # Confirm the broadcasted value in the output assert np.array_equiv(outputs[0].storage[0], 2039) + @pytest.mark.parametrize("inplace", [True, False]) + def test_memory_leak(self, inplace): + import gc + + n = 100_000 + + x = aesara.shared(np.ones(n, dtype=np.float64)) + + y = x.dimshuffle([0, "x"]) + y.owner.op.inplace = inplace + + f = aesara.function([], y, mode=Mode(optimizer=None)) + + assert len(f.maker.fgraph.apply_nodes) == 2 + assert isinstance(f.maker.fgraph.toposort()[0].op, DimShuffle) + + assert f.maker.fgraph.toposort()[0].op.inplace is inplace + + tracemalloc.start() + + blocks_last = None + block_diffs = [] + for i in range(50): + x.set_value(np.ones(n)) + _ = f() + _ = gc.collect() + blocks_i, _ = tracemalloc.get_traced_memory() + if blocks_last is not None: + blocks_diff = (blocks_i - blocks_last) // 10 ** 3 + block_diffs.append(blocks_diff) + blocks_last = blocks_i + + tracemalloc.stop() + assert np.allclose(np.mean(block_diffs), 0) + class TestBroadcast: # this is to allow other types to reuse this class to test their ops	Memory leak in `DimShuffle` ## Description of your problem or feature request Please provide a minimal, self-contained, and reproducible example. ```python import os import psutil import aesara from aesara import tensor as at process = psutil.Process(os.getpid()) old_rss = None n = 100_000 x = at.sharedvar.TensorSharedVariable( "test", at.type.dvector, np.ones(n), strict=True ) y = x.dimshuffle([0, "x"]) f = aesara.function([], y) for i in range(100): x.set_value(np.ones(n)) f() if i % 10 == 0: new_rss = process.memory_info().rss if old_rss is not None: print(f"Python process increased RSS by {round((new_rss - old_rss) / 10242, 2)} MB") old_rss = new_rss ``` Please provide the full traceback of any errors. ```python Python process increased RSS by 6.62 MB Python process increased RSS by 7.74 MB Python process increased RSS by 7.64 MB Python process increased RSS by 7.68 MB Python process increased RSS by 7.64 MB Python process increased RSS by 7.68 MB Python process increased RSS by 7.41 MB Python process increased RSS by 7.63 MB Python process increased RSS by 7.85 MB ``` Please provide any additional information below.** This happens when the reshape operation is compiled to C. When I run the same code setting `aesara.config.cxx = ""`, the Python process does not increase RSS. ## Versions and main components * Aesara version: 2.4.0 * Aesara config (`python -c "import aesara; print(aesara.config)"`) * Python version: 3.9 * Operating system: Ubuntu 18.04 * How did you install Aesara: (conda/pip) pip	3d8553f7b56caed8686e3db9bfbe5ffea110b70a	[ "tests/tensor/test_elemwise.py::TestDimShuffle::test_memory_leak[True]", "tests/tensor/test_elemwise.py::TestDimShuffle::test_memory_leak[False]" ]	[ "tests/tensor/test_elemwise.py::TestDimShuffle::test_perform", "tests/tensor/test_elemwise.py::TestDimShuffle::test_c_or_py", "tests/tensor/test_elemwise.py::TestDimShuffle::test_infer_shape", "tests/tensor/test_elemwise.py::TestDimShuffle::test_c_views", "tests/tensor/test_elemwise.py::TestBroadcast::test_perform", "tests/tensor/test_elemwise.py::TestBroadcast::test_c", "tests/tensor/test_elemwise.py::TestBroadcast::test_perform_inplace", "tests/tensor/test_elemwise.py::TestBroadcast::test_c_inplace", "tests/tensor/test_elemwise.py::TestBroadcast::test_fill", "tests/tensor/test_elemwise.py::TestBroadcast::test_fill_var", "tests/tensor/test_elemwise.py::TestBroadcast::test_fill_grad", "tests/tensor/test_elemwise.py::TestBroadcast::test_weird_strides", "tests/tensor/test_elemwise.py::TestBroadcast::test_same_inputs", "tests/tensor/test_elemwise.py::TestCAReduce::test_perform_noopt", "tests/tensor/test_elemwise.py::TestCAReduce::test_perform_nan", "tests/tensor/test_elemwise.py::TestCAReduce::test_c_noopt", "tests/tensor/test_elemwise.py::TestCAReduce::test_infer_shape", "tests/tensor/test_elemwise.py::TestBitOpReduceGrad::test_all_grad", "tests/tensor/test_elemwise.py::TestBitOpReduceGrad::test_any_grad", "tests/tensor/test_elemwise.py::TestElemwise::test_elemwise_grad_bool", "tests/tensor/test_elemwise.py::TestElemwise::test_infer_shape", "tests/tensor/test_elemwise.py::TestElemwise::test_input_dimensions_overflow", "tests/tensor/test_elemwise.py::TestElemwise::test_input_dimensions_match_python", "tests/tensor/test_elemwise.py::test_not_implemented_elemwise_grad" ]	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2022-03-11 02:00:34+00:00	bsd-3-clause	909
aesara-devs__aesara-902	diff --git a/aesara/compile/builders.py b/aesara/compile/builders.py index b714138eb..4328e95e7 100644 --- a/aesara/compile/builders.py +++ b/aesara/compile/builders.py @@ -375,6 +375,11 @@ class OpFromGraph(Op, HasInnerGraph): self.kwargs = kwargs self.input_types = [inp.type for inp in inputs] self.output_types = [out.type for out in outputs] + + self.lop_overrides = lop_overrides + self.grad_overrides = grad_overrides + self.rop_overrides = rop_overrides + if lop_overrides != "default": if grad_overrides != "default": raise ValueError( @@ -732,19 +737,71 @@ class OpFromGraph(Op, HasInnerGraph): ] return ret_l + def __call__(self, inputs, kwargs): + # The user interface doesn't expect the shared variable inputs of the + # inner-graph, but, since `Op.make_node` does (and `Op.__call__` + # dispatches to `Op.make_node`), we need to compensate here + num_expected_inps = len(self.inner_inputs) - len(self.shared_inputs) + + if len(inputs) == num_expected_inps: + actual_inputs = inputs + tuple(self.shared_inputs) + return super().__call__(actual_inputs, *kwargs) + elif len(inputs) == len(self.inner_inputs): + return super().__call__(inputs, *kwargs) + else: + raise ValueError(f"Expected at least {num_expected_inps} input(s)") + def make_node(self, inputs): + # The `inputs` received here should correspond to the inputs in the + # `Apply` nodes we produce below + if len(inputs) != len(self.inner_inputs): + raise ValueError(f"Expected {len(self.inner_inputs)} input(s)") + num_expected_inps = len(self.inner_inputs) - len(self.shared_inputs) - if len(inputs) != num_expected_inps: - raise ValueError( - f"Expected {int(num_expected_inps)} inputs, got {len(inputs)}" - ) - inputs = [ - inp_t.filter_variable(inp) for inp, inp_t in zip(inputs, self.input_types) + non_shared_inputs = inputs[:num_expected_inps] + + non_shared_inputs = [ + inp_t.filter_variable(inp) + for inp, inp_t in zip(non_shared_inputs, self.input_types) ] + + shared_inputs = inputs[num_expected_inps:] + local_shared_inputs = self.inner_inputs[num_expected_inps:] + + inner_and_input_shareds = list(zip(local_shared_inputs, shared_inputs)) + + if not all(inp_s == inn_s for inn_s, inp_s in inner_and_input_shareds): + # The shared variables are not equal to the original shared + # variables, so we construct a new `Op` that uses the new shared + # variables instead + replace = { + old_inp: new_inp for old_inp, new_inp in zip(self.inner_inputs, inputs) + } + replace.update(inner_and_input_shareds) + + # If the new shared variables are inconsistent with the inner-graph, + # such errors should arise in this step + new_outputs = clone_replace( + self.inner_outputs, replace=replace, share_inputs=True + ) + + new_op = type(self)( + inputs=non_shared_inputs, + outputs=new_outputs, + inline=self.is_inline, + lop_overrides=self.lop_overrides, + grad_overrides=self.grad_overrides, + rop_overrides=self.rop_overrides, + connection_pattern=self._connection_pattern, + name=self.name, + ) + else: + new_op = self + apply_node = Apply( - self, - list(inputs) + self.shared_inputs, - [type() for type in self.output_types], + new_op, + list(non_shared_inputs) + new_op.shared_inputs, + [type() for type in new_op.output_types], ) return apply_node	aesara-devs/aesara	6ef1452a83681e2ccd582ba12aaa7be778e1ff15	diff --git a/tests/compile/test_builders.py b/tests/compile/test_builders.py index a552c7a09..9d894aae7 100644 --- a/tests/compile/test_builders.py +++ b/tests/compile/test_builders.py @@ -3,6 +3,7 @@ from functools import partial import numpy as np import pytest +import aesara.tensor as at from aesara.compile import shared from aesara.compile.builders import OpFromGraph from aesara.compile.function import function @@ -29,6 +30,12 @@ class TestOpFromGraph(unittest_tools.InferShapeTester): def test_valid_input(self): x, y, z = matrices("xyz") + with pytest.raises(ValueError, match="Expected at least."): + OpFromGraph([x], [x])() + + with pytest.raises(ValueError, match=r"Expected 1 input\(s\)"): + OpFromGraph([x], [x]).make_node() + with pytest.raises(TypeError): OpFromGraph((x,), (x,)) @@ -451,6 +458,39 @@ class TestOpFromGraph(unittest_tools.InferShapeTester): grad_f = grad(f, y) assert grad_f.tag.test_value is not None + def test_make_node_shared(self): + """Make sure we can provide `OpFromGraph.make_node` new shared inputs and get a valid `OpFromGraph`.""" + + x = at.scalar("x") + y = shared(1.0, name="y") + + test_ofg = OpFromGraph([x], [x + y]) + assert test_ofg.inputs == [x] + assert test_ofg.shared_inputs == [y] + + out = test_ofg(x) + + y_clone = y.clone() + assert y_clone != y + y_clone.name = "y_clone" + + out_new = test_ofg.make_node((out.owner.inputs[:1] + [y_clone])).outputs[0] + + assert out_new.owner.op.inputs == [x] + assert out_new.owner.op.shared_inputs == [y_clone] + + out_fn = function([x], out_new) + + assert np.array_equal(out_fn(1.0), 2.0) + + y_clone.set_value(2.0) + + assert np.array_equal(out_fn(1.0), 3.0) + + # This should also work, because the containers are the same: + # y.set_value(1.0) + # assert np.array_equal(out_fn(1.0), 2.0) + def test_debugprint(): x, y, z = matrices("xyz") diff --git a/tests/scan/test_opt.py b/tests/scan/test_opt.py index 06eb27372..af14b7930 100644 --- a/tests/scan/test_opt.py +++ b/tests/scan/test_opt.py @@ -4,6 +4,7 @@ import pytest import aesara import aesara.tensor.basic as at from aesara import function, scan, shared +from aesara.compile.builders import OpFromGraph from aesara.compile.io import In from aesara.compile.mode import get_default_mode from aesara.configdefaults import config @@ -550,6 +551,28 @@ class TestPushOutNonSeqScan: utt.assert_allclose(output_opt[0], output_no_opt[0]) utt.assert_allclose(output_opt[1], output_no_opt[1]) + def test_OpFromGraph_shared(self): + """Make sure that a simple `OpFromGraph` with a shared variable can be pushed out.""" + + y = shared(1.0, name="y") + + test_ofg = OpFromGraph([], [1 + y]) + + def inner_func(): + return test_ofg() + + out, out_updates = aesara.scan(inner_func, n_steps=10) + + out_fn = function([], out, updates=out_updates) + + res = out_fn() + assert np.array_equal(res, np.repeat(2.0, 10)) + + y.set_value(2.0) + + res = out_fn() + assert np.array_equal(res, np.repeat(3.0, 10)) + class TestPushOutAddScan: """	`OpFromGraph.make_node`'s expected inputs and actual inputs are inconsistent `OpFromGraph.make_node` expects inputs corresponding to each of its inner-graph inputs, except for the shared variables; however, `OpFromGraph.make_node` also constructs `Apply` nodes such that `Apply.inputs` _contains_ the shared variable inputs of the inner-graph. This leads to an inherent inconsistency that prevents rewrites from reconstructing nodes via `Op.make_node(Apply.inputs)`. Here's an example in which this issue results in an optimization failure: ```python import aesara import aesara.tensor as at from aesara.compile.builders import OpFromGraph y = aesara.shared(1.0, name="y") test_ofg = OpFromGraph([], [1 + y]) test_ofg.inputs # [] test_ofg.shared_inputs # [y] def inner_func(): return test_ofg() out, out_updates = aesara.scan(inner_func, n_steps=10) with aesara.config.change_flags(on_opt_error="raise"): out_fn = aesara.function([], out) # ERROR (aesara.graph.opt): Optimization failure due to: push_out_non_seq_scan # ERROR (aesara.graph.opt): node: for{cpu,scan_fn}(TensorConstant{10}, TensorConstant{10}, y) # ERROR (aesara.graph.opt): TRACEBACK: # ERROR (aesara.graph.opt): Traceback (most recent call last): # File ".../Aesara/aesara/graph/opt.py", line 1850, in process_node # replacements = lopt.transform(fgraph, node) # File ".../Aesara/aesara/graph/opt.py", line 1055, in transform # return self.fn(fgraph, node) # File ".../Aesara/aesara/scan/opt.py", line 282, in push_out_non_seq_scan # nw_outer_node = nd.op.make_node(outside_ins) # File ".../Aesara/aesara/compile/builders.py", line 738, in make_node # raise ValueError( # ValueError: Expected 1 inputs, got 2 ```	6ef1452a83681e2ccd582ba12aaa7be778e1ff15	[ "tests/compile/test_builders.py::TestOpFromGraph::test_valid_input", "tests/compile/test_builders.py::TestOpFromGraph::test_make_node_shared", "tests/scan/test_opt.py::TestPushOutNonSeqScan::test_OpFromGraph_shared" ]	[ "tests/compile/test_builders.py::TestOpFromGraph::test_straightforward[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_straightforward[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_size_changes[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_size_changes[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_grad[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_grad[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_grad_grad[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_grad_grad[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_shared[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_shared[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_shared_grad[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_shared_grad[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_grad_override[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_grad_override[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_lop_override[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_lop_override[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_rop[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_rop[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_rop_override[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_rop_override[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_connection_pattern_override[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_connection_pattern_override[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_nested[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_nested[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_connection_pattern[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_connection_pattern[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_infer_shape", "tests/compile/test_builders.py::TestOpFromGraph::test_compute_test_value", "tests/compile/test_builders.py::test_debugprint", "tests/scan/test_opt.py::TestPushOutDot::test_pushout_all", "tests/scan/test_opt.py::TestScanMerge::test_belongs_to_set", "tests/scan/test_opt.py::TestSaveMem::test_save_mem_reduced_number_of_steps", "tests/scan/test_opt.py::TestSaveMem::test_save_mem_store_steps", "tests/scan/test_opt.py::test_opt_order" ]	{ "failed_lite_validators": [ "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2022-04-13 21:10:22+00:00	bsd-3-clause	910
aesara-devs__aesara-928	diff --git a/aesara/scalar/basic.py b/aesara/scalar/basic.py index 0bf12a70a..36a05c387 100644 --- a/aesara/scalar/basic.py +++ b/aesara/scalar/basic.py @@ -2307,6 +2307,8 @@ class Pow(BinaryScalarOp): if ( node.inputs[0].type == node.outputs[0].type and node.inputs[1].type == node.outputs[0].type + and None not in node.inputs[0].type.shape + and None not in node.inputs[1].type.shape and # amdlibm 3.0 do not have a float64 version of this SIMD function node.inputs[0].dtype == "float32" diff --git a/aesara/tensor/elemwise.py b/aesara/tensor/elemwise.py index b678ad16b..ce7d67b5f 100644 --- a/aesara/tensor/elemwise.py +++ b/aesara/tensor/elemwise.py @@ -913,7 +913,7 @@ second dimension checks = cgen.make_checks(orders, idtypes, sub) # Check if all inputs (except broadcasted scalar) are fortran. - # In that case, create an fortran output ndarray. + # In that case, create a fortran output ndarray. z = list(zip(inames, inputs)) alloc_fortran = " && ".join( [ @@ -1071,7 +1071,7 @@ second dimension # If all inputs and outputs are contiguous # and the scalar op define optimized code for that case - # use it! The scalar_op need to check the broadcast flag himself. + # use it! The scalar_op needs to check the type-level shapes itself. if ( all(o.ndim >= 1 for o in node.outputs) and @@ -1088,11 +1088,19 @@ second dimension # compiler to vectorize the code as their won't be as # many ptr and the stride will be hard coded. if all( - [ - io.broadcastable == node.outputs[0].broadcastable - or all(io.broadcastable) - for io in node.inputs + node.outputs - ] + # io.type.shape == node.outputs[1].type.shape + # Elemwise does not specify non-broadcastable static/type-levelshape + # information for its outputs yet + node.outputs[0].type.is_super(io.type) + for io in node.inputs + node.outputs + ) and ( + len(node.inputs) <= 1 + # If either one of the inputs has a `None` shape, we cannot + # assume they will have the same size + or all( + len(set(inp_shape)) == 1 and None not in inp_shape + for inp_shape in zip((inp.type.shape for inp in node.inputs)) + ) ): z = onames[0] contig = f""" @@ -1188,7 +1196,7 @@ second dimension return support_code def c_code_cache_version_apply(self, node): - version = [13] # the version corresponding to the c code in this Op + version = [14] # the version corresponding to the c code in this Op # now we insert versions for the ops on which we depend... scalar_node = Apply( diff --git a/aesara/tensor/elemwise_cgen.py b/aesara/tensor/elemwise_cgen.py index cfc5abde8..9e50369fb 100644 --- a/aesara/tensor/elemwise_cgen.py +++ b/aesara/tensor/elemwise_cgen.py @@ -66,10 +66,12 @@ def make_checks(loop_orders, dtypes, sub): if index != "x": # Initialize the variables associated to the jth loop # jump = stride - adjust + # If the variable has size 1 in that dim, we set the stride to zero to + # emulate broadcasting jump = f"({var}_stride{index}) - ({adjust})" init += f""" {var}_n{index} = PyArray_DIMS({var})[{index}]; - {var}_stride{index} = PyArray_STRIDES({var})[{index}] / sizeof({dtype}); + {var}_stride{index} = ({var}_n{index} == 1)? 0 : PyArray_STRIDES({var})[{index}] / sizeof({dtype}); {var}_jump{index}_{j} = {jump}; """ adjust = f"{var}_n{index}{var}_stride{index}" @@ -90,26 +92,85 @@ def make_checks(loop_orders, dtypes, sub): # elements of to_compare are pairs ( input_variable_idx, input_variable_dim_idx ) if len(to_compare) < 2: continue - j0, x0 = to_compare[0] - for (j, x) in to_compare[1:]: - check += f""" - if (%(lv{j0})s_n{x0} != %(lv{j})s_n{x}) + + # Find first dimension size that is != 1 + jl, xl = to_compare[-1] + non1size_dim_check = f""" + npy_intp non1size_dim{xl}; + non1size_dim{xl} = """ + for (j, x) in to_compare[:-1]: + non1size_dim_check += f"(%(lv{j})s_n{x} != 1) ? %(lv{j})s_n{x} : " + non1size_dim_check += f"%(lv{jl})s_n{xl};" + check += non1size_dim_check + + # Check the nonsize1 dims match + # TODO: This is a bit inefficient because we are comparing one dimension against itself + check += f""" + if (non1size_dim{xl} != 1) {{ - PyErr_Format(PyExc_ValueError, "Input dimension mismatch. (input[%%i].shape[%%i] = %%lld, input[%%i].shape[%%i] = %%lld)", - {j0}, - {x0}, - (long long int) %(lv{j0})s_n{x0}, - {j}, - {x}, - (long long int) %(lv{j})s_n{x} - ); - %(fail)s - }} + """ + for (j, x) in to_compare: + check += f""" + if ((%(lv{j})s_n{x} != non1size_dim{x}) && (%(lv{j})s_n{x} != 1)) + {{ + PyErr_Format(PyExc_ValueError, "Input dimension mismatch. One other input has shape[%%i] = %%lld, but input[%%i].shape[%%i] = %%lld.", + {x}, + (long long int) non1size_dim{x}, + {j}, + {x}, + (long long int) %(lv{j})s_n{x} + ); + %(fail)s + }} """ + check += """ + } + """ return init % sub + check % sub +def compute_broadcast_dimensions(array_name: str, loop_orders, sub) -> str: + """Create c_code to compute broadcasted dimensions of multiple arrays, arising from + Elemwise operations. + + The code returned by this function populates the array `array_name`, but does not + initialize it. + + TODO: We can decide to either specialize C code even further given the input types + or make it general, regardless of whether static broadcastable information is given + """ + dims_c_code = "" + for i, candidates in enumerate(zip(loop_orders)): + # TODO: Are candidates always either "x" or "i"? If that's the case we can + # simplify some logic here (e.g., we don't need to track the `idx`). + nonx_candidates = tuple( + (idx, c) for idx, c in enumerate(candidates) if c != "x" + ) + + # All inputs are known to be broadcastable + if not nonx_candidates: + dims_c_code += f"{array_name}[{i}] = 1;\n" + continue + + # There is only one informative source of size + if len(nonx_candidates) == 1: + idx, candidate = nonx_candidates[0] + var = sub[f"lv{int(idx)}"] + dims_c_code += f"{array_name}[{i}] = {var}_n{candidate};\n" + continue + + # In this case any non-size 1 variable will define the right size + dims_c_code += f"{array_name}[{i}] = " + for (idx, candidate) in nonx_candidates[:-1]: + var = sub[f"lv{int(idx)}"] + dims_c_code += f"({var}_n{candidate} != 1)? {var}_n{candidate}: " + idx, candidate = nonx_candidates[-1] + var = sub[f"lv{idx}"] + dims_c_code += f"{var}_n{candidate};\n" + return dims_c_code + + def make_alloc(loop_orders, dtype, sub, fortran="0"): """Generate C code to allocate outputs. @@ -125,20 +186,7 @@ def make_alloc(loop_orders, dtype, sub, fortran="0"): if type.startswith("AESARA_COMPLEX"): type = type.replace("AESARA_COMPLEX", "NPY_COMPLEX") nd = len(loop_orders[0]) - init_dims = "" - # For each dimension, the tensors are either all broadcasted, in - # which case the output will also be broadcastable (dimension = - # 1), or one or more are not broadcasted, in which case the number - # of elements of the output in that dimension will be equal to the - # number of elements of any of them. - for i, candidates in enumerate(zip(loop_orders)): - for j, candidate in enumerate(candidates): - if candidate != "x": - var = sub[f"lv{int(j)}"] - init_dims += f"dims[{i}] = {var}_n{candidate};\n" - break - else: - init_dims += f"dims[{i}] = 1;\n" + init_dims = compute_broadcast_dimensions("dims", loop_orders, sub) # TODO: it would be interesting to allocate the output in such a # way that its contiguous dimensions match one of the input's @@ -310,26 +358,8 @@ def make_reordered_loop( """ # Get the (sorted) total number of iterations of each loop - # Get totals in the initial order - # For each dimension, the tensors are either all broadcasted, in - # which case there is only one iteration of the loop, or one or - # more are not broadcasted, in which case the number of elements - # of any of them will be equal to the number of iterations we have - # to do. - totals = [] - for i, candidates in enumerate(zip(*init_loop_orders)): - for j, candidate in enumerate(candidates): - if candidate != "x": - var = sub[f"lv{int(j)}"] - total = f"{var}_n{candidate}" - break - else: - total = "1" - totals.append(total) - - declare_totals = f""" - int init_totals[{nnested}] = {{{", ".join(totals)}}}; - """ + declare_totals = f"int init_totals[{nnested}];\n" + declare_totals += compute_broadcast_dimensions("init_totals", init_loop_orders, sub) # Sort totals to match the new order that was computed by sorting # the loop vector. One integer variable per loop is declared.	aesara-devs/aesara	b60cf7240a6d17ed80db2bd9b43c6faf377d64fe	diff --git a/tests/tensor/test_elemwise.py b/tests/tensor/test_elemwise.py index c2b2d230b..1b298a92a 100644 --- a/tests/tensor/test_elemwise.py +++ b/tests/tensor/test_elemwise.py @@ -206,77 +206,117 @@ class TestBroadcast: return np.asarray(np.random.random(shp), dtype=aesara.config.floatX) def with_linker(self, linker, op, type, rand_val): - for xsh, ysh in [ - ((3, 5), (3, 5)), - ((3, 5), (1, 5)), - ((3, 5), (3, 1)), - ((1, 5), (5, 1)), - ((1, 1), (1, 1)), - ((self.openmp_minsize,), (self.openmp_minsize,)), - ( - (self.openmp_minsize_sqrt, self.openmp_minsize_sqrt), - (self.openmp_minsize_sqrt, self.openmp_minsize_sqrt), - ), - ((2, 3, 4, 5), (2, 3, 4, 5)), - ((2, 3, 4, 5), (1, 3, 1, 5)), - ((2, 3, 4, 5), (1, 1, 1, 1)), - ((), ()), - ]: - x = type(aesara.config.floatX, [(entry == 1) for entry in xsh])("x") - y = type(aesara.config.floatX, [(entry == 1) for entry in ysh])("y") - e = op(aes.add)(x, y) - f = make_function(copy(linker).accept(FunctionGraph([x, y], [e]))) - xv = rand_val(xsh) - yv = rand_val(ysh) - zv = xv + yv - - unittest_tools.assert_allclose(f(xv, yv), zv) + for shape_info in ("complete", "only_broadcastable", "none"): + for xsh, ysh in [ + ((3, 5), (3, 5)), + ((3, 5), (1, 5)), + ((3, 5), (3, 1)), + ((1, 5), (5, 1)), + ((1, 1), (1, 1)), + ((self.openmp_minsize,), (self.openmp_minsize,)), + ( + (self.openmp_minsize_sqrt, self.openmp_minsize_sqrt), + (self.openmp_minsize_sqrt, self.openmp_minsize_sqrt), + ), + ((2, 3, 4, 5), (2, 3, 4, 5)), + ((2, 3, 4, 5), (1, 3, 1, 5)), + ((2, 3, 4, 5), (1, 1, 1, 1)), + ((), ()), + ]: + if shape_info == "complete": + x_type = type(aesara.config.floatX, shape=xsh) + y_type = type(aesara.config.floatX, shape=ysh) + elif shape_info == "only_broadcastable": + # This condition is here for backwards compatibility, when the only + # type shape provided by Aesara was broadcastable/non-broadcastable + x_type = type( + aesara.config.floatX, + broadcastable=[(entry == 1) for entry in xsh], + ) + y_type = type( + aesara.config.floatX, + broadcastable=[(entry == 1) for entry in ysh], + ) + else: + x_type = type(aesara.config.floatX, shape=[None for _ in xsh]) + y_type = type(aesara.config.floatX, shape=[None for _ in ysh]) - # test Elemwise.infer_shape - # the Shape op don't implement c_code! - if isinstance(linker, PerformLinker): - x = type(aesara.config.floatX, [(entry == 1) for entry in xsh])("x") - y = type(aesara.config.floatX, [(entry == 1) for entry in ysh])("y") + x = x_type("x") + y = y_type("y") e = op(aes.add)(x, y) - f = make_function(copy(linker).accept(FunctionGraph([x, y], [e.shape]))) - assert tuple(f(xv, yv)) == tuple(zv.shape) + f = make_function(copy(linker).accept(FunctionGraph([x, y], [e]))) + xv = rand_val(xsh) + yv = rand_val(ysh) + zv = xv + yv - def with_linker_inplace(self, linker, op, type, rand_val): - for xsh, ysh in [ - ((5, 5), (5, 5)), - ((5, 5), (1, 5)), - ((5, 5), (5, 1)), - ((1, 1), (1, 1)), - ((2, 3, 4, 5), (2, 3, 4, 5)), - ((2, 3, 4, 5), (1, 3, 1, 5)), - ((2, 3, 4, 5), (1, 1, 1, 1)), - ((), ()), - ]: - x = type(aesara.config.floatX, [(entry == 1) for entry in xsh])("x") - y = type(aesara.config.floatX, [(entry == 1) for entry in ysh])("y") - e = op(aes.Add(aes.transfer_type(0)), {0: 0})(x, y) - f = make_function(copy(linker).accept(FunctionGraph([x, y], [e]))) - xv = rand_val(xsh) - yv = rand_val(ysh) - zv = xv + yv + unittest_tools.assert_allclose(f(xv, yv), zv) - f(xv, yv) + # test Elemwise.infer_shape + # the Shape op don't implement c_code! + if isinstance(linker, PerformLinker): + x = x_type("x") + y = y_type("y") + e = op(aes.add)(x, y) + f = make_function( + copy(linker).accept(FunctionGraph([x, y], [e.shape])) + ) + assert tuple(f(xv, yv)) == tuple(zv.shape) - assert (xv == zv).all() - # test Elemwise.infer_shape - # the Shape op don't implement c_code! - if isinstance(linker, PerformLinker): - x = type(aesara.config.floatX, [(entry == 1) for entry in xsh])("x") - y = type(aesara.config.floatX, [(entry == 1) for entry in ysh])("y") + def with_linker_inplace(self, linker, op, type, rand_val): + for shape_info in ("complete", "only_broadcastable", "none"): + for xsh, ysh in [ + ((5, 5), (5, 5)), + ((5, 5), (1, 5)), + ((5, 5), (5, 1)), + ((1, 1), (1, 1)), + ((2, 3, 4, 5), (2, 3, 4, 5)), + ((2, 3, 4, 5), (1, 3, 1, 5)), + ((2, 3, 4, 5), (1, 1, 1, 1)), + ((), ()), + ]: + if shape_info == "complete": + x_type = type(aesara.config.floatX, shape=xsh) + y_type = type(aesara.config.floatX, shape=ysh) + elif shape_info == "only_broadcastable": + # This condition is here for backwards compatibility, when the only + # type shape provided by Aesara was broadcastable/non-broadcastable + x_type = type( + aesara.config.floatX, + broadcastable=[(entry == 1) for entry in xsh], + ) + y_type = type( + aesara.config.floatX, + broadcastable=[(entry == 1) for entry in ysh], + ) + else: + x_type = type(aesara.config.floatX, shape=[None for _ in xsh]) + y_type = type(aesara.config.floatX, shape=[None for _ in ysh]) + + x = x_type("x") + y = y_type("y") e = op(aes.Add(aes.transfer_type(0)), {0: 0})(x, y) - f = make_function(copy(linker).accept(FunctionGraph([x, y], [e.shape]))) + f = make_function(copy(linker).accept(FunctionGraph([x, y], [e]))) xv = rand_val(xsh) yv = rand_val(ysh) zv = xv + yv f(xv, yv) - assert xv.shape == zv.shape + assert (xv == zv).all() + # test Elemwise.infer_shape + # the Shape op don't implement c_code! + if isinstance(linker, PerformLinker): + x = x_type("x") + y = y_type("y") + e = op(aes.Add(aes.transfer_type(0)), {0: 0})(x, y) + f = make_function( + copy(linker).accept(FunctionGraph([x, y], [e.shape])) + ) + xv = rand_val(xsh) + yv = rand_val(ysh) + zv = xv + yv + assert xv.shape == zv.shape + assert tuple(f(xv, yv)) == zv.shape def test_perform(self): self.with_linker(PerformLinker(), self.op, self.type, self.rand_val) @@ -746,10 +786,6 @@ class TestElemwise(unittest_tools.InferShapeTester): def test_input_dimensions_match_python(self): self.check_input_dimensions_match(Mode(linker="py")) - @pytest.mark.xfail( - reason="Elemwise C implementation does not broadcast parameters", - exception=ValueError, - ) @pytest.mark.skipif( not aesara.config.cxx, reason="G++ not available, so we need to skip this test." )	C Elemwise implementation doesn't broadcast variables I'm seeing a very weird error in `Elemwise`: First, here's a basic broadcasting operations in NumPy: ```python import numpy as np x = np.array([[-1.32720483], [ 0.23442016]]) m = np.array([0., 0.]) z = x - m ``` ```python >>> z array([[-1.32720483, -1.32720483], [ 0.23442016, 0.23442016]]) ``` In Aesara, here's the equivalent operation using `TensorConstant`s: ```python import aesara import aesara.tensor as at x_at = at.as_tensor(x) m_at = at.as_tensor(m) z_at = x_at - m_at ``` ```python >>> aesara.dprint(z_at) Elemwise{sub,no_inplace} [id A] '' \|TensorConstant{[[-1.32720..23442016]]} [id B] \|InplaceDimShuffle{x,0} [id C] '' \|TensorConstant{(2,) of 0.0} [id D] ``` The resulting graph is a simple `Elemwise` for the subtraction `Op`–as expected. There's also an `InplaceDimShuffle` that adds a broadcastable dimension to the second argument, so that both inputs have the same number of dimensions. This `InplaceDimShuffle` is equivalent to `np.expand_dims(m, 0)`, which–when subtracted from `x`–yields the same value as `z`. So far, everything is good, because ```python >>> np.array_equal(aesara.function([], z_at)(), z) True ``` Now, when we replace the `TensorConstant`s with generic `TensorVariable`s, we get a strange error: ```python x_v = at.matrix("x") m_v = at.vector("m") z_v = x_v - m_v ``` ```python >>> aesara.function([x_v, m_v], z_v)(x, m) <ipython-input-23-66cc28afa70f> in <module> ----> 1 aesara.function([x_v, m_v], z_v)(x, m) ~/projects/code/python/Aesara/aesara/compile/function/types.py in __call__(self, args, kwargs) 989 node=self.fn.nodes[self.fn.position_of_error], 990 thunk=thunk, --> 991 storage_map=getattr(self.fn, "storage_map", None), 992 ) 993 else: ~/projects/code/python/Aesara/aesara/link/utils.py in raise_with_op(fgraph, node, thunk, exc_info, storage_map) 506 # Some exception need extra parameter in inputs. So forget the 507 # extra long error message in that case. --> 508 raise exc_value.with_traceback(exc_trace) 509 510 ~/projects/code/python/Aesara/aesara/compile/function/types.py in __call__(self, args, *kwargs) 973 outputs = ( 974 self.fn() --> 975 if output_subset is None 976 else self.fn(output_subset=output_subset) 977 ) ValueError: Input dimension mis-match. (input[0].shape[1] = 1, input[1].shape[1] = 2) Apply node that caused the error: Elemwise{sub,no_inplace}(x, InplaceDimShuffle{x,0}.0) Toposort index: 1 Inputs types: [TensorType(float64, matrix), TensorType(float64, row)] Inputs shapes: [(2, 1), (1, 2)] Inputs strides: [(8, 8), (16, 8)] Inputs values: [array([[-1.32720483], [ 0.23442016]]), array([[0., 0.]])] Outputs clients: [['output']] ``` We can emulate this issue using the Python implementation of `Elemwise`, as well: ```python >>> aesara.function([x_v, m_v], z_v, mode="FAST_COMPILE")(x, m) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) ~/projects/code/python/Aesara/aesara/link/vm.py in __call__(self) 312 ): --> 313 thunk() 314 for old_s in old_storage: ~/projects/code/python/Aesara/aesara/graph/op.py in rval(p, i, o, n) 472 def rval(p=p, i=node_input_storage, o=node_output_storage, n=node): --> 473 r = p(n, [x[0] for x in i], o) 474 for o in node.outputs: ~/projects/code/python/Aesara/aesara/tensor/elemwise.py in perform(self, node, inputs, output_storage) 760 base_exc_str = f"Dimension mismatch; shapes are {', '.join(msg)}" --> 761 raise ValueError(base_exc_str) 762 ValueError: Dimension mismatch; shapes are (2, 1), (, 2) ``` From this output, we can see that this erroneous error is apparently the result of some bad input validation code in `Elemwise`. The same is true for the C implementation, although that's a little less apparent from the output. In this case, the C code for this validation step is [here](https://github.com/pymc-devs/aesara/blob/master/aesara/tensor/elemwise_cgen.py#L98).	b60cf7240a6d17ed80db2bd9b43c6faf377d64fe	[ "tests/tensor/test_elemwise.py::TestBroadcast::test_c", "tests/tensor/test_elemwise.py::TestBroadcast::test_c_inplace", "tests/tensor/test_elemwise.py::TestElemwise::test_input_dimensions_match_c" ]	[ "tests/tensor/test_elemwise.py::TestDimShuffle::test_perform", "tests/tensor/test_elemwise.py::TestDimShuffle::test_c_or_py", "tests/tensor/test_elemwise.py::TestDimShuffle::test_infer_shape", "tests/tensor/test_elemwise.py::TestDimShuffle::test_c_views", "tests/tensor/test_elemwise.py::TestDimShuffle::test_memory_leak[True]", "tests/tensor/test_elemwise.py::TestDimShuffle::test_memory_leak[False]", "tests/tensor/test_elemwise.py::TestDimShuffle::test_static_shape", "tests/tensor/test_elemwise.py::TestBroadcast::test_perform", "tests/tensor/test_elemwise.py::TestBroadcast::test_perform_inplace", "tests/tensor/test_elemwise.py::TestBroadcast::test_fill", "tests/tensor/test_elemwise.py::TestBroadcast::test_fill_var", "tests/tensor/test_elemwise.py::TestBroadcast::test_fill_grad", "tests/tensor/test_elemwise.py::TestBroadcast::test_weird_strides", "tests/tensor/test_elemwise.py::TestBroadcast::test_same_inputs", "tests/tensor/test_elemwise.py::TestCAReduce::test_perform_noopt", "tests/tensor/test_elemwise.py::TestCAReduce::test_perform_nan", "tests/tensor/test_elemwise.py::TestCAReduce::test_c_noopt", "tests/tensor/test_elemwise.py::TestCAReduce::test_infer_shape", "tests/tensor/test_elemwise.py::TestCAReduce::test_str", "tests/tensor/test_elemwise.py::TestBitOpReduceGrad::test_all_grad", "tests/tensor/test_elemwise.py::TestBitOpReduceGrad::test_any_grad", "tests/tensor/test_elemwise.py::TestElemwise::test_elemwise_grad_bool", "tests/tensor/test_elemwise.py::TestElemwise::test_infer_shape", "tests/tensor/test_elemwise.py::TestElemwise::test_input_dimensions_overflow", "tests/tensor/test_elemwise.py::TestElemwise::test_input_dimensions_match_python", "tests/tensor/test_elemwise.py::TestElemwise::test_str", "tests/tensor/test_elemwise.py::test_not_implemented_elemwise_grad" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-04-25 12:50:52+00:00	bsd-3-clause	911
aesara-devs__aesara-968	diff --git a/aesara/compile/function/types.py b/aesara/compile/function/types.py index 8aa1e3ee8..d1f9eae2f 100644 --- a/aesara/compile/function/types.py +++ b/aesara/compile/function/types.py @@ -785,6 +785,8 @@ class Function: f_cpy.finder[swap[in_ori.variable]] = container in_cpy.variable = swap[in_ori.variable] + f_cpy.trust_input = self.trust_input + f_cpy.unpack_single = self.unpack_single f_cpy.name = name f_cpy.maker.fgraph.name = name return f_cpy	aesara-devs/aesara	104dc0379c3585a0bc8ebb87f61f2ae38d101b83	diff --git a/tests/compile/function/test_types.py b/tests/compile/function/test_types.py index 61322a2e7..ea8b81986 100644 --- a/tests/compile/function/test_types.py +++ b/tests/compile/function/test_types.py @@ -299,7 +299,7 @@ class TestFunction: t() def test_copy(self): - a = scalar() # the a is for 'anonymous' (un-named). + a = scalar() x, s = scalars("xs") f = function( @@ -312,26 +312,34 @@ class TestFunction: ) g = copy.copy(f) - # if they both return, assume that they return equivalent things. + + assert f.unpack_single == g.unpack_single + assert f.trust_input == g.trust_input assert g.container[x].storage is not f.container[x].storage assert g.container[a].storage is not f.container[a].storage assert g.container[s].storage is not f.container[s].storage - assert g.value[a] is f.value[a] # should not have been copied - assert ( - g.value[s] is not f.value[s] - ) # should have been copied because it is mutable. - assert not (g.value[s] != f.value[s]).any() # its contents should be identical + # Should not have been copied + assert g.value[a] is f.value[a] - assert f(2, 1) == g( - 2 - ) # they should be in sync, default value should be copied. - assert f(2, 1) == g( - 2 - ) # they should be in sync, default value should be copied. - f(1, 2) # put them out of sync - assert f(1, 2) != g(1, 2) # they should not be equal anymore. + # Should have been copied because it is mutable + assert g.value[s] is not f.value[s] + + # Their contents should be equal, though + assert np.array_equal(g.value[s], f.value[s]) + + # They should be in sync, default value should be copied + assert np.array_equal(f(2, 1), g(2)) + + # They should be in sync, default value should be copied + assert np.array_equal(f(2, 1), g(2)) + + # Put them out of sync + f(1, 2) + + # They should not be equal anymore + assert not np.array_equal(f(1, 2), g(1, 2)) def test_copy_share_memory(self): x = fscalar("x") @@ -478,9 +486,9 @@ class TestFunction: ori = function([x], out, mode=mode, updates={z: z * 2}) cpy = ori.copy(delete_updates=True) - assert cpy(1)[0] == 4 - assert cpy(1)[0] == 4 - assert cpy(1)[0] == 4 + assert cpy(1) == 4 + assert cpy(1) == 4 + assert cpy(1) == 4 # Test if unused implicit and explicit inputs from delete_updates # are ignored as intended.	Copied function does not respect original single output format ```python import aesara import aesara.tensor as at f1 = aesara.function([], at.constant(1.0)) f2 = f1.copy() print(f1(), f2()) # 1.0 [array(1., dtype=float32)] ```	104dc0379c3585a0bc8ebb87f61f2ae38d101b83	[ "tests/compile/function/test_types.py::TestFunction::test_copy", "tests/compile/function/test_types.py::TestFunction::test_copy_delete_updates" ]	[ "tests/compile/function/test_types.py::TestFunction::test_empty", "tests/compile/function/test_types.py::TestFunction::test_extra_inputs", "tests/compile/function/test_types.py::TestFunction::test_missing_inputs", "tests/compile/function/test_types.py::TestFunction::test_input_anon_singleton", "tests/compile/function/test_types.py::TestFunction::test_input_anon_unpack", "tests/compile/function/test_types.py::TestFunction::test_naming_rule0", "tests/compile/function/test_types.py::TestFunction::test_naming_rule1", "tests/compile/function/test_types.py::TestFunction::test_naming_rule2", "tests/compile/function/test_types.py::TestFunction::test_naming_rule3", "tests/compile/function/test_types.py::TestFunction::test_naming_rule4", "tests/compile/function/test_types.py::TestFunction::test_state_access[mode0]", "tests/compile/function/test_types.py::TestFunction::test_state_access[mode2]", "tests/compile/function/test_types.py::TestFunction::test_state_access[mode3]", "tests/compile/function/test_types.py::TestFunction::test_same_names", "tests/compile/function/test_types.py::TestFunction::test_weird_names", "tests/compile/function/test_types.py::TestFunction::test_copy_share_memory", "tests/compile/function/test_types.py::TestFunction::test_swap_SharedVariable", "tests/compile/function/test_types.py::TestFunction::test_swap_SharedVariable_with_given", "tests/compile/function/test_types.py::TestFunction::test_shared_state0", "tests/compile/function/test_types.py::TestFunction::test_shared_state1", "tests/compile/function/test_types.py::TestFunction::test_shared_state2", "tests/compile/function/test_types.py::TestFunction::test_shared_state_not_implicit", "tests/compile/function/test_types.py::TestFunction::test_constant_output", "tests/compile/function/test_types.py::TestFunction::test_borrow_input", "tests/compile/function/test_types.py::TestFunction::test_borrow_output", "tests/compile/function/test_types.py::TestFunction::test_disconnected_input", "tests/compile/function/test_types.py::TestFunction::test_masked_input", "tests/compile/function/test_types.py::TestFunction::test_givens_input_var", "tests/compile/function/test_types.py::TestFunction::test_free", "tests/compile/function/test_types.py::TestFunction::test_default_values", "tests/compile/function/test_types.py::TestFunction::test_check_for_aliased_inputs", "tests/compile/function/test_types.py::TestPicklefunction::test_deepcopy", "tests/compile/function/test_types.py::TestPicklefunction::test_deepcopy_trust_input", "tests/compile/function/test_types.py::TestPicklefunction::test_output_keys", "tests/compile/function/test_types.py::TestPicklefunction::test_deepcopy_shared_container", "tests/compile/function/test_types.py::TestPicklefunction::test_pickle", "tests/compile/function/test_types.py::TestPicklefunction::test_multiple_functions", "tests/compile/function/test_types.py::TestPicklefunction::test_pickle_class_with_functions", "tests/compile/function/test_types.py::test_empty_givens_updates" ]	{ "failed_lite_validators": [ "has_short_problem_statement" ], "has_test_patch": true, "is_lite": false }	2022-05-20 03:14:15+00:00	bsd-3-clause	912
aesara-devs__aesara-995	diff --git a/aesara/graph/type.py b/aesara/graph/type.py index f26d72664..f35a6d969 100644 --- a/aesara/graph/type.py +++ b/aesara/graph/type.py @@ -180,10 +180,10 @@ class Type(MetaObject): return None - def is_valid_value(self, data: D) -> bool: + def is_valid_value(self, data: D, strict: bool = True) -> bool: """Return ``True`` for any python object that would be a legal value for a `Variable` of this `Type`.""" try: - self.filter(data, strict=True) + self.filter(data, strict=strict) return True except (TypeError, ValueError): return False diff --git a/aesara/tensor/random/type.py b/aesara/tensor/random/type.py index ff00669c4..68373b08c 100644 --- a/aesara/tensor/random/type.py +++ b/aesara/tensor/random/type.py @@ -1,9 +1,14 @@ +from typing import Generic, TypeVar + import numpy as np import aesara from aesara.graph.type import Type +T = TypeVar("T", np.random.RandomState, np.random.Generator) + + gen_states_keys = { "MT19937": (["state"], ["key", "pos"]), "PCG64": (["state", "has_uint32", "uinteger"], ["state", "inc"]), @@ -18,22 +23,15 @@ gen_states_keys = { numpy_bit_gens = {0: "MT19937", 1: "PCG64", 2: "Philox", 3: "SFC64"} -class RandomType(Type): +class RandomType(Type, Generic[T]): r"""A Type wrapper for `numpy.random.Generator` and `numpy.random.RandomState`.""" - @classmethod - def filter(cls, data, strict=False, allow_downcast=None): - if cls.is_valid_value(data, strict): - return data - else: - raise TypeError() - @staticmethod - def may_share_memory(a, b): + def may_share_memory(a: T, b: T): return a._bit_generator is b._bit_generator -class RandomStateType(RandomType): +class RandomStateType(RandomType[np.random.RandomState]): r"""A Type wrapper for `numpy.random.RandomState`. The reason this exists (and `Generic` doesn't suffice) is that @@ -49,28 +47,38 @@ class RandomStateType(RandomType): def __repr__(self): return "RandomStateType" - @staticmethod - def is_valid_value(a, strict): - if isinstance(a, np.random.RandomState): - return True + def filter(self, data, strict: bool = False, allow_downcast=None): + """ + XXX: This doesn't convert `data` to the same type of underlying RNG type + as `self`. It really only checks that `data` is of the appropriate type + to be a valid `RandomStateType`. + + In other words, it serves as a `Type.is_valid_value` implementation, + but, because the default `Type.is_valid_value` depends on + `Type.filter`, we need to have it here to avoid surprising circular + dependencies in sub-classes. + """ + if isinstance(data, np.random.RandomState): + return data - if not strict and isinstance(a, dict): + if not strict and isinstance(data, dict): gen_keys = ["bit_generator", "gauss", "has_gauss", "state"] state_keys = ["key", "pos"] for key in gen_keys: - if key not in a: - return False + if key not in data: + raise TypeError() for key in state_keys: - if key not in a["state"]: - return False + if key not in data["state"]: + raise TypeError() - state_key = a["state"]["key"] + state_key = data["state"]["key"] if state_key.shape == (624,) and state_key.dtype == np.uint32: - return True + # TODO: Add an option to convert to a `RandomState` instance? + return data - return False + raise TypeError() @staticmethod def values_eq(a, b): @@ -114,7 +122,7 @@ aesara.compile.register_view_op_c_code( random_state_type = RandomStateType() -class RandomGeneratorType(RandomType): +class RandomGeneratorType(RandomType[np.random.Generator]): r"""A Type wrapper for `numpy.random.Generator`. The reason this exists (and `Generic` doesn't suffice) is that @@ -130,16 +138,25 @@ class RandomGeneratorType(RandomType): def __repr__(self): return "RandomGeneratorType" - @staticmethod - def is_valid_value(a, strict): - if isinstance(a, np.random.Generator): - return True + def filter(self, data, strict=False, allow_downcast=None): + """ + XXX: This doesn't convert `data` to the same type of underlying RNG type + as `self`. It really only checks that `data` is of the appropriate type + to be a valid `RandomGeneratorType`. + + In other words, it serves as a `Type.is_valid_value` implementation, + but, because the default `Type.is_valid_value` depends on + `Type.filter`, we need to have it here to avoid surprising circular + dependencies in sub-classes. + """ + if isinstance(data, np.random.Generator): + return data - if not strict and isinstance(a, dict): - if "bit_generator" not in a: - return False + if not strict and isinstance(data, dict): + if "bit_generator" not in data: + raise TypeError() else: - bit_gen_key = a["bit_generator"] + bit_gen_key = data["bit_generator"] if hasattr(bit_gen_key, "_value"): bit_gen_key = int(bit_gen_key._value) @@ -148,16 +165,16 @@ class RandomGeneratorType(RandomType): gen_keys, state_keys = gen_states_keys[bit_gen_key] for key in gen_keys: - if key not in a: - return False + if key not in data: + raise TypeError() for key in state_keys: - if key not in a["state"]: - return False + if key not in data["state"]: + raise TypeError() - return True + return data - return False + raise TypeError() @staticmethod def values_eq(a, b):	aesara-devs/aesara	174117f9b0a2c1ddb13e6244bbb31d6c75c12245	diff --git a/tests/tensor/random/test_type.py b/tests/tensor/random/test_type.py index 5f45af2fe..a34d4cbad 100644 --- a/tests/tensor/random/test_type.py +++ b/tests/tensor/random/test_type.py @@ -56,15 +56,17 @@ class TestRandomStateType: with pytest.raises(TypeError): rng_type.filter(1) - rng = rng.get_state(legacy=False) - assert rng_type.is_valid_value(rng, strict=False) + rng_dict = rng.get_state(legacy=False) - rng["state"] = {} + assert rng_type.is_valid_value(rng_dict) is False + assert rng_type.is_valid_value(rng_dict, strict=False) - assert rng_type.is_valid_value(rng, strict=False) is False + rng_dict["state"] = {} - rng = {} - assert rng_type.is_valid_value(rng, strict=False) is False + assert rng_type.is_valid_value(rng_dict, strict=False) is False + + rng_dict = {} + assert rng_type.is_valid_value(rng_dict, strict=False) is False def test_values_eq(self): @@ -147,15 +149,17 @@ class TestRandomGeneratorType: with pytest.raises(TypeError): rng_type.filter(1) - rng = rng.__getstate__() - assert rng_type.is_valid_value(rng, strict=False) + rng_dict = rng.__getstate__() + + assert rng_type.is_valid_value(rng_dict) is False + assert rng_type.is_valid_value(rng_dict, strict=False) - rng["state"] = {} + rng_dict["state"] = {} - assert rng_type.is_valid_value(rng, strict=False) is False + assert rng_type.is_valid_value(rng_dict, strict=False) is False - rng = {} - assert rng_type.is_valid_value(rng, strict=False) is False + rng_dict = {} + assert rng_type.is_valid_value(rng_dict, strict=False) is False def test_values_eq(self):	Error w/ deepcopy of pymc v4 model ## Generating a deep copy of pymc v4 model results in aesara error Please provide a minimal, self-contained, and reproducible example. ```python from copy import deepcopy import numpy as np import pymc as pm RANDOM_SEED = 8927 rng = np.random.default_rng(RANDOM_SEED) # True parameter values alpha, sigma = 1, 1 beta = [1, 2.5] # Size of dataset size = 100 # Predictor variable X1 = np.random.randn(size) X2 = np.random.randn(size) * 0.2 # Simulate outcome variable Y = alpha + beta[0] * X1 + beta[1] * X2 + rng.normal(size=size) * sigma basic_model = pm.Model() with basic_model: # Priors for unknown model parameters alpha = pm.Normal("alpha", mu=0, sigma=10) beta = pm.Normal("beta", mu=0, sigma=10, shape=2) sigma = pm.HalfNormal("sigma", sigma=1) # Expected value of outcome mu = alpha + beta[0] * X1 + beta[1] * X2 # Likelihood (sampling distribution) of observations Y_obs = pm.Normal("Y_obs", mu=mu, sigma=sigma, observed=Y) model_copy = deepcopy(basic_model) ``` Please provide the full traceback of any errors. ```python --------------------------------------------------------------------------- TypeError Traceback (most recent call last) Input In [9], in <cell line: 41>() 38 # Likelihood (sampling distribution) of observations 39 Y_obs = pm.Normal("Y_obs", mu=mu, sigma=sigma, observed=Y) ---> 41 model_copy = deepcopy(basic_model) File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:172, in deepcopy(x, memo, _nil) 170 y = x 171 else: --> 172 y = _reconstruct(x, memo, rv) 174 # If is its own copy, don't memoize. 175 if y is not x: File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:270, in _reconstruct(x, memo, func, args, state, listiter, dictiter, deepcopy) 268 if state is not None: 269 if deep: --> 270 state = deepcopy(state, memo) 271 if hasattr(y, '__setstate__'): 272 y.__setstate__(state) File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:146, in deepcopy(x, memo, _nil) 144 copier = _deepcopy_dispatch.get(cls) 145 if copier is not None: --> 146 y = copier(x, memo) 147 else: 148 if issubclass(cls, type): File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:230, in _deepcopy_dict(x, memo, deepcopy) 228 memo[id(x)] = y 229 for key, value in x.items(): --> 230 y[deepcopy(key, memo)] = deepcopy(value, memo) 231 return y File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:146, in deepcopy(x, memo, _nil) 144 copier = _deepcopy_dispatch.get(cls) 145 if copier is not None: --> 146 y = copier(x, memo) 147 else: 148 if issubclass(cls, type): File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:230, in _deepcopy_dict(x, memo, deepcopy) 228 memo[id(x)] = y 229 for key, value in x.items(): --> 230 y[deepcopy(key, memo)] = deepcopy(value, memo) 231 return y File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:172, in deepcopy(x, memo, _nil) 170 y = x 171 else: --> 172 y = _reconstruct(x, memo, rv) 174 # If is its own copy, don't memoize. 175 if y is not x: File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:270, in _reconstruct(x, memo, func, args, state, listiter, dictiter, deepcopy) 268 if state is not None: 269 if deep: --> 270 state = deepcopy(state, memo) 271 if hasattr(y, '__setstate__'): 272 y.__setstate__(state) [... skipping similar frames: _deepcopy_dict at line 230 (1 times), deepcopy at line 146 (1 times)] File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:172, in deepcopy(x, memo, _nil) 170 y = x 171 else: --> 172 y = _reconstruct(x, memo, rv) 174 # If is its own copy, don't memoize. 175 if y is not x: File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:270, in _reconstruct(x, memo, func, args, state, listiter, dictiter, deepcopy) 268 if state is not None: 269 if deep: --> 270 state = deepcopy(state, memo) 271 if hasattr(y, '__setstate__'): 272 y.__setstate__(state) [... skipping similar frames: deepcopy at line 146 (1 times)] File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:230, in _deepcopy_dict(x, memo, deepcopy) 228 memo[id(x)] = y 229 for key, value in x.items(): --> 230 y[deepcopy(key, memo)] = deepcopy(value, memo) 231 return y File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:146, in deepcopy(x, memo, _nil) 144 copier = _deepcopy_dispatch.get(cls) 145 if copier is not None: --> 146 y = copier(x, memo) 147 else: 148 if issubclass(cls, type): File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:205, in _deepcopy_list(x, memo, deepcopy) 203 append = y.append 204 for a in x: --> 205 append(deepcopy(a, memo)) 206 return y File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:172, in deepcopy(x, memo, _nil) 170 y = x 171 else: --> 172 y = _reconstruct(x, memo, rv) 174 # If is its own copy, don't memoize. 175 if y is not x: File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:270, in _reconstruct(x, memo, func, args, state, listiter, dictiter, deepcopy) 268 if state is not None: 269 if deep: --> 270 state = deepcopy(state, memo) 271 if hasattr(y, '__setstate__'): 272 y.__setstate__(state) File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:146, in deepcopy(x, memo, _nil) 144 copier = _deepcopy_dispatch.get(cls) 145 if copier is not None: --> 146 y = copier(x, memo) 147 else: 148 if issubclass(cls, type): File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:230, in _deepcopy_dict(x, memo, deepcopy) 228 memo[id(x)] = y 229 for key, value in x.items(): --> 230 y[deepcopy(key, memo)] = deepcopy(value, memo) 231 return y File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:153, in deepcopy(x, memo, _nil) 151 copier = getattr(x, "__deepcopy__", None) 152 if copier is not None: --> 153 y = copier(memo) 154 else: 155 reductor = dispatch_table.get(cls) File ~\.virtualenvs\pymc4-venv\lib\site-packages\aesara\link\basic.py:142, in Container.__deepcopy__(self, memo) 132 r = type(self)( 133 deepcopy(self.type, memo=memo), 134 deepcopy(self.storage, memo=memo), (...) 138 name=deepcopy(self.name, memo=memo), 139 ) 140 # Work around NumPy deepcopy of ndarray with 0 dimension that 141 # don't return an ndarray. --> 142 if r.storage[0] is not None and not self.type.is_valid_value(r.storage[0]): 143 assert not data_was_in_memo 144 assert self.type.is_valid_value(self.storage[0]) TypeError: is_valid_value() missing 1 required positional argument: 'strict' ``` This used to work on pymc3 and theano-pymc ## Versions and main components * Aesara version: 2.66 * Aesara config (`python -c "import aesara; print(aesara.config)"`) * Python version: 3.9 * Operating system: Windows * How did you install Aesara: pip * Pymc version: 4.0	174117f9b0a2c1ddb13e6244bbb31d6c75c12245	[ "tests/tensor/random/test_type.py::TestRandomStateType::test_filter" ]	[ "tests/tensor/random/test_type.py::test_view_op_c_code", "tests/tensor/random/test_type.py::TestRandomStateType::test_pickle", "tests/tensor/random/test_type.py::TestRandomStateType::test_repr", "tests/tensor/random/test_type.py::TestRandomStateType::test_values_eq", "tests/tensor/random/test_type.py::TestRandomStateType::test_may_share_memory", "tests/tensor/random/test_type.py::TestRandomGeneratorType::test_pickle", "tests/tensor/random/test_type.py::TestRandomGeneratorType::test_repr", "tests/tensor/random/test_type.py::TestRandomGeneratorType::test_may_share_memory" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-06-14 17:50:52+00:00	bsd-3-clause	913
agrc__sweeper-51	diff --git a/.gitignore b/.gitignore index 9fbddef..1fe895c 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,4 @@ __pycache__ dist/ build/ +.env/ diff --git a/.vscode/settings.json b/.vscode/settings.json index 1d21cf6..40c0fd3 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -12,6 +12,7 @@ "pformat", "posix", "pypi", + "pytest", "sdist", "usaddress", "xxhash" diff --git a/readme.md b/readme.md index b9dcff1..d9d1c5f 100644 --- a/readme.md +++ b/readme.md @@ -80,7 +80,7 @@ A normalized string representing the entire address that was passed into the con 1. install required dependencies to work on sweeper - `pip install -e ".[develop]"` 1. install required dependencies to run sweeper tests - - `pip install -e ".[test]"` + - `pip install -e ".[tests]"` 1. run tests: `pytest` ### Uploading to pypi.org diff --git a/src/sweeper/address_parser.py b/src/sweeper/address_parser.py index 5e61825..5cccd1d 100644 --- a/src/sweeper/address_parser.py +++ b/src/sweeper/address_parser.py @@ -7,19 +7,20 @@ A module that parses street addresses into their various parts. import json import pprint from os.path import dirname, join, realpath +from re import compile import usaddress TAG_MAPPING = { 'AddressNumber': 'address_number', - # 'AddressNumberPrefix': 'address1', + 'AddressNumberPrefix': 'address_number', 'AddressNumberSuffix': 'address_number_suffix', 'StreetNamePreDirectional': 'prefix_direction', 'StreetName': 'street_name', - # 'StreetNamePreModifier': 'address1', - # 'StreetNamePreType': 'address1', + # 'StreetNamePreModifier': 'street_name', #: handled in class below + # 'StreetNamePreType': 'street_name', #: handled in class below 'StreetNamePostDirectional': 'street_direction', - # 'StreetNamePostModifier': 'address1', + 'StreetNamePostModifier': 'street_type', 'StreetNamePostType': 'street_type', # 'CornerOf': 'address1', # 'IntersectionSeparator': 'address1', @@ -28,7 +29,7 @@ TAG_MAPPING = { # 'USPSBoxGroupType': 'address1', # 'USPSBoxID': 'address1', # 'USPSBoxType': 'address1', - # 'BuildingName': 'address2', + 'BuildingName': 'unit_id', 'OccupancyType': 'unit_type', 'OccupancyIdentifier': 'unit_id', # 'SubaddressIdentifier': 'address2', @@ -41,6 +42,7 @@ TAG_MAPPING = { TWO_CHAR_DIRECTIONS = ['NO', 'SO', 'EA', 'WE'] with open(join(dirname(realpath(__file__)), 'street_types.json'), 'r') as file: STREET_TYPES = json.loads(file.read()) +HWY_REGEX = compile('(SR\|STATE ROUTE\|HIGHWAY)') class Address(): @@ -77,6 +79,19 @@ class Address(): if self.po_box is not None: return + try: + #: e.g. US HWY + self.street_name = f'{normalize_street_name_pre_type(self.StreetNamePreType)} {self.street_name}' + del self.StreetNamePreType + except AttributeError: + pass + + try: + self.street_name = f'{self.StreetNamePreModifier} {self.street_name}' + del self.StreetNamePreModifier + except AttributeError: + pass + #: look for two-character prefix directions which usaddress does not handle if self.street_name: street_name_parts = self.street_name.split(' ') @@ -135,6 +150,7 @@ def normalize_direction(direction_text): return direction_text[0].upper() + def normalize_street_type(type_text): ''' returns the standard abbreviation for the input street type @@ -148,6 +164,14 @@ def normalize_street_type(type_text): raise InvalidStreetTypeError(type_text) +def normalize_street_name_pre_type(text): + '''normalizes highways by doing things like replaces SR with HWY and removes US + + No need to worried about casing or "."s because usaddress has already taken care of them by this point. + ''' + return HWY_REGEX.sub('HWY', text).replace('US ', '') + + class InvalidStreetTypeError(Exception): ''' exception for when the street type does not have a corresponding value in street_types.json	agrc/sweeper	75254926a9de985e82bb2fa116948302d4fb8abe	diff --git a/src/sweeper/tests/test_address_parser.py b/src/sweeper/tests/test_address_parser.py index c4f2caf..ae08739 100644 --- a/src/sweeper/tests/test_address_parser.py +++ b/src/sweeper/tests/test_address_parser.py @@ -386,3 +386,89 @@ class TestBadAddresses(): assert address.street_name is None assert address.address_number == '100' assert address.prefix_direction == 'S' + + +class TestHighways(): + '''tests to make sure that state routes and us highways are parsed correctly + ''' + + def test_state_routes(self): + address = Address('910 S SR 22') + + assert address.address_number == '910' + assert address.prefix_direction == 'S' + assert address.street_name == 'HWY 22' + assert address.normalized == '910 S HWY 22' + + def test_state_route_expanded(self): + address = Address('910 S State Route 22') + + assert address.address_number == '910' + assert address.prefix_direction == 'S' + assert address.street_name == 'HWY 22' + assert address.normalized == '910 S HWY 22' + + def test_state_route_with_punctuation(self): + address = Address('910 S S.R. 22') + + assert address.address_number == '910' + assert address.prefix_direction == 'S' + assert address.street_name == 'HWY 22' + assert address.normalized == '910 S HWY 22' + + def test_state_route_casing(self): + address = Address('910 S sr 22') + + assert address.address_number == '910' + assert address.prefix_direction == 'S' + assert address.street_name == 'HWY 22' + assert address.normalized == '910 S HWY 22' + + + def test_highways(self): + address = Address('1910 N US HWY 89') + + assert address.address_number == '1910' + assert address.prefix_direction == 'N' + assert address.street_name == 'HWY 89' + assert address.normalized == '1910 N HWY 89' + + address = Address('1106 S OLD HWY 89') + + assert address.address_number == '1106' + assert address.prefix_direction == 'S' + assert address.street_name == 'OLD HWY 89' + assert address.normalized == '1106 S OLD HWY 89' + + def test_highway_expanded(self): + address = Address('1910 N US highway 89') + + assert address.address_number == '1910' + assert address.prefix_direction == 'N' + assert address.street_name == 'HWY 89' + assert address.normalized == '1910 N HWY 89' + + def test_highway_with_punctuation(self): + address = Address('1910 N U.S. highway 89') + + assert address.address_number == '1910' + assert address.prefix_direction == 'N' + assert address.street_name == 'HWY 89' + assert address.normalized == '1910 N HWY 89' + + def test_highway_casing(self): + address = Address('1910 N u.s. highway 89') + + assert address.address_number == '1910' + assert address.prefix_direction == 'N' + assert address.street_name == 'HWY 89' + assert address.normalized == '1910 N HWY 89' + + def test_street_name_with_sr(self): + address = Address('1910 s woodsrow dr') + + assert address.address_number == '1910' + assert address.prefix_direction == 'S' + assert address.street_name == 'WOODSROW' + assert address.street_type == 'DR' + assert address.normalized == '1910 S WOODSROW DR'	State Routes SR Addresses like 910 S SR 22 or 1910 N US HWY 89 will return 22 and 89 for the street_name	75254926a9de985e82bb2fa116948302d4fb8abe	[ "src/sweeper/tests/test_address_parser.py::TestHighways::test_state_routes", "src/sweeper/tests/test_address_parser.py::TestHighways::test_state_route_expanded", "src/sweeper/tests/test_address_parser.py::TestHighways::test_state_route_with_punctuation", "src/sweeper/tests/test_address_parser.py::TestHighways::test_state_route_casing", "src/sweeper/tests/test_address_parser.py::TestHighways::test_highways", "src/sweeper/tests/test_address_parser.py::TestHighways::test_highway_expanded", "src/sweeper/tests/test_address_parser.py::TestHighways::test_highway_with_punctuation", "src/sweeper/tests/test_address_parser.py::TestHighways::test_highway_casing" ]	[ "src/sweeper/tests/test_address_parser.py::TestAddressNumber::test_parses_address_number", "src/sweeper/tests/test_address_parser.py::TestAddressNumberSuffix::test_parses_number_suffix", "src/sweeper/tests/test_address_parser.py::TestPrefixDirection::test_parses_prefix_direction", "src/sweeper/tests/test_address_parser.py::TestPrefixDirection::test_no_prefix_direction", "src/sweeper/tests/test_address_parser.py::TestStreetName::test_parses_street_name", "src/sweeper/tests/test_address_parser.py::TestStreetName::test_multi_word_street_name", "src/sweeper/tests/test_address_parser.py::TestStreetName::test_no_prefix_direction_street", "src/sweeper/tests/test_address_parser.py::TestStreetDirection::test_street_direction", "src/sweeper/tests/test_address_parser.py::TestNormalizeDirection::test_normalize_direction", "src/sweeper/tests/test_address_parser.py::TestNormalizeDirection::test_two_characters", "src/sweeper/tests/test_address_parser.py::TestWhiteSpace::test_white_space", "src/sweeper/tests/test_address_parser.py::TestWhiteSpace::test_double_spaces", "src/sweeper/tests/test_address_parser.py::TestNormalizeStreetType::test_normalize_street_type", "src/sweeper/tests/test_address_parser.py::TestNormalizeStreetType::test_raises_exceptions", "src/sweeper/tests/test_address_parser.py::TestNormalizeStreetType::test_street_names_with_types", "src/sweeper/tests/test_address_parser.py::TestUnitParts::test_add_hash_if_no_type", "src/sweeper/tests/test_address_parser.py::TestUnitParts::test_strip_hash_if_type", "src/sweeper/tests/test_address_parser.py::TestPOBox::test_parses_po_boxes", "src/sweeper/tests/test_address_parser.py::test_normalized_address_string", "src/sweeper/tests/test_address_parser.py::test_strip_periods", "src/sweeper/tests/test_address_parser.py::test_steve", "src/sweeper/tests/test_address_parser.py::TestBadAddresses::test_missing_street_names", "src/sweeper/tests/test_address_parser.py::TestHighways::test_street_name_with_sr" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-03-26 22:39:19+00:00	mit	914
agronholm__anyio-137	diff --git a/src/anyio/__init__.py b/src/anyio/__init__.py index 2b2cfec..cb1fd4b 100644 --- a/src/anyio/__init__.py +++ b/src/anyio/__init__.py @@ -14,6 +14,7 @@ from typing import TypeVar, Callable, Union, Optional, Awaitable, Coroutine, Any import sniffio +from ._utils import convert_ipv6_sockaddr from .abc import ( Lock, Condition, Event, Semaphore, CapacityLimiter, CancelScope, TaskGroup, IPAddressType, SocketStream, UDPSocket, ConnectedUDPSocket, IPSockAddrType, Listener, SocketListener) @@ -32,8 +33,7 @@ IPPROTO_IPV6 = getattr(socket, 'IPPROTO_IPV6', 41) # https://bugs.python.org/is T_Retval = TypeVar('T_Retval', covariant=True) T_Agen = TypeVar('T_Agen') T_Item = TypeVar('T_Item') -GetAddrInfoReturnType = List[Tuple[AddressFamily, SocketKind, int, str, - Union[Tuple[str, int], Tuple[str, int, int, int]]]] +GetAddrInfoReturnType = List[Tuple[AddressFamily, SocketKind, int, str, Tuple[str, int]]] AnyIPAddressFamily = Literal[AddressFamily.AF_UNSPEC, AddressFamily.AF_INET, AddressFamily.AF_INET6] IPAddressFamily = Literal[AddressFamily.AF_INET, AddressFamily.AF_INET6] @@ -607,15 +607,18 @@ async def create_connected_udp_socket( reuse_port) -def getaddrinfo(host: Union[bytearray, bytes, str], port: Union[str, int, None], , - family: Union[int, AddressFamily] = 0, type: Union[int, SocketKind] = 0, - proto: int = 0, flags: int = 0) -> Awaitable[GetAddrInfoReturnType]: +async def getaddrinfo(host: Union[bytearray, bytes, str], port: Union[str, int, None], , + family: Union[int, AddressFamily] = 0, type: Union[int, SocketKind] = 0, + proto: int = 0, flags: int = 0) -> GetAddrInfoReturnType: """ Look up a numeric IP address given a host name. Internationalized domain names are translated according to the (non-transitional) IDNA 2008 standard. + .. note:: 4-tuple IPv6 socket addresses are automatically converted to 2-tuples of + (host, port), unlike what :func:`socket.getaddrinfo` does. + :param host: host name :param port: port number :param family: socket family (`'AF_INET``, ...) @@ -637,8 +640,10 @@ def getaddrinfo(host: Union[bytearray, bytes, str], port: Union[str, int, None], else: encoded_host = host - return _get_asynclib().getaddrinfo(encoded_host, port, family=family, type=type, proto=proto, - flags=flags) + gai_res = await _get_asynclib().getaddrinfo(encoded_host, port, family=family, type=type, + proto=proto, flags=flags) + return [(family, type, proto, canonname, convert_ipv6_sockaddr(sockaddr)) + for family, type, proto, canonname, sockaddr in gai_res] def getnameinfo(sockaddr: IPSockAddrType, flags: int = 0) -> Awaitable[Tuple[str, str]]: diff --git a/src/anyio/_backends/_asyncio.py b/src/anyio/_backends/_asyncio.py index 03d3093..d85e45d 100644 --- a/src/anyio/_backends/_asyncio.py +++ b/src/anyio/_backends/_asyncio.py @@ -854,23 +854,12 @@ class ConnectedUDPSocket(abc.ConnectedUDPSocket): self._transport.sendto(item) -def _convert_ipv6_sockaddr(sockaddr: Optional[IPSockAddrType]) -> Optional[Tuple[str, int]]: - # This is more complicated than it should be because of MyPy - if sockaddr is None: - return None - elif len(sockaddr) == 4 and sockaddr[-1]: - # Add scopeid to the address - return sockaddr[0] + '%' + str(sockaddr[-1]), sockaddr[1] - else: - return sockaddr[:2] - - async def connect_tcp(host: str, port: int, - local_addr: Optional[IPSockAddrType] = None) -> SocketStream: + local_addr: Optional[Tuple[str, int]] = None) -> SocketStream: transport, protocol = cast( Tuple[asyncio.Transport, StreamProtocol], await get_running_loop().create_connection(StreamProtocol, host, port, - local_addr=_convert_ipv6_sockaddr(local_addr)) + local_addr=local_addr) ) transport.pause_reading() return SocketStream(transport, protocol) @@ -892,8 +881,8 @@ async def create_udp_socket( reuse_port: bool ) -> Union[UDPSocket, ConnectedUDPSocket]: result = await get_running_loop().create_datagram_endpoint( - DatagramProtocol, local_addr=_convert_ipv6_sockaddr(local_address), - remote_addr=_convert_ipv6_sockaddr(remote_address), family=family, reuse_port=reuse_port) + DatagramProtocol, local_addr=local_address, remote_addr=remote_address, family=family, + reuse_port=reuse_port) transport = cast(asyncio.DatagramTransport, result[0]) protocol = cast(DatagramProtocol, result[1]) if protocol.exception: diff --git a/src/anyio/_utils.py b/src/anyio/_utils.py index ff68d2c..0f7bdac 100644 --- a/src/anyio/_utils.py +++ b/src/anyio/_utils.py @@ -16,3 +16,26 @@ class ResourceGuard: def __exit__(self, exc_type, exc_val, exc_tb): self._guarded = False + + +def convert_ipv6_sockaddr(sockaddr): + """ + Convert a 4-tuple IPv6 socket address to a 2-tuple (address, port) format. + + If the scope ID is nonzero, it is added to the address, separated with ``%``. + Otherwise the flow id and scope id are simply cut off from the tuple. + Any other kinds of socket addresses are returned as-is. + + :param sockaddr: the result of :meth:`~socket.socket.getsockname` + :return: the converted socket address + + """ + # This is more complicated than it should be because of MyPy + if isinstance(sockaddr, tuple) and len(sockaddr) == 4: + if sockaddr[3]: + # Add scopeid to the address + return sockaddr[0] + '%' + str(sockaddr[3]), sockaddr[1] + else: + return sockaddr[:2] + else: + return sockaddr diff --git a/src/anyio/abc/sockets.py b/src/anyio/abc/sockets.py index f02d1c8..50d8a4d 100644 --- a/src/anyio/abc/sockets.py +++ b/src/anyio/abc/sockets.py @@ -6,7 +6,7 @@ from typing import TypeVar, Tuple, Union, Generic from .streams import UnreliableObjectStream, ByteStream, Listener IPAddressType = Union[str, IPv4Address, IPv6Address] -IPSockAddrType = Union[Tuple[str, int], Tuple[str, int, int, int]] +IPSockAddrType = Tuple[str, int] SockAddrType = Union[IPSockAddrType, str] UDPPacketType = Tuple[bytes, IPSockAddrType] T_Retval = TypeVar('T_Retval') @@ -41,8 +41,7 @@ class _SocketMixin(Generic[T_SockAddr]): """ The bound address of the underlying local socket. - For IPv4 TCP streams, this is a tuple of (IP address, port). - For IPv6 TCP streams, this is a tuple of (IP address, port, flowinfo, scopeid). + For TCP streams, this is a tuple of (IP address, port). For UNIX socket streams, this is the path to the socket. """ @@ -56,8 +55,7 @@ class SocketStream(Generic[T_SockAddr], ByteStream, _SocketMixin[T_SockAddr]): """ The address this socket is connected to. - For IPv4 TCP streams, this is a tuple of (IP address, port). - For IPv6 TCP streams, this is a tuple of (IP address, port, flowinfo, scopeid). + For TCP streams, this is a tuple of (IP address, port). For UNIX socket streams, this is the path to the socket. """ @@ -80,9 +78,4 @@ class ConnectedUDPSocket(UnreliableObjectStream[bytes], _SocketMixin[IPSockAddrT @property @abstractmethod def remote_address(self) -> IPSockAddrType: - """ - The address this socket is connected to. - - For IPv4 sockets, this is a tuple of (IP address, port). - For IPv6 sockets, this is a tuple of (IP address, port, flowinfo, scopeid). - """ + """The address this socket is connected to."""	agronholm/anyio	cfba438b71237aeb93bfb955a8e70edd8f101ac9	diff --git a/tests/test_sockets.py b/tests/test_sockets.py index 24fb5de..7f47bb6 100644 --- a/tests/test_sockets.py +++ b/tests/test_sockets.py @@ -747,8 +747,7 @@ async def test_getaddrinfo_ipv6addr(sock_type): # IDNA trips up over raw IPv6 addresses proto = 0 if platform.system() == 'Windows' else 6 assert await getaddrinfo('::1', 0, type=sock_type) == [ - (socket.AddressFamily.AF_INET6, socket.SocketKind.SOCK_STREAM, proto, '', - ('::1', 0, 0, 0)) + (socket.AddressFamily.AF_INET6, socket.SocketKind.SOCK_STREAM, proto, '', ('::1', 0)) ]	Should we expose the user to 4-tuple IPv6 socket addresses? The result of `sock.getsockname()` for IPv6 sockets is a 4-tuple (address, port, flowinfo, scopeid). The last two fields are specific to IPv6. The flowinfo field is useless/deprecated and the scopeid is only meaningful for link-local addresses. The important part here is that the address field can carry a scope ID by appending it to the address with a `%` separator, like `fe80::dead:beef%1`. Most people are not used to dealing with 4-tuple socket addresses, so maybe it would make sense to make it part of the address always. On the other hand, others might expect the usual behavior and get confused when they get 2-tuples instead!	cfba438b71237aeb93bfb955a8e70edd8f101ac9	[ "tests/test_sockets.py::test_getaddrinfo_ipv6addr[asyncio-SocketKind.SOCK_STREAM0]", "tests/test_sockets.py::test_getaddrinfo_ipv6addr[asyncio-SocketKind.SOCK_STREAM1]", "tests/test_sockets.py::test_getaddrinfo_ipv6addr[asyncio+uvloop-SocketKind.SOCK_STREAM0]", "tests/test_sockets.py::test_getaddrinfo_ipv6addr[asyncio+uvloop-SocketKind.SOCK_STREAM1]" ]	[ "tests/test_sockets.py::TestTCPStream::test_send_receive[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_send_receive[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_send_receive[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_send_receive[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_send_large_buffer[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_send_large_buffer[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_send_large_buffer[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_send_large_buffer[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_send_eof[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_send_eof[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_send_eof[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_send_eof[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_iterate[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_iterate[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_iterate[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_iterate[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_socket_options[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_socket_options[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_socket_options[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_socket_options[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_happy_eyeballs[asyncio-dualstack]", "tests/test_sockets.py::TestTCPStream::test_happy_eyeballs[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_happy_eyeballs[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_happy_eyeballs[asyncio+uvloop-dualstack]", "tests/test_sockets.py::TestTCPStream::test_happy_eyeballs[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_happy_eyeballs[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_connection_refused[asyncio-multi]", "tests/test_sockets.py::TestTCPStream::test_connection_refused[asyncio-single]", "tests/test_sockets.py::TestTCPStream::test_connection_refused[asyncio+uvloop-multi]", "tests/test_sockets.py::TestTCPStream::test_connection_refused[asyncio+uvloop-single]", "tests/test_sockets.py::TestTCPStream::test_receive_timeout[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_receive_timeout[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_receive_timeout[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_receive_timeout[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_concurrent_send[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_concurrent_send[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_concurrent_send[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_concurrent_send[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_concurrent_receive[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_concurrent_receive[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_concurrent_receive[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_concurrent_receive[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_close_during_receive[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_close_during_receive[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_close_during_receive[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_close_during_receive[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_receive_after_close[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_receive_after_close[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_receive_after_close[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_receive_after_close[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_send_after_close[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_send_after_close[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_send_after_close[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_send_after_close[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_connect_tcp_with_tls[asyncio-ipv4]", 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"tests/test_sockets.py::TestConnectedUDPSocket::test_send_after_close[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestConnectedUDPSocket::test_send_after_close[asyncio+uvloop-ipv6]", "tests/test_sockets.py::test_getaddrinfo[asyncio]", "tests/test_sockets.py::test_getaddrinfo[asyncio+uvloop]", "tests/test_sockets.py::test_getnameinfo[asyncio]", "tests/test_sockets.py::test_getnameinfo[asyncio+uvloop]" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-07-31 12:55:49+00:00	mit	915
agronholm__anyio-227	diff --git a/docs/versionhistory.rst b/docs/versionhistory.rst index b9fa806..466bc78 100644 --- a/docs/versionhistory.rst +++ b/docs/versionhistory.rst @@ -54,6 +54,7 @@ This library adheres to `Semantic Versioning 2.0 <http://semver.org/>`_. - Added the ``run_sync_from_thread()`` function - Added ``UNIXSocketStream`` as a ``SocketStream`` subclass, capable of sending and receiving file descriptors +- Added thread pooling for asyncio - Added the ``FileReadStream`` and ``FileWriteStream`` classes - Added the ``TaskGroup.start()`` method and a corresponding ``BlockingPortal.start_task()`` method - Added the ``name`` argument to ``BlockingPortal.spawn_task()`` @@ -81,6 +82,8 @@ This library adheres to `Semantic Versioning 2.0 <http://semver.org/>`_. - Changed the asyncio ``TaskGroup.spawn()`` method to avoid the use of a coroutine wrapper on Python 3.8+ and added a hint for hiding the wrapper in tracebacks on earlier Pythons (supported by Pytest, Sentry etc.) +- Changed the default thread limiter on asyncio to be scoped to an event loop so that multiple + running event loops don't conflict with each other 2.2.0 diff --git a/src/anyio/_backends/_asyncio.py b/src/anyio/_backends/_asyncio.py index ac67930..2ba1e8d 100644 --- a/src/anyio/_backends/_asyncio.py +++ b/src/anyio/_backends/_asyncio.py @@ -4,6 +4,7 @@ import concurrent.futures import math import socket import sys +from asyncio.base_events import _run_until_complete_cb # type: ignore from collections import OrderedDict, deque from concurrent.futures import Future from dataclasses import dataclass @@ -11,8 +12,9 @@ from functools import partial, wraps from inspect import ( CORO_RUNNING, CORO_SUSPENDED, GEN_RUNNING, GEN_SUSPENDED, getcoroutinestate, getgeneratorstate) from io import IOBase +from queue import Empty, Queue from socket import AddressFamily, SocketKind, SocketType -from threading import Thread +from threading import Thread, current_thread from types import TracebackType from typing import ( Any, Awaitable, Callable, Collection, Coroutine, Deque, Dict, Generator, List, Optional, @@ -40,6 +42,15 @@ else: if sys.version_info >= (3, 7): from asyncio import all_tasks, create_task, current_task, get_running_loop from asyncio import run as native_run + + def find_root_task() -> asyncio.Task: + for task in all_tasks(): + if task._callbacks: + for cb, context in task._callbacks: # type: ignore + if cb is _run_until_complete_cb or cb.__module__ == 'uvloop.loop': + return task + + raise RuntimeError('Cannot find root task for setting cleanup callback') else: _T = TypeVar('_T') @@ -115,6 +126,14 @@ else: return asyncio.Task.current_task(loop) + def find_root_task() -> asyncio.Task: + for task in all_tasks(): + for cb in task._callbacks: + if cb is _run_until_complete_cb or cb.__module__ == 'uvloop.loop': + return task + + raise RuntimeError('Cannot find root task for setting cleanup callback') + T_Retval = TypeVar('T_Retval') # Check whether there is native support for task names in asyncio (3.8+) @@ -619,47 +638,87 @@ class TaskGroup(abc.TaskGroup): _Retval_Queue_Type = Tuple[Optional[T_Retval], Optional[BaseException]] -async def run_sync_in_worker_thread( - func: Callable[..., T_Retval], args, cancellable: bool = False, - limiter: Optional['CapacityLimiter'] = None) -> T_Retval: - def thread_worker(): +def _thread_pool_worker(work_queue: Queue, workers: Set[Thread], + idle_workers: Set[Thread]) -> None: + func: Callable + args: tuple + future: asyncio.Future + limiter: CapacityLimiter + thread = current_thread() + while True: try: + func, args, future = work_queue.get(timeout=10) + except Empty: + workers.remove(thread) + return + finally: + idle_workers.discard(thread) + + if func is None: + # Shutdown command received + workers.remove(thread) + return + + if not future.cancelled(): with claim_worker_thread('asyncio'): - threadlocals.loop = loop - result = func(args) - except BaseException as exc: - if not loop.is_closed(): - loop.call_soon_threadsafe(limiter.release_on_behalf_of, task) - if not cancelled: - loop.call_soon_threadsafe(queue.put_nowait, (None, exc)) + loop = threadlocals.loop = future._loop + try: + result = func(args) + except BaseException as exc: + idle_workers.add(thread) + if not loop.is_closed() and not future.cancelled(): + loop.call_soon_threadsafe(future.set_exception, exc) + else: + idle_workers.add(thread) + if not loop.is_closed() and not future.cancelled(): + loop.call_soon_threadsafe(future.set_result, result) else: - if not loop.is_closed(): - loop.call_soon_threadsafe(limiter.release_on_behalf_of, task) - if not cancelled: - loop.call_soon_threadsafe(queue.put_nowait, (result, None)) + idle_workers.add(thread) + + work_queue.task_done() + +_threadpool_work_queue: RunVar[Queue] = RunVar('_threadpool_work_queue') +_threadpool_idle_workers: RunVar[Set[Thread]] = RunVar('_threadpool_idle_workers') +_threadpool_workers: RunVar[Set[Thread]] = RunVar('_threadpool_workers') + + +def _loop_shutdown_callback(f: asyncio.Future) -> None: + """This is called when the root task has finished.""" + for _ in range(len(_threadpool_workers.get())): + _threadpool_work_queue.get().put_nowait((None, None, None)) + + +async def run_sync_in_worker_thread( + func: Callable[..., T_Retval], args, cancellable: bool = False, + limiter: Optional['CapacityLimiter'] = None) -> T_Retval: await checkpoint() - loop = get_running_loop() - task = current_task() - queue: asyncio.Queue[_Retval_Queue_Type] = asyncio.Queue(1) - cancelled = False - limiter = limiter or _default_thread_limiter - await limiter.acquire_on_behalf_of(task) - thread = Thread(target=thread_worker, daemon=True) - thread.start() - exception: Optional[BaseException] = None - with CancelScope(shield=not cancellable): - try: - retval, exception = await queue.get() - except BaseException as exc: - exception = exc - finally: - cancelled = True - if exception is not None: - raise exception - else: - return cast(T_Retval, retval) + # If this is the first run in this event loop thread, set up the necessary variables + try: + work_queue = _threadpool_work_queue.get() + idle_workers = _threadpool_idle_workers.get() + workers = _threadpool_workers.get() + except LookupError: + work_queue = Queue() + idle_workers = set() + workers = set() + _threadpool_work_queue.set(work_queue) + _threadpool_idle_workers.set(idle_workers) + _threadpool_workers.set(workers) + find_root_task().add_done_callback(_loop_shutdown_callback) + + async with (limiter or current_default_thread_limiter()): + with CancelScope(shield=not cancellable): + future: asyncio.Future = asyncio.Future() + work_queue.put_nowait((func, args, future)) + if not idle_workers: + args = (work_queue, workers, idle_workers) + thread = Thread(target=_thread_pool_worker, args=args, name='AnyIO worker thread') + workers.add(thread) + thread.start() + + return await future def run_sync_from_thread(func: Callable[..., T_Retval], *args, @@ -1536,11 +1595,16 @@ class CapacityLimiter(abc.CapacityLimiter): tuple(self._borrowers), len(self._wait_queue)) -def current_default_thread_limiter(): - return _default_thread_limiter +_default_thread_limiter: RunVar[CapacityLimiter] = RunVar('_default_thread_limiter') -_default_thread_limiter = CapacityLimiter(40) +def current_default_thread_limiter(): + try: + return _default_thread_limiter.get() + except LookupError: + limiter = CapacityLimiter(40) + _default_thread_limiter.set(limiter) + return limiter #	agronholm/anyio	8c136ffff989fb12c738bf87183046285b738a63	diff --git a/tests/test_threads.py b/tests/test_threads.py index 9d07ed7..56eb5b8 100644 --- a/tests/test_threads.py +++ b/tests/test_threads.py @@ -9,7 +9,7 @@ import pytest from anyio import ( create_blocking_portal, create_capacity_limiter, create_event, create_task_group, - get_cancelled_exc_class, get_current_task, run_async_from_thread, run_sync_from_thread, + get_cancelled_exc_class, get_current_task, run, run_async_from_thread, run_sync_from_thread, run_sync_in_worker_thread, sleep, start_blocking_portal, wait_all_tasks_blocked) if sys.version_info < (3, 7): @@ -48,6 +48,23 @@ async def test_run_sync_from_thread(): assert result == 3 +def test_run_sync_from_thread_pooling(): + async def main(): + thread_ids = set() + for _ in range(5): + thread_ids.add(await run_sync_in_worker_thread(threading.get_ident)) + + # Expects that all the work has been done in the same worker thread + assert len(thread_ids) == 1 + assert thread_ids.pop() != threading.get_ident() + assert threading.active_count() == initial_count + 1 + + # The thread should not exist after the event loop has been closed + initial_count = threading.active_count() + run(main, backend='asyncio') + assert threading.active_count() == initial_count + + async def test_run_async_from_thread_exception(): async def add(a, b): assert threading.get_ident() == event_loop_thread_id	Use thread pools in run_sync_in_worker_thread() Right now, the asyncio implementation of this starts a new thread every time this function is called. We should be using thread pools instead, like trio does.	8c136ffff989fb12c738bf87183046285b738a63	[ "tests/test_threads.py::test_run_sync_from_thread_pooling" ]	[ "tests/test_threads.py::test_run_async_from_thread[asyncio]", "tests/test_threads.py::test_run_async_from_thread[asyncio+uvloop]", "tests/test_threads.py::test_run_sync_from_thread[asyncio]", "tests/test_threads.py::test_run_sync_from_thread[asyncio+uvloop]", "tests/test_threads.py::test_run_async_from_thread_exception[asyncio]", "tests/test_threads.py::test_run_async_from_thread_exception[asyncio+uvloop]", "tests/test_threads.py::test_run_sync_from_thread_exception[asyncio]", "tests/test_threads.py::test_run_sync_from_thread_exception[asyncio+uvloop]", "tests/test_threads.py::test_run_anyio_async_func_from_thread[asyncio]", "tests/test_threads.py::test_run_anyio_async_func_from_thread[asyncio+uvloop]", "tests/test_threads.py::test_run_in_thread_cancelled[asyncio]", "tests/test_threads.py::test_run_in_thread_cancelled[asyncio+uvloop]", "tests/test_threads.py::test_run_in_thread_exception[asyncio]", "tests/test_threads.py::test_run_in_thread_exception[asyncio+uvloop]", "tests/test_threads.py::test_run_in_custom_limiter[asyncio]", "tests/test_threads.py::test_run_in_custom_limiter[asyncio+uvloop]", "tests/test_threads.py::test_run_async_from_unclaimed_thread", "tests/test_threads.py::test_run_sync_from_unclaimed_thread", "tests/test_threads.py::test_cancel_worker_thread[asyncio-uncancellable]", "tests/test_threads.py::test_cancel_worker_thread[asyncio-cancellable]", "tests/test_threads.py::test_cancel_worker_thread[asyncio+uvloop-uncancellable]", "tests/test_threads.py::test_cancel_worker_thread[asyncio+uvloop-cancellable]", "tests/test_threads.py::test_cancel_asyncio_native_task[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_successful_call[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_successful_call[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_aexit_with_exception[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_aexit_with_exception[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_aexit_without_exception[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_aexit_without_exception[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_call_portal_from_event_loop_thread[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_call_portal_from_event_loop_thread[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_start_with_new_event_loop[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_start_with_new_event_loop[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_start_with_nonexistent_backend", "tests/test_threads.py::TestBlockingPortal::test_call_stopped_portal[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_call_stopped_portal[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_spawn_task[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_spawn_task[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_spawn_task_cancel_later[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_spawn_task_cancel_later[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_spawn_task_cancel_immediately[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_spawn_task_cancel_immediately[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_spawn_task_with_name[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_spawn_task_with_name[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_async_context_manager_success[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_async_context_manager_success[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_async_context_manager_error[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_async_context_manager_error[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_async_context_manager_error_ignore[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_async_context_manager_error_ignore[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_start_no_value[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_start_no_value[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_start_with_value[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_start_with_value[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_start_crash_before_started_call[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_start_crash_before_started_call[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_start_crash_after_started_call[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_start_crash_after_started_call[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_start_no_started_call[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_start_no_started_call[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_start_with_name[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_start_with_name[asyncio+uvloop]" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-03-03 21:08:05+00:00	mit	916

ValvePython__steam-359

diff --git a/requirements.txt b/requirements.txt index 92661a9..14293fb 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,7 +3,8 @@ pycryptodomex>=3.7.0 requests>=2.9.1 vdf>=3.3 gevent>=1.3.0 -protobuf>=3.0.0 +protobuf>~3.0; python_version >= '3' +protobuf<3.18.0; python_version < '3' gevent-eventemitter~=2.1 cachetools>=3.0.0 enum34==1.1.2; python_version < '3.4' diff --git a/setup.py b/setup.py index 16b8870..382f8f2 100644 --- a/setup.py +++ b/setup.py @@ -26,7 +26,8 @@ install_requires = [ install_extras = { 'client': [ 'gevent>=1.3.0', - 'protobuf>=3.0.0', + 'protobuf>~3.0; python_version >= "3"', + 'protobuf<3.18.0; python_version < "3"', 'gevent-eventemitter~=2.1', ], } diff --git a/steam/game_servers.py b/steam/game_servers.py index 07b09f1..80bf108 100644 --- a/steam/game_servers.py +++ b/steam/game_servers.py @@ -142,8 +142,11 @@ def _u(data): class StructReader(_StructReader): - def read_cstring(self): - return _u(super(StructReader, self).read_cstring()) + def read_cstring(self, binary=False): + raw = super(StructReader, self).read_cstring() + if binary: + return raw + return _u(raw) class MSRegion(IntEnum): @@ -526,7 +529,7 @@ def a2s_players(server_addr, timeout=2, challenge=0): return players -def a2s_rules(server_addr, timeout=2, challenge=0): +def a2s_rules(server_addr, timeout=2, challenge=0, binary=False): """Get rules from server :param server_addr: (ip, port) for the server @@ -535,9 +538,11 @@ def a2s_rules(server_addr, timeout=2, challenge=0): :type timeout: float :param challenge: (optional) challenge number :type challenge: int + :param binary: (optional) return rules as raw bytes + :type binary: bool :raises: :class:`RuntimeError`, :class:`socket.timeout` :returns: a list of rules - :rtype: :class:`list` + :rtype: :class:`dict` """ ss = socket.socket(socket.AF_INET, socket.SOCK_DGRAM) ss.connect(server_addr) @@ -571,13 +576,14 @@ def a2s_rules(server_addr, timeout=2, challenge=0): rules = {} while len(rules) != num_rules: - name = data.read_cstring() - value = data.read_cstring() - - if _re_match(r'^\-?[0-9]+$', value): - value = int(value) - elif _re_match(r'^\-?[0-9]+\.[0-9]+$', value): - value = float(value) + name = data.read_cstring(binary=binary) + value = data.read_cstring(binary=binary) + + if not binary: + if _re_match(r'^\-?[0-9]+$', value): + value = int(value) + elif _re_match(r'^\-?[0-9]+\.[0-9]+$', value): + value = float(value) rules[name] = value

ValvePython/steam

061ca33842c9ec5aa7c0866d20cbeed0759d5ea5

diff --git a/tests/test_game_servers.py b/tests/test_game_servers.py new file mode 100644 index 0000000..47fc89e --- /dev/null +++ b/tests/test_game_servers.py @@ -0,0 +1,64 @@ +import mock +import socket +import unittest + +from steam.game_servers import a2s_rules + + +class TestA2SRules(unittest.TestCase): + @mock.patch("socket.socket") + def test_returns_rules_with_default_arguments(self, mock_socket_class): + mock_socket = mock_socket_class.return_value + mock_socket.recv.side_effect = [ + b"\xff\xff\xff\xffA\x01\x02\x03\x04", + b"\xff\xff\xff\xffE\x03\0text\0b\x99r\0int\x0042\0float\x0021.12\0" + ] + + rules = a2s_rules(("addr", 1234)) + + self.assertEqual( + { + "text": u"b\ufffdr", + "int": 42, + "float": 21.12 + }, + rules) + + mock_socket_class.assert_called_once_with( + socket.AF_INET, socket.SOCK_DGRAM) + + mock_socket.connect.assert_called_once_with(("addr", 1234)) + mock_socket.settimeout.assert_called_once_with(2) + + self.assertEqual(2, mock_socket.send.call_count) + mock_socket.send.assert_has_calls([ + mock.call(b"\xff\xff\xff\xffV\0\0\0\0"), + mock.call(b"\xff\xff\xff\xffV\x01\x02\x03\x04") + ]) + + self.assertEqual(2, mock_socket.recv.call_count) + mock_socket.recv.assert_has_calls([ + mock.call(512), + mock.call(2048) + ]) + + mock_socket.close.assert_called_once_with() + + @mock.patch("socket.socket") + def test_returns_rules_as_bytes_when_binary_is_true( + self, mock_socket_class): + mock_socket = mock_socket_class.return_value + mock_socket.recv.side_effect = [ + b"\xff\xff\xff\xffA\x01\x02\x03\x04", + b"\xff\xff\xff\xffE\x03\0text\0b\x99r\0int\x0042\0float\x0021.12\0" + ] + + rules = a2s_rules(("addr", 1234), binary=True) + + self.assertEqual( + { + b"text": b"b\x99r", + b"int": b"42", + b"float": b"21.12" + }, + rules)

Option to return a2s_rules as bytes instead of strings The `steam.game_servers.a2s_rules` function currently returns the server rules as a dictionary of strings to strings (`Dict[str, str]`), which is suitable for plain text rules. However, some game servers use the Steam `A2S_RULES` API to return binary data. For example, Bohemia Interactive's Arma and DayZ servers use the rules API to return required DLC and Mod information (see https://community.bistudio.com/wiki/Arma_3:_ServerBrowserProtocol3 for details). Unfortunately, because `steam.game_servers.a2s_rules` decodes the A2S_RULES server response data as UTF-8 **with `"replace"` as the `errors` option**, important binary data is lost when querying an Arma or DayZ server's rules. For example: ```python >>> pprint(a2s_rules(("192.169.82.235",2303))) {'\x01\x01': '\x01\x01\x01\x02\x01\x02\x01\x02\x02��_\x04ITv�\x0eNamalsk ' 'Island#�:\x13Ԓ\x11\x0b' 'Livonia DLC\x03\x0eCrimsonZamboni\x04dayz\x06sumrak', 'allowedBuild': 0, 'dedicated': 1, 'island': 'namalsk', 'language': 65545, 'platform': 'win', 'requiredBuild': 0, 'requiredVersion': 113, 'timeLeft': 15} ``` It would be very helpful if we could get a server's `A2S_RULES` information as raw `bytes`, instead of `str` objects. Perhaps an optional keyword argument could be added to the `steam.game_servers.a2s_rules` function? For example: ```python a2s_rules(("192.169.82.235",2303), binary=True) ``` The default should be `binary=False` to maintain backwards compatibility but when `binary=True`, the resulting rule names and values would be returned as `bytes` objects (i.e. `Dict[bytes, bytes]`), allowing the caller to further decode the binary data, as needed.

0.0

061ca33842c9ec5aa7c0866d20cbeed0759d5ea5

[ "tests/test_game_servers.py::TestA2SRules::test_returns_rules_as_bytes_when_binary_is_true" ]

[ "tests/test_game_servers.py::TestA2SRules::test_returns_rules_with_default_arguments" ]

{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-09-25 17:38:38+00:00

mit

817

Viatorus__quom-34

diff --git a/README.md b/README.md index db84fbb..4486b8c 100644 --- a/README.md +++ b/README.md @@ -44,6 +44,10 @@ optional arguments: --trim, -t Reduce continuous line breaks to one. Default: True --include_directory INCLUDE_DIRECTORY, -I INCLUDE_DIRECTORY Add include directories for header files. + --source_directory SOURCE_DIRECTORY, -S SOURCE_DIRECTORY + Set the source directories for source files. + Use ./ in front of a path to mark as relative to the header file. + ``` ## Simple example diff --git a/quom/__main__.py b/quom/__main__.py index d717853..ed25d0b 100644 --- a/quom/__main__.py +++ b/quom/__main__.py @@ -1,12 +1,12 @@ import argparse import sys -import traceback from pathlib import Path +from typing import List from .quom import Quom -def main(): +def main(args: List[str]): parser = argparse.ArgumentParser(prog='quom', description='Single header generator for C/C++ libraries.') parser.add_argument('input_path', metavar='input', type=Path, help='Input file path of the main file.') parser.add_argument('output_path', metavar='output', type=Path, @@ -20,12 +20,33 @@ def main(): help='Reduce continuous line breaks to one. Default: %(default)s') parser.add_argument('--include_directory', '-I', type=Path, action='append', default=[], help='Add include directories for header files.') + parser.add_argument('--source_directory', '-S', type=str, action='append', default=['.'], + help='Set the source directories for source files. ' + 'Use ./ in front of a path to mark as relative to the header file.') - args = parser.parse_args() + args = parser.parse_args(args) + + # Transform source directories to distingue between: + # - relative from header file (starting with dot) + # - relative from workdir + # - absolute path + relative_source_directories = [] + source_directories = [] + for src in args.source_directory: + path = Path(src) + if src == '.' or src.startswith('./'): + relative_source_directories.append(path) + else: + source_directories.append(path.resolve()) with args.output_path.open('w+') as file: - Quom(args.input_path, file, args.stitch, args.include_guard, args.trim, args.include_directory) + Quom(args.input_path, file, args.stitch, args.include_guard, args.trim, args.include_directory, + relative_source_directories, source_directories) + + +def run(): + main(sys.argv[1:]) if __name__ == '__main__': - sys.exit(main()) + run() diff --git a/quom/quom.py b/quom/quom.py index 20bc83e..d366219 100644 --- a/quom/quom.py +++ b/quom/quom.py @@ -1,3 +1,4 @@ +import os import re from pathlib import Path from queue import Queue @@ -29,12 +30,17 @@ def contains_only_whitespace_and_comment_tokens(tokens: List[Token]): class Quom: def __init__(self, src_file_path: Union[Path, str], dst: TextIO, stitch_format: str = None, include_guard_format: str = None, trim: bool = True, - include_directories: List[Union[Path, str]] = None): + include_directories: List[Union[Path, str]] = None, + relative_source_directories: List[Union[Path]] = None, + source_directories: List[Union[Path]] = None): self.__dst = dst self.__stitch_format = stitch_format self.__include_guard_format = re.compile('^{}$'.format(include_guard_format)) if include_guard_format else None self.__trim = trim self.__include_directories = [Path(x) for x in include_directories] if include_directories else [] + self.__relative_source_directories = relative_source_directories if relative_source_directories else [] \ + if source_directories else [Path('.')] + self.__source_directories = source_directories if source_directories else [Path('.')] self.__processed_files = set() self.__source_files = Queue() @@ -87,7 +93,9 @@ class Quom: self.__write_token(token, is_main_header) - self.__find_possible_source_file(file_path) + file_path = self.__find_possible_source_file(file_path) + if file_path: + self.__source_files.put(file_path) def __write_token(self, token: Token, is_main_header: bool): if isinstance(token, StartToken) or isinstance(token, EndToken): @@ -129,16 +137,21 @@ class Quom: contains_only_whitespace_and_comment_tokens(token.preprocessor_arguments[i + 1:]): return True - def __find_possible_source_file(self, header_file_path: Path): + def __find_possible_source_file(self, header_file_path: Path) -> Union[Path, None]: if header_file_path.suffix in ['.c', '.cpp', '.cxx', '.cc', '.c++', '.cp', '.C']: return # Checks if a equivalent compilation unit exits. for extension in ['.c', '.cpp', '.cxx', '.cc', '.c++', '.cp', '.C']: - file_path = header_file_path.with_suffix(extension) - if file_path.exists(): - self.__source_files.put(file_path) - break + for src_dir in self.__relative_source_directories: + file_path = (header_file_path.parent / src_dir / header_file_path.name).with_suffix(extension) + if file_path.exists(): + return file_path + for src_dir in self.__source_directories: + file_path = (src_dir / header_file_path.name).with_suffix(extension).resolve() + if file_path.exists(): + return file_path + return None def __scan_for_include(self, file_path: Path, token: Token, is_source_file: bool) -> Union[Token, None]: if not isinstance(token, PreprocessorIncludeToken) or not token.is_local_include:

Viatorus/quom

b4bb7665357892411081b86b7c33c0ffc18d2f1b

diff --git a/tests/test_quom/test_normal.py b/tests/test_quom/test_normal.py index f0928dd..38d53f0 100644 --- a/tests/test_quom/test_normal.py +++ b/tests/test_quom/test_normal.py @@ -4,6 +4,7 @@ from pathlib import Path import pytest from quom import Quom, QuomError +from quom.__main__ import main FILE_MAIN_HPP = """\ #pragma once @@ -247,3 +248,13 @@ def test_with_missing_source_file(fs): Quom(Path('main.hpp'), dst) assert dst.getvalue() == RESULT_NORMAL_WITHOUT_SOURCES + + +def test_main(fs): + init() + + main(['main.hpp', 'result.hpp']) + assert Path('result.hpp').read_text() == RESULT_NORMAL + + main(['main.hpp', 'result.hpp', '-S', '.']) + assert Path('result.hpp').read_text() == RESULT_NORMAL diff --git a/tests/test_quom/test_source_directory.py b/tests/test_quom/test_source_directory.py new file mode 100644 index 0000000..790d417 --- /dev/null +++ b/tests/test_quom/test_source_directory.py @@ -0,0 +1,62 @@ +import os +from io import StringIO +from pathlib import Path + +from quom import Quom +from quom.__main__ import main + +FILE_MAIN_HPP = """ +int foo = 3; + +int foo(); +""" + +FILE_MAIN_CPP = """ +int foo() { return 42; } +""" + +RESULT = """ +int foo = 3; + +int foo(); + +int foo() { return 42; } +""" + + +def test_source_directory(fs): + os.makedirs('project/') + os.chdir('project/') + os.makedirs('include/') + os.makedirs('src/') + + with open('include/main.hpp', 'w+') as file: + file.write(FILE_MAIN_HPP) + + with open('src/main.cpp', 'w+') as file: + file.write(FILE_MAIN_CPP) + + dst = StringIO() + Quom(Path('include/main.hpp'), dst) + assert dst.getvalue() != RESULT + + dst = StringIO() + Quom(Path('include/main.hpp'), dst, relative_source_directories=[Path('../src')]) + assert dst.getvalue() == RESULT + + dst = StringIO() + Quom(Path('include/main.hpp'), dst, source_directories=[Path('src').resolve()]) + assert dst.getvalue() == RESULT + + dst = StringIO() + Quom(Path('include/main.hpp'), dst, source_directories=[Path('/project/src')]) + assert dst.getvalue() == RESULT + + main(['include/main.hpp', 'result.hpp', '-S', './../src']) + assert Path('result.hpp').read_text() == RESULT + + main(['include/main.hpp', 'result.hpp', '-S', 'src']) + assert Path('result.hpp').read_text() == RESULT + + main(['include/main.hpp', 'result.hpp', '-S', '/project/src']) + assert Path('result.hpp').read_text() == RESULT

Feature request - Additional directories to search for sources Hi, I found this package very useful, but when trying to use it - encounter with a small problem. The case when sources are located in different directory then their headers - are not supported. The common folder structure of any project can be as follows: _project/_    _public/_    _include/_    _src/_ So it would be nice if it will be possible to specify source directories relative to include directories. For instance via `--relative_source_dir` or `-SI` argument. The most common use can be: `-SI "./" -SI "../" -SI "../src"` By default the directory suffixes array is ["./'] but if at least one -SI argument provided it should be overwritten.

0.0

b4bb7665357892411081b86b7c33c0ffc18d2f1b

[ "tests/test_quom/test_normal.py::test_main", "tests/test_quom/test_source_directory.py::test_source_directory" ]

[ "tests/test_quom/test_normal.py::test_with_missing_source_file", "tests/test_quom/test_normal.py::test_with_include_guard_format", "tests/test_quom/test_normal.py::test_with_mismatching_include_guard_format", "tests/test_quom/test_normal.py::test_normal", "tests/test_quom/test_normal.py::test_normal_without_trim", "tests/test_quom/test_normal.py::test_with_mismatching_stitch", "tests/test_quom/test_normal.py::test_with_stitch_location", "tests/test_quom/test_normal.py::test_with_missing_header_file" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-04-22 19:15:57+00:00

mit

818

Viatorus__quom-43

diff --git a/src/quom/quom.py b/src/quom/quom.py index 5dbaad9..5f7d51c 100644 --- a/src/quom/quom.py +++ b/src/quom/quom.py @@ -80,6 +80,7 @@ class Quom: raise QuomError('Include not found: "{}"'.format(include_path)) # Skip already processed files. + file_path = file_path.resolve() if file_path in self.__processed_files: return self.__processed_files.add(file_path)

Viatorus/quom

8d13a41baea1a930d27a869ff468aa72fe25b100

diff --git a/tests/test_quom/same_file_different_include.py b/tests/test_quom/same_file_different_include.py new file mode 100644 index 0000000..8ef3b9d --- /dev/null +++ b/tests/test_quom/same_file_different_include.py @@ -0,0 +1,41 @@ +import os +from io import StringIO + +from quom import Quom + +FILE_FOO_HPP = """ +#include "../b/bar.hpp" +""" + +FILE_BAR_HPP = """ +int foo(); +""" + +FILE_MAIN_CPP = """ +#include "a/foo.hpp" +#include "b/bar.hpp" +""" + +RESULT = """ + +int foo(); +""" + + +def test_same_file_different_include(fs): + os.makedirs('a') + os.makedirs('b') + + with open('main.cpp', 'w+') as file: + file.write(FILE_MAIN_CPP) + + with open('a/foo.hpp', 'w+') as file: + file.write(FILE_FOO_HPP) + + with open('b/bar.hpp', 'w+') as file: + file.write(FILE_BAR_HPP) + + dst = StringIO() + Quom('main.cpp', dst) + + assert dst.getvalue() == RESULT

option to skip already included files Hello and thanks for creating such awesome utility! I'm using it in my [CTRE](https://github.com/hanickadot/compile-time-regular-expressions) project. I noticed sometimes quom include same file multiple times. Would be possible to add an option to ignore already included files? Based on normalised URL preferably. Thanks! ❤️

0.0

8d13a41baea1a930d27a869ff468aa72fe25b100

[ "tests/test_quom/same_file_different_include.py::test_same_file_different_include" ]

[]

{ "failed_lite_validators": [ "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }

2021-06-15 18:54:32+00:00

mit

819

Viatorus__quom-44

diff --git a/src/quom/__main__.py b/src/quom/__main__.py index 77d99b3..bb62485 100644 --- a/src/quom/__main__.py +++ b/src/quom/__main__.py @@ -29,6 +29,8 @@ def main(args: List[str]): parser.add_argument('--source_directory', '-S', type=str, action='append', default=['.'], help='Set the source directories for source files. ' 'Use ./ or .\\ in front of a path to mark as relative to the header file.') + parser.add_argument('--encoding', '-e', type=str, default='utf-8', + help='The encoding used to read and write all files.') args = parser.parse_args(args) @@ -45,9 +47,9 @@ def main(args: List[str]): else: source_directories.append(path.resolve()) - with args.output_path.open('w+') as file: + with args.output_path.open('w+', encoding=args.encoding) as file: Quom(args.input_path, file, args.stitch, args.include_guard, args.trim, args.include_directory, - relative_source_directories, source_directories) + relative_source_directories, source_directories, args.encoding) def run(): diff --git a/src/quom/quom.py b/src/quom/quom.py index 5f7d51c..3cf4e13 100644 --- a/src/quom/quom.py +++ b/src/quom/quom.py @@ -31,7 +31,8 @@ class Quom: include_guard_format: str = None, trim: bool = True, include_directories: List[Union[Path, str]] = None, relative_source_directories: List[Union[Path]] = None, - source_directories: List[Union[Path]] = None): + source_directories: List[Union[Path]] = None, + encoding: str = 'utf-8'): self.__dst = dst self.__stitch_format = stitch_format self.__include_guard_format = re.compile('^{}$'.format(include_guard_format)) if include_guard_format else None @@ -40,6 +41,7 @@ class Quom: self.__relative_source_directories = relative_source_directories if relative_source_directories else [] \ if source_directories else [Path('.')] self.__source_directories = source_directories if source_directories else [Path('.')] + self.__encoding = encoding self.__processed_files = set() self.__source_files = Queue() @@ -65,16 +67,11 @@ class Quom: is_main_header=False): # First check if file exists relative. file_path = relative_path / include_path - if file_path.exists(): - with file_path.open() as file: - tokens = tokenize(file.read()) - else: + if not file_path.exists(): # Otherwise search in include directories. for include_directory in self.__include_directories: file_path = include_directory / include_path if file_path.exists(): - with file_path.open() as file: - tokens = tokenize(file.read()) break else: raise QuomError('Include not found: "{}"'.format(include_path)) @@ -85,6 +82,9 @@ class Quom: return self.__processed_files.add(file_path) + # Tokenize the file. + tokens = tokenize(file_path.read_text(encoding=self.__encoding)) + for token in tokens: # Find local includes. token = self.__scan_for_include(file_path, token, is_source_file)

Viatorus/quom

1c180ae75c91edf5c174053332aa96007fe13caa

diff --git a/tests/test_quom/same_file_different_include.py b/tests/test_quom/same_file_different_include.py index 8ef3b9d..a913dbc 100644 --- a/tests/test_quom/same_file_different_include.py +++ b/tests/test_quom/same_file_different_include.py @@ -26,13 +26,13 @@ def test_same_file_different_include(fs): os.makedirs('a') os.makedirs('b') - with open('main.cpp', 'w+') as file: + with open('main.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_MAIN_CPP) - with open('a/foo.hpp', 'w+') as file: + with open('a/foo.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_FOO_HPP) - with open('b/bar.hpp', 'w+') as file: + with open('b/bar.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_BAR_HPP) dst = StringIO() diff --git a/tests/test_quom/test_file_encoding.py b/tests/test_quom/test_file_encoding.py new file mode 100644 index 0000000..416a993 --- /dev/null +++ b/tests/test_quom/test_file_encoding.py @@ -0,0 +1,40 @@ +from pathlib import Path + +import pytest + +from quom.__main__ import main + +FILE_MAIN_HPP = """ +int foo(); // qθομ""" + + +def test_file_encoding_default_encoding(fs): + with open('main.hpp', 'w+', encoding='utf-8') as file: + file.write(FILE_MAIN_HPP) + + main(['main.hpp', 'result.hpp']) + assert Path('result.hpp').read_text('utf-8') == FILE_MAIN_HPP + + with pytest.raises(UnicodeDecodeError): + Path('result.hpp').read_text('ascii') + + with pytest.raises(UnicodeDecodeError): + Path('result.hpp').read_text('utf-32') + + +def test_file_encoding_custom_encoding(fs): + with open('main.hpp', 'w+', encoding='utf-32') as file: + file.write(FILE_MAIN_HPP) + + main(['main.hpp', 'result.hpp', '--encoding=utf-32']) + + assert Path('result.hpp').read_text('utf-32') == FILE_MAIN_HPP + + with pytest.raises(UnicodeDecodeError): + Path('result.hpp').read_text('utf-8') + + with pytest.raises(UnicodeDecodeError): + main(['main.hpp', 'result.hpp']) + + with pytest.raises(UnicodeDecodeError): + main(['main.hpp', 'result.hpp', '--encoding=utf-8']) diff --git a/tests/test_quom/test_include_directory.py b/tests/test_quom/test_include_directory.py index 1d8e572..1666ecf 100644 --- a/tests/test_quom/test_include_directory.py +++ b/tests/test_quom/test_include_directory.py @@ -79,28 +79,28 @@ def test_include_directory(fs): os.makedirs('include/my_lib/util') os.makedirs('include/my_other_lib/') - with open('include/my_lib/main.hpp', 'w+') as file: + with open('include/my_lib/main.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_MAIN_HPP) - with open('include/my_lib/core/core.hpp', 'w+') as file: + with open('include/my_lib/core/core.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_CORE_HPP) - with open('include/my_lib/core/core.cpp', 'w+') as file: + with open('include/my_lib/core/core.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_CORE_CPP) - with open('include/my_lib/util/foo.hpp', 'w+') as file: + with open('include/my_lib/util/foo.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_FOO_HPP) - with open('include/my_lib/util/foo.cpp', 'w+') as file: + with open('include/my_lib/util/foo.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_FOO_CPP) - with open('include/my_other_lib/bar.hpp', 'w+') as file: + with open('include/my_other_lib/bar.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_BAR_HPP) - with open('include/my_other_lib/bar.cpp', 'w+') as file: + with open('include/my_other_lib/bar.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_BAR_CPP) - with open('include/my_other_lib/info.hpp', 'w+') as file: + with open('include/my_other_lib/info.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_INFO_HPP) dst = StringIO() diff --git a/tests/test_quom/test_last_source_file.py b/tests/test_quom/test_last_source_file.py index 96e2c98..c227c21 100644 --- a/tests/test_quom/test_last_source_file.py +++ b/tests/test_quom/test_last_source_file.py @@ -82,13 +82,13 @@ int foo = 42;""" def init(): - with open('main.hpp', 'w+') as file: + with open('main.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_MAIN_HPP) - with open('foo.hpp', 'w+') as file: + with open('foo.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_FOO_HPP) - with open('foo.cpp', 'w+') as file: + with open('foo.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_FOO_CPP) @@ -111,7 +111,7 @@ def test_normal_without_trim(fs): def test_without_newline_at_end(fs): - with open('main.hpp', 'w+') as file: + with open('main.hpp', 'w+', encoding='utf-8') as file: file.write('int a;') dst = StringIO() diff --git a/tests/test_quom/test_normal.py b/tests/test_quom/test_normal.py index a718b87..48dd016 100644 --- a/tests/test_quom/test_normal.py +++ b/tests/test_quom/test_normal.py @@ -166,13 +166,13 @@ int foo = 42; def init(): - with open('main.hpp', 'w+') as file: + with open('main.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_MAIN_HPP) - with open('foo.hpp', 'w+') as file: + with open('foo.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_FOO_HPP) - with open('foo.cpp', 'w+') as file: + with open('foo.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_FOO_CPP) diff --git a/tests/test_quom/test_source_directory.py b/tests/test_quom/test_source_directory.py index 790d417..9bd63bc 100644 --- a/tests/test_quom/test_source_directory.py +++ b/tests/test_quom/test_source_directory.py @@ -30,10 +30,10 @@ def test_source_directory(fs): os.makedirs('include/') os.makedirs('src/') - with open('include/main.hpp', 'w+') as file: + with open('include/main.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_MAIN_HPP) - with open('src/main.cpp', 'w+') as file: + with open('src/main.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_MAIN_CPP) dst = StringIO()

Open files with UTF-8 encoding On Windows, Python uses ANSI encoding as its default text encoding when opening files. This is fine if you only use ASCII characters since ANSI is compatible with ASCII. But otherwise you will get errors like the following: ```py File "C:\Users\Username\AppData\Roaming\Python\Python39\site-packages\quom\__main__.py", line 54, in run main(sys.argv[1:]) File "C:\Users\Username\AppData\Roaming\Python\Python39\site-packages\quom\__main__.py", line 49, in main Quom(args.input_path, file, args.stitch, args.include_guard, args.trim, args.include_directory, File "C:\Users\Username\AppData\Roaming\Python\Python39\site-packages\quom\quom.py", line 49, in __init__ self.__process_file(Path(), src_file_path, False, True) File "C:\Users\Username\AppData\Roaming\Python\Python39\site-packages\quom\quom.py", line 70, in __process_file tokens = tokenize(file.read()) UnicodeDecodeError: 'gbk' codec can't decode byte 0xbf in position 2: illegal multibyte sequence ``` (GBK, or CP936, is the ANSI encoding under Simplified Chinese) My suggestion is to change to using UTF-8 encoding to open files, which is more appropriate for most programmers: ```py file_path.open(encoding='utf-8') ```

0.0

1c180ae75c91edf5c174053332aa96007fe13caa

[ "tests/test_quom/test_file_encoding.py::test_file_encoding_custom_encoding" ]

[ "tests/test_quom/same_file_different_include.py::test_same_file_different_include", "tests/test_quom/test_file_encoding.py::test_file_encoding_default_encoding", "tests/test_quom/test_include_directory.py::test_include_directory", "tests/test_quom/test_last_source_file.py::test_normal", "tests/test_quom/test_last_source_file.py::test_normal_without_trim", "tests/test_quom/test_last_source_file.py::test_without_newline_at_end", "tests/test_quom/test_normal.py::test_normal", "tests/test_quom/test_normal.py::test_normal_without_trim", "tests/test_quom/test_normal.py::test_with_include_guard_format", "tests/test_quom/test_normal.py::test_with_mismatching_include_guard_format", "tests/test_quom/test_normal.py::test_with_stitch_location", "tests/test_quom/test_normal.py::test_with_mismatching_stitch", "tests/test_quom/test_normal.py::test_with_missing_header_file", "tests/test_quom/test_normal.py::test_with_missing_source_file", "tests/test_quom/test_normal.py::test_main", "tests/test_quom/test_source_directory.py::test_source_directory" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-06-15 19:31:50+00:00

mit

820

Viatorus__quom-46

diff --git a/src/quom/quom.py b/src/quom/quom.py index 3cf4e13..0f6f7cd 100644 --- a/src/quom/quom.py +++ b/src/quom/quom.py @@ -1,3 +1,4 @@ +import os import re from pathlib import Path from queue import Queue @@ -46,6 +47,7 @@ class Quom: self.__processed_files = set() self.__source_files = Queue() self.__cont_lb = CONTINUOUS_LINE_BREAK_START + self.__used_linesep = None self.__prev_token = EmptyToken() self.__process_file(Path(), src_file_path, False, True) @@ -56,12 +58,7 @@ class Quom: .format(stitch_format)) while not self.__source_files.empty(): self.__process_file(Path(), self.__source_files.get(), True) - # Write last token. - self.__write_token(self.__prev_token, True) - elif self.__cont_lb == CONTINUOUS_LINE_BREAK_START or not isinstance(self.__prev_token, - LinebreakWhitespaceToken): - # Write last token, if not a continuous line break. - self.__write_token(self.__prev_token, True) + self.__write_line_break_if_missing() def __process_file(self, relative_path: Path, include_path: Path, is_source_file: bool, is_main_header=False): @@ -109,9 +106,8 @@ class Quom: if self.__is_cont_line_break(token): return - # Write previous token, store current. - if self.__prev_token: - self.__dst.write(str(self.__prev_token.raw)) + # Write token and store. + self.__dst.write(str(token.raw)) self.__prev_token = token @staticmethod @@ -171,10 +167,15 @@ class Quom: while not self.__source_files.empty(): self.__process_file(Path(), self.__source_files.get(), True) + self.__write_line_break_if_missing() return True def __is_cont_line_break(self, token: Token) -> bool: + # Save a used line break for later. + if self.__used_linesep is None and isinstance(token, LinebreakWhitespaceToken): + self.__used_linesep = token.raw + if not self.__trim: return False @@ -187,3 +188,9 @@ class Quom: self.__cont_lb = CONTINUOUS_LINE_BREAK_START return self.__cont_lb >= CONTINUOUS_BREAK_REACHED + + def __write_line_break_if_missing(self): + if not isinstance(self.__prev_token, LinebreakWhitespaceToken): + if self.__used_linesep is None: + self.__used_linesep = os.linesep # fallback + self.__dst.write(self.__used_linesep)

Viatorus/quom

4633b5aaba35454c425227ec498ea1e19caade39

diff --git a/tests/test_quom/test_last_source_file.py b/tests/test_quom/test_last_source_file.py index c227c21..7f148d2 100644 --- a/tests/test_quom/test_last_source_file.py +++ b/tests/test_quom/test_last_source_file.py @@ -53,7 +53,8 @@ extern int foo; #include <algorithm> -int foo = 42;""" +int foo = 42; +""" RESULT_NORMAL_WITHOUT_TRIM = """\ #pragma once @@ -78,7 +79,8 @@ extern int foo; #include <algorithm> -int foo = 42;""" +int foo = 42; +""" def init(): diff --git a/tests/test_quom/test_line_breaks_when_stitching.py b/tests/test_quom/test_line_breaks_when_stitching.py new file mode 100644 index 0000000..0bb6c37 --- /dev/null +++ b/tests/test_quom/test_line_breaks_when_stitching.py @@ -0,0 +1,98 @@ +from io import StringIO +from pathlib import Path + +from quom import Quom + +FILE_MAIN_CPP = """\ +#include "a.hpp" +int main() { + return 0; +} +// Stitch Begin +// End +""" + +FILE_A_HPP = 'int a;' + +FILE_A_CPP = """\ +#include "b.hpp" +#include "c.hpp" +void mid() {}""" + +FILE_B_HPP = 'int b;' +FILE_C_HPP = 'int c;' + +FILE_B_CPP = """\ +#include """ + +FILE_C_CPP = """\ +#include <c>""" + +RESULT = """\ +int a; +int main() { + return 0; +} +// Stitch Begin +// End +int b; +int c; +void mid() {} +#include +#include <c> +""" + +RESULT_STITCH = """\ +int a; +int main() { + return 0; +} +int b; +int c; +void mid() {} +#include +#include <c> + +// End +""" + + +def init(): + with open('main.hpp', 'w+', encoding='utf-8') as file: + file.write(FILE_MAIN_CPP) + + with open('a.hpp', 'w+', encoding='utf-8') as file: + file.write(FILE_A_HPP) + + with open('a.cpp', 'w+', encoding='utf-8') as file: + file.write(FILE_A_CPP) + + with open('b.hpp', 'w+', encoding='utf-8') as file: + file.write(FILE_B_HPP) + + with open('b.cpp', 'w+', encoding='utf-8') as file: + file.write(FILE_B_CPP) + + with open('c.hpp', 'w+', encoding='utf-8') as file: + file.write(FILE_C_HPP) + + with open('c.cpp', 'w+', encoding='utf-8') as file: + file.write(FILE_C_CPP) + + +def test_add_line_break_in_stitched_files_if_missing(fs): + init() + + dst = StringIO() + Quom(Path('main.hpp'), dst) + + assert dst.getvalue() == RESULT + + +def test_add_line_break_in_stitched_files_if_missing_at_stitch_location(fs): + init() + + dst = StringIO() + Quom(Path('main.hpp'), dst, stitch_format='Stitch Begin') + + assert dst.getvalue() == RESULT_STITCH

when source files have no newline at EOF, content of next file is concatenated right after last closing curly bracket When one of source files has no newline at EOF, the "#include ..."s of the next file appears right after the last closing curly bracket and that causes a compilation error. I know it's a trivial problem to resolve when compiling fails but it would be nice to ensure the content of all source files are separated by newline. ```c++ // bad.cpp void foo(){ // there is no newline at EOF, file ends right after this closing curly bracket. } // b.cpp #include <iostream> // this include is at first line and located outside current build directory // main.cpp include "bad.hpp" include "b.hpp" ... ``` And the source file quom produces has something like: ```c++ void foo(){ }#include <iostream> // this include comes from b.cpp ``` I wrote a test to demonstrate this problem. The following test will fail at current commit which is ```4633b5aa```. ---- ```python from io import StringIO from pathlib import Path from quom import Quom FILE_MAIN_CPP = """\ #include "a.hpp" #include "b.hpp" int main() { return 0; } """ FILE_A_HPP = """\ #ifndef A_HPP_ #define A_HPP_ #endif //A_HPP_ """ FILE_A_CPP = """\ #include "a.hpp" #include "b.hpp" int mid() { }""" FILE_B_HPP = """\ #ifndef B_HPP_ #define B_HPP_ #endif //B_HPP_ """ FILE_B_CPP = """\ #include <memory> """ RESULT = """\ #ifndef A_HPP_ #define A_HPP_ #endif //A_HPP_ #ifndef B_HPP_ #define B_HPP_ #endif //B_HPP_ int main() { return 0; } void mid() { } #include <memory> """ def init(): with open('main.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_MAIN_CPP) with open('a.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_A_HPP) with open('a.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_A_CPP) with open('b.hpp', 'w+', encoding='utf-8') as file: file.write(FILE_B_HPP) with open('b.cpp', 'w+', encoding='utf-8') as file: file.write(FILE_B_CPP) def test_issue_one(fs): init() dst = StringIO() Quom(Path('main.hpp'), dst) assert dst.getvalue() == RESULT ```

0.0

4633b5aaba35454c425227ec498ea1e19caade39

[ "tests/test_quom/test_last_source_file.py::test_normal", "tests/test_quom/test_last_source_file.py::test_normal_without_trim", "tests/test_quom/test_line_breaks_when_stitching.py::test_add_line_break_in_stitched_files_if_missing", "tests/test_quom/test_line_breaks_when_stitching.py::test_add_line_break_in_stitched_files_if_missing_at_stitch_location" ]

[ "tests/test_quom/test_last_source_file.py::test_without_newline_at_end" ]

{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-07-27 20:35:58+00:00

mit

821

VictorPelaez__coral-reef-optimization-algorithm-43

diff --git a/cro/cro.py b/cro/cro.py index 44c17ae..ebc560b 100644 --- a/cro/cro.py +++ b/cro/cro.py @@ -20,6 +20,7 @@ class CRO(object): self.Pd = Pd self.fitness_coral = fitness_coral self.opt = opt + self.opt_multiplier = -1 if opt == "max" else 1 self.L = L self.ke = ke self.seed = seed @@ -83,7 +84,7 @@ class CRO(object): coral_fitness = self.fitness_coral(coral) REEF_fitness.append(coral_fitness) - return np.array(REEF_fitness) + return self.opt_multiplier*np.array(REEF_fitness) def broadcastspawning(self, REEF, REEFpob): """ @@ -197,7 +198,6 @@ class CRO(object): - REEFfitness: new reef fitness """ k = self.k - opt = self.opt np.random.seed(seed=self.seed) Nlarvae = larvae.shape[0] @@ -222,10 +222,7 @@ class CRO(object): REEFfitness[reef_index] = larva_fitness REEF[reef_index] = 1 else: # occupied coral - if opt == "max": - fitness_comparison = larva_fitness > REEFfitness[reef_indices] - else: - fitness_comparison = larva_fitness < REEFfitness[reef_indices] + fitness_comparison = larva_fitness < REEFfitness[reef_indices] if np.any(fitness_comparison): reef_index = reef_indices[np.where(fitness_comparison)[0][0]] @@ -243,7 +240,6 @@ class CRO(object): - pob: reef population - fitness: reef fitness - Fa: fraction of corals to be duplicated - - opt: type of optimization ('max' or 'min') Output: - Alarvae: created larvae, - Afitness: larvae's fitness @@ -255,8 +251,7 @@ class CRO(object): N = pob.shape[0] NA = int(np.round(Fa*N)) - if self.opt=='max': ind = np.argsort(-fitness); - else: ind = np.argsort(fitness) + ind = np.argsort(fitness) fitness = fitness[ind] Alarvae = pob[ind[0:NA], :] @@ -284,10 +279,8 @@ class CRO(object): Pd = self.Pd np.random.seed(seed = self.seed) - if (self.opt=='max'): - ind = np.argsort(REEFfitness) - else: - ind = np.argsort(-REEFfitness) + # Sort by worse fitness (hence the minus sign) + ind = np.argsort(-REEFfitness) sortind = ind[:int(np.round(Fd*REEFpob.shape[0]))] p = np.random.rand(len(sortind)) @@ -390,13 +383,10 @@ class CRO(object): Bestfitness = [] Meanfitness = [] - if opt=='max': - if verbose: print('Reef initialization:', np.max(REEFfitness)) - Bestfitness.append(np.max(REEFfitness)) - else: - if verbose: print('Reef initialization:', np.min(REEFfitness)) - Bestfitness.append(np.min(REEFfitness)) - Meanfitness.append(np.mean(REEFfitness)) + Bestfitness.append(self.opt_multiplier*np.min(REEFfitness)) + Meanfitness.append(self.opt_multiplier*np.mean(REEFfitness)) + if verbose: + print('Reef initialization:', self.opt_multiplier*np.min(REEFfitness)) for n in range(Ngen): @@ -420,23 +410,18 @@ class CRO(object): (REEF, REEFpob, REEFfitness) = self.depredation(REEF, REEFpob, REEFfitness) (REEF, REEFpob, REEFfitness) = self.extremedepredation(REEF, REEFpob, REEFfitness, int(np.round(self.ke*N*M))) - if opt=='max': Bestfitness.append(np.max(REEFfitness)) - else: Bestfitness.append(np.min(REEFfitness)) - Meanfitness.append(np.mean(REEFfitness)) + Bestfitness.append(self.opt_multiplier*np.min(REEFfitness)) + Meanfitness.append(self.opt_multiplier*np.mean(REEFfitness)) - if (n%10==0) & (n!=Ngen): - if (opt=='max') & (verbose): print('Best-fitness:', np.max(REEFfitness), '\n', str(n/Ngen*100) + '% completado \n' ); - if (opt=='min') & (verbose): print('Best-fitness:', np.min(REEFfitness), '\n', str(n/Ngen*100) + '% completado \n' ); + if all([n%10 == 0, n != Ngen, verbose]): + print('Best-fitness:', self.opt_multiplier*np.min(REEFfitness), '\n', str(n/Ngen*100) + '% completado \n' ); - if opt=='max': - if verbose: print('Best-fitness:', np.max(REEFfitness), '\n', str(100) + '% completado \n' ) - ind_best = np.where(REEFfitness == np.max(REEFfitness))[0][0] - else: - if verbose: print('Best-fitness:', np.min(REEFfitness), '\n', str(100) + '% completado \n' ) - ind_best = np.where(REEFfitness == np.min(REEFfitness))[0][0] + if verbose: + print('Best-fitness:', self.opt_multiplier*np.min(REEFfitness), '\n', str(100) + '% completado \n' ) + ind_best = np.where(REEFfitness == np.min(REEFfitness))[0][0] self.plot_results(Bestfitness, Meanfitness) print('Best coral: ', REEFpob[ind_best, :]) - print('Best solution:', REEFfitness[ind_best]) + print('Best solution:', self.opt_multiplier*REEFfitness[ind_best]) return (REEF, REEFpob, REEFfitness, ind_best, Bestfitness, Meanfitness)

VictorPelaez/coral-reef-optimization-algorithm

9939a280c87090b7ae575a23670f49a265ad017a

diff --git a/cro/tests.py b/cro/tests.py index abd19cf..9bde3df 100644 --- a/cro/tests.py +++ b/cro/tests.py @@ -91,14 +91,14 @@ def test_larvaesettling_nonemptyreef(): [1,0,1,1]]) REEF = np.array([0,1,1,1]) - REEFfitness = np.array([0,1,2,11]) + REEFfitness = -np.array([0,1,2,11]) larvae = np.array([[1,0,0,0], [0,1,1,0], [0,1,0,0], [1,0,0,1]]) - larvaefitness = np.array([8,6,4,9]) + larvaefitness = -np.array([8,6,4,9]) N, L = REEFpob.shape M = 1 @@ -126,7 +126,7 @@ def test_larvaesettling_nonemptyreef(): [1,0,0,1], [0,0,1,0], [1,0,1,1]]) - REEFfitness_exp = np.array([8,9,2,11]) + REEFfitness_exp = -np.array([8,9,2,11]) np.testing.assert_almost_equal(REEF_res, np.array([1,1,1,1])) np.testing.assert_almost_equal(REEFpob_res, REEFpob_exp)

create a opt_multiplier (-1 or 1) with opt argument One of the main point suggested in Issue #22. Using opt argument, create a self.opt_multiplier (1, -1) It looks an improvement in 2 functions: - budding() ``` if self.opt=='max': ind = np.argsort(-fitness); else: ind = np.argsort(fitness) ``` - depredation() ``` if (self.opt=='max'): ind = np.argsort(REEFfitness) else: ind = np.argsort(-REEFfitness) ``` @apastors Did your proposal cover anything else? regards

0.0

9939a280c87090b7ae575a23670f49a265ad017a

[ "cro/tests.py::test_larvaesettling_nonemptyreef" ]

[ "cro/tests.py::test_croCreation", "cro/tests.py::test_croInit", "cro/tests.py::test_reefinitializationDisc", "cro/tests.py::test_larvaesettling_emptyreef" ]

{ "failed_lite_validators": [ "has_issue_reference", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2017-10-29 08:56:15+00:00

mit

822

VictorPelaez__coral-reef-optimization-algorithm-45

diff --git a/.travis.yml b/.travis.yml index 8bc2fee..15ab2f9 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,7 +9,6 @@ install: - pip install -r requirements.txt script: - pytest tests/ - deploy: provider: pypi user: victorpelaez diff --git a/cro/cro.py b/cro/cro.py index b7231dd..7c24105 100644 --- a/cro/cro.py +++ b/cro/cro.py @@ -1,15 +1,24 @@ #!/usr/bin/env python # coding=utf-8 ############################################################################### - -from __future__ import division +from __future__ import division, print_function +import sys +import logging import numpy as np + +from .reef_initialization import get_reefinit_function from .larvaemutation import get_larvaemutation_function class CRO(object): def __init__(self, Ngen, N, M, Fb, Fa, Fd, r0, k, Pd, fitness_coral, opt, L=None, ke=0.2, npolyps=1, seed=None, mode='bin', param_grid={}, verbose=False): + # Set logging configuration + logging_level = logging.INFO if verbose else logging.WARNING + logging.basicConfig(stream=sys.stdout, + format="%(message)s") + logging.getLogger().setLevel(logging_level) + self.Ngen = Ngen self.N = N self.M = M @@ -29,9 +38,11 @@ class CRO(object): self.mode = mode self.param_grid = param_grid self.verbose = verbose - - print("[*Running] Initialization: ", self.opt) + self.reefinit_function = get_reefinit_function(mode) + self.larvaemutation_function = get_larvaemutation_function(mode) + logging.info("Running Initialization: %s", self.opt) + def reefinitialization (self): """ function [REEF,REEFpob]=reefinitialization(M,N,r0,L) @@ -45,37 +56,9 @@ class CRO(object): - REEF: reef matrix - REEFpob: population matrix """ - - # print error. Maybe use other place for all arg-checks - if ( (self.param_grid=={}) & (self.mode =='disc') ): - print('\nThis mode (', self.mode, ') needs a param_grid as a dictionary') - return -1 - - # commom for all modes - np.random.seed(seed = self.seed) - O = int(np.round(self.N*self.M*self.r0)) # number of occupied reefs - - # Binary mode - if self.mode =='bin': - A = np.random.randint(2, size=[O, self.L]) - B = np.zeros([( (self.N*self.M)-O), self.L], int) - REEFpob = np.concatenate([A,B]) # Population creation - REEF = np.array((REEFpob.any(axis=1)),int) - return (REEF, REEFpob) - - # Discrete mode - elif self.mode =='disc': - for key, value in self.param_grid.items(): - valmax = (value[1] - value[0] + 1) - A = np.random.randint(valmax, size=[O, self.L]) + value[0] - B = np.zeros([( (self.N*self.M)-O), self.L], int) - REEFpob = np.concatenate([A,B]) # Population creation - REEF = np.array((REEFpob.any(axis=1)),int) - return (REEF, REEFpob) - - else: - print('\nThis mode (', self.mode, ') is not available') - return -1 + np.random.seed(seed = self.seed) # commom for all modes + REEF, REEFpob = self.reefinit_function(self.M, self.N, self.r0, self.L, param_grid=self.param_grid) + return REEF, REEFpob def fitness(self, REEFpob): """ @@ -163,8 +146,8 @@ class CRO(object): pos = np.random.randint(brooders.shape[1], size=(npolyps, nbrooders)) - larvaemutation_function = get_larvaemutation_function(self.mode) - brooders = larvaemutation_function(brooders, pos, delta=1, param_grid=self.param_grid, seed=self.seed) + brooders = self.larvaemutation_function(brooders, pos, delta=1, + param_grid=self.param_grid, seed=self.seed) return brooders @@ -384,8 +367,7 @@ class CRO(object): Bestfitness.append(self.opt_multiplier*np.min(REEFfitness)) Meanfitness.append(self.opt_multiplier*np.mean(REEFfitness)) - if verbose: - print('Reef initialization:', self.opt_multiplier*np.min(REEFfitness)) + logging.info('Reef initialization: %s', self.opt_multiplier*np.min(REEFfitness)) for n in range(Ngen): @@ -413,14 +395,13 @@ class CRO(object): Meanfitness.append(self.opt_multiplier*np.mean(REEFfitness)) if all([n%10 == 0, n != Ngen, verbose]): - print('Best-fitness:', self.opt_multiplier*np.min(REEFfitness), '\n', str(n/Ngen*100) + '% completado \n' ); + logging.info('Best-fitness: %s, (%.2f%% completado)', self.opt_multiplier*np.min(REEFfitness), n/Ngen*100) - if verbose: - print('Best-fitness:', self.opt_multiplier*np.min(REEFfitness), '\n', str(100) + '% completado \n' ) + logging.info('Best-fitness: %s. (100%% completado)', self.opt_multiplier*np.min(REEFfitness)) ind_best = np.where(REEFfitness == np.min(REEFfitness))[0][0] self.plot_results(Bestfitness, Meanfitness) print('Best coral: ', REEFpob[ind_best, :]) - print('Best solution:', self.opt_multiplier*REEFfitness[ind_best]) + print('Best solution: ', self.opt_multiplier*REEFfitness[ind_best]) return (REEF, REEFpob, REEFfitness, ind_best, Bestfitness, Meanfitness) diff --git a/cro/larvaemutation.py b/cro/larvaemutation.py index 835e7f6..20211a7 100644 --- a/cro/larvaemutation.py +++ b/cro/larvaemutation.py @@ -87,6 +87,6 @@ def get_larvaemutation_function(mode): logging.info("Using {}".format(name)) else: name, func = mode_functions[0] - logging.info("Using {} for initializing the reef".format(name)) + logging.info("Using {} for the brooding operator".format(name)) - return func \ No newline at end of file + return func diff --git a/cro/reef_initialization.py b/cro/reef_initialization.py new file mode 100644 index 0000000..211b87f --- /dev/null +++ b/cro/reef_initialization.py @@ -0,0 +1,86 @@ +""" +Module that contains all the functions that perform the reef +initialization. + +Every function should start with the mode name it performs, +followed by an underscore and the function name. + +It should accept the following arguments: + - M: Reef size + - N: Reef size + - r0: occupied/total ratio + - L: coral length + - kwargs: extra arguments that the function might need (see + https://stackoverflow.com/a/1769475 for an + explanation on kwargs) + +It should return a tuple with (REEF, REEFpob) +""" +import logging + +import numpy as np + +from .utils import get_module_functions + +def bin_binary(M, N, r0, L, **kwargs): + """ + Each value in each coral in the reef is a boolean value, i.e, + either a 0 or a 1 + """ + O = int(np.round(N*M*r0)) # number of occupied reefs + A = np.random.randint(2, size=[O, L]) + B = np.zeros([((N*M)-O), L], int) + REEFpob = np.concatenate([A, B]) # Population creation + REEF = np.array((REEFpob.any(axis=1)),int) + return (REEF, REEFpob) + +def disc_equal_range(M, N, r0, L, **kwargs): + """ + Each value in each coral in the reef is an integer in the range + specified by the keyword argument `param_grid`. `param_grid` + must have the next format: + + >>> param_grid = { + "x": [2, 10] + } + + where "x" can be basically anything, and its value is a list + with both minimum and maximum value. + In this example each coral will contain integers between 2 and 10 + """ + try: + param_grid = kwargs["param_grid"] + except KeyError: + raise ValueError("disc mode needs a param_grid as a dictionary") + + O = int(np.round(N*M*r0)) # number of occupied reefs + for _, value in param_grid.items(): + valmax = (value[1] - value[0] + 1) + A = np.random.randint(valmax, size=[O, L]) + value[0] + B = np.zeros([((N*M)-O), L], int) + REEFpob = np.concatenate([A,B]) # Population creation + REEF = np.array((REEFpob.any(axis=1)),int) + return (REEF, REEFpob) + +""""" +UTILS +""""" +def get_reefinit_function(mode): + """ + Returns the init function for the given mode. + If more than one function exists, return one randomly. + """ + reef_init_functions = get_module_functions(__name__) + mode_functions = [(name, func) for name, func in reef_init_functions.items() + if name.startswith(mode)] + if not mode_functions: + raise ValueError("No initialization function for mode {}".format(mode)) + elif len(mode_functions) > 1: + logging.warning("More than one initialization function for mode {}".format(mode)) + name, func = mode_functions[0] + logging.info("Using {}".format(name)) + else: + name, func = mode_functions[0] + logging.info("Using {} for initializing the reef".format(name)) + + return func diff --git a/cro/utils.py b/cro/utils.py index 5ffd7ff..980e657 100644 --- a/cro/utils.py +++ b/cro/utils.py @@ -31,5 +31,3 @@ def get_module_functions(module_name): """ current_module = sys.modules[module_name] return dict(getmembers(current_module, predicate=isfunction)) - - diff --git a/examples/example_advanced.py b/examples/example_advanced.py index 9b5d55b..39e1378 100644 --- a/examples/example_advanced.py +++ b/examples/example_advanced.py @@ -90,9 +90,9 @@ if __name__ == '__main__': get_prediction=lambda gbr, X: gbr.predict(X), metric=mean_squared_error) start = time.time() - cro = CRO(Ngen, N, M, Fb, Fa, Fd, r0, k, Pd, fitness_coral, opt, L, verbose=True) + cro = CRO(Ngen, N, M, Fb, Fa, Fd, r0, k, Pd, fitness_coral, opt, L, seed=13, verbose=True) (REEF, REEFpob, REEFfitness, ind_best, Bestfitness, Meanfitness) = cro.fit(X, y, gbr) print("Example II: feature selection, regression (min mse): ", time.time() - start, "seconds.") names = np.array(['CRIM', 'ZN', 'INDUS', 'CHAS', 'NOX', 'RM', 'AGE', 'DIS', 'RAD', 'TAX', 'PTRATIO', 'B', 'LSTAT']) - print(names[REEFpob[ind_best, :]>0]) \ No newline at end of file + print(names[REEFpob[ind_best, :]>0])

VictorPelaez/coral-reef-optimization-algorithm

bc0b2fd006187f3e269c6e1898241866f502bd25

diff --git a/tests/__init__.py b/tests/__init__.py index e69de29..1581836 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -0,0 +1,4 @@ +import sys +import os + +sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) diff --git a/tests/test_cro.py b/tests/test_cro.py index f71a78f..5c8a9ed 100644 --- a/tests/test_cro.py +++ b/tests/test_cro.py @@ -3,11 +3,6 @@ ############################################################################### # run with: # python -m pytest tests/test_cro.py - -import sys -import os -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) - import numpy as np from cro.cro import CRO @@ -119,7 +114,6 @@ def test_larvaesettling_nonemptyreef(): """ Due to the passed seed, [1,0,0,0] will be placed in the empty coral (index 0) - Then, larva [0,1,1,0] will try to settle in indices [0,3,1], settling in the third try (index 1) Larva [0,1,0,0] will try in indices [0,3,3], being discarded Larva [1,0,0,1] will try in indices [3,3,1], settling in the third try (index 1) @@ -176,4 +170,4 @@ def test_settle_larvae(): assert REEF_res[indices] == 1 np.testing.assert_almost_equal(REEFpob_res[indices, :], larvae) - np.testing.assert_almost_equal(REEFfitness_res[indices], larvaefitness) \ No newline at end of file + np.testing.assert_almost_equal(REEFfitness_res[indices], larvaefitness) diff --git a/tests/test_fitness.py b/tests/test_fitness.py index 30f0a0e..73eafe7 100644 --- a/tests/test_fitness.py +++ b/tests/test_fitness.py @@ -3,11 +3,6 @@ ############################################################################### # run with: # python -m pytest tests/test_fitness.py - -import sys -import os -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) - import numpy as np from cro.fitness import max_ones @@ -37,4 +32,4 @@ def test_feature_selection(): """ To be added """ - pass \ No newline at end of file + pass diff --git a/tests/test_larvaemutation.py b/tests/test_larvaemutation.py index 9713491..c564422 100644 --- a/tests/test_larvaemutation.py +++ b/tests/test_larvaemutation.py @@ -3,11 +3,6 @@ ############################################################################### # run with: # python -m pytest tests/test_larvaemutation.py - -import sys -import os -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) - import numpy as np from cro.larvaemutation import get_larvaemutation_function @@ -79,4 +74,4 @@ def test_get_larvaemutation_function(): f = get_larvaemutation_function('bin') assert 'function bin_larvaemutation' in str(f) f = get_larvaemutation_function('disc') - assert 'function disc_larvaemutation' in str(f) \ No newline at end of file + assert 'function disc_larvaemutation' in str(f) diff --git a/tests/test_reefinitialization.py b/tests/test_reefinitialization.py index 567c7dd..198f6bd 100644 --- a/tests/test_reefinitialization.py +++ b/tests/test_reefinitialization.py @@ -3,28 +3,28 @@ ############################################################################### # run with: # python -m pytest tests/test_larvaemutation.py - -import sys -import os -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) - import numpy as np -#from cro.reefinitialization import bin_binary, disc_equal_range +from cro.reef_initialization import bin_binary, disc_equal_range # ------------------------------------------------------ # reefinitialization module # ------------------------------------------------------ - def test_bin_binary(): """ Test that corals in the population only contain values in {0, 1} """ - pass - - + M, N, r0, L = 2, 2, 0.6, 8 + REEF, REEFpob = bin_binary(M, N, r0, L) + assert set(REEFpob.ravel()) == {0, 1} + def test_disc_equal_range(): """ Test that corals in population contain values specified in the grid """ - pass \ No newline at end of file + M, N, r0, L = 2, 2, 0.6, 8 + grid = {'x': [2, 10]} # Discrete values between 2 and 10 + + REEF, REEFpob = disc_equal_range(M, N, r0, L, param_grid=grid) + p = sum(REEFpob[np.where(REEFpob!=0)]<grid['x'][0]) + sum(REEFpob[np.where(REEFpob!=0)]>grid['x'][1]) + assert p == 0

Refactor Reef initialization To improve the code architecture, a module with different initialization functions should be considered: one function per mode that accepts all the parameters it needs (`M`, `N`, `L`, `param_grid`, ...) and have it return `REEFpob`. This way we could add documentation for each initialization explaining how it is done and which parameters it needs. Also each function could be easily testable.

0.0

bc0b2fd006187f3e269c6e1898241866f502bd25

[ "tests/test_cro.py::test_croCreation", "tests/test_cro.py::test_croInit", "tests/test_cro.py::test_reefinitializationDisc", "tests/test_cro.py::test_larvaesettling_emptyreef", "tests/test_cro.py::test_larvaesettling_nonemptyreef", "tests/test_cro.py::test_brooding", "tests/test_cro.py::test_settle_larvae", "tests/test_fitness.py::test_max_ones", "tests/test_fitness.py::test_feature_selection", "tests/test_larvaemutation.py::test_bin_larvaemutattion", "tests/test_larvaemutation.py::test_disc_larvaemutattion", "tests/test_larvaemutation.py::test_cont_larvaemutattion", "tests/test_larvaemutation.py::test_get_larvaemutation_function", "tests/test_reefinitialization.py::test_bin_binary", "tests/test_reefinitialization.py::test_disc_equal_range" ]

[]

{ "failed_lite_validators": [ "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2017-11-02 21:28:47+00:00

mit

823

Vipul-Cariappa__py-utility-7

diff --git a/README.md b/README.md index e6336ee..47feb7f 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,8 @@ Utility functions for managing and monitoring python resources. ## installation <pre><code>pip install py-utility</code></pre> -## Decorator Function + +## Documentation ### memoryit memoryit returns the total memory used by the function at runtime in bytes. @@ -12,25 +13,32 @@ memoryit returns the total memory used by the function at runtime in bytes. Example Code: <pre><code>from pyutility import memoryit -@memoryit + def prime_check(x): for i in range(2, x): if x % i == 0: return False - return True</code></pre> + return True + +if __name__ == "__main__": + ... + memoryit(prime_check, args=(89,)) + ... + + </code></pre> ### limit_memory -limit_memory limits the memory consumption of function at runtime. It takes the limit in MB. You will find unexpected behaviour if too low value is set. The default value is 25 MB. It is throw MemoryError if it exceeds the limit. +limit_memory limits the memory consumption of function at runtime. It takes the limit in MB. You will find unexpected behaviour if too low value is set. The default value is 25 MB. It throws MemoryError if it exceeds the limit. Example Code: <pre><code>from pyutility import limit_memory -@limit_memory(30) -def prime_check(x): - for i in range(2, x): - if x % i == 0: - return False - return True</code></pre> + +if __name__ == "__main__": + ... + limit_memory(prime_check, memory=30, args=(89,)) + ... + </code></pre> ### timeit timeit returns the total time take to execute the function in seconds. @@ -38,12 +46,11 @@ timeit returns the total time take to execute the function in seconds. Example Code: <pre><code>from pyutility import timeit -@timeit -def prime_check(x): - for i in range(2, x): - if x % i == 0: - return False - return True</code></pre> + +if __name__ == "__main__": + ... + timeit(prime_check, args=(89,)) + ...</code></pre> ### limit_time limit_time limits the time used to execute the function. It takes limit as seconds. The default value is 10 seconds. It throws TimeoutError if it exceeds the limit. @@ -51,12 +58,12 @@ limit_time limits the time used to execute the function. It takes limit as secon Example Code: <pre><code>from pyutility import limit_time -@limit_time(30) -def prime_check(x): - for i in range(2, x): - if x % i == 0: - return False - return True</code></pre> + +if __name__ == "__main__": + ... + limit_time(prime_check, time=2, args=(89,)) + ...</code></pre> ## Contribution All contributions are welcomed. If it is a bug fix or new feature, creating new issue is highly recommend before any pull request. + If you want any new feature to be included create new issue asking for the feature with a use case and example code if possible. diff --git a/pyutility/memoryutil.py b/pyutility/memoryutil.py index 29c5f3f..ca8d3ed 100644 --- a/pyutility/memoryutil.py +++ b/pyutility/memoryutil.py @@ -4,7 +4,7 @@ import resource def me_worker(func, storage, *args, **kwargs): - """measures the peak memory consumption of given function; should be run by memoryit decorator as a new process + """measures the peak memory consumption of given function Args: func (`function`): function to execute @@ -30,11 +30,11 @@ def me_worker(func, storage, *args, **kwargs): def li_worker(func, limit, storage, *args, **kwargs): - """limits the memory consumption of given function; should be run by limit_memory decorator as a new process + """limits the memory consumption of given function Args: func (`function`): function to execute - limit (`int`): maximum allowed memory consuption + limit (`int`): maximum allowed memory consumption storage (`list`): multiprocessing.Manager().List() to store the peak memory args (`tuple`): arguments for the function kwargs(`dict`): keyword arguments for the function @@ -57,53 +57,51 @@ def li_worker(func, limit, storage, *args, **kwargs): return 0 -def memoryit(func): - """decorator function to measures the peak memory consumption of given function +def memoryit(func, args=(), kwargs={}): + """measures the peak memory consumption of given function Args: func (`function`): function to execute + args (`tuple`): arguments for the function + kwargs(`dict`): keyword arguments for the function Return: peak memory used during the execution of given function in bytes (`int`) """ - def wrapper(*args, **kwargs): - ctx = mp.get_context('spawn') - manager = ctx.Manager() - com_obj = manager.list() - p = ctx.Process(target=me_worker, args=( - func, com_obj, *args), kwargs=kwargs) - p.start() - p.join() - - return com_obj[-1] + ctx = mp.get_context('spawn') + manager = ctx.Manager() + com_obj = manager.list() + p = ctx.Process(target=me_worker, args=( + func, com_obj, *args), kwargs=kwargs) + p.start() + p.join() - return wrapper + return com_obj[-1] -def limit_memory(value=15): - """decorator function to limits the memory consumption of given function +def limit_memory(func, memory=25, args=(), kwargs={}): + """limits the memory consumption of given function. + If limit set is very low it will not behave in expected way. Args: - value (`int`): maximum allowed memory consumption in MB func (`function`): function to execute + limit (`int`): maximum allowed memory consumption in MB default is 25 MB + args (`tuple`): arguments for the function + kwargs(`dict`): keyword arguments for the function Return: return value of function or MemoryError """ - def decorator(func): - def wrapper(*args, **kwargs): - ctx = mp.get_context('spawn') - manager = ctx.Manager() - com_obj = manager.list() - p = ctx.Process(target=li_worker, args=( - func, value, com_obj, *args), kwargs=kwargs) - p.start() - p.join() - - if isinstance(com_obj[-1], Exception): - raise com_obj[-1] - else: - return com_obj[-1] - - return wrapper - return decorator + + ctx = mp.get_context('spawn') + manager = ctx.Manager() + com_obj = manager.list() + p = ctx.Process(target=li_worker, args=( + func, memory, com_obj, *args), kwargs=kwargs) + p.start() + p.join() + + if isinstance(com_obj[-1], Exception): + raise com_obj[-1] + else: + return com_obj[-1] diff --git a/pyutility/timeutil.py b/pyutility/timeutil.py index 325830a..dc2c0bd 100644 --- a/pyutility/timeutil.py +++ b/pyutility/timeutil.py @@ -4,8 +4,7 @@ import signal def me_worker(func, storage, *args, **kwargs): - """measures the time taken to execute given function should be run by timeit decorator as a new process - + """measures the time taken to execute given function Args: func (`function`): function to execute storage (`list`): multiprocessing.Manager().List() to store the time taken to excute @@ -13,7 +12,7 @@ def me_worker(func, storage, *args, **kwargs): kwargs(`dict`): keyword arguments for the function Return: - time taken to execute the given function in seconds (`int`) + time taken to execute the given function in seconds (`float`) """ t1 = time() func(*args, **kwargs) @@ -23,7 +22,7 @@ def me_worker(func, storage, *args, **kwargs): def li_worker(func, time, storage, *args, **kwargs): - """limits the time taken for exection of given function; should be run by limit_time decorator as a new process + """limits the time taken for exection of given function Args: func (`function`): function to execute @@ -52,53 +51,51 @@ def li_worker(func, time, storage, *args, **kwargs): return 0 -def timeit(func): - """decorator function to measure time taken to execute a given function in new process +def timeit(func, args=(), kwargs={}): + """measures the time taken to execute given function Args: func (`function`): function to execute + args (`tuple`): arguments for the function + kwargs(`dict`): keyword arguments for the function Return: - time taken to execute the given function in seconds (`int`) + time taken to execute the given function in seconds (`float`) """ - def wrapper(*args, **kwargs): - ctx = mp.get_context('spawn') - manager = ctx.Manager() - com_obj = manager.list() - p = ctx.Process(target=me_worker, args=( - func, com_obj, *args), kwargs=kwargs) - p.start() - p.join() - return com_obj[-1] - return wrapper + ctx = mp.get_context('spawn') + manager = ctx.Manager() + com_obj = manager.list() + p = ctx.Process(target=me_worker, args=( + func, com_obj, *args), kwargs=kwargs) + p.start() + p.join() + + return com_obj[-1] -def limit_time(time=10): - """decorator function to limits the time taken to execute given function +def limit_time(func, time=10, args=(), kwargs={}): + """limits the time taken for exection of given function Args: - value (`int`): maximum allowed time in seconds func (`function`): function to execute + limit (`int`): maximum allowed time in seconds, default is 10 + args (`tuple`): arguments for the function + kwargs(`dict`): keyword arguments for the function Return: return value of function or TimeoutError """ - def inner(func): - def wrapper(*args, **kwargs): - - ctx = mp.get_context('spawn') - manager = ctx.Manager() - com_obj = manager.list() - p = ctx.Process(target=li_worker, args=( - func, time, com_obj, *args), kwargs=kwargs) - p.start() - p.join() - - if isinstance(com_obj[-1], Exception): - raise com_obj[-1] - else: - return com_obj[-1] - - return wrapper - return inner + + ctx = mp.get_context('spawn') + manager = ctx.Manager() + com_obj = manager.list() + p = ctx.Process(target=li_worker, args=( + func, time, com_obj, *args), kwargs=kwargs) + p.start() + p.join() + + if isinstance(com_obj[-1], Exception): + raise com_obj[-1] + else: + return com_obj[-1] diff --git a/pyutility/utility.py b/pyutility/utility.py index d0eefbc..841fd7e 100644 --- a/pyutility/utility.py +++ b/pyutility/utility.py @@ -15,7 +15,7 @@ def me_worker(func, storage, *args, **kwargs): kwargs(`dict`): keyword arguments for the function Return: - peak memory used, time taken during the execution of given function in bytes (`list` of 'int', 'float') + peak memory used, time taken for the execution of given function (`list` of 'int', 'float') """ tm.start() @@ -74,58 +74,54 @@ def li_worker(func, storage, time, memory, *args, **kwargs): return 0 -def measureit(func): - """decorator function to measures the peak memory consumption and time taken to execute given function +def measureit(func, args=(), kwargs={}): + """measures the peak memory consumption and time taken for execution of given function Args: func (`function`): function to execute + args (`tuple`): arguments for the function + kwargs(`dict`): keyword arguments for the function Return: - peak memory used, time taken during the execution of given function in bytes (`tuple` of 'int', 'float') + peak memory used (MB), time taken (seconds) during the execution of given function (`list` of 'int', 'float') """ - def wrapper(*args, **kwargs): - ctx = mp.get_context('spawn') - manager = ctx.Manager() - com_obj = manager.list() - p = ctx.Process(target=me_worker, args=( - func, com_obj, *args), kwargs=kwargs) - p.start() - p.join() - - if len(com_obj) == 2: - return tuple(com_obj) - - # else - raise com_obj[-1] + ctx = mp.get_context('spawn') + manager = ctx.Manager() + com_obj = manager.list() + p = ctx.Process(target=me_worker, args=( + func, com_obj, *args), kwargs=kwargs) + p.start() + p.join() - return wrapper + if len(com_obj) == 2: + return tuple(com_obj) + # else + raise com_obj[-1] -def limit_resource(time=10, memory=25): - """decorator function to limits the memory consumption and time taken to execute given function + +def limit_resource(func, time=10, memory=25, args=(), kwargs={}): + """limits the memory consumption and time taken to execute given function Args: - time (`int`): maximum allowed time consuption in seconds - memory (`int`): maximum allowed memory consuption in MB func (`function`): function to execute + time (`int`): maximum allowed time in seconds, default is 10 + memory (`int`): maximum allowed memory consumption in MB, default is 25 + args (`tuple`): arguments for the function + kwargs(`dict`): keyword arguments for the function Return: return value of function or MemoryError or TimeoutError """ - def decorator(func): - def wrapper(*args, **kwargs): - ctx = mp.get_context('spawn') - manager = ctx.Manager() - com_obj = manager.list() - p = ctx.Process(target=li_worker, args=( - func, com_obj, time, memory, *args), kwargs=kwargs) - p.start() - p.join() - - if isinstance(com_obj[-1], Exception): - raise com_obj[-1] - else: - return com_obj[-1] - - return wrapper - return decorator + ctx = mp.get_context('spawn') + manager = ctx.Manager() + com_obj = manager.list() + p = ctx.Process(target=li_worker, args=( + func, com_obj, time, memory, *args), kwargs=kwargs) + p.start() + p.join() + + if isinstance(com_obj[-1], Exception): + raise com_obj[-1] + # else + return com_obj[-1]

Vipul-Cariappa/py-utility

8f66fc1fc569c34798865ab063f1da4e7753c9d5

diff --git a/tests/func.py b/tests/func.py new file mode 100644 index 0000000..cbe21ea --- /dev/null +++ b/tests/func.py @@ -0,0 +1,20 @@ +def memory(x): + x = [i for i in range(x)] + return -1 + + +def time(x): + # recursive function to find xth fibonacci number + if x < 3: + return 1 + return time(x-1) + time(x-2) + + +def error(x=None): + # error function + return "a" / 2 + + +def return_check(*args, **kwagrs): + # args and kwargs function + return list(args) + list(kwagrs.values()) diff --git a/tests/test_memory.py b/tests/test_memory.py index c5b3197..437a8ac 100644 --- a/tests/test_memory.py +++ b/tests/test_memory.py @@ -1,50 +1,46 @@ from unittest import TestCase from pyutility import limit_memory, memoryit - -def func1(x): - x = [i for i in range(x)] - return -1 - - -def func2(): - # error function - return "a" / 2 - - -def func3(*args, **kwagrs): - # args and kwargs function - return list(args) + list(kwagrs.values()) +from .func import memory, error, return_check class MemoryitTest(TestCase): - def setUp(self): - self.er_func = memoryit(func2) - self.func = memoryit(func1) - self.ka_func = memoryit(func3) - def test_memoryit_1(self): - self.assertIsInstance(self.func(5), int) + def test_memoryit1(self): + v = memoryit(memory, args=(5,)) + self.assertIsInstance(v, int) - def test_memoryit_2(self): - self.assertRaises(Exception, self.er_func) + def test_memoryit2(self): + self.assertRaises(Exception, memoryit, error, 5) class LimitMemoryTest(TestCase): - def setUp(self): - self.er_func = limit_memory()(func2) - self.func = limit_memory()(func1) - self.ka_func = limit_memory()(func3) def test_limit_memory_1(self): - self.assertEqual(self.func(3), -1) + v = limit_memory(memory, args=(10,)) + self.assertEqual(v, -1) def test_limit_memory_2(self): - self.assertRaises(Exception, self.er_func) + self.assertRaises( + Exception, + limit_memory, + error, + args=(100_000_000,) + ) def test_limit_memory_3(self): - self.assertRaises(MemoryError, self.func, 100_000_000) + self.assertRaises( + MemoryError, + limit_memory, + memory, + args=(500_000_000,) + ) def test_limit_memory_4(self): - self.assertEqual(self.ka_func( - 1, 2, 3, four=4, five=5), [1, 2, 3, 4, 5]) + v = limit_memory( + return_check, + args=(1, 2, 3), + kwargs={"four": 4, "five": 5} + ) + + self.assertEqual(v, [1, 2, 3, 4, 5]) diff --git a/tests/test_time.py b/tests/test_time.py index ce5ec03..78bbd2c 100644 --- a/tests/test_time.py +++ b/tests/test_time.py @@ -1,52 +1,49 @@ from unittest import TestCase from pyutility import limit_time, timeit - -def func1(x): - # recursive function to find xth fibonacci number - if x < 3: - return 1 - return func1(x-1) + func1(x-2) - - -def func2(): - # error function - return "a" / 2 - - -def func3(*args, **kwagrs): - # args and kwargs function - return list(args) + list(kwagrs.values()) +from .func import time, error, return_check class TimeitTest(TestCase): - def setUp(self): - self.er_func = timeit(func2) - self.func = timeit(func1) - self.ka_func = timeit(func3) def test_timeit1(self): - self.assertIsInstance(self.func(5), float) + v = timeit(time, args=(5,)) + self.assertIsInstance(v, float) def test_timeit2(self): - self.assertRaises(Exception, self.er_func) + self.assertRaises(Exception, timeit, error, 5) class LimitTimeTest(TestCase): - def setUp(self): - self.er_func = limit_time(2)(func2) - self.func = limit_time(2)(func1) - self.ka_func = limit_time(2)(func3) def test_limit_time_1(self): - self.assertEqual(self.func(10), 55) + v = limit_time(time, time=2, args=(10,)) + self.assertEqual(v, 55) def test_limit_time_2(self): - self.assertRaises(Exception, self.er_func) + self.assertRaises( + Exception, + limit_time, + error, + time=2, + args=(2,) + ) def test_limit_time_3(self): - self.assertRaises(TimeoutError, self.func, 50) + self.assertRaises( + TimeoutError, + limit_time, + time, + time=2, + args=(50,) + ) def test_limit_time_4(self): - self.assertEqual(self.ka_func( - 1, 2, 3, four=4, five=5), [1, 2, 3, 4, 5]) + v = limit_time( + return_check, + time=2, + args=(1, 2, 3), + kwargs={"four": 4, "five": 5} + ) + + self.assertEqual(v, [1, 2, 3, 4, 5]) diff --git a/tests/test_utility.py b/tests/test_utility.py index 603316a..266cdfa 100644 --- a/tests/test_utility.py +++ b/tests/test_utility.py @@ -1,73 +1,65 @@ from unittest import TestCase from pyutility import limit_resource, measureit - -def func1a(x): - x = [i for i in range(x)] - return -1 - - -def func1b(x): - # recursive function to find xth fibonacci number - if x < 3: - return 1 - return func1b(x-1) + func1b(x-2) - - -def func2(): - # error function - return "a" / 2 - - -def func3(*args, **kwagrs): - # args and kwargs function - return list(args) + list(kwagrs.values()) +from .func import memory, time, return_check, error class MeasureitTest(TestCase): - def setUp(self): - self.er_func = measureit(func2) - self.func_m = measureit(func1a) - self.func_t = measureit(func1b) - self.ka_func = measureit(func3) def test_measureit_1(self): - self.assertIsInstance(self.func_m(100), tuple) + v = measureit(memory, args=(100,)) + self.assertIsInstance(v, tuple) def test_measureit_2(self): - x = self.func_t(10) - self.assertIsInstance(x[0], int) - self.assertIsInstance(x[1], float) + v = measureit(time, args=(15,)) + self.assertIsInstance(v[0], int) + self.assertIsInstance(v[1], float) def test_measureit_3(self): - self.assertIsInstance(self.func_t(15), tuple) + v = measureit(time, args=(15,)) + self.assertIsInstance(v, tuple) def test_measureit_4(self): - self.assertRaises(Exception, self.er_func) + self.assertRaises(Exception, measureit, error, 100) class LimitResourceTest(TestCase): - def setUp(self): - self.er_func = limit_resource(time=2)(func2) - self.func_m = limit_resource(time=2)(func1a) - self.func_t = limit_resource(time=2)(func1b) - self.ka_func = limit_resource(time=2)(func3) def test_limit_resource_1(self): - self.assertEqual(self.func_m(300), -1) + v = limit_resource(memory, time=2, args=(300,)) + self.assertEqual(v, -1) def test_limit_resource_2(self): - self.assertEqual(self.func_t(3), 2) + v = limit_resource(time, time=2, args=(3,)) + self.assertEqual(v, 2) def test_limit_resource_3(self): - self.assertRaises(Exception, self.er_func) + self.assertRaises(Exception, error) def test_limit_resource_4(self): - self.assertRaises(MemoryError, self.func_m, 100_000_000) + self.assertRaises( + MemoryError, + limit_resource, + memory, + args=(100_000_000,), + time=2 + ) def test_limit_resource_5(self): - self.assertRaises(TimeoutError, self.func_t, 50) + self.assertRaises( + TimeoutError, + limit_resource, + time, + args=(50,), + time=2 + ) def test_limit_resource_6(self): - self.assertEqual(self.ka_func( - 1, 2, 3, four=4, five=5), [1, 2, 3, 4, 5]) + v = limit_resource( + return_check, + time=2, + args=(1, 2, 3), + kwargs={"four": 4, "five": 5} + ) + + self.assertEqual(v, [1, 2, 3, 4, 5])

Multiprocessing Errors Python throws EOFError and RuntimeError, when decorator is used. Even when `__name__ == __main__` if statement is present it throws PicklingError. This is because multiprocessing is using spawn to create new processes. Some details can be found here: [StackOverFlow Question](https://stackoverflow.com/questions/41385708/multiprocessing-example-giving-attributeerror) Either using other method to create new process or changing it to function may resolve the problem.

0.0

8f66fc1fc569c34798865ab063f1da4e7753c9d5

[ "tests/test_memory.py::MemoryitTest::test_memoryit1", "tests/test_memory.py::LimitMemoryTest::test_limit_memory_1", "tests/test_memory.py::LimitMemoryTest::test_limit_memory_3", "tests/test_memory.py::LimitMemoryTest::test_limit_memory_4", "tests/test_time.py::TimeitTest::test_timeit1", "tests/test_time.py::LimitTimeTest::test_limit_time_1", "tests/test_time.py::LimitTimeTest::test_limit_time_3", "tests/test_time.py::LimitTimeTest::test_limit_time_4", "tests/test_utility.py::MeasureitTest::test_measureit_1", "tests/test_utility.py::MeasureitTest::test_measureit_2", "tests/test_utility.py::MeasureitTest::test_measureit_3", "tests/test_utility.py::LimitResourceTest::test_limit_resource_1", "tests/test_utility.py::LimitResourceTest::test_limit_resource_2", "tests/test_utility.py::LimitResourceTest::test_limit_resource_4", "tests/test_utility.py::LimitResourceTest::test_limit_resource_5", "tests/test_utility.py::LimitResourceTest::test_limit_resource_6" ]

[ "tests/test_memory.py::MemoryitTest::test_memoryit2", "tests/test_memory.py::LimitMemoryTest::test_limit_memory_2", "tests/test_time.py::TimeitTest::test_timeit2", "tests/test_time.py::LimitTimeTest::test_limit_time_2", "tests/test_utility.py::MeasureitTest::test_measureit_4", "tests/test_utility.py::LimitResourceTest::test_limit_resource_3" ]

{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }

2020-12-05 14:07:56+00:00

mit

824

VirtusLab__git-machete-179

diff --git a/git_machete/cmd.py b/git_machete/cmd.py index 03f722b..9772a79 100644 --- a/git_machete/cmd.py +++ b/git_machete/cmd.py @@ -89,7 +89,7 @@ class MacheteClient: def read_definition_file(self, verify_branches: bool = True) -> None: with open(self._definition_file_path) as f: - lines: List[str] = [line.rstrip() for line in f.readlines() if not line.isspace()] + lines: List[str] = [line.rstrip() for line in f.readlines()] at_depth = {} last_depth = -1 @@ -98,6 +98,8 @@ class MacheteClient: invalid_branches: List[str] = [] for index, line in enumerate(lines): + if line == "" or line.isspace(): + continue prefix = "".join(itertools.takewhile(str.isspace, line)) if prefix and not self.__indent: self.__indent = prefix @@ -1819,7 +1821,6 @@ def launch(orig_args: List[str]) -> None: cli_opts = CommandLineOptions() git = GitContext(cli_opts) - machete_client = MacheteClient(cli_opts, git) if sys.version_info.major == 2 or (sys.version_info.major == 3 and sys.version_info.minor < 6): version_str = f"{sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}" @@ -1967,6 +1968,7 @@ def launch(orig_args: List[str]) -> None: return in_args[0] try: + machete_client = MacheteClient(cli_opts, git) cmd = None # Let's first extract the common options like `--help` or `--verbose` that might appear BEFORE the command, # as in e.g. `git machete --verbose status`.

VirtusLab/git-machete

974914523542045104806e52be8135027603f771

diff --git a/git_machete/tests/functional/test_machete.py b/git_machete/tests/functional/test_machete.py index f549acf..fb587a0 100644 --- a/git_machete/tests/functional/test_machete.py +++ b/git_machete/tests/functional/test_machete.py @@ -10,8 +10,10 @@ from contextlib import redirect_stdout from typing import Iterable from git_machete import cmd +from git_machete.exceptions import MacheteException from git_machete.git_operations import GitContext from git_machete.options import CommandLineOptions +from git_machete.utils import fmt cli_opts: CommandLineOptions = CommandLineOptions() git: GitContext = GitContext(cli_opts) @@ -92,6 +94,12 @@ class MacheteTester(unittest.TestCase): git.flush_caches() return out.getvalue() + @staticmethod + def rewrite_definition_file(new_body: str) -> None: + definition_file_path = git.get_git_subpath("machete") + with open(os.path.join(os.getcwd(), definition_file_path), 'w') as def_file: + def_file.writelines(new_body) + def assert_command(self, cmds: Iterable[str], expected_result: str) -> None: self.assertEqual(self.launch_command(*cmds), self.adapt(expected_result)) @@ -175,6 +183,25 @@ class MacheteTester(unittest.TestCase): """, ) + def test_branch_reappers_in_definition(self) -> None: + body: str = \ + """master + \tdevelop + \t\n + develop + """ + expected_error_msg: str = fmt('.git/machete, line 5: branch `develop` re-appears in the tree definition. Edit the definition file manually with `git machete edit`') + + self.repo_sandbox.new_branch("root") + self.rewrite_definition_file(body) + + machete_client = cmd.MacheteClient(cli_opts, git) # Only to workaround sys.exit while calling launch(['status']) + try: + machete_client.read_definition_file() + except MacheteException as e: + if e.parameter != expected_error_msg: + self.fail(f'Actual Exception message: {e} \nis not equal to expected message: {expected_error_msg}') + def test_show(self) -> None: self.setup_discover_standard_tree()

Line numbers displayed in errors refer to non-empty lines, not all lines .git/machete file: ``` master develop develop ``` The empty lines lead to an error in `git machete status`: `.git/machete, line 3: branch develop re-appears in the tree definition. Edit the definition file manually with git machete edit` while it should say: `.git/machete, line 5: branch develop re-appears in the tree definition. Edit the definition file manually with git machete edit` This is due to how `read_definition_file` is implemented, should be pretty easy to fix.

0.0

974914523542045104806e52be8135027603f771

[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_branch_reappers_in_definition" ]

[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_few_possible_downstream_branches_and_yes_option", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_no_downstream_branches", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_one_downstream_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_discover_traverse_squash", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_with_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_without_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_help", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_first", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_next", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_prev", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_merge", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_override", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_untracked", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_not_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_specified" ]

{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-08-19 13:47:27+00:00

mit

825

VirtusLab__git-machete-330

diff --git a/git_machete/cli.py b/git_machete/cli.py index 19a6a38..8824ec9 100644 --- a/git_machete/cli.py +++ b/git_machete/cli.py @@ -358,15 +358,25 @@ def create_cli_parser() -> argparse.ArgumentParser: def update_cli_opts_using_parsed_args( cli_opts: git_machete.options.CommandLineOptions, parsed_args: argparse.Namespace) -> None: + + # Warning: In mypy, Arguments that come from untyped functions/variables are silently treated by mypy as Any. + # Since argparse is not typed, everything that comes from argparse.Namespace will be taken as Any :( + # Even if we add type=LocalBranchShortName into argument parser for branch, + # python debugger will see branch as LocalBranchShortName but mypy always will see it as Any, + # until you specifically tell mypy what is the exact type by casting (right now it's done this way below, but casting does not solve all of the problems). + # + # The reasonable solution here would be to use Typed Argument Parser which is a wrapper over argparse with modernised solution for typing. + # But it would add external dependency to git-machete, so let's stick to current casting. + for opt, arg in vars(parsed_args).items(): if opt == "branch": - cli_opts.opt_branch = arg + cli_opts.opt_branch = LocalBranchShortName.of(arg) elif opt == "checked_out_since": cli_opts.opt_checked_out_since = arg elif opt == "color": cli_opts.opt_color = arg elif opt == "down_fork_point": - cli_opts.opt_down_fork_point = arg + cli_opts.opt_down_fork_point = AnyRevision.of(arg) elif opt == "debug": cli_opts.opt_debug = True elif opt == "draft": @@ -374,7 +384,7 @@ def update_cli_opts_using_parsed_args( elif opt == "fetch": cli_opts.opt_fetch = True elif opt == "fork_point": - cli_opts.opt_fork_point = arg + cli_opts.opt_fork_point = AnyRevision.of(arg) elif opt == "inferred": cli_opts.opt_inferred = True elif opt == "list_commits_with_hashes": @@ -397,7 +407,7 @@ def update_cli_opts_using_parsed_args( elif opt == "no_push_untracked": cli_opts.opt_push_untracked = False elif opt == "onto": - cli_opts.opt_onto = arg + cli_opts.opt_onto = LocalBranchShortName.of(arg) elif opt == "override_to": cli_opts.opt_override_to = arg elif opt == "override_to_inferred": @@ -412,7 +422,7 @@ def update_cli_opts_using_parsed_args( elif opt == "as_root": cli_opts.opt_as_root = True elif opt == "roots": - cli_opts.opt_roots = arg.split(",") + cli_opts.opt_roots = list(map(LocalBranchShortName.of, arg.split(","))) elif opt == "return_to": cli_opts.opt_return_to = arg elif opt == "stat":

VirtusLab/git-machete

18f7e32640cab8483c32a231a478c23c1a50ec67

diff --git a/git_machete/tests/functional/test_machete.py b/git_machete/tests/functional/test_machete.py index e6f934d..36165d7 100644 --- a/git_machete/tests/functional/test_machete.py +++ b/git_machete/tests/functional/test_machete.py @@ -2647,3 +2647,31 @@ class MacheteTester(unittest.TestCase): roots_only_commit_hash, log_content, msg="Verify that commits from parent branch are not visible when " "executing `git machete log`.") + + @mock.patch('git_machete.utils.run_cmd', mock_run_cmd) # to hide git outputs in tests + def test_add(self) -> None: + """ + Verify behaviour of a 'git machete add' command. + """ + ( + self.repo_sandbox.new_branch("master") + .commit("master commit.") + .new_branch("develop") + .commit("develop commit.") + .new_branch("feature") + .commit("feature commit.") + .check_out("develop") + .commit("New commit on develop") + ) + self.launch_command("discover", "-y") + self.repo_sandbox.new_branch("bugfix/feature_fail") + + self.assert_command(['add', '-y', 'bugfix/feature_fail'], 'Adding `bugfix/feature_fail` onto the inferred upstream (parent) branch `develop`\n' + 'Added branch `bugfix/feature_fail` onto `develop`\n', strip_indentation=False) + + # test with --onto option + self.repo_sandbox.new_branch("chore/remove_indentation") + + self.assert_command(['add', '--onto=feature'], + 'Added branch `chore/remove_indentation` onto `feature`\n', + strip_indentation=False)

`AttributeError: 'str' object has no attribute 'full_name'` due to (?) mistyped `CommandLineOptions.opt_branch` For an already existing, but not yet managed branch `foo/bar`: ``` $ git machete add foo/bar Traceback (most recent call last): File "/usr/local/bin/git-machete", line 4, in <module> __import__('pkg_resources').run_script('git-machete==3.5.0', 'git-machete') File "/usr/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1469, in run_script exec(script_code, namespace, namespace) File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/EGG-INFO/scripts/git-machete", line 19, in <module> File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/git_machete/cli.py", line 803, in main File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/git_machete/cli.py", line 522, in launch File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/git_machete/client.py", line 263, in add File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/git_machete/client.py", line 1502, in __infer_upstream File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/git_machete/client.py", line 1479, in __match_log_to_filtered_reflogs File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/git_machete/git_operations.py", line 495, in spoonfeed_log_shas File "/usr/local/lib/python3.7/site-packages/git_machete-3.5.0-py3.7.egg/git_machete/git_operations.py", line 487, in __get_log_shas AttributeError: 'str' object has no attribute 'full_name' ``` This is most likely due to assignment `cli_opts.opt_branch = arg`, with `arg` being `str`-typed (?)... not sure why it passed mypy in the first place, pls investigate. Also, regression test + preferable a systematic solution against this kind of errors would be very useful.

0.0

18f7e32640cab8483c32a231a478c23c1a50ec67

[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_add" ]

[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_few_possible_downstream_branches_and_yes_option", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_no_downstream_branches", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_one_downstream_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_anno_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_branch_reappers_in_definition", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_freshly_cloned", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_from_fork_with_deleted_repo", "git_machete/tests/functional/test_machete.py::MacheteTester::test_discover_traverse_squash", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_with_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_without_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_help", "git_machete/tests/functional/test_machete.py::MacheteTester::test_log", "git_machete/tests/functional/test_machete.py::MacheteTester::test_retarget_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_first", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_next", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_prev", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_down_fork_point_and_multiple_children_of_last_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_invalid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_valid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_merge", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_invalid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_valid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_override", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_untracked", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_not_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_invalid_fork_point" ]

{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-11-03 12:50:09+00:00

mit

826

VirtusLab__git-machete-348

diff --git a/git_machete/client.py b/git_machete/client.py index 556fa3d..d1d9146 100644 --- a/git_machete/client.py +++ b/git_machete/client.py @@ -1631,6 +1631,7 @@ class MacheteClient: *, branch: LocalBranchShortName, is_called_from_traverse: bool, + is_called_from_create_pr: bool, opt_push_untracked: bool, opt_push_tracked: bool, opt_yes: bool @@ -1654,6 +1655,7 @@ class MacheteClient: new_remote=rems[index], branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=is_called_from_create_pr, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes) @@ -1667,12 +1669,13 @@ class MacheteClient: new_remote: str, branch: LocalBranchShortName, is_called_from_traverse: bool, + is_called_from_create_pr: bool, opt_push_untracked: bool, opt_push_tracked: bool, opt_yes: bool ) -> None: rems: List[str] = self.__git.get_remotes() - can_pick_other_remote = len(rems) > 1 + can_pick_other_remote = len(rems) > 1 and not is_called_from_create_pr other_remote_choice = "o[ther-remote]" if can_pick_other_remote else "" remote_branch = RemoteBranchShortName.of(f"{new_remote}/{branch}") if not self.__git.get_commit_sha_by_revision(remote_branch): @@ -1694,6 +1697,7 @@ class MacheteClient: self.__pick_remote( branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=is_called_from_create_pr, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes) @@ -1708,6 +1712,7 @@ class MacheteClient: self.__pick_remote( branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=is_called_from_create_pr, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes) @@ -1783,6 +1788,7 @@ class MacheteClient: self.__pick_remote( branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=is_called_from_create_pr, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes) @@ -1994,9 +2000,24 @@ class MacheteClient: self.flush_caches() base: Optional[LocalBranchShortName] = self.up_branch.get(LocalBranchShortName.of(head)) + if not base: + raise MacheteException(f'Could not determine base branch for PR. Branch `{head}` is a root branch.') org: str repo: str - _, (org, repo) = self.__derive_remote_and_github_org_and_repo() + remote, (org, repo) = self.__derive_remote_and_github_org_and_repo() + print(f"Fetching {remote}...") + self.__git.fetch_remote(remote) + if '/'.join([remote, base]) not in self.__git.get_remote_branches(): + warn(f'Base branch for this PR (`{base}`) is not found on remote, pushing...') + self.handle_untracked_branch( + branch=base, + new_remote=remote, + is_called_from_traverse=False, + is_called_from_create_pr=True, + opt_push_tracked=False, + opt_push_untracked=True, + opt_yes=False) + current_user: Optional[str] = git_machete.github.derive_current_user_login() debug(f'create_github_pr({head})', f'organization is {org}, repository is {repo}') debug(f'create_github_pr({head})', 'current GitHub user is ' + (current_user or '<none>')) @@ -2079,13 +2100,16 @@ class MacheteClient: new_remote=rmt, branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=False, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes) elif len(rems) == 1: self.handle_untracked_branch( - new_remote=rems[0], branch=branch, + new_remote=rems[0], + branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=False, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes) @@ -2094,6 +2118,7 @@ class MacheteClient: new_remote="origin", branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=False, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes) @@ -2103,6 +2128,7 @@ class MacheteClient: self.__pick_remote( branch=branch, is_called_from_traverse=is_called_from_traverse, + is_called_from_create_pr=False, opt_push_untracked=opt_push_untracked, opt_push_tracked=opt_push_tracked, opt_yes=opt_yes)

VirtusLab/git-machete

931fd2c58aaebdc325e1fd2c9ceacecee80f72e7

diff --git a/git_machete/tests/functional/test_machete.py b/git_machete/tests/functional/test_machete.py index 36165d7..55749e7 100644 --- a/git_machete/tests/functional/test_machete.py +++ b/git_machete/tests/functional/test_machete.py @@ -1927,6 +1927,8 @@ class MacheteTester(unittest.TestCase): git_api_state_for_test_create_pr = MockGithubAPIState([{'head': {'ref': 'ignore-trailing', 'repo': mock_repository_info}, 'user': {'login': 'github_user'}, 'base': {'ref': 'hotfix/add-trigger'}, 'number': '3', 'html_url': 'www.github.com', 'state': 'open'}], issues=[{'number': '4'}, {'number': '5'}, {'number': '6'}]) + # We need to mock GITHUB_REMOTE_PATTERNS in the tests for `test_github_create_pr` due to `git fetch` executed by `create-pr` subcommand. + @mock.patch('git_machete.github.GITHUB_REMOTE_PATTERNS', FAKE_GITHUB_REMOTE_PATTERNS) @mock.patch('git_machete.utils.run_cmd', mock_run_cmd) # to hide git outputs in tests @mock.patch('git_machete.options.CommandLineOptions', FakeCommandLineOptions) @mock.patch('git_machete.client.MacheteClient.ask_if', mock_ask_if) @@ -2093,6 +2095,47 @@ class MacheteTester(unittest.TestCase): self.assertEqual(e.exception.parameter, expected_error_message, 'Verify that expected error message has appeared when creating PR from root branch.') + git_api_state_for_test_create_pr_missing_base_branch_on_remote = MockGithubAPIState([{'head': {'ref': 'chore/redundant_checks', 'repo': mock_repository_info}, 'user': {'login': 'github_user'}, 'base': {'ref': 'restrict_access'}, 'number': '18', 'html_url': 'www.github.com', 'state': 'open'}]) + + # We need to mock GITHUB_REMOTE_PATTERNS in the tests for `test_github_create_pr` due to `git fetch` executed by `create-pr` subcommand. + @mock.patch('git_machete.github.GITHUB_REMOTE_PATTERNS', FAKE_GITHUB_REMOTE_PATTERNS) + @mock.patch('git_machete.utils.run_cmd', mock_run_cmd) # to hide git outputs in tests + @mock.patch('git_machete.options.CommandLineOptions', FakeCommandLineOptions) + @mock.patch('git_machete.client.MacheteClient.ask_if', mock_ask_if) + @mock.patch('urllib.request.urlopen', MockContextManager) + @mock.patch('urllib.request.Request', git_api_state_for_test_create_pr_missing_base_branch_on_remote.new_request()) + def test_github_create_pr_missing_base_branch_on_remote(self) -> None: + ( + self.repo_sandbox.new_branch("root") + .commit("initial commit") + .new_branch("develop") + .commit("first commit on develop") + .push() + .new_branch("feature/api_handling") + .commit("Introduce GET and POST methods on API") + .new_branch("feature/api_exception_handling") + .commit("catch exceptions coming from API") + .push() + .delete_branch("root") + ) + + self.launch_command('discover') + + expected_msg = ("Fetching origin...\n" + "Warn: Base branch for this PR (`feature/api_handling`) is not found on remote, pushing...\n" + "Creating a PR from `feature/api_exception_handling` to `feature/api_handling`... OK, see www.github.com\n") + self.assert_command(['github', 'create-pr'], expected_msg, strip_indentation=False) + self.assert_command( + ['status'], + """ + develop + | + o-feature/api_handling + | + o-feature/api_exception_handling * PR #19 + """, + ) + git_api_state_for_test_checkout_prs = MockGithubAPIState([ {'head': {'ref': 'chore/redundant_checks', 'repo': mock_repository_info}, 'user': {'login': 'github_user'}, 'base': {'ref': 'restrict_access'}, 'number': '18', 'html_url': 'www.github.com', 'state': 'open'}, {'head': {'ref': 'restrict_access', 'repo': mock_repository_info}, 'user': {'login': 'github_user'}, 'base': {'ref': 'allow-ownership-link'}, 'number': '17', 'html_url': 'www.github.com', 'state': 'open'},

`github create-pr`: check if base branch for PR exists in remote Attempt to create a pull request with base branch being already deleted from remote ends up with `Unprocessable Entity` error. (example in #332). Proposed solution: Perform `git fetch <remote>` at the beginning of `create-pr`. if base branch is not present in remote branches, perform `handle_untracked_branch` with relevant remote for missing base branch.

0.0

931fd2c58aaebdc325e1fd2c9ceacecee80f72e7

[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr_missing_base_branch_on_remote" ]

[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_add", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_few_possible_downstream_branches_and_yes_option", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_no_downstream_branches", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_one_downstream_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_anno_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_branch_reappers_in_definition", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_freshly_cloned", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_from_fork_with_deleted_repo", "git_machete/tests/functional/test_machete.py::MacheteTester::test_discover_traverse_squash", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_with_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_without_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_help", "git_machete/tests/functional/test_machete.py::MacheteTester::test_log", "git_machete/tests/functional/test_machete.py::MacheteTester::test_retarget_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_first", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_next", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_prev", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_down_fork_point_and_multiple_children_of_last_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_invalid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_valid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_merge", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_invalid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_valid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_override", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_untracked", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_not_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_invalid_fork_point" ]

{ "failed_lite_validators": [ "has_issue_reference", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-11-16 14:09:49+00:00

mit

827

VirtusLab__git-machete-350

diff --git a/git_machete/exceptions.py b/git_machete/exceptions.py index a1f9893..ae09ea3 100644 --- a/git_machete/exceptions.py +++ b/git_machete/exceptions.py @@ -21,7 +21,7 @@ class UnprocessableEntityHTTPError(MacheteException): or creating a pull request for a branch that already has a PR. """ def __init__(self, msg: str) -> None: - self.msg: str = 'UnprocessableEntityHTTPError: ' + msg + self.msg: str = msg def __str__(self) -> str: return str(self.msg) diff --git a/git_machete/github.py b/git_machete/github.py index 031bcb5..8b246d4 100644 --- a/git_machete/github.py +++ b/git_machete/github.py @@ -9,9 +9,9 @@ import subprocess from pathlib import Path from typing import Any, Dict, List, Optional, Tuple import urllib.request -from urllib.error import HTTPError +import urllib.error -from git_machete.utils import debug, fmt, find_or_none +from git_machete.utils import debug, fmt from git_machete.exceptions import MacheteException, UnprocessableEntityHTTPError from git_machete.git_operations import GitContext, LocalBranchShortName @@ -158,7 +158,7 @@ def __fire_github_api_request(method: str, path: str, token: Optional[str], requ with urllib.request.urlopen(http_request) as response: parsed_response_body: Any = json.loads(response.read().decode()) return parsed_response_body - except HTTPError as err: + except urllib.error.HTTPError as err: if err.code == http.HTTPStatus.UNPROCESSABLE_ENTITY: error_response = json.loads(err.read().decode()) error_reason: str = __extract_failure_info_from_422(error_response) @@ -193,13 +193,8 @@ def create_pull_request(org: str, repo: str, head: str, base: str, title: str, d 'body': description, 'draft': draft } - prs: List[GitHubPullRequest] = derive_pull_requests(org, repo) - pr_found: Optional[GitHubPullRequest] = find_or_none(lambda pr: pr.base == base and pr.head == head, prs) - if not pr_found: - pr = __fire_github_api_request('POST', f'/repos/{org}/{repo}/pulls', token, request_body) - return __parse_pr_json(pr) - else: - raise MacheteException(f'Pull request for branch {head} is already created under link {pr_found.html_url}!\nPR details: {pr_found}') + pr = __fire_github_api_request('POST', f'/repos/{org}/{repo}/pulls', token, request_body) + return __parse_pr_json(pr) def add_assignees_to_pull_request(org: str, repo: str, number: int, assignees: List[str]) -> None:

VirtusLab/git-machete

5c5bef4a52ef72bdb4bc095210d15acdc1826ffd

diff --git a/git_machete/tests/functional/test_machete.py b/git_machete/tests/functional/test_machete.py index 55749e7..24e5542 100644 --- a/git_machete/tests/functional/test_machete.py +++ b/git_machete/tests/functional/test_machete.py @@ -174,6 +174,9 @@ class MockGithubAPIRequest: def update_pull_request(self) -> "MockGithubAPIResponse": pull_no: str = self.find_number(self.parsed_url.path, 'pulls') if not pull_no: + if self.is_pull_created(): + return self.make_response_object(HTTPStatus.UNPROCESSABLE_ENTITY, {'message': 'Validation Failed', 'errors': [ + {'message': f'A pull request already exists for test_repo:{json.loads(self.json_data)["head"]}.'}]}) return self.create_pull_request() pull: Dict[str, Any] = self.github_api_state.get_pull(pull_no) return self.fill_pull_request_data(json.loads(self.json_data), pull) @@ -221,6 +224,17 @@ class MockGithubAPIRequest: self.github_api_state.issues.append(issue) return self.make_response_object(HTTPStatus.CREATED, issue) + def is_pull_created(self) -> bool: + deserialized_json_data = json.loads(self.json_data) + head: str = deserialized_json_data['head'] + base: str = deserialized_json_data['base'] + for pull in self.github_api_state.pulls: + pull_head: str = pull['head']['ref'] + pull_base: str = pull['base']['ref'] + if (head, base) == (pull_head, pull_base): + return True + return False + @staticmethod def get_index_or_none(entity: Dict[str, Any], base: List[Dict[str, Any]]) -> Optional[int]: try: @@ -245,6 +259,15 @@ class MockGithubAPIRequest: return str(max(numbers) + 1) +class MockHTTPError(HTTPError): + def __init__(self, url: str, code: int, msg: Any, hdrs: Dict[str, str], fp: Any) -> None: + super().__init__(url, code, msg, hdrs, fp) + self.msg = msg + + def read(self, n: int = 1) -> bytes: + return json.dumps(self.msg).encode() + + class MockContextManager: def __init__(self, obj: MockGithubAPIResponse) -> None: self.obj = obj @@ -252,6 +275,8 @@ class MockContextManager: def __enter__(self) -> MockGithubAPIResponse: if self.obj.status_code == HTTPStatus.NOT_FOUND: raise HTTPError(None, 404, 'Not found', None, None) + elif self.obj.status_code == HTTPStatus.UNPROCESSABLE_ENTITY: + raise MockHTTPError(None, 422, self.obj.response_data, None, None) return self.obj def __exit__(self, *args: Any) -> None: @@ -1927,6 +1952,7 @@ class MacheteTester(unittest.TestCase): git_api_state_for_test_create_pr = MockGithubAPIState([{'head': {'ref': 'ignore-trailing', 'repo': mock_repository_info}, 'user': {'login': 'github_user'}, 'base': {'ref': 'hotfix/add-trigger'}, 'number': '3', 'html_url': 'www.github.com', 'state': 'open'}], issues=[{'number': '4'}, {'number': '5'}, {'number': '6'}]) + @mock.patch('urllib.error.HTTPError', MockHTTPError) # need to provide read() method, which does not actually reads error from url # We need to mock GITHUB_REMOTE_PATTERNS in the tests for `test_github_create_pr` due to `git fetch` executed by `create-pr` subcommand. @mock.patch('git_machete.github.GITHUB_REMOTE_PATTERNS', FAKE_GITHUB_REMOTE_PATTERNS) @mock.patch('git_machete.utils.run_cmd', mock_run_cmd) # to hide git outputs in tests @@ -2062,12 +2088,12 @@ class MacheteTester(unittest.TestCase): ) # check against attempt to create already existing pull request machete_client = MacheteClient(git) - expected_error_message = "Pull request for branch hotfix/add-trigger is already created under link www.github.com!\nPR details: PR #6 by github_user: hotfix/add-trigger -> master" + expected_error_message = "A pull request already exists for test_repo:hotfix/add-trigger." machete_client.read_definition_file() with self.assertRaises(MacheteException) as e: machete_client.create_github_pr(head=LocalBranchShortName.of('hotfix/add-trigger'), opt_draft=False, opt_onto=None) if e: - self.assertEqual(e.exception.parameter, expected_error_message, + self.assertEqual(e.exception.msg, expected_error_message, # type: ignore 'Verify that expected error message has appeared when given pull request to create is already created.') # check against head branch is ancestor or equal to base branch

Is the check for PR existence still needed now that we read the body of 422 response? `git_machete.github.create_pull_request`: ``` prs: List[GitHubPullRequest] = derive_pull_requests(org, repo) pr_found: Optional[GitHubPullRequest] = find_or_none(lambda pr: pr.base == base and pr.head == head, prs) if not pr_found: pr = __fire_github_api_request('POST', f'/repos/{org}/{repo}/pulls', token, request_body) return __parse_pr_json(pr) else: raise MacheteException(f'Pull request for branch {head} is already created under link {pr_found.html_url}!\nPR details: {pr_found}') ``` Maybe we can skip one request to the API (`derive_pull_requests`) and rely on our new handling for 422 now?

0.0

5c5bef4a52ef72bdb4bc095210d15acdc1826ffd

[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr" ]

[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_add", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_few_possible_downstream_branches_and_yes_option", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_no_downstream_branches", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_one_downstream_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_anno_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_branch_reappers_in_definition", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_freshly_cloned", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_from_fork_with_deleted_repo", "git_machete/tests/functional/test_machete.py::MacheteTester::test_discover_traverse_squash", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr_missing_base_branch_on_remote", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_with_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_without_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_help", "git_machete/tests/functional/test_machete.py::MacheteTester::test_log", "git_machete/tests/functional/test_machete.py::MacheteTester::test_retarget_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_first", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_next", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_prev", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_down_fork_point_and_multiple_children_of_last_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_invalid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_valid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_merge", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_invalid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_valid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_override", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_untracked", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_not_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_invalid_fork_point" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }

2021-11-18 14:42:19+00:00

mit

828

VirtusLab__git-machete-353

diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index 4cb7056..395fed7 100644 --- a/RELEASE_NOTES.md +++ b/RELEASE_NOTES.md @@ -1,5 +1,9 @@ # Release notes +## New in git-machete 3.6.0 + +- added: `t` alias for `traverse` command + ## New in git-machete 3.5.0 - added: new way of acquiring the github token (from `~/.github-token`) diff --git a/docs/source/cli_help/traverse.rst b/docs/source/cli_help/traverse.rst index 8b23310..d74e384 100644 --- a/docs/source/cli_help/traverse.rst +++ b/docs/source/cli_help/traverse.rst @@ -13,10 +13,10 @@ traverse .. code-block:: shell - git machete traverse [-F|--fetch] [-l|--list-commits] [-M|--merge] - [-n|--no-edit-merge|--no-interactive-rebase] [--no-detect-squash-merges] - [--[no-]push] [--[no-]push-untracked] - [--return-to=WHERE] [--start-from=WHERE] [-w|--whole] [-W] [-y|--yes] + git machete t[raverse] [-F|--fetch] [-l|--list-commits] [-M|--merge] + [-n|--no-edit-merge|--no-interactive-rebase] [--no-detect-squash-merges] + [--[no-]push] [--[no-]push-untracked] + [--return-to=WHERE] [--start-from=WHERE] [-w|--whole] [-W] [-y|--yes] Traverses the branch dependency tree in pre-order (i.e. simply in the order as they occur in the definition file). By default traverse starts from current branch, however this behaviour can be customized using options: ``--start-from=``, ``--whole`` or ``-w``, ``-W``. diff --git a/git_machete/__init__.py b/git_machete/__init__.py index bf5afe7..826cf62 100644 --- a/git_machete/__init__.py +++ b/git_machete/__init__.py @@ -1,1 +1,1 @@ -__version__ = '3.5.1' +__version__ = '3.6.0' diff --git a/git_machete/cli.py b/git_machete/cli.py index 0a4398c..34d369c 100644 --- a/git_machete/cli.py +++ b/git_machete/cli.py @@ -26,7 +26,8 @@ alias_by_command: Dict[str, str] = { "edit": "e", "go": "g", "log": "l", - "status": "s" + "status": "s", + "traverse": "t" } command_groups: List[Tuple[str, List[str]]] = [ @@ -316,6 +317,7 @@ def create_cli_parser() -> argparse.ArgumentParser: traverse_parser = subparsers.add_parser( 'traverse', + aliases=['t'], argument_default=argparse.SUPPRESS, usage=argparse.SUPPRESS, add_help=False, @@ -748,7 +750,7 @@ def launch(orig_args: List[str]) -> None: opt_list_commits=cli_opts.opt_list_commits, opt_list_commits_with_hashes=cli_opts.opt_list_commits_with_hashes, opt_no_detect_squash_merges=cli_opts.opt_no_detect_squash_merges) - elif cmd == "traverse": + elif cmd in {"traverse", alias_by_command["traverse"]}: if cli_opts.opt_start_from not in {"here", "root", "first-root"}: raise MacheteException( "Invalid argument for `--start-from`. " diff --git a/git_machete/docs.py b/git_machete/docs.py index 513561d..803bb3d 100644 --- a/git_machete/docs.py +++ b/git_machete/docs.py @@ -606,10 +606,10 @@ long_docs: Dict[str, str] = { when detecting if a branch is merged into its upstream (parent). """, "traverse": """ - Usage: git machete traverse [-F|--fetch] [-l|--list-commits] [-M|--merge] - [-n|--no-edit-merge|--no-interactive-rebase] [--no-detect-squash-merges] - [--[no-]push] [--[no-]push-untracked] - [--return-to=WHERE] [--start-from=WHERE] [-w|--whole] [-W] [-y|--yes] + Usage: git machete t[raverse] [-F|--fetch] [-l|--list-commits] [-M|--merge] + [-n|--no-edit-merge|--no-interactive-rebase] [--no-detect-squash-merges] + [--[no-]push] [--[no-]push-untracked] + [--return-to=WHERE] [--start-from=WHERE] [-w|--whole] [-W] [-y|--yes] Traverses the branch dependency tree in pre-order (i.e. simply in the order as they occur in the definition file). By default traverse starts from current branch, however this behaviour can be customized using options: `--starts-from=`, `--whole` or `-w`, `-W`.

VirtusLab/git-machete

b5ce4b7f67ea347ff0e1357a61d5412027218a87

diff --git a/git_machete/tests/functional/test_machete.py b/git_machete/tests/functional/test_machete.py index 24e5542..53cef1e 100644 --- a/git_machete/tests/functional/test_machete.py +++ b/git_machete/tests/functional/test_machete.py @@ -538,8 +538,39 @@ class MacheteTester(unittest.TestCase): @mock.patch('git_machete.utils.run_cmd', mock_run_cmd) # to hide git outputs in tests def test_traverse_no_push_override(self) -> None: self.setup_discover_standard_tree() + self.repo_sandbox.check_out("hotfix/add-trigger") + self.launch_command("t", "-Wy", "--no-push", "--push", "--start-from=here") + self.assert_command( + ["status", "-l"], + """ + develop + | + | Allow ownership links + | 1st round of fixes + x-allow-ownership-link (ahead of origin) + | | + | | Build arbitrarily long chains + | x-build-chain (untracked) + | + | Call web service + | 1st round of fixes + | 2nd round of fixes + o-call-ws (ahead of origin) + | + | Drop unneeded SQL constraints + x-drop-constraint (untracked) - self.launch_command("traverse", "-Wy", "--no-push", "--push") + master + | + | HOTFIX Add the trigger (amended) + o-hotfix/add-trigger * + | + | Ignore trailing data (amended) + o-ignore-trailing + """, + ) + self.repo_sandbox.check_out("ignore-trailing") + self.launch_command("t", "-Wy", "--no-push", "--push") self.assert_command( ["status", "-l"], """

Add `t` as an alias for `traverse` (just as `s` is for `status`)

0.0

b5ce4b7f67ea347ff0e1357a61d5412027218a87

[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_override" ]

[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_add", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_few_possible_downstream_branches_and_yes_option", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_no_downstream_branches", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_one_downstream_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_anno_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_branch_reappers_in_definition", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_freshly_cloned", "git_machete/tests/functional/test_machete.py::MacheteTester::test_checkout_prs_from_fork_with_deleted_repo", "git_machete/tests/functional/test_machete.py::MacheteTester::test_discover_traverse_squash", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr_missing_base_branch_on_remote", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_with_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_without_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_help", "git_machete/tests/functional/test_machete.py::MacheteTester::test_log", "git_machete/tests/functional/test_machete.py::MacheteTester::test_retarget_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_first", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_next", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_prev", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_down_fork_point_and_multiple_children_of_last_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_invalid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_valid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_merge", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_invalid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_valid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_untracked", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_not_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_invalid_fork_point" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-11-22 09:53:54+00:00

mit

829

VirtusLab__git-machete-463

diff --git a/git_machete/client.py b/git_machete/client.py index b8a55b1..0e44ae6 100644 --- a/git_machete/client.py +++ b/git_machete/client.py @@ -1947,28 +1947,27 @@ class MacheteClient: if pr_from_github: result.append(pr_from_github) else: - if len(prs_list) > 1: - warn(f"PR #{pr_no} is not found in repository `{org}/{repo}`, skipping.") - else: - raise MacheteException(f"PR #{pr_no} is not found in repository `{org}/{repo}`") + raise MacheteException(f"PR #{pr_no} is not found in repository `{org}/{repo}`") if not result: raise MacheteException( f"Given PRs: {', '.join(map(str, prs_list))} are not found in repository `{org}/{repo}`") return result if all: if not all_opened_prs_from_github: - raise MacheteException(f"Currently there is not any pull request opened in repository `{org}/{repo}`") + warn(f"Currently there are no pull requests opened in repository `{org}/{repo}`") + return [] return all_opened_prs_from_github elif my and user: result = [pr for pr in all_opened_prs_from_github if pr.user == user] if not result: - raise MacheteException( - f"Current user {user} has no open pull request in repository `{org}/{repo}`") + warn(f"Current user `{user}` has no open pull request in repository `{org}/{repo}`") + return [] return result elif by: result = [pr for pr in all_opened_prs_from_github if pr.user == by] if not result: - raise MacheteException(f"User {by} has no open pull request in repository `{org}/{repo}`") + warn(f"User `{by}` has no open pull request in repository `{org}/{repo}`") + return [] return result return []

VirtusLab/git-machete

d5093f1a6f16a6f834fe71ddae9e4e63a2b18a03

diff --git a/git_machete/tests/functional/test_machete.py b/git_machete/tests/functional/test_machete.py index fc4d788..7718ce8 100644 --- a/git_machete/tests/functional/test_machete.py +++ b/git_machete/tests/functional/test_machete.py @@ -2220,6 +2220,7 @@ class MacheteTester(unittest.TestCase): @mock.patch('git_machete.github.GITHUB_REMOTE_PATTERNS', FAKE_GITHUB_REMOTE_PATTERNS) @mock.patch('git_machete.options.CommandLineOptions', FakeCommandLineOptions) @mock.patch('git_machete.utils.run_cmd', mock_run_cmd) # to hide git outputs in tests + @mock.patch('git_machete.github.__get_github_token', mock__get_github_token) @mock.patch('urllib.request.Request', git_api_state_for_test_checkout_prs.new_request()) @mock.patch('urllib.request.urlopen', MockContextManager) def test_github_checkout_prs(self) -> None: @@ -2416,6 +2417,16 @@ class MacheteTester(unittest.TestCase): self.assertEqual(e.exception.parameter, expected_error_message, 'Verify that expected error message has appeared when given pull request to checkout does not exists.') + with self.assertRaises(MacheteException) as e: + self.launch_command('github', 'checkout-prs', '19', '100') + if e: + self.assertEqual(e.exception.parameter, expected_error_message, + 'Verify that expected error message has appeared when one of the given pull requests to checkout does not exists.') + + # check against user with no open pull requests + expected_msg = f"Warn: User `tester` has no open pull request in repository `{org}/{repo}`\n" + self.assert_command(['github', 'checkout-prs', '--by', 'tester'], expected_msg, strip_indentation=False) + # Check against closed pull request with head branch deleted from remote local_path = popen("mktemp -d") self.repo_sandbox.new_repo(GitRepositorySandbox.second_remote_path)

`checkout_github_prs()` should NOT fail if no PRs for the given criteria are found

0.0

d5093f1a6f16a6f834fe71ddae9e4e63a2b18a03

[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_checkout_prs" ]

[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_add", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_few_possible_downstream_branches_and_yes_option", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_no_downstream_branches", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_one_downstream_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_anno_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_branch_reappears_in_definition", "git_machete/tests/functional/test_machete.py::MacheteTester::test_discover_traverse_squash", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_checkout_prs_freshly_cloned", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_checkout_prs_from_fork_with_deleted_repo", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr_missing_base_branch_on_remote", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_with_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_without_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_help", "git_machete/tests/functional/test_machete.py::MacheteTester::test_log", "git_machete/tests/functional/test_machete.py::MacheteTester::test_retarget_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_first", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_next", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_prev", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_down_fork_point_and_multiple_children_of_last_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_invalid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_valid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_merge", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_invalid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_valid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_override", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_untracked", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_not_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_invalid_fork_point" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }

2022-03-08 10:15:24+00:00

mit

830

VirtusLab__git-machete-483

diff --git a/docs/source/cli_help/github.rst b/docs/source/cli_help/github.rst index 0bfdb25..a5cef47 100644 --- a/docs/source/cli_help/github.rst +++ b/docs/source/cli_help/github.rst @@ -25,7 +25,7 @@ Creates, checks out and manages GitHub PRs while keeping them reflected in branc Check out the head branch of the given pull requests (specified by number), also traverse chain of pull requests upwards, adding branches one by one to git-machete and check them out locally. Once the specified pull requests are checked out locally, annotate local branches with corresponding pull request numbers. - If only one PR is given, then switch the local repository's HEAD to its head branch. + If only one PR has been checked out, then switch the local repository's HEAD to its head branch. **Options:** diff --git a/git_machete/cli.py b/git_machete/cli.py index d90f1a2..ec291d9 100644 --- a/git_machete/cli.py +++ b/git_machete/cli.py @@ -546,7 +546,9 @@ def launch(orig_args: List[str]) -> None: branch=branch, opt_onto=cli_opts.opt_onto, opt_as_root=cli_opts.opt_as_root, - opt_yes=cli_opts.opt_yes) + opt_yes=cli_opts.opt_yes, + verbose=True, + switch_head_if_new_branch=True) elif cmd == "advance": machete_client.read_definition_file(perform_interactive_slide_out=should_perform_interactive_slide_out) git.expect_no_operation_in_progress() diff --git a/git_machete/client.py b/git_machete/client.py index 7871c51..1a42aa7 100644 --- a/git_machete/client.py +++ b/git_machete/client.py @@ -219,7 +219,8 @@ class MacheteClient: opt_onto: Optional[LocalBranchShortName], opt_as_root: bool, opt_yes: bool, - verbose: bool = True + verbose: bool, + switch_head_if_new_branch: bool ) -> None: if branch in self.managed_branches: raise MacheteException( @@ -237,7 +238,7 @@ class MacheteClient: msg = common_line + f"Check out `{branch}` locally?" + get_pretty_choices('y', 'N') opt_yes_msg = common_line + f"Checking out `{branch}` locally..." if self.ask_if(msg, opt_yes_msg, opt_yes=opt_yes, verbose=verbose) in ('y', 'yes'): - self.__git.create_branch(branch, remote_branch.full_name()) + self.__git.create_branch(branch, remote_branch.full_name(), switch_head=switch_head_if_new_branch) else: return # Not dealing with `onto` here. If it hasn't been explicitly @@ -256,7 +257,7 @@ class MacheteClient: current_branch = self.__git.get_current_branch_or_none() if current_branch and current_branch in self.managed_branches: opt_onto = current_branch - self.__git.create_branch(branch, out_of) + self.__git.create_branch(branch, out_of, switch_head=switch_head_if_new_branch) else: return @@ -1913,21 +1914,23 @@ class MacheteClient: opt_as_root=True, opt_onto=None, opt_yes=True, - verbose=verbose) + verbose=verbose, + switch_head_if_new_branch=False) else: self.add( branch=branch, opt_onto=reversed_path[index - 1], opt_as_root=False, opt_yes=True, - verbose=verbose) + verbose=verbose, + switch_head_if_new_branch=False) if pr not in checked_out_prs: print(fmt(f"Pull request `#{pr.number}` checked out at local branch `{pr.head}`")) checked_out_prs.append(pr) debug('Current GitHub user is ' + (current_user or '<none>')) self.__sync_annotations_to_definition_file(all_open_prs, current_user, verbose=verbose) - if pr and len(applicable_prs) == 1 and len(checked_out_prs) == 1: + if pr and len(checked_out_prs) == 1: self.__git.checkout(LocalBranchShortName.of(pr.head)) if verbose: print(fmt(f"Switched to local branch `{pr.head}`")) @@ -2266,7 +2269,12 @@ class MacheteClient: current_branch = self.__git.get_current_branch() if current_branch not in self.managed_branches: - self.add(branch=current_branch, opt_onto=opt_onto, opt_as_root=False, opt_yes=opt_yes) + self.add(branch=current_branch, + opt_onto=opt_onto, + opt_as_root=False, + opt_yes=opt_yes, + verbose=True, + switch_head_if_new_branch=True) if current_branch not in self.managed_branches: raise MacheteException( "Command `github create-pr` can NOT be executed on the branch" diff --git a/git_machete/docs.py b/git_machete/docs.py index f6ad05e..b697234 100644 --- a/git_machete/docs.py +++ b/git_machete/docs.py @@ -351,7 +351,7 @@ long_docs: Dict[str, str] = { Check out the head branch of the given pull requests (specified by number), also traverse chain of pull requests upwards, adding branches one by one to git-machete and check them out locally. Once the specified pull requests are checked out locally, annotate local branches with corresponding pull request numbers. - If only one PR is given, then switch the local repository's HEAD to its head branch. + If only one PR has been checked out, then switch the local repository's HEAD to its head branch. Options: --all Checkout all open PRs. diff --git a/git_machete/git_operations.py b/git_machete/git_operations.py index d83eaed..ca3a753 100644 --- a/git_machete/git_operations.py +++ b/git_machete/git_operations.py @@ -580,8 +580,10 @@ class GitContext: )) return self.__reflogs_cached[branch] - def create_branch(self, branch: LocalBranchShortName, out_of_revision: AnyRevision) -> None: - self._run_git("checkout", "-b", branch, out_of_revision) + def create_branch(self, branch: LocalBranchShortName, out_of_revision: AnyRevision, switch_head: bool) -> None: + self._run_git("branch", branch, out_of_revision) + if switch_head: + self._run_git("checkout", branch) self.flush_caches() # the repository state has changed because of a successful branch creation, let's defensively flush all the caches def flush_caches(self) -> None:

VirtusLab/git-machete

5a2b68e1a7a7fff7e226f2e6ff96f7936bf98439

diff --git a/git_machete/tests/functional/test_machete.py b/git_machete/tests/functional/test_machete.py index b76db02..38a3d45 100644 --- a/git_machete/tests/functional/test_machete.py +++ b/git_machete/tests/functional/test_machete.py @@ -50,8 +50,7 @@ def mock_exit_script(status_code: Optional[int] = None, error: Optional[BaseExce def mock_fetch_ref(cls: Any, remote: str, ref: str) -> None: branch: LocalBranchShortName = LocalBranchShortName.of(ref[ref.index(':') + 1:]) - git.create_branch(branch, get_current_commit_hash()) - git.checkout(branch) + git.create_branch(branch, get_current_commit_hash(), switch_head=True) def mock_run_cmd(cmd: str, *args: str, **kwargs: Any) -> int: @@ -2404,13 +2403,13 @@ class MacheteTester(unittest.TestCase): | | | o-chore/redundant_checks PR #18 (github_user) | - o-enhance/add_user * PR #19 (github_user) + o-enhance/add_user PR #19 (github_user) bugfix/add_user | o-testing/add_user PR #22 (github_user) | - o-chore/comments PR #24 (github_user) + o-chore/comments * PR #24 (github_user) """ )

`github checkout-prs --by=...` switches to ALL checked out branches one by one Installed version from PR #435 (commit `6ee6681e33cf037e8c86b1cf340a443b4d77fcee`). Testing on this very repo: ``` ➜ 12:29 ~/git-machete develop $ g m s master v3.7.2 │ └─develop v3.8.0 ➜ 12:29 ~/git-machete develop $ gb * develop master ➜ 12:30 ~/git-machete develop $ g m github checkout-prs --by=amalota Checking for open GitHub PRs... branch 'feature/command_clean' set up to track 'origin/feature/command_clean'. Switched to a new branch 'feature/command_clean' Pull request #435 checked out at local branch feature/command_clean branch 'code_quality/github_token_msg' set up to track 'origin/code_quality/github_token_msg'. Switched to a new branch 'code_quality/github_token_msg' Pull request #469 checked out at local branch code_quality/github_token_msg branch 'feature/advance_with_push_to_remote' set up to track 'origin/feature/advance_with_push_to_remote'. Switched to a new branch 'feature/advance_with_push_to_remote' Pull request #473 checked out at local branch feature/advance_with_push_to_remote ➜ 12:30 ~/git-machete feature/advance_with_push_to_remote PR #473 (amalota) $ ``` So... first HEAD hsa been switched to `feature/command_clean`, then to `code_quality/github_token_msg`, finally to `feature/advance_with_push_to_remote`. This is contrary to docs in github.rst: ``` If only one PR is given, then switch the local repository's HEAD to its head branch. ``` In fact, the doc should probably say: ``` If only one PR has been checked out, then switch the local repository's HEAD to its head branch. ``` and `github checkout-prs` should behave adequately (i.e. for the sample above, it should **never** switch HEAD). Pls provide regression tests as well.

0.0

5a2b68e1a7a7fff7e226f2e6ff96f7936bf98439

[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_checkout_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_checkout_prs_from_fork_with_deleted_repo" ]

[ "git_machete/tests/functional/test_machete.py::MacheteTester::test_add", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_few_possible_downstream_branches_and_yes_option", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_no_downstream_branches", "git_machete/tests/functional/test_machete.py::MacheteTester::test_advance_with_one_downstream_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_anno_prs", "git_machete/tests/functional/test_machete.py::MacheteTester::test_branch_reappears_in_definition", "git_machete/tests/functional/test_machete.py::MacheteTester::test_clean", "git_machete/tests/functional/test_machete.py::MacheteTester::test_discover_traverse_squash", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_checkout_prs_freshly_cloned", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_create_pr_missing_base_branch_on_remote", "git_machete/tests/functional/test_machete.py::MacheteTester::test_github_sync", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_with_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_first_root_without_downstream", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_next_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_exists", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_prev_successor_on_another_root_tree", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_go_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_help", "git_machete/tests/functional/test_machete.py::MacheteTester::test_log", "git_machete/tests/functional/test_machete.py::MacheteTester::test_retarget_pr", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_down", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_first", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_last", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_next", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_prev", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_root", "git_machete/tests/functional/test_machete.py::MacheteTester::test_show_up", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_down_fork_point_and_multiple_children_of_last_branch", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_invalid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_slide_out_with_valid_down_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_merge", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_invalid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_squash_with_valid_fork_point", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_override", "git_machete/tests/functional/test_machete.py::MacheteTester::test_traverse_no_push_untracked", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_not_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_fork_point_specified", "git_machete/tests/functional/test_machete.py::MacheteTester::test_update_with_invalid_fork_point" ]

{ "failed_lite_validators": [ "has_issue_reference", "has_git_commit_hash", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2022-04-05 12:58:57+00:00

mit

831

VirtusLab__git-machete-534

diff --git a/git_machete/client.py b/git_machete/client.py index d063583..19ef0c4 100644 --- a/git_machete/client.py +++ b/git_machete/client.py @@ -2109,7 +2109,7 @@ class MacheteClient: description_path = self.__git.get_main_git_subpath('info', 'description') description: str = utils.slurp_file_or_empty(description_path) - ok_str = ' <green>OK</green>' + ok_str = ' <green>-> OK</green>' print(fmt(f'Creating a {"draft " if opt_draft else ""}PR from `{head}` to `{base}`...'), end='', flush=True) pr: GitHubPullRequest = create_pull_request(org, repo, head=head, base=base, title=commits[0].subject, description=description, draft=opt_draft) diff --git a/git_machete/github.py b/git_machete/github.py index f8dc8c4..49f089b 100644 --- a/git_machete/github.py +++ b/git_machete/github.py @@ -181,8 +181,9 @@ def __fire_github_api_request(method: str, path: str, token: Optional[str], requ 'Visit `https://github.com/settings/tokens` to generate a new one.') elif err.code == http.HTTPStatus.NOT_FOUND: raise MacheteException( - f'Given endpoint: {url}, not found in GitHub or you don\'t have' - f' the permission to access it (expired token?).') # TODO (#164): make dedicated exception here + f'`{method} {url}` request ended up in 404 response from GitHub. A valid GitHub API token is required.\n' + f'Provide a GitHub API token with `repo` access via one of the: {get_github_token_possible_providers()} ' + 'Visit `https://github.com/settings/tokens` to generate a new one.') # TODO (#164): make dedicated exception here else: first_line = fmt(f'GitHub API returned {err.code} HTTP status with error message: `{err.reason}`\n') raise MacheteException(first_line + "Please open an issue regarding this topic under link: https://github.com/VirtusLab/git-machete/issues/new")

VirtusLab/git-machete

7a72f615bfa9bd8e9c436dfb726216dfa07d0839

diff --git a/tests/test_github.py b/tests/test_github.py index 90fe555..d8fce10 100644 --- a/tests/test_github.py +++ b/tests/test_github.py @@ -454,7 +454,7 @@ class TestGithub: expected_msg = ("Fetching origin...\n" "Warn: Base branch for this PR (`feature/api_handling`) is not found on remote, pushing...\n" - "Creating a PR from `feature/api_exception_handling` to `feature/api_handling`... OK, see www.github.com\n") + "Creating a PR from `feature/api_exception_handling` to `feature/api_handling`... -> OK, see www.github.com\n") assert_command(['github', 'create-pr'], expected_msg, strip_indentation=False) assert_command( ['status'],

Does `/pulls` endpoint for a public GitHub repository really require authentication? As @mkondratek reported: I've tried to use `create-pr` with that result: ```sh mikko@mikko-MS-7C91:~/IdeaProjects/git-machete-intellij-plugin$ git machete github create-pr Fetching origin... Creating a PR from hook-executors-improvements to develop...Given endpoint: https://api.github.com/repos/VirtusLab/git-machete-intellij-plugin/pulls, not found in GitHub or you don't have the permission to access it (expired token?). ``` I have no token (generated and) set so that's the reason. After that - works. _Originally posted by @mkondratek in https://github.com/VirtusLab/git-machete/issues/493#issuecomment-1113174706_ --- My addition: note that https://api.github.com/repos/VirtusLab/git-machete-intellij-plugin/pulls can be readily accessed from browser and returns legit results. Let's check why this error happens when accessing GitHub API from git-machete CLI. If this can't be circumvented (e.g. for private repos), let's at least improve the error message (since it doesn't even clearly state that the token might be missing, only mentions expiry) :thinking:

0.0

7a72f615bfa9bd8e9c436dfb726216dfa07d0839

[ "tests/test_github.py::TestGithub::test_github_create_pr_missing_base_branch_on_remote" ]

[ "tests/test_github.py::TestGithub::test_github_retarget_pr", "tests/test_github.py::TestGithub::test_github_anno_prs", "tests/test_github.py::TestGithub::test_github_create_pr", "tests/test_github.py::TestGithub::test_github_checkout_prs", "tests/test_github.py::TestGithub::test_github_checkout_prs_freshly_cloned", "tests/test_github.py::TestGithub::test_github_checkout_prs_from_fork_with_deleted_repo", "tests/test_github.py::TestGithub::test_github_sync" ]

{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2022-05-27 10:32:01+00:00

mit

832

WIPACrepo__iceprod-339

diff --git a/iceprod/core/functions.py b/iceprod/core/functions.py index 964f20b9..619cc991 100644 --- a/iceprod/core/functions.py +++ b/iceprod/core/functions.py @@ -270,16 +270,11 @@ def get_local_ip_address(): def gethostname(): """Get hostname of this computer.""" ret = socket.getfqdn() - try: - resp = requests.get('http://simprod.icecube.wisc.edu/downloads/getip.php', timeout=1) - resp.raise_for_status() - logging.info('getip: %r', resp.text) - ret2 = resp.text.split(' ')[-1] - if len(ret2.split('.')) > 1: - ret = '.'.join(ret.split('.')[:1]+ret2.split('.')[1:]) - except Exception: - logging.info('error getting global ip', exc_info=True) - return ret + ret2 = socket.gethostname() + if len(ret2) > len(ret): + return ret2 + else: + return ret @contextmanager

WIPACrepo/iceprod

168fdf0ddea222567e6c87401d11b121d7369927

diff --git a/tests/core/functions_test.py b/tests/core/functions_test.py index ffe9f4ac..9ece4946 100644 --- a/tests/core/functions_test.py +++ b/tests/core/functions_test.py @@ -672,29 +672,25 @@ class functions_test(AsyncTestCase): logging.info('%s',e) @patch('socket.getfqdn') - @requests_mock.mock() + @patch('socket.gethostname') @unittest_reporter - def test_301_gethostname(self, fqdn, http_mock): + def test_301_gethostname(self, fqdn, hostname): fqdn.return_value = 'myhost' - http_mock.get('/downloads/getip.php', text='123 myhost') + hostname.return_value = 'myhost' host = iceprod.core.functions.gethostname() self.assertEqual(host, 'myhost') - self.assertEqual(http_mock.call_count, 1) - http_mock.get('/downloads/getip.php', text='123 dyn.test.com') + hostname.return_value = 'myhost.test.com' host = iceprod.core.functions.gethostname() self.assertEqual(host, 'myhost.test.com') - self.assertEqual(http_mock.call_count, 2) fqdn.return_value = 'myhost.foo.bar' host = iceprod.core.functions.gethostname() self.assertEqual(host, 'myhost.test.com') - self.assertEqual(http_mock.call_count, 3) fqdn.return_value = 'myhost.foo.bar.baz' host = iceprod.core.functions.gethostname() - self.assertEqual(host, 'myhost.test.com') - self.assertEqual(http_mock.call_count, 4) + self.assertEqual(host, 'myhost.foo.bar.baz') @unittest_reporter def test_302_isurl(self):

remove getip.php request This request: http://simprod.icecube.wisc.edu/downloads/getip.php is on an old SL6 server. We'd like to decommission that server. Replace this lookup with something else, or remove entirely.

0.0

168fdf0ddea222567e6c87401d11b121d7369927

[ "tests/core/functions_test.py::functions_test::test_301_gethostname" ]

[ "tests/core/functions_test.py::functions_test::test_001_uncompress", "tests/core/functions_test.py::functions_test::test_002_uncompress_tar", "tests/core/functions_test.py::functions_test::test_003_uncompress_tar", "tests/core/functions_test.py::functions_test::test_020_iscompressed", "tests/core/functions_test.py::functions_test::test_021_istarred", "tests/core/functions_test.py::functions_test::test_100_md5sum", "tests/core/functions_test.py::functions_test::test_101_check_md5sum", "tests/core/functions_test.py::functions_test::test_102_sha1sum", "tests/core/functions_test.py::functions_test::test_103_check_sha1sum", "tests/core/functions_test.py::functions_test::test_104_sha256sum", "tests/core/functions_test.py::functions_test::test_105_check_sha256sum", "tests/core/functions_test.py::functions_test::test_106_sha512sum", "tests/core/functions_test.py::functions_test::test_107_check_sha512sum", "tests/core/functions_test.py::functions_test::test_200_removedirs", "tests/core/functions_test.py::functions_test::test_201_copy", "tests/core/functions_test.py::functions_test::test_300_getInterfaces", "tests/core/functions_test.py::functions_test::test_302_isurl", "tests/core/functions_test.py::functions_test::test_304_download", "tests/core/functions_test.py::functions_test::test_305_download", "tests/core/functions_test.py::functions_test::test_320_download", "tests/core/functions_test.py::functions_test::test_404_upload", "tests/core/functions_test.py::functions_test::test_405_upload", "tests/core/functions_test.py::functions_test::test_410_upload", "tests/core/functions_test.py::functions_test::test_420_upload", "tests/core/functions_test.py::functions_test::test_504_delete", "tests/core/functions_test.py::functions_test::test_505_delete", "tests/core/functions_test.py::functions_test::test_510_delete" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }

2023-04-19 18:14:54+00:00

mit

833

WPI-MMR__gym_solo-38

diff --git a/examples/solo8_vanilla/interactive_pos_control.py b/examples/solo8_vanilla/interactive_pos_control.py index 8773e53..446e3c4 100644 --- a/examples/solo8_vanilla/interactive_pos_control.py +++ b/examples/solo8_vanilla/interactive_pos_control.py @@ -17,8 +17,7 @@ if __name__ == '__main__': env.obs_factory.register_observation(obs.TorsoIMU(env.robot)) env.reward_factory.register_reward(1,rewards.UprightReward(env.robot)) - env.termination_factory.register_termination( - terms.TimeBasedTermination(10000000)) + env.termination_factory.register_termination(terms.PerpetualTermination()) joint_params = [] num_joints = env.client.getNumJoints(env.robot) diff --git a/examples/solo8_vanilla/observation_dump.py b/examples/solo8_vanilla/observation_dump.py index 68bdde0..3dc3df9 100644 --- a/examples/solo8_vanilla/observation_dump.py +++ b/examples/solo8_vanilla/observation_dump.py @@ -19,8 +19,7 @@ if __name__ == '__main__': env.obs_factory.register_observation(obs.TorsoIMU(env.robot)) env.reward_factory.register_reward(1,rewards.UprightReward(env.robot)) - env.termination_factory.register_termination( - terms.TimeBasedTermination(100000000)) + env.termination_factory.register_termination(terms.PerpetualTermination()) try: print("""\n diff --git a/gym_solo/core/termination.py b/gym_solo/core/termination.py index 6135f8a..72a7b33 100644 --- a/gym_solo/core/termination.py +++ b/gym_solo/core/termination.py @@ -80,4 +80,19 @@ class TimeBasedTermination(Termination): Otherwise return false. """ self.step_delta += 1 - return self.step_delta > self.max_step_delta \ No newline at end of file + return self.step_delta > self.max_step_delta + + +class PerpetualTermination(Termination): + """Termination condition that never ends. Useful for demos / testing.""" + def reset(self): + """Unneeded.""" + pass + + def is_terminated(self) -> bool: + """Always returns that the episode is *not* terminated. + + Returns: + bool: False + """ + return False \ No newline at end of file

WPI-MMR/gym_solo

fdf8acff06a8d143e0d9890eb15d86fc643a6843

diff --git a/gym_solo/core/test_termination_conditions.py b/gym_solo/core/test_termination_conditions.py index bad6698..a6979b4 100644 --- a/gym_solo/core/test_termination_conditions.py +++ b/gym_solo/core/test_termination_conditions.py @@ -27,4 +27,13 @@ class TestTimeBasedTermination(unittest.TestCase): self.assertEqual(i+1, term.step_delta) self.assertEqual(True, term.is_terminated()) - self.assertEqual(max_step_delta + 1, term.step_delta) \ No newline at end of file + self.assertEqual(max_step_delta + 1, term.step_delta) + + +class TestPerpetualTermination(unittest.TestCase): + def test_is_terminated(self): + term = termination.PerpetualTermination() + + # Arbitrary count, just need to ensure that always returns False + for i in range(1000): + self.assertFalse(term.is_terminated()) \ No newline at end of file

Create Never Ending Termination A couple of PRs have this issue (#33, #35), but if a user wants to run gym indefinitely, they would need to create a `TimeBasedTermination` with a really big number. While that works, it's pretty jank and we should just make a `NoTermination` which just goes on forever instead.

0.0

fdf8acff06a8d143e0d9890eb15d86fc643a6843

[ "gym_solo/core/test_termination_conditions.py::TestPerpetualTermination::test_is_terminated" ]

[ "gym_solo/core/test_termination_conditions.py::TestTimeBasedTermination::test_attributes", "gym_solo/core/test_termination_conditions.py::TestTimeBasedTermination::test_is_terminated", "gym_solo/core/test_termination_conditions.py::TestTimeBasedTermination::test_reset" ]

{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2021-01-16 19:53:13+00:00

mit

834

WPI-MMR__gym_solo-6

diff --git a/gym_solo/core/rewards.py b/gym_solo/core/rewards.py new file mode 100644 index 0000000..d364f98 --- /dev/null +++ b/gym_solo/core/rewards.py @@ -0,0 +1,63 @@ +from abc import ABC, abstractmethod +from dataclasses import dataclass +from typing import List + +from gym_solo import solo_types + + +class Reward(ABC): + @abstractmethod + def compute(self) -> solo_types.reward: + """Compute the reward for the current state. + + Returns: + solo_types.reward: The reward evalulated at the current state. + """ + pass + + +@dataclass +class _WeightedReward: + reward: Reward + weight: float + + +class RewardFactory: + """A factory to dynamically create rewards. + + Note that this factory is currently implemented to combined rewards via + a linear combination. For example, if the user wanted to register rewards + r1, r2, and r3, the final reward would be r1 + r2 + r3. + + Obviously, you can add coefficients to the rewards, and that functionality + is further explained in register_reward() below. + + If you need more functionality then a linear combination (exponential + temporal decay), then it's probably in your best interest to implement that + in a custom Reward. + """ + def __init__(self): + """Create a new RewardFactory.""" + self._rewards: List[_WeightedReward] = [] + + def register_reward(self, weight: float, reward: Reward): + """Register a reward to be computed per state. + + Args: + weight (float): The weight to be applied to this reward when it is + is combined linearly with the other rewards. The domain for this + value is (-∞, ∞). + reward (Reward): A Reward object which .compute() will be called on at + reward computation time. + """ + self._rewards.append(_WeightedReward(reward=reward, weight=weight)) + + def get_reward(self) -> float: + """Evaluate the current state and get the combined reward. + + Returns: + float: The reward from the current state. Note that this reward is a + combination of multiple atomic sub-rewards, as explained by the + strategies earlier. + """ + return sum(wr.weight * wr.reward.compute() for wr in self._rewards) \ No newline at end of file diff --git a/gym_solo/solo_types.py b/gym_solo/solo_types.py index 85dc7ae..365d7e8 100644 --- a/gym_solo/solo_types.py +++ b/gym_solo/solo_types.py @@ -3,4 +3,7 @@ from typing import List import numpy as np # A state observation -obs = np.ndarray \ No newline at end of file +obs = np.ndarray + +# A reward after a step +reward = float \ No newline at end of file

WPI-MMR/gym_solo

e4bcb11fb1b18da997494d56acf95bdd512a076a

diff --git a/gym_solo/core/test_rewards_factory.py b/gym_solo/core/test_rewards_factory.py new file mode 100644 index 0000000..fd70bea --- /dev/null +++ b/gym_solo/core/test_rewards_factory.py @@ -0,0 +1,35 @@ +import unittest +from gym_solo.core import rewards + +from parameterized import parameterized + + +class TestReward(rewards.Reward): + def __init__(self, return_value): + self._return_value = return_value + + def compute(self): + return self._return_value + + +class TestRewardsFactory(unittest.TestCase): + def test_empty(self): + rf = rewards.RewardFactory() + self.assertListEqual(rf._rewards, []) + + @parameterized.expand([ + ('single', {1: 2.5}, 2.5), + ('two_happy', {1: 1, 2: 2}, 5), + ('0-weight', {0: 1, 2: 2}, 4), + ('negative-weight', {-1: 1, 2: 2}, 3), + ('three', {1: 1, 2: 2, 3: 3}, 14), + ]) + def test_register_and_compute(self, name, rewards_dict, expected_reward): + rf = rewards.RewardFactory() + for weight, reward in rewards_dict.items(): + rf.register_reward(weight, TestReward(reward)) + self.assertEqual(rf.get_reward(), expected_reward) + + +if __name__ == '__main__': + unittest.main() \ No newline at end of file

Create Rewards Factory Similar to the observation factory. The reward factory should be able to take in `Reward` objects, similar to an `Observation` object, evaluate the rewards for the state, and combine them. I'm thinking of making the final reward a linear combination of the registered rewards. With that in mind, consider the following example: ```python r1 = Reward() r2 = Reward() r3 = Reward() rf = RewardFactory() r1.register_reward(-1, r1) r1.register_reward(.1, r2) r1.register_reward(.9, r3) ``` Notice that `register_reward()` has two args: `weight: float` and `reward: gym_solo.core.rewards.Reward`. Thus, the final reward would evaluate to: `-r1() + 0.1 * r2() + 0.9 * r3()`. Figure that if you need functionality more elaborate than a linear combination, you should be offloading that processing into a `Reward` class. @mahajanrevant thoughts on this? lmk if you think we need anything stronger than linear combinations in the `RewardFactory`.

0.0

e4bcb11fb1b18da997494d56acf95bdd512a076a

[ "gym_solo/core/test_rewards_factory.py::TestRewardsFactory::test_empty", "gym_solo/core/test_rewards_factory.py::TestRewardsFactory::test_register_and_compute_0_single", "gym_solo/core/test_rewards_factory.py::TestRewardsFactory::test_register_and_compute_1_two_happy", "gym_solo/core/test_rewards_factory.py::TestRewardsFactory::test_register_and_compute_2_0_weight", "gym_solo/core/test_rewards_factory.py::TestRewardsFactory::test_register_and_compute_3_negative_weight", "gym_solo/core/test_rewards_factory.py::TestRewardsFactory::test_register_and_compute_4_three" ]

[]

{ "failed_lite_validators": [ "has_added_files" ], "has_test_patch": true, "is_lite": false }

2020-10-27 21:14:37+00:00

mit

835

Workday__prism-python-8

diff --git a/.travis.yml b/.travis.yml index 4da15ef..478c235 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,4 +7,4 @@ python: install: - pip install . script: -- echo "skipping tests" +- pytest diff --git a/environment.yml b/environment.yml index de104b0..9049cf6 100644 --- a/environment.yml +++ b/environment.yml @@ -4,3 +4,4 @@ channels: dependencies: - python=3.7 - requests + - pytest diff --git a/prism/data/schema.json b/prism/data/schema.json new file mode 100644 index 0000000..896c055 --- /dev/null +++ b/prism/data/schema.json @@ -0,0 +1,42 @@ +{ + "fields": [ + { + "defaultValue": "textField", + "description": "this is a Text Field", + "name": "State2", + "parseFormat": "", + "precision": 0, + "ordinal": 1, + "scale": 0, + "type": { + "id": "Schema_Field_Type=Text" + } + }, + { + "defaultValue": "0", + "description": "this is an Integer Field", + "name": "Population2", + "parseFormat": "", + "precision": 9, + "ordinal": 2, + "scale": 0, + "type": { + "id": "Schema_Field_Type=Numeric" + } + } + ], + "parseOptions": { + "charset": { + "id": "Encoding=UTF-8" + }, + "fieldsDelimitedBy": ",", + "fieldsEnclosedBy": "\"", + "headerLinesToIgnore": 1, + "type": { + "id": "Schema_File_Type=Delimited" + } + }, + "schemaVersion": { + "id": "Schema_Version=1.0" + } +} \ No newline at end of file diff --git a/setup.py b/setup.py index f8e5ce8..5ea16f2 100644 --- a/setup.py +++ b/setup.py @@ -13,7 +13,13 @@ setup( author_email='[email protected]', url='https://github.com/Workday/prism-python', packages=['prism'], + package_data={'prism': ['data/*']}, install_requires=requirements, + extras_require={ + 'dev': [ + 'pytest', + ] + }, keywords='prism', classifiers=[ 'Programming Language :: Python :: 3.6',

Workday/prism-python

11b6c089a2d2c5b65e4ecc1caf57ccf30e426612

diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..317f19d --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,11 @@ +import os +import pytest + [email protected] +def rootdir(): + return os.path.join(os.path.dirname(os.path.abspath(__file__)), '..') + [email protected] +def schema_file(rootdir): + """Path to example JSON schema""" + return os.path.join(rootdir, 'prism', 'data', 'schema.json') diff --git a/tests/test_prism.py b/tests/test_prism.py new file mode 100644 index 0000000..bfaad2f --- /dev/null +++ b/tests/test_prism.py @@ -0,0 +1,5 @@ +import prism + +def test_load_schema(schema_file): + schema = prism.load_schema(schema_file) + assert type(schema) is dict

Add PyTest Add a simple unit test to make sure the package successfully imports. Unit tests can be expanded in the future to offer greater coverage.

0.0

11b6c089a2d2c5b65e4ecc1caf57ccf30e426612

[ "tests/test_prism.py::test_load_schema" ]

[]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_added_files", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2019-12-09 23:44:53+00:00

apache-2.0

836

WorksApplications__SudachiPy-158

diff --git a/sudachipy/dictionarylib/dictionarybuilder.py b/sudachipy/dictionarylib/dictionarybuilder.py index 5f3512a..bde5871 100644 --- a/sudachipy/dictionarylib/dictionarybuilder.py +++ b/sudachipy/dictionarylib/dictionarybuilder.py @@ -334,7 +334,7 @@ class DictionaryBuilder(object): @staticmethod def __is_id(text): - return re.match(r'U?\d+', text) + return re.match(r'U?\d+$', text) def parse_id(self, text): if text.startswith('U'): diff --git a/sudachipy/dictionarylib/doublearraylexicon.py b/sudachipy/dictionarylib/doublearraylexicon.py index 6e1a7ce..fb77ee8 100644 --- a/sudachipy/dictionarylib/doublearraylexicon.py +++ b/sudachipy/dictionarylib/doublearraylexicon.py @@ -78,14 +78,22 @@ class DoubleArrayLexicon(Lexicon): return self.word_params.size def get_word_id(self, headword: str, pos_id: int, reading_form: str) -> int: + for wid, _ in self.lookup(headword.encode('utf-8'), 0): + if self._compare_word_id(wid, headword, pos_id, reading_form): + return wid + for wid in range(self.word_infos.size()): - info = self.word_infos.get_word_info(wid) - if info.surface == headword \ - and info.pos_id == pos_id \ - and info.reading_form == reading_form: + if self._compare_word_id(wid, headword, pos_id, reading_form): return wid + return -1 + def _compare_word_id(self, wid: int, headword: str, pos_id: int, reading_form: str) -> bool: + info = self.word_infos.get_word_info(wid) + return info.surface == headword \ + and info.pos_id == pos_id \ + and info.reading_form == reading_form + def get_dictionary_id(self, word_id: int) -> int: return 0

WorksApplications/SudachiPy

7e5b501111920cef057b821412af595db248a7b8

diff --git a/tests/dictionarylib/test_dictionarybuilder.py b/tests/dictionarylib/test_dictionarybuilder.py index f1ead7a..a07a647 100644 --- a/tests/dictionarylib/test_dictionarybuilder.py +++ b/tests/dictionarylib/test_dictionarybuilder.py @@ -39,6 +39,8 @@ class TestDictionaryBuilder(TestCase): wf.write("東京都,0,0,0,東京都,名詞,固有名詞,地名,一般,*,*,ヒガシキョウト,東京都,*,B,\"東,名詞,普通名詞,一般,*,*,*,ヒガシ/2\",*,1/2,1/2\n") wf.write("東,-1,-1,0,東,名詞,普通名詞,一般,*,*,*,ヒガシ,ひがし,*,A,*,*,*,*\n") wf.write("京都,0,0,0,京都,名詞,固有名詞,地名,一般,*,*,キョウト,京都,*,A,*,*,*,*\n") + wf.write("1,-1,-1,0,1,名詞,数詞,*,*,*,*,イチ,1,*,A,*,*,*,*\n") + wf.write("東1,0,0,0,東1,名詞,普通名詞,一般,*,*,*,ヒガシイチ,東1,*,C,\"東,名詞,普通名詞,一般,*,*,*,ヒガシ/1,名詞,数詞,*,*,*,*,イチ\",\"東,名詞,普通名詞,一般,*,*,*,ヒガシ/U3\",*") self.logger = getLogger() self.logger.disabled = True @@ -218,13 +220,13 @@ class TestDictionaryBuilder(TestCase): self.assertEqual('test', header.description) # grammar - self.assertEqual(2, grammar.get_part_of_speech_size()) + self.assertEqual(3, grammar.get_part_of_speech_size()) self.assertEqual(["名詞", "固有名詞", "地名", "一般", "*", "*"], grammar.get_part_of_speech_string(0)) self.assertEqual(["名詞", "普通名詞", "一般", "*", "*", "*"], grammar.get_part_of_speech_string(1)) self.assertEqual(200, grammar.get_connect_cost(0, 0)) # lexicon - self.assertEqual(3, lexicon.size()) + self.assertEqual(5, lexicon.size()) self.assertEqual(0, lexicon.get_cost(0)) wi = lexicon.get_word_info(0) self.assertEqual('東京都', wi.surface)

Slow building of user dictionary with surface form split info It seems take 30+ seconds per entry to build user dictionary, if its words have split info with word info (構成語情報). ``` $ sudachipy ubuild user.csv -o user.dic reading the source file...1 words writing the POS table...2 bytes writing the connection matrix...4 bytes building the trie...done writing the trie...1028 bytes writing the word-ID table...9 bytes writing the word parameters...10 bytes writing the word_infos...70 bytes writing word_info offsets...4 bytes real 0m38.654s user 0m38.499s sys 0m0.139s ``` user.csv: ```csv 舞台藝術,5146,5146,8000,舞台藝術,名詞,普通名詞,一般,*,*,*,ブタイゲイジュツ,舞台芸術,*,C,"舞台,名詞,普通名詞,一般,*,*,*,ブタイ/藝術,名詞,普通名詞,一般,*,*,*,ゲイジュツ","舞台,名詞,普通名詞,一般,*,*,*,ブタイ/藝術,名詞,普通名詞,一般,*,*,*,ゲイジュツ","舞台,名詞,普通名詞,一般,*,*,*,ブタイ/藝術,名詞,普通名詞,一般,*,*,*,ゲイジュツ",* ``` If I have two lines then it takes 1m. ※ No problem with **word id** split info ```csv 舞台藝術,5146,5146,8000,舞台藝術,名詞,普通名詞,一般,*,*,*,ブタイゲイジュツ,舞台芸術,*,C,647312/659236,647312/659236,647312/659236,* ``` ``` $ sudachipy ubuild user.csv -o user.dic real 0m0.925s user 0m0.776s sys 0m0.159s ``` ---- ``` $ sudachipy --version sudachipy 0.5.2 ```

0.0

7e5b501111920cef057b821412af595db248a7b8

[ "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_build" ]

[ "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_add_to_trie", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_convert_matrix", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_convert_postable", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_decode", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_line_empty_headword", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_line_invalid_columns", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_line_same_readingform", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_line_toolong_headword", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_line_toomany_split", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_splitinfo", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_splitinfo_invalid_system_wordid_in_userdict", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_splitinfo_invalid_wordid", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parse_splitinfo_invalid_wordid_userdict", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_parseline", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_write_intarray", "tests/dictionarylib/test_dictionarybuilder.py::TestDictionaryBuilder::test_write_string" ]

{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2021-06-24 03:14:56+00:00

apache-2.0

837

Wortmeister-HQ__zahlwort2num-6

diff --git a/zahlwort2num/__init__.py b/zahlwort2num/__init__.py index cacf7d9..2e0a2b5 100644 --- a/zahlwort2num/__init__.py +++ b/zahlwort2num/__init__.py @@ -12,6 +12,7 @@ class ZahlConverter: 'eine': 1, 'er': 1, 'zwei': 2, + 'zwo': 2, 'drei': 3, 'drit': 3, 'vier': 4,

Wortmeister-HQ/zahlwort2num

325417a06bc6f79ca13605bb54b0dbc6d45c8f6e

diff --git a/zahlwort2num/tests/test_convert.py b/zahlwort2num/tests/test_convert.py index 91fd15f..905ec5c 100644 --- a/zahlwort2num/tests/test_convert.py +++ b/zahlwort2num/tests/test_convert.py @@ -6,6 +6,7 @@ class TestConverter(TestCase): def test_hardcoded_values_upto_100(self): self.assertTrue(w2n.convert('eins') == 1) self.assertTrue(w2n.convert('zwei') == 2) + self.assertTrue(w2n.convert('zwo') == 2) self.assertTrue(w2n.convert('drei') == 3) self.assertTrue(w2n.convert('vier') == 4) self.assertTrue(w2n.convert('fünf') == 5) @@ -128,12 +129,14 @@ class TestConverter(TestCase): 'zwei milliarden', 'eintausend', 'null', - 'neunundvierzig' + 'neunundvierzig', + 'zwohundertzwoundzwanzig', + 'zwotausend' ] numbers = [7, 99, 1000, 200000, 4504, 4511, 225, 3625, 12854, 653521, 99, 500002, 1004000, 700000000009001009001, 9000000000000000000000000011, - 2000000000, 1000, 0, 49] + 2000000000, 1000, 0, 49, 222, 2000] self.compare_sets(numbers, words)

Does not work with alternative pronunciation "zwo" ```py >>> from zahlwort2num import convert >>> convert("zwo") Traceback (most recent call last): File "<stdin>", line 1, in <module> File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 137, in convert return c.convert() File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 123, in convert return self.ordBn(number) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 108, in ordBn return self.ordWithBN(number, 0) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 88, in ordWithBN return self.convOrd(number) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 81, in convOrd return self.convt2(number) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 129, in <lambda> self.convt2 = lambda number: self.mult(number, 'tausend', 1000, self.convh2) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 60, in mult return fun(spliter[0]) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 130, in <lambda> self.convh2 = lambda number: self.mult(number, 'hundert', 100, self.convu2) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 60, in mult return fun(spliter[0]) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 131, in <lambda> self.convu2 = lambda number: self.mult(number, 'und', 1, lambda word: self.CONST_NUMS[word]) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 60, in mult return fun(spliter[0]) File "C:\ProgramData\miniforge3\lib\site-packages\zahlwort2num\__init__.py", line 131, in <lambda> self.convu2 = lambda number: self.mult(number, 'und', 1, lambda word: self.CONST_NUMS[word]) KeyError: 'zwo' ```

0.0

325417a06bc6f79ca13605bb54b0dbc6d45c8f6e

[ "zahlwort2num/tests/test_convert.py::TestConverter::test_hardcoded_values_upto_100", "zahlwort2num/tests/test_convert.py::TestConverter::test_more_specific" ]

[ "zahlwort2num/tests/test_convert.py::TestConverter::test_bugs_found_by_users", "zahlwort2num/tests/test_convert.py::TestConverter::test_negative_values", "zahlwort2num/tests/test_convert.py::TestConverter::test_negative_with_ordinal", "zahlwort2num/tests/test_convert.py::TestConverter::test_ordinal_numbers", "zahlwort2num/tests/test_convert.py::TestConverter::test_swiss_variant", "zahlwort2num/tests/test_convert.py::TestConverter::test_yet_another_ordinal_edge_case" ]

{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }

2022-10-28 09:45:02+00:00

mit

838

XKNX__xknx-1008

diff --git a/docs/changelog.md b/docs/changelog.md index 98a4c42b..9a9e0700 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -6,6 +6,12 @@ nav_order: 2 # Changelog +## Unreleased changes + +### Internal + +- Fix DPT2ByteFloat numeric range issues + ## 0.22.1 Wrong delivery 2022-07-29 ### Management diff --git a/xknx/dpt/dpt_2byte_float.py b/xknx/dpt/dpt_2byte_float.py index ead6abdc..c5858011 100644 --- a/xknx/dpt/dpt_2byte_float.py +++ b/xknx/dpt/dpt_2byte_float.py @@ -49,33 +49,23 @@ class DPT2ByteFloat(DPTNumeric): @classmethod def to_knx(cls, value: float) -> tuple[int, int]: """Serialize to KNX/IP raw data.""" - - def calc_exponent(float_value: float, sign: bool) -> tuple[int, int]: - """Return float exponent.""" - exponent = 0 - significand = abs(int(float_value * 100)) - - while significand < -2048 or significand > 2048: - exponent += 1 - significand >>= 1 - - if sign: - significand ^= 0x7FF # invert - significand += 1 # and add 1 - - return exponent, significand - try: knx_value = float(value) if not cls._test_boundaries(knx_value): raise ValueError - sign = knx_value < 0 - exponent, significand = calc_exponent(knx_value, sign) + value = knx_value * 100 + exponent = 0 + while value < -2048 or value > 2047: + exponent += 1 + value /= 2 + + mantisse = int(round(value)) & 0x7FF + msb = exponent << 3 | mantisse >> 8 + if value < 0: + msb |= 0x80 - return (sign << 7) | (exponent << 3) | ( - significand >> 8 - ), significand & 0xFF + return msb, mantisse & 0xFF except ValueError: raise ConversionError(f"Could not serialize {cls.__name__}", value=value) diff --git a/xknx/secure/keyring.py b/xknx/secure/keyring.py index e23bc7e7..1727e5e9 100644 --- a/xknx/secure/keyring.py +++ b/xknx/secure/keyring.py @@ -222,7 +222,7 @@ class XMLDevice(AttributeReader): class Keyring(AttributeReader): """Class for loading and decrypting knxkeys XML files.""" - backbone: XMLBackbone + backbone: XMLBackbone | None = None interfaces: list[XMLInterface] group_addresses: list[XMLGroupAddress] devices: list[XMLDevice]

XKNX/xknx

180ec53481c40f8bebf4b9fcaad2b450857d7109

diff --git a/requirements/testing.txt b/requirements/testing.txt index 76aac084..ee9c39d4 100644 --- a/requirements/testing.txt +++ b/requirements/testing.txt @@ -8,6 +8,6 @@ pylint==2.14.5 pytest==7.1.2 pytest-asyncio==0.19.0 pytest-cov==3.0.0 -setuptools==63.4.2 +setuptools==64.0.1 tox==3.25.1 mypy==0.971 diff --git a/test/dpt_tests/dpt_float_test.py b/test/dpt_tests/dpt_float_test.py index 0a9dc336..083fa7c1 100644 --- a/test/dpt_tests/dpt_float_test.py +++ b/test/dpt_tests/dpt_float_test.py @@ -79,6 +79,13 @@ class TestDPTFloat: assert DPT2ByteFloat.to_knx(DPT2ByteFloat.value_max) == (0x7F, 0xFF) assert DPT2ByteFloat.from_knx((0x7F, 0xFF)) == DPT2ByteFloat.value_max + def test_close_to_limit(self): + """Test parsing and streaming of DPT2ByteFloat with numeric limit.""" + assert DPT2ByteFloat.to_knx(20.48) == (0x0C, 0x00) + assert DPT2ByteFloat.from_knx((0x0C, 0x00)) == 20.48 + assert DPT2ByteFloat.to_knx(-20.48) == (0x80, 0x00) + assert DPT2ByteFloat.from_knx((0x80, 0x00)) == -20.48 + def test_min(self): """Test parsing and streaming of DPT2ByteFloat with minimum value.""" assert DPT2ByteFloat.to_knx(DPT2ByteFloat.value_min) == (0xF8, 0x00)

AttributeError: 'Keyring' object has no attribute 'backbone' Hi. My ETS generates a .knxkeys file that doesn't have a "backbone" parameter: ``` <?xml version="1.0" encoding="utf-8"?> <Keyring Project="Apartment" CreatedBy="ETS 5.7.4 (Build 1093)" Created="2022-08-09T15:53:32" Signature="yaIT..." xmlns="http://knx.org/xml/keyring/1"> <Interface Type="Tunneling" Host="1.1.251" UserID="2" Password="HIDDEN" IndividualAddress="HIDDEN" Authentication="HIDDEN" /> <Interface Type="Tunneling" Host="1.1.251" UserID="3" Password="HIDDEN" IndividualAddress="HIDDEN" Authentication="HIDDEN" /> <Interface Type="Tunneling" Host="1.1.251" UserID="4" Password="HIDDEN" IndividualAddress="HIDDEN" Authentication="HIDDEN" /> <Interface Type="Tunneling" Host="1.1.251" UserID="5" Password="HIDDEN" IndividualAddress="HIDDEN" Authentication="HIDDEN" /> <Devices> <Device IndividualAddress="1.1.251" SequenceNumber="24" /> </Devices> </Keyring> ``` Because of that i get the following error: ``` There was an error during loading the knxkeys file. Traceback (most recent call last): File "/opt/homebrew/lib/python3.9/site-packages/xknx/secure/keyring.py", line 316, in load_key_ring keyring.decrypt(password) File "/opt/homebrew/lib/python3.9/site-packages/xknx/secure/keyring.py", line 299, in decrypt if self.backbone is not None: AttributeError: 'Keyring' object has no attribute 'backbone' Traceback (most recent call last): File "/opt/homebrew/lib/python3.9/site-packages/xknx/secure/keyring.py", line 316, in load_key_ring keyring.decrypt(password) File "/opt/homebrew/lib/python3.9/site-packages/xknx/secure/keyring.py", line 299, in decrypt if self.backbone is not None: AttributeError: 'Keyring' object has no attribute 'backbone' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/max/Projects/KNX/example_telegram_monitor.py", line 69, in <module> asyncio.run(main(sys.argv[1:])) File "/opt/homebrew/Cellar/[email protected]/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/runners.py", line 44, in run return loop.run_until_complete(main) File "/opt/homebrew/Cellar/[email protected]/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete return future.result() File "/Users/max/Projects/KNX/example_telegram_monitor.py", line 65, in main await monitor(address_filters) File "/Users/max/Projects/KNX/example_telegram_monitor.py", line 47, in monitor await xknx.start() File "/opt/homebrew/lib/python3.9/site-packages/xknx/xknx.py", line 128, in start await self.knxip_interface.start() File "/opt/homebrew/lib/python3.9/site-packages/xknx/io/knxip_interface.py", line 69, in start await self._start() File "/opt/homebrew/lib/python3.9/site-packages/xknx/io/knxip_interface.py", line 105, in _start keyring: Keyring = load_key_ring( File "/opt/homebrew/lib/python3.9/site-packages/xknx/secure/keyring.py", line 321, in load_key_ring raise InvalidSecureConfiguration() from exception xknx.exceptions.exception.InvalidSecureConfiguration ``` I get the same error in the standalone version of XKNX and in Home Assistant when using the "TCP with IP Secure" connection mode. My code: ``` connection_config = ConnectionConfig( connection_type=ConnectionType.TUNNELING_TCP_SECURE, gateway_ip="192.168.11.24", secure_config=SecureConfig( user_id=3, knxkeys_file_path="/Users/max/KNX/Deployment/Apartment.knxkeys", knxkeys_password="HIDDEN", ), ) xknx = XKNX(connection_config=connection_config, daemon_mode=True) ``` As a temporary fix i've applied the following patch: ``` --- xknx/secure/keyring.py 2022-08-09 19:49:28.000000000 +0300 +++ xknx/secure/keyring_fixed.py 2022-08-09 20:27:51.000000000 +0300 @@ -233,6 +233,7 @@ def __init__(self) -> None: """Initialize the Keyring.""" + self.backbone = None self.interfaces = [] self.devices = [] self.group_addresses = [] ``` - [X] using xknx standalone - [X] using Home-Assistant knx integration **Version information:** - Standalone xknx: 0.22.1 - xknx / Home-Assistant release with the issue: 2022.7.7 **KNX installation:** ETS 5.7.4 KNX IP Interface: MDT SCN-IP000.03

0.0

180ec53481c40f8bebf4b9fcaad2b450857d7109

[ "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_close_to_limit" ]

[ "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_value_from_documentation", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_value_taken_from_live_thermostat", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_zero_value", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_room_temperature", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_high_temperature", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_minor_negative_temperature", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_very_cold_temperature", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_max", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_min", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_close_to_max", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_close_to_min", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_to_knx_min_exceeded", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_to_knx_max_exceeded", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_to_knx_wrong_parameter", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_from_knx_wrong_parameter", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_from_knx_wrong_parameter2", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_temperature_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_temperature_assert_min_exceeded", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_temperature_assert_min_exceeded_from_knx", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_lux_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_lux_assert_min_exceeded", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_humidity_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_humidity_assert_min_exceeded", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_enthalpy_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_partspermillion_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_voltage_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_float_values_from_power_meter", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_14_033", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_14_055", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_14_057", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_float_values_from_voltage_meter", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_float_zero_value", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_float_special_value", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_float_to_knx_wrong_parameter", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_float_from_knx_wrong_parameter", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_float_from_knx_wrong_parameter2", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_4byte_flaot_from_knx_unpack_error", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_electric_current_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_electric_potential_settings", "test/dpt_tests/dpt_float_test.py::TestDPTFloat::test_power_settings" ]

{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2022-08-10 08:07:07+00:00

mit

839

XKNX__xknx-1114

diff --git a/docs/changelog.md b/docs/changelog.md index 2cc605ca..b056f7de 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -12,6 +12,10 @@ nav_order: 2 - ExposeSensor: Add `cooldown` option to allow rate-limiting of sent telegrams. +### Connection + +- Disconnect when tunnelling sequence number (UDP) gets out of sync. + ### Internals - Add `task.done()` to TaskRegistry tasks. diff --git a/xknx/io/tunnel.py b/xknx/io/tunnel.py index 20833f81..e57c871d 100644 --- a/xknx/io/tunnel.py +++ b/xknx/io/tunnel.py @@ -607,6 +607,9 @@ class UDPTunnel(_Tunnel): self.expected_sequence_number, tunneling_request, ) + # Tunnelling server should repeat that frame and disconnect after that was also not ACKed. + # some don't seem to initiate disconnection here so we take a shortcut and disconnect ourselves + self._tunnel_lost() def _send_tunnelling_ack( self, communication_channel_id: int, sequence_counter: int

XKNX/xknx

d1d6085102331fe9430004e55085612fd993b2f7

diff --git a/requirements/testing.txt b/requirements/testing.txt index 7954b357..e07b3e32 100644 --- a/requirements/testing.txt +++ b/requirements/testing.txt @@ -1,13 +1,13 @@ -r production.txt -pre-commit==2.20.0 -isort==5.11.3 +pre-commit==2.21.0 +isort==5.11.4 flake8==6.0.0 -flake8-isort==5.0.3 +flake8-isort==6.0.0 pydocstyle==6.1.1 pylint==2.15.9 pytest==7.2.0 pytest-asyncio==0.20.3 pytest-cov==4.0.0 setuptools==65.6.3 -tox==4.0.16 +tox==4.0.17 mypy==0.991 diff --git a/test/io_tests/tunnel_test.py b/test/io_tests/tunnel_test.py index cd177980..53178978 100644 --- a/test/io_tests/tunnel_test.py +++ b/test/io_tests/tunnel_test.py @@ -155,7 +155,9 @@ class TestUDPTunnel: assert self.tunnel.expected_sequence_number == 11 assert self.tg_received_mock.call_count == 1 # wrong sequence number - no ACK, not processed - self.tunnel._request_received(test_frame_9, None, None) + # reconnect if `auto_reconnect` was True + with pytest.raises(CommunicationError): + self.tunnel._request_received(test_frame_9, None, None) await time_travel(0) assert self.tunnel.transport.send.call_args_list == [] self.tunnel.transport.send.reset_mock()

'TunnellingRequest with sequence number not equal to expected' error every few hours Every few hours 'Received TunnellingRequest with sequence number not equal to expected' error is stuck while the sequence finally loops around. During that time messages are sent but not read. - [ ] using xknx standalone - [x] using Home-Assistant knx integration **Version information:** - xknx / Home-Assistant release with the issue: 1.2.1 - last working xknx / Home-Assistant release (if known): unknown **KNX installation:** `configuration.yaml` [knx.yaml.txt](https://github.com/XKNX/xknx/files/10067390/knx.yaml.txt) **Diagnostic data of the config entry (only when Home Assistant is used)** [config_entry-knx-ed093e5771cbc5d18e4307a64fd3a504.json.txt](https://github.com/XKNX/xknx/files/10067378/config_entry-knx-ed093e5771cbc5d18e4307a64fd3a504.json.txt) **Traceback (if applicable):** [log.txt](https://github.com/XKNX/xknx/files/10067435/log.txt)

0.0

d1d6085102331fe9430004e55085612fd993b2f7

[ "test/io_tests/tunnel_test.py::TestUDPTunnel::test_repeated_tunnel_request" ]

[ "test/io_tests/tunnel_test.py::TestUDPTunnel::test_tunnel_request_received[\\x06\\x10\\x04", "test/io_tests/tunnel_test.py::TestUDPTunnel::test_tunnel_request_received_callback", "test/io_tests/tunnel_test.py::TestUDPTunnel::test_tunnel_request_received_cemi_too_small", "test/io_tests/tunnel_test.py::TestUDPTunnel::test_tunnel_request_received_apci_unsupported", "test/io_tests/tunnel_test.py::TestUDPTunnel::test_tunnel_connect_send_disconnect[False-data_endpoint_addr0-local_endpoint0]", "test/io_tests/tunnel_test.py::TestUDPTunnel::test_tunnel_connect_send_disconnect[True-None-local_endpoint1]", "test/io_tests/tunnel_test.py::TestUDPTunnel::test_tunnel_request_description", "test/io_tests/tunnel_test.py::TestTCPTunnel::test_tunnel_heartbeat", "test/io_tests/tunnel_test.py::TestTCPTunnel::test_tunnel_heartbeat_no_answer", "test/io_tests/tunnel_test.py::TestTCPTunnel::test_tunnel_heartbeat_error" ]

{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2022-12-21 21:20:28+00:00

mit

840

XKNX__xknx-1190

diff --git a/docs/changelog.md b/docs/changelog.md index 03b50890..5834d7d3 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -17,6 +17,7 @@ nav_order: 2 - Parse Data Secure credentials form Keyring from non-IP-Secure interfaces. - Parse Data Secure credentials from Keyrings exported for specific interfaces. +- Fix callback for Cover target position when called with same value consecutively. - Fix Windows TCP transport bug when using IP Secure Tunnelling. ### Protocol diff --git a/xknx/devices/cover.py b/xknx/devices/cover.py index 750913e1..489c1364 100644 --- a/xknx/devices/cover.py +++ b/xknx/devices/cover.py @@ -360,7 +360,7 @@ class Cover(Device): await self._stop_position_update() await self.position_current.process(telegram, always_callback=True) - await self.position_target.process(telegram) + await self.position_target.process(telegram, always_callback=True) await self.angle.process(telegram) await self.locked.process(telegram)

XKNX/xknx

88fc1ead4cdb10bdacee6824905540365588bf9d

diff --git a/test/devices_tests/cover_test.py b/test/devices_tests/cover_test.py index 2617622e..9dbe67ad 100644 --- a/test/devices_tests/cover_test.py +++ b/test/devices_tests/cover_test.py @@ -830,6 +830,9 @@ class TestCover: ("1/2/1", DPTBinary(1), "long"), ("1/2/2", DPTBinary(1), "short"), ("1/2/4", DPTArray(42), "position"), + ("1/2/3", DPTBinary(1), "stop"), + # call position with same value again to make sure `always_callback` is set for target position + ("1/2/4", DPTArray(42), "position"), ("1/2/5", DPTArray(42), "position state"), ("1/2/6", DPTArray(42), "angle"), ("1/2/7", DPTArray(51), "angle state"),

Cover update callback stops in some special case Hello! My intention is to use `device_updated_cb` callback for Cover to process some logic during its movement etc.. I faced the problem when callback stops working in some special case, for example: Pretend the blind initial position is 0% and we need to move it to 90% 1) start moving the blind to some position `await cover.set_position(90)` 2) send Stop during movement `cover.stop()` 3) then continue to move it to the previously given position `await cover.set_position(90)` Here the `device_updated_cb` stops 4) if then or instead to send the blind to any other position but except 90%, the callback gets back to work, for example, sending to any of 0-89 or 91-100% . Not sure if I'm doing something not correctly. Here is the reduced example: ` async def cover_update_cb(cover: Cover): print('Something inside cover update callback') cover: Cover = None async def test(): global cover await asyncio.sleep(1) await cover.set_position(90) await asyncio.sleep(4) print('STOP command') await cover.stop() await asyncio.sleep(2) print(f'Continue to move to 90') await cover.set_position(90) # here cover_update_cb stops. If instead set any different position from a position that the blind started moving from at the beginning (in our case 90) then callback will work. async def main(): global cover xknx = XKNX(daemon_mode=True) cover = Cover( xknx, 'Cover', group_address_stop = "1/1/2", group_address_position = "1/1/3", group_address_position_state = "1/1/4", device_updated_cb=cover_update_cb ) loop = asyncio.get_running_loop() loop.create_task(test()) await xknx.start() await xknx.stop() asyncio.run(main()) `

0.0

88fc1ead4cdb10bdacee6824905540365588bf9d

[ "test/devices_tests/cover_test.py::TestCover::test_process_callback" ]

[ "test/devices_tests/cover_test.py::TestCover::test_supports_stop_true", "test/devices_tests/cover_test.py::TestCover::test_supports_stop_false", "test/devices_tests/cover_test.py::TestCover::test_supports_position_true", "test/devices_tests/cover_test.py::TestCover::test_supports_position_false", "test/devices_tests/cover_test.py::TestCover::test_supports_angle_true", "test/devices_tests/cover_test.py::TestCover::test_support_angle_false", "test/devices_tests/cover_test.py::TestCover::test_support_locked", "test/devices_tests/cover_test.py::TestCover::test_sync", "test/devices_tests/cover_test.py::TestCover::test_sync_state", "test/devices_tests/cover_test.py::TestCover::test_sync_angle", "test/devices_tests/cover_test.py::TestCover::test_sync_angle_state", "test/devices_tests/cover_test.py::TestCover::test_set_up", "test/devices_tests/cover_test.py::TestCover::test_set_short_down", "test/devices_tests/cover_test.py::TestCover::test_set_down_inverted", "test/devices_tests/cover_test.py::TestCover::test_set_short_up", "test/devices_tests/cover_test.py::TestCover::test_set_up_inverted", "test/devices_tests/cover_test.py::TestCover::test_set_down", "test/devices_tests/cover_test.py::TestCover::test_stop", "test/devices_tests/cover_test.py::TestCover::test_stop_angle", "test/devices_tests/cover_test.py::TestCover::test_position", "test/devices_tests/cover_test.py::TestCover::test_position_without_binary", "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_up", "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_down", "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_uninitialized_up", "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_uninitialized_down", "test/devices_tests/cover_test.py::TestCover::test_angle", "test/devices_tests/cover_test.py::TestCover::test_angle_not_supported", "test/devices_tests/cover_test.py::TestCover::test_process_position", "test/devices_tests/cover_test.py::TestCover::test_process_angle", "test/devices_tests/cover_test.py::TestCover::test_process_locked", "test/devices_tests/cover_test.py::TestCover::test_process_up", "test/devices_tests/cover_test.py::TestCover::test_process_down", "test/devices_tests/cover_test.py::TestCover::test_process_stop", "test/devices_tests/cover_test.py::TestCover::test_process_short_stop", "test/devices_tests/cover_test.py::TestCover::test_is_traveling", "test/devices_tests/cover_test.py::TestCover::test_auto_stop", "test/devices_tests/cover_test.py::TestCover::test_periodic_update", "test/devices_tests/cover_test.py::TestCover::test_has_group_address" ]

{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2023-02-11 06:57:04+00:00

mit

841

XKNX__xknx-234

diff --git a/examples/example_light_rgbw.py b/examples/example_light_rgbw.py new file mode 100644 index 00000000..dd060c98 --- /dev/null +++ b/examples/example_light_rgbw.py @@ -0,0 +1,49 @@ +"""Example for setting different colors on a RGBW light.""" +import asyncio + +from xknx import XKNX +from xknx.devices import RemoteValueColorRGBW + + +async def main(): + """Connect to KNX/IP bus and set different colors.""" + xknx = XKNX() + await xknx.start() + + rgbw = RemoteValueColorRGBW(xknx, + group_address='1/1/40', + group_address_state='1/1/41', + device_name="RGBWLight") + + await rgbw.set([255, 255, 255, 0, 15]) # cold-white + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 255, 15]) # warm-white + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 0, 15]) # off + await asyncio.sleep(1) + + await rgbw.set([255, 0, 0, 0]) # red + await asyncio.sleep(1) + await rgbw.set([0, 255, 0, 0]) # green + await asyncio.sleep(1) + await rgbw.set([0, 0, 255, 0]) # blue + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 0, 15]) # off + await asyncio.sleep(1) + + await rgbw.set([255, 255, 0, 0, 15]) + await asyncio.sleep(1) + await rgbw.set([0, 255, 255, 0, 15]) + await asyncio.sleep(1) + await rgbw.set([255, 0, 255, 0, 15]) + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 0, 15]) # off + await asyncio.sleep(1) + + await xknx.stop() + + +# pylint: disable=invalid-name +loop = asyncio.get_event_loop() +loop.run_until_complete(main()) +loop.close() diff --git a/xknx/devices/remote_value_color_rgbw.py b/xknx/devices/remote_value_color_rgbw.py index 6c2e436e..beea0ca9 100644 --- a/xknx/devices/remote_value_color_rgbw.py +++ b/xknx/devices/remote_value_color_rgbw.py @@ -35,19 +35,23 @@ class RemoteValueColorRGBW(RemoteValue): Convert value (4-6 bytes) to payload (6 bytes). * Structure of DPT 251.600 - ** Bytes 0, 1: - *** Bit 0-11: 0 - *** Bit 12,13,14,15: R,G,B,W value valid? - ** Byte 2: R value - ** Byte 3: G value - ** Byte 4: B value - ** Byte 5: W value + ** Byte 0: R value + ** Byte 1: G value + ** Byte 2: B value + ** Byte 3: W value + ** Byte 4: 0x00 (reserved) + ** Byte 5: + *** Bit 0: W value valid? + *** Bit 1: B value valid? + *** Bit 2: G value valid? + *** Bit 3: R value valid? + *** Bit 4-7: 0 In case we receive * > 6 bytes: error * 6 bytes: all bytes are passed through - * 5 bytes: 0x00 left padding - * 4 bytes: 0x000f left padding + * 5 bytes: 0x00?? fill up to 6 bytes + * 4 bytes: 0x000f right padding to 6 bytes * < 4 bytes: error """ if not isinstance(value, (list, tuple)): @@ -56,12 +60,16 @@ class RemoteValueColorRGBW(RemoteValue): if len(value) < 4 or len(value) > 6: raise ConversionError("Cannot serialize value to DPT 251.600 (wrong length, expecting list of 4-6 bytes)", value=value, type=type(value)) - rgbw = value[len(value)-4:] + rgbw = value[:4] if any(not isinstance(color, int) for color in rgbw) \ or any(color < 0 for color in rgbw) \ or any(color > 255 for color in rgbw): raise ConversionError("Cannot serialize DPT 251.600 (wrong RGBW values)", value=value) - return DPTArray([0x00, 0x0f][:6-len(value)] + list(value)) + if len(value) < 5: + return DPTArray(list(rgbw) + [0x00, 0x0f]) + if len(value) < 6: + return DPTArray(list(rgbw) + [0x00] + list(value[4:])) + return DPTArray(value) def from_knx(self, payload): """ @@ -72,7 +80,7 @@ class RemoteValueColorRGBW(RemoteValue): """ result = [] for i in range(0, len(payload.value) - 2): - valid = payload.value[1] & (0x08 >> i) != 0 - result.append(payload.value[2 + i] if valid else self.previous_value[i]) + valid = (payload.value[5] & (0x08 >> i)) != 0 # R,G,B,W value valid? + result.append(payload.value[i] if valid else self.previous_value[i]) self.previous_value = result return result diff --git a/xknx/exceptions/exception.py b/xknx/exceptions/exception.py index 879e14b2..626299bd 100644 --- a/xknx/exceptions/exception.py +++ b/xknx/exceptions/exception.py @@ -6,7 +6,15 @@ class XKNXException(Exception): def __eq__(self, other): """Equal operator.""" - return self.__dict__ == other.__dict__ + return repr(self) == repr(other) + + def __hash__(self): + """Hash function.""" + return hash(str(self)) + + def __repr__(self): + """Representation of object.""" + return str(self) class CouldNotParseTelegram(XKNXException): @@ -14,7 +22,7 @@ class CouldNotParseTelegram(XKNXException): def __init__(self, description, **kwargs): """Initialize CouldNotParseTelegram class.""" - super().__init__("Could not parse Telegram") + super().__init__() self.description = description self.parameter = kwargs @@ -32,7 +40,7 @@ class CouldNotParseKNXIP(XKNXException): def __init__(self, description=""): """Initialize CouldNotParseTelegram class.""" - super().__init__("Could not parse KNXIP") + super().__init__() self.description = description def __str__(self): @@ -46,7 +54,7 @@ class ConversionError(XKNXException): def __init__(self, description, **kwargs): """Initialize ConversionError class.""" - super().__init__("Conversion Error") + super().__init__() self.description = description self.parameter = kwargs @@ -63,7 +71,7 @@ class CouldNotParseAddress(XKNXException): def __init__(self, address=None): """Initialize CouldNotParseAddress class.""" - super().__init__("Could not parse address") + super().__init__() self.address = address def __str__(self): @@ -76,7 +84,7 @@ class DeviceIllegalValue(XKNXException): def __init__(self, value, description): """Initialize DeviceIllegalValue class.""" - super().__init__("Illegal value for device") + super().__init__() self.value = value self.description = description

XKNX/xknx

4b71c28db4cde694695da3dfad0072dd5383717f

diff --git a/test/core_tests/exceptions_test.py b/test/core_tests/exceptions_test.py new file mode 100644 index 00000000..41fc1b74 --- /dev/null +++ b/test/core_tests/exceptions_test.py @@ -0,0 +1,51 @@ +"""Unit tests for exceptions""" +import pytest + +from xknx.exceptions import ( + ConversionError, CouldNotParseAddress, CouldNotParseKNXIP, + CouldNotParseTelegram, DeviceIllegalValue, XKNXException) + + [email protected]( + "base,equal,diff", + [ + ( + ConversionError("desc1"), + ConversionError("desc1"), + ConversionError("desc2"), + ), + ( + CouldNotParseAddress(123), + CouldNotParseAddress(123), + CouldNotParseAddress(321), + ), + ( + CouldNotParseKNXIP("desc1"), + CouldNotParseKNXIP("desc1"), + CouldNotParseKNXIP("desc2"), + ), + ( + CouldNotParseTelegram("desc", arg1=1, arg2=2), + CouldNotParseTelegram("desc", arg1=1, arg2=2), + CouldNotParseTelegram("desc", arg1=2, arg2=1), + ), + ( + DeviceIllegalValue("value1", "desc"), + DeviceIllegalValue("value1", "desc"), + DeviceIllegalValue("value1", "desc2"), + ), + ( + XKNXException("desc1"), + XKNXException("desc1"), + XKNXException("desc2"), + ), + ], +) +def test_exceptions(base, equal, diff): + """Test hashability and repr of exceptions.""" + assert hash(base) == hash(equal) + assert hash(base) != hash(diff) + assert base == equal + assert base != diff + assert repr(base) == repr(equal) + assert repr(base) != repr(diff) diff --git a/test/devices_tests/light_test.py b/test/devices_tests/light_test.py index b6283672..5de6eddf 100644 --- a/test/devices_tests/light_test.py +++ b/test/devices_tests/light_test.py @@ -318,7 +318,7 @@ class TestLight(unittest.TestCase): self.assertEqual(xknx.telegrams.qsize(), 1) telegram = xknx.telegrams.get_nowait() self.assertEqual(telegram, - Telegram(GroupAddress('1/2/5'), payload=DPTArray((0, 15, 23, 24, 25, 26)))) + Telegram(GroupAddress('1/2/5'), payload=DPTArray((23, 24, 25, 26, 0, 15)))) self.assertEqual(light.current_color, ([23, 24, 25], 26)) def test_set_color_rgbw_not_possible(self): @@ -489,7 +489,7 @@ class TestLight(unittest.TestCase): group_address_color='1/2/4', group_address_rgbw='1/2/5') self.assertEqual(light.current_color, (None, None)) - telegram = Telegram(GroupAddress('1/2/5'), payload=DPTArray((0, 15, 23, 24, 25, 26))) + telegram = Telegram(GroupAddress('1/2/5'), payload=DPTArray((23, 24, 25, 26, 0, 15))) self.loop.run_until_complete(asyncio.Task(light.process(telegram))) self.assertEqual(light.current_color, ([23, 24, 25], 26)) diff --git a/test/devices_tests/remote_value_color_rgbw_test.py b/test/devices_tests/remote_value_color_rgbw_test.py index 2a56d3b0..d352c299 100644 --- a/test/devices_tests/remote_value_color_rgbw_test.py +++ b/test/devices_tests/remote_value_color_rgbw_test.py @@ -26,32 +26,32 @@ class TestRemoteValueColorRGBW(unittest.TestCase): remote_value = RemoteValueColorRGBW(xknx) input_list = [100, 101, 102, 127] input_tuple = (100, 101, 102, 127) - expected = DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x7f)) + expected = DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x0f)) self.assertEqual(remote_value.to_knx(input_tuple), expected) self.assertEqual(remote_value.to_knx(input_list), expected) - self.assertEqual(remote_value.to_knx((15,) + input_tuple), expected) - self.assertEqual(remote_value.to_knx([15] + input_list), expected) - self.assertEqual(remote_value.to_knx((0, 15) + input_tuple), expected) - self.assertEqual(remote_value.to_knx([0, 15] + input_list), expected) + self.assertEqual(remote_value.to_knx(input_tuple + (15,)), expected) + self.assertEqual(remote_value.to_knx(input_list + [15]), expected) + self.assertEqual(remote_value.to_knx(input_tuple + (0, 15)), expected) + self.assertEqual(remote_value.to_knx(input_list + [0, 15]), expected) def test_from_knx(self): """Test from_knx function with normal operation.""" xknx = XKNX(loop=self.loop) remote_value = RemoteValueColorRGBW(xknx) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x00, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x00))), [0, 0, 0, 0]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x0f))), [100, 101, 102, 127]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x00, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x00))), [100, 101, 102, 127]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x09, 0xff, 0x65, 0x66, 0xff))), + remote_value.from_knx(DPTArray((0xff, 0x65, 0x66, 0xff, 0x00, 0x09))), [255, 101, 102, 255]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x01, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x01))), [255, 101, 102, 127]) def test_to_knx_error(self): @@ -90,7 +90,7 @@ class TestRemoteValueColorRGBW(unittest.TestCase): telegram, Telegram( GroupAddress('1/2/3'), - payload=DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x67)))) + payload=DPTArray((0x64, 0x65, 0x66, 0x67, 0x00, 0x0f)))) self.loop.run_until_complete(asyncio.Task(remote_value.set((100, 101, 104, 105)))) self.assertEqual(xknx.telegrams.qsize(), 1) telegram = xknx.telegrams.get_nowait() @@ -98,7 +98,7 @@ class TestRemoteValueColorRGBW(unittest.TestCase): telegram, Telegram( GroupAddress('1/2/3'), - payload=DPTArray((0x00, 0x0f, 0x64, 0x65, 0x68, 0x69)))) + payload=DPTArray((0x64, 0x65, 0x68, 0x69, 0x00, 0x0f)))) def test_process(self): """Test process telegram.""" @@ -108,7 +108,7 @@ class TestRemoteValueColorRGBW(unittest.TestCase): group_address=GroupAddress("1/2/3")) telegram = Telegram( group_address=GroupAddress("1/2/3"), - payload=DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x67))) + payload=DPTArray((0x64, 0x65, 0x66, 0x67, 0x00, 0x0f))) self.loop.run_until_complete(asyncio.Task(remote_value.process(telegram))) self.assertEqual(remote_value.value, [100, 101, 102, 103])

XKNXException is an unhashable exception **Description of problem:** Seem the XKNXException exception is not hashable causing problems with python traceback module: https://bugs.python.org/issue28603. Oddly that aught to have been solved already. - [ ] using xknx standalone - [X] using Home-Assistant knx plugin **Version information:** - xknx / Home-Assistant release with the issue: - last working xknx / Home-Assistant release (if known): 0.98 **KNX installation:**  **Problem-relevant `xknx.yaml` or `configuration.yaml` entries (fill out even if it seems unimportant):** **Traceback (if applicable):** Aug 22 08:18:24 hass hass[35975]: TypeError: unhashable type: 'XKNXException' Aug 22 08:18:24 hass hass[35975]: _seen.add(exc_value) Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/traceback.py", line 462, in __init__ Aug 22 08:18:24 hass hass[35975]: type(value), value, tb, limit=limit).format(chain=chain): Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/traceback.py", line 100, in print_exception Aug 22 08:18:24 hass hass[35975]: traceback.print_exception(ei[0], ei[1], tb, None, sio) Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/logging/__init__.py", line 533, in formatException Aug 22 08:18:24 hass hass[35975]: record.exc_text = self.formatException(record.exc_info) Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/logging/__init__.py", line 583, in format Aug 22 08:18:24 hass hass[35975]: return fmt.format(record) Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/logging/__init__.py", line 838, in format Aug 22 08:18:24 hass hass[35975]: msg = self.format(record) Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/logging/__init__.py", line 992, in emit

0.0

4b71c28db4cde694695da3dfad0072dd5383717f

[ "test/core_tests/exceptions_test.py::test_exceptions[base0-equal0-diff0]", "test/core_tests/exceptions_test.py::test_exceptions[base1-equal1-diff1]", "test/core_tests/exceptions_test.py::test_exceptions[base2-equal2-diff2]", "test/core_tests/exceptions_test.py::test_exceptions[base3-equal3-diff3]", "test/core_tests/exceptions_test.py::test_exceptions[base4-equal4-diff4]", "test/core_tests/exceptions_test.py::test_exceptions[base5-equal5-diff5]", "test/devices_tests/light_test.py::TestLight::test_process_color_rgbw", "test/devices_tests/light_test.py::TestLight::test_set_color_rgbw", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_from_knx", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_process", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_set", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_to_knx" ]

[ "test/devices_tests/light_test.py::TestLight::test_do", "test/devices_tests/light_test.py::TestLight::test_has_group_address", "test/devices_tests/light_test.py::TestLight::test_process_color", "test/devices_tests/light_test.py::TestLight::test_process_color_temperature", "test/devices_tests/light_test.py::TestLight::test_process_color_temperature_payload_invalid_length", "test/devices_tests/light_test.py::TestLight::test_process_color_temperature_wrong_payload", "test/devices_tests/light_test.py::TestLight::test_process_dimm", "test/devices_tests/light_test.py::TestLight::test_process_dimm_payload_invalid_length", "test/devices_tests/light_test.py::TestLight::test_process_dimm_wrong_payload", "test/devices_tests/light_test.py::TestLight::test_process_switch", "test/devices_tests/light_test.py::TestLight::test_process_switch_callback", "test/devices_tests/light_test.py::TestLight::test_process_tunable_white", "test/devices_tests/light_test.py::TestLight::test_process_tunable_white_payload_invalid_length", "test/devices_tests/light_test.py::TestLight::test_process_tunable_white_wrong_payload", "test/devices_tests/light_test.py::TestLight::test_set_brightness", "test/devices_tests/light_test.py::TestLight::test_set_brightness_not_dimmable", "test/devices_tests/light_test.py::TestLight::test_set_color", "test/devices_tests/light_test.py::TestLight::test_set_color_not_possible", "test/devices_tests/light_test.py::TestLight::test_set_color_rgbw_not_possible", "test/devices_tests/light_test.py::TestLight::test_set_color_temp", "test/devices_tests/light_test.py::TestLight::test_set_color_temp_unsupported", "test/devices_tests/light_test.py::TestLight::test_set_off", "test/devices_tests/light_test.py::TestLight::test_set_on", "test/devices_tests/light_test.py::TestLight::test_set_tw", "test/devices_tests/light_test.py::TestLight::test_set_tw_unsupported", "test/devices_tests/light_test.py::TestLight::test_supports_color_false", "test/devices_tests/light_test.py::TestLight::test_supports_color_temp_false", "test/devices_tests/light_test.py::TestLight::test_supports_color_temp_true", "test/devices_tests/light_test.py::TestLight::test_supports_color_true", "test/devices_tests/light_test.py::TestLight::test_supports_dimm_no", "test/devices_tests/light_test.py::TestLight::test_supports_dimm_yes", "test/devices_tests/light_test.py::TestLight::test_supports_rgbw_false", "test/devices_tests/light_test.py::TestLight::test_supports_rgbw_true", "test/devices_tests/light_test.py::TestLight::test_supports_tw_no", "test/devices_tests/light_test.py::TestLight::test_supports_tw_yes", "test/devices_tests/light_test.py::TestLight::test_sync", "test/devices_tests/light_test.py::TestLight::test_sync_state_address", "test/devices_tests/light_test.py::TestLight::test_wrong_do", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_to_knx_error", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_to_process_error" ]

{ "failed_lite_validators": [ "has_hyperlinks", "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2019-09-10 16:14:51+00:00

mit

842

XKNX__xknx-235

diff --git a/examples/example_light_rgbw.py b/examples/example_light_rgbw.py new file mode 100644 index 00000000..dd060c98 --- /dev/null +++ b/examples/example_light_rgbw.py @@ -0,0 +1,49 @@ +"""Example for setting different colors on a RGBW light.""" +import asyncio + +from xknx import XKNX +from xknx.devices import RemoteValueColorRGBW + + +async def main(): + """Connect to KNX/IP bus and set different colors.""" + xknx = XKNX() + await xknx.start() + + rgbw = RemoteValueColorRGBW(xknx, + group_address='1/1/40', + group_address_state='1/1/41', + device_name="RGBWLight") + + await rgbw.set([255, 255, 255, 0, 15]) # cold-white + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 255, 15]) # warm-white + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 0, 15]) # off + await asyncio.sleep(1) + + await rgbw.set([255, 0, 0, 0]) # red + await asyncio.sleep(1) + await rgbw.set([0, 255, 0, 0]) # green + await asyncio.sleep(1) + await rgbw.set([0, 0, 255, 0]) # blue + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 0, 15]) # off + await asyncio.sleep(1) + + await rgbw.set([255, 255, 0, 0, 15]) + await asyncio.sleep(1) + await rgbw.set([0, 255, 255, 0, 15]) + await asyncio.sleep(1) + await rgbw.set([255, 0, 255, 0, 15]) + await asyncio.sleep(1) + await rgbw.set([0, 0, 0, 0, 15]) # off + await asyncio.sleep(1) + + await xknx.stop() + + +# pylint: disable=invalid-name +loop = asyncio.get_event_loop() +loop.run_until_complete(main()) +loop.close() diff --git a/xknx/devices/remote_value_color_rgbw.py b/xknx/devices/remote_value_color_rgbw.py index 6c2e436e..beea0ca9 100644 --- a/xknx/devices/remote_value_color_rgbw.py +++ b/xknx/devices/remote_value_color_rgbw.py @@ -35,19 +35,23 @@ class RemoteValueColorRGBW(RemoteValue): Convert value (4-6 bytes) to payload (6 bytes). * Structure of DPT 251.600 - ** Bytes 0, 1: - *** Bit 0-11: 0 - *** Bit 12,13,14,15: R,G,B,W value valid? - ** Byte 2: R value - ** Byte 3: G value - ** Byte 4: B value - ** Byte 5: W value + ** Byte 0: R value + ** Byte 1: G value + ** Byte 2: B value + ** Byte 3: W value + ** Byte 4: 0x00 (reserved) + ** Byte 5: + *** Bit 0: W value valid? + *** Bit 1: B value valid? + *** Bit 2: G value valid? + *** Bit 3: R value valid? + *** Bit 4-7: 0 In case we receive * > 6 bytes: error * 6 bytes: all bytes are passed through - * 5 bytes: 0x00 left padding - * 4 bytes: 0x000f left padding + * 5 bytes: 0x00?? fill up to 6 bytes + * 4 bytes: 0x000f right padding to 6 bytes * < 4 bytes: error """ if not isinstance(value, (list, tuple)): @@ -56,12 +60,16 @@ class RemoteValueColorRGBW(RemoteValue): if len(value) < 4 or len(value) > 6: raise ConversionError("Cannot serialize value to DPT 251.600 (wrong length, expecting list of 4-6 bytes)", value=value, type=type(value)) - rgbw = value[len(value)-4:] + rgbw = value[:4] if any(not isinstance(color, int) for color in rgbw) \ or any(color < 0 for color in rgbw) \ or any(color > 255 for color in rgbw): raise ConversionError("Cannot serialize DPT 251.600 (wrong RGBW values)", value=value) - return DPTArray([0x00, 0x0f][:6-len(value)] + list(value)) + if len(value) < 5: + return DPTArray(list(rgbw) + [0x00, 0x0f]) + if len(value) < 6: + return DPTArray(list(rgbw) + [0x00] + list(value[4:])) + return DPTArray(value) def from_knx(self, payload): """ @@ -72,7 +80,7 @@ class RemoteValueColorRGBW(RemoteValue): """ result = [] for i in range(0, len(payload.value) - 2): - valid = payload.value[1] & (0x08 >> i) != 0 - result.append(payload.value[2 + i] if valid else self.previous_value[i]) + valid = (payload.value[5] & (0x08 >> i)) != 0 # R,G,B,W value valid? + result.append(payload.value[i] if valid else self.previous_value[i]) self.previous_value = result return result diff --git a/xknx/exceptions/exception.py b/xknx/exceptions/exception.py index 879e14b2..626299bd 100644 --- a/xknx/exceptions/exception.py +++ b/xknx/exceptions/exception.py @@ -6,7 +6,15 @@ class XKNXException(Exception): def __eq__(self, other): """Equal operator.""" - return self.__dict__ == other.__dict__ + return repr(self) == repr(other) + + def __hash__(self): + """Hash function.""" + return hash(str(self)) + + def __repr__(self): + """Representation of object.""" + return str(self) class CouldNotParseTelegram(XKNXException): @@ -14,7 +22,7 @@ class CouldNotParseTelegram(XKNXException): def __init__(self, description, **kwargs): """Initialize CouldNotParseTelegram class.""" - super().__init__("Could not parse Telegram") + super().__init__() self.description = description self.parameter = kwargs @@ -32,7 +40,7 @@ class CouldNotParseKNXIP(XKNXException): def __init__(self, description=""): """Initialize CouldNotParseTelegram class.""" - super().__init__("Could not parse KNXIP") + super().__init__() self.description = description def __str__(self): @@ -46,7 +54,7 @@ class ConversionError(XKNXException): def __init__(self, description, **kwargs): """Initialize ConversionError class.""" - super().__init__("Conversion Error") + super().__init__() self.description = description self.parameter = kwargs @@ -63,7 +71,7 @@ class CouldNotParseAddress(XKNXException): def __init__(self, address=None): """Initialize CouldNotParseAddress class.""" - super().__init__("Could not parse address") + super().__init__() self.address = address def __str__(self): @@ -76,7 +84,7 @@ class DeviceIllegalValue(XKNXException): def __init__(self, value, description): """Initialize DeviceIllegalValue class.""" - super().__init__("Illegal value for device") + super().__init__() self.value = value self.description = description diff --git a/xknx/knxip/cemi_frame.py b/xknx/knxip/cemi_frame.py index ec925a83..3f023c62 100644 --- a/xknx/knxip/cemi_frame.py +++ b/xknx/knxip/cemi_frame.py @@ -105,7 +105,10 @@ class CEMIFrame(KNXIPBody): def from_knx(self, raw): """Parse/deserialize from KNX/IP raw data.""" - self.code = CEMIMessageCode(raw[0]) + try: + self.code = CEMIMessageCode(raw[0]) + except ValueError: + raise CouldNotParseKNXIP("Could not understand CEMIMessageCode: {0} ".format(raw[0])) if self.code == CEMIMessageCode.L_DATA_IND or \ self.code == CEMIMessageCode.L_Data_REQ or \ @@ -140,7 +143,11 @@ class CEMIFrame(KNXIPBody): tpci_apci = cemi[9 + addil] * 256 + cemi[10 + addil] - self.cmd = APCICommand(tpci_apci & 0xFFC0) + try: + self.cmd = APCICommand(tpci_apci & 0xFFC0) + except ValueError: + raise CouldNotParseKNXIP( + "APCI not supported: {0:#012b}".format(tpci_apci & 0xFFC0)) apdu = cemi[10 + addil:] if len(apdu) != self.mpdu_len:

XKNX/xknx

4b71c28db4cde694695da3dfad0072dd5383717f

diff --git a/test/core_tests/exceptions_test.py b/test/core_tests/exceptions_test.py new file mode 100644 index 00000000..41fc1b74 --- /dev/null +++ b/test/core_tests/exceptions_test.py @@ -0,0 +1,51 @@ +"""Unit tests for exceptions""" +import pytest + +from xknx.exceptions import ( + ConversionError, CouldNotParseAddress, CouldNotParseKNXIP, + CouldNotParseTelegram, DeviceIllegalValue, XKNXException) + + [email protected]( + "base,equal,diff", + [ + ( + ConversionError("desc1"), + ConversionError("desc1"), + ConversionError("desc2"), + ), + ( + CouldNotParseAddress(123), + CouldNotParseAddress(123), + CouldNotParseAddress(321), + ), + ( + CouldNotParseKNXIP("desc1"), + CouldNotParseKNXIP("desc1"), + CouldNotParseKNXIP("desc2"), + ), + ( + CouldNotParseTelegram("desc", arg1=1, arg2=2), + CouldNotParseTelegram("desc", arg1=1, arg2=2), + CouldNotParseTelegram("desc", arg1=2, arg2=1), + ), + ( + DeviceIllegalValue("value1", "desc"), + DeviceIllegalValue("value1", "desc"), + DeviceIllegalValue("value1", "desc2"), + ), + ( + XKNXException("desc1"), + XKNXException("desc1"), + XKNXException("desc2"), + ), + ], +) +def test_exceptions(base, equal, diff): + """Test hashability and repr of exceptions.""" + assert hash(base) == hash(equal) + assert hash(base) != hash(diff) + assert base == equal + assert base != diff + assert repr(base) == repr(equal) + assert repr(base) != repr(diff) diff --git a/test/devices_tests/light_test.py b/test/devices_tests/light_test.py index b6283672..5de6eddf 100644 --- a/test/devices_tests/light_test.py +++ b/test/devices_tests/light_test.py @@ -318,7 +318,7 @@ class TestLight(unittest.TestCase): self.assertEqual(xknx.telegrams.qsize(), 1) telegram = xknx.telegrams.get_nowait() self.assertEqual(telegram, - Telegram(GroupAddress('1/2/5'), payload=DPTArray((0, 15, 23, 24, 25, 26)))) + Telegram(GroupAddress('1/2/5'), payload=DPTArray((23, 24, 25, 26, 0, 15)))) self.assertEqual(light.current_color, ([23, 24, 25], 26)) def test_set_color_rgbw_not_possible(self): @@ -489,7 +489,7 @@ class TestLight(unittest.TestCase): group_address_color='1/2/4', group_address_rgbw='1/2/5') self.assertEqual(light.current_color, (None, None)) - telegram = Telegram(GroupAddress('1/2/5'), payload=DPTArray((0, 15, 23, 24, 25, 26))) + telegram = Telegram(GroupAddress('1/2/5'), payload=DPTArray((23, 24, 25, 26, 0, 15))) self.loop.run_until_complete(asyncio.Task(light.process(telegram))) self.assertEqual(light.current_color, ([23, 24, 25], 26)) diff --git a/test/devices_tests/remote_value_color_rgbw_test.py b/test/devices_tests/remote_value_color_rgbw_test.py index 2a56d3b0..d352c299 100644 --- a/test/devices_tests/remote_value_color_rgbw_test.py +++ b/test/devices_tests/remote_value_color_rgbw_test.py @@ -26,32 +26,32 @@ class TestRemoteValueColorRGBW(unittest.TestCase): remote_value = RemoteValueColorRGBW(xknx) input_list = [100, 101, 102, 127] input_tuple = (100, 101, 102, 127) - expected = DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x7f)) + expected = DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x0f)) self.assertEqual(remote_value.to_knx(input_tuple), expected) self.assertEqual(remote_value.to_knx(input_list), expected) - self.assertEqual(remote_value.to_knx((15,) + input_tuple), expected) - self.assertEqual(remote_value.to_knx([15] + input_list), expected) - self.assertEqual(remote_value.to_knx((0, 15) + input_tuple), expected) - self.assertEqual(remote_value.to_knx([0, 15] + input_list), expected) + self.assertEqual(remote_value.to_knx(input_tuple + (15,)), expected) + self.assertEqual(remote_value.to_knx(input_list + [15]), expected) + self.assertEqual(remote_value.to_knx(input_tuple + (0, 15)), expected) + self.assertEqual(remote_value.to_knx(input_list + [0, 15]), expected) def test_from_knx(self): """Test from_knx function with normal operation.""" xknx = XKNX(loop=self.loop) remote_value = RemoteValueColorRGBW(xknx) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x00, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x00))), [0, 0, 0, 0]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x0f))), [100, 101, 102, 127]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x00, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x00))), [100, 101, 102, 127]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x09, 0xff, 0x65, 0x66, 0xff))), + remote_value.from_knx(DPTArray((0xff, 0x65, 0x66, 0xff, 0x00, 0x09))), [255, 101, 102, 255]) self.assertEqual( - remote_value.from_knx(DPTArray((0x00, 0x01, 0x64, 0x65, 0x66, 0x7f))), + remote_value.from_knx(DPTArray((0x64, 0x65, 0x66, 0x7f, 0x00, 0x01))), [255, 101, 102, 127]) def test_to_knx_error(self): @@ -90,7 +90,7 @@ class TestRemoteValueColorRGBW(unittest.TestCase): telegram, Telegram( GroupAddress('1/2/3'), - payload=DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x67)))) + payload=DPTArray((0x64, 0x65, 0x66, 0x67, 0x00, 0x0f)))) self.loop.run_until_complete(asyncio.Task(remote_value.set((100, 101, 104, 105)))) self.assertEqual(xknx.telegrams.qsize(), 1) telegram = xknx.telegrams.get_nowait() @@ -98,7 +98,7 @@ class TestRemoteValueColorRGBW(unittest.TestCase): telegram, Telegram( GroupAddress('1/2/3'), - payload=DPTArray((0x00, 0x0f, 0x64, 0x65, 0x68, 0x69)))) + payload=DPTArray((0x64, 0x65, 0x68, 0x69, 0x00, 0x0f)))) def test_process(self): """Test process telegram.""" @@ -108,7 +108,7 @@ class TestRemoteValueColorRGBW(unittest.TestCase): group_address=GroupAddress("1/2/3")) telegram = Telegram( group_address=GroupAddress("1/2/3"), - payload=DPTArray((0x00, 0x0f, 0x64, 0x65, 0x66, 0x67))) + payload=DPTArray((0x64, 0x65, 0x66, 0x67, 0x00, 0x0f))) self.loop.run_until_complete(asyncio.Task(remote_value.process(telegram))) self.assertEqual(remote_value.value, [100, 101, 102, 103]) diff --git a/test/knxip_tests/cemi_frame_test.py b/test/knxip_tests/cemi_frame_test.py new file mode 100644 index 00000000..dae3f63c --- /dev/null +++ b/test/knxip_tests/cemi_frame_test.py @@ -0,0 +1,71 @@ +"""Tests for the CEMIFrame object""" + +from unittest.mock import MagicMock + +from pytest import fixture, raises + +from xknx.exceptions import CouldNotParseKNXIP +from xknx.knx import DPTBinary, PhysicalAddress +from xknx.knxip.cemi_frame import CEMIFrame +from xknx.knxip.knxip_enum import APCICommand, CEMIMessageCode + + +def get_data(code, adil, flags, src, dst, mpdu_len, tpci_apci, payload): + return [ + code, + adil, # adil + (flags >> 8) & 255, # flags + flags & 255, # flags + (src >> 8) & 255, # src + src & 255, # src + (dst >> 8) & 255, # dst + dst & 255, # dst + mpdu_len, # mpdu_len + (tpci_apci >> 8) & 255, # tpci_apci + tpci_apci & 255, # tpci_apci + *payload, # payload + ] + + +@fixture(name="frame") +def fixture_frame(): + """Fixture to get a simple mocked frame""" + xknx = MagicMock() + return CEMIFrame(xknx) + + +def test_valid_command(frame): + """Test for valid frame parsing""" + packet_len = frame.from_knx(get_data(0x29, 0, 0, 0, 0, 1, 0, [])) + assert frame.code == CEMIMessageCode.L_DATA_IND + assert frame.cmd == APCICommand.GROUP_READ + assert frame.flags == 0 + assert frame.mpdu_len == 1 + assert frame.payload == DPTBinary(0) + assert frame.src_addr == PhysicalAddress(0) + assert frame.dst_addr == PhysicalAddress(0) + assert packet_len == 11 + + +def test_invalid_tpci_apci(frame): + """Test for invalid APCICommand""" + with raises(CouldNotParseKNXIP, match=r".*APCI not supported: .*"): + frame.from_knx(get_data(0x29, 0, 0, 0, 0, 1, 0xFFC0, [])) + + +def test_invalid_apdu_len(frame): + """Test for invalid apdu len""" + with raises(CouldNotParseKNXIP, match=r".*APDU LEN should be .*"): + frame.from_knx(get_data(0x29, 0, 0, 0, 0, 2, 0, [])) + + +def test_invalid_invalid_len(frame): + """Test for invalid cemi len""" + with raises(CouldNotParseKNXIP, match=r".*CEMI too small"): + frame.from_knx(get_data(0x29, 0, 0, 0, 0, 2, 0, [])[:5]) + + +def test_invalid_invalid_code(frame): + """Test for invalid cemi code""" + with raises(CouldNotParseKNXIP, match=r".*Could not understand CEMIMessageCode"): + frame.from_knx(get_data(0x0, 0, 0, 0, 0, 2, 0, []))

ValueError: [448,256] is not a valid APCICommand **Description of problem:** Exception during processing of messages, likely while ETS is communicating with new Secure IP Interface. - [ ] using xknx standalone - [X] using Home-Assistant knx plugin **Version information:** - xknx / Home-Assistant release with the issue: 0.98 - last working xknx / Home-Assistant release (if known): None **KNX installation:**  ETS 5.7.2 **Problem-relevant `xknx.yaml` or `configuration.yaml` entries (fill out even if it seems unimportant):** **Traceback (if applicable):** ``` Aug 19 19:09:24 hass hass[32967]: Traceback (most recent call last): Aug 19 19:09:24 hass hass[32967]: File "/usr/lib/python3.6/asyncio/events.py", line 127, in _run Aug 19 19:09:24 hass hass[32967]: self._callback(*self._args) Aug 19 19:09:24 hass hass[32967]: File "/usr/lib/python3.6/asyncio/selector_events.py", line 1078, in _read_ready Aug 19 19:09:24 hass hass[32967]: self._protocol.datagram_received(data, addr) Aug 19 19:09:24 hass hass[32967]: File "/home/homeassistant/env/lib/python3.6/site-packages/xknx/io/udp_client.py", line 55, in datagram_received Aug 19 19:09:24 hass hass[32967]: self.data_received_callback(data) Aug 19 19:09:24 hass hass[32967]: File "/home/homeassistant/env/lib/python3.6/site-packages/xknx/io/udp_client.py", line 87, in data_received_callback Aug 19 19:09:24 hass hass[32967]: knxipframe.from_knx(raw) Aug 19 19:09:24 hass hass[32967]: File "/home/homeassistant/env/lib/python3.6/site-packages/xknx/knxip/knxip.py", line 78, in from_knx Aug 19 19:09:24 hass hass[32967]: pos += self.body.from_knx(data[pos:]) Aug 19 19:09:24 hass hass[32967]: File "/home/homeassistant/env/lib/python3.6/site-packages/xknx/knxip/tunnelling_request.py", line 48, in from_knx Aug 19 19:09:24 hass hass[32967]: pos += self.cemi.from_knx(raw[pos:]) Aug 19 19:09:24 hass hass[32967]: File "/home/homeassistant/env/lib/python3.6/site-packages/xknx/knxip/cemi_frame.py", line 113, in from_knx Aug 19 19:09:24 hass hass[32967]: return self.from_knx_data_link_layer(raw) Aug 19 19:09:24 hass hass[32967]: File "/home/homeassistant/env/lib/python3.6/site-packages/xknx/knxip/cemi_frame.py", line 143, in from_knx_data_link_layer Aug 19 19:09:24 hass hass[32967]: self.cmd = APCICommand(tpci_apci & 0xFFC0) Aug 19 19:09:24 hass hass[32967]: File "/usr/lib/python3.6/enum.py", line 291, in __call__ Aug 19 19:09:24 hass hass[32967]: return cls.__new__(cls, value) Aug 19 19:09:24 hass hass[32967]: File "/usr/lib/python3.6/enum.py", line 533, in __new__ Aug 19 19:09:24 hass hass[32967]: return cls._missing_(value) Aug 19 19:09:24 hass hass[32967]: File "/usr/lib/python3.6/enum.py", line 546, in _missing_ Aug 19 19:09:24 hass hass[32967]: raise ValueError("%r is not a valid %s" % (value, cls.__name__)) Aug 19 19:09:24 hass hass[32967]: ValueError: 448 is not a valid APCICommand ``` ``` Aug 22 08:15:49 hass hass[35975]: ValueError: 256 is not a valid APCICommand Aug 22 08:15:49 hass hass[35975]: raise ValueError("%r is not a valid %s" % (value, cls.__name__)) Aug 22 08:15:49 hass hass[35975]: File "/usr/lib/python3.6/enum.py", line 546, in _missing_ Aug 22 08:15:49 hass hass[35975]: return cls._missing_(value) Aug 22 08:15:49 hass hass[35975]: File "/usr/lib/python3.6/enum.py", line 533, in __new__ Aug 22 08:15:49 hass hass[35975]: return cls.__new__(cls, value) Aug 22 08:15:49 hass hass[35975]: File "/usr/lib/python3.6/enum.py", line 291, in __call__ Aug 22 08:15:49 hass hass[35975]: self.cmd = APCICommand(tpci_apci & 0xFFC0) Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/asyncio/base_events.py", line 1426, in _run_once Aug 22 08:18:24 hass hass[35975]: self._run_once() Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/asyncio/base_events.py", line 421, in run_forever Aug 22 08:18:24 hass hass[35975]: self.run_forever() Aug 22 08:18:24 hass hass[35975]: File "/usr/lib/python3.6/asyncio/base_events.py", line 454, in run_until_complete Aug 22 08:18:24 hass hass[35975]: return loop.run_until_complete(main) Aug 22 08:18:24 hass hass[35975]: File "/home/homeassistant/env/lib/python3.6/site-packages/homeassistant/util/async_.py", line 37, in asyncio_run Aug 22 08:18:24 hass hass[35975]: exit_code = asyncio_run(setup_and_run_hass(config_dir, args)) Aug 22 08:18:24 hass hass[35975]: File "/home/homeassistant/env/lib/python3.6/site-packages/homeassistant/__main__.py", line 419, in main Aug 22 08:18:24 hass hass[35975]: sys.exit(main()) Aug 22 08:18:24 hass hass[35975]: File "/home/homeassistant/env/bin/hass", line 10, in <module> ```

0.0

4b71c28db4cde694695da3dfad0072dd5383717f

[ "test/core_tests/exceptions_test.py::test_exceptions[base0-equal0-diff0]", "test/core_tests/exceptions_test.py::test_exceptions[base1-equal1-diff1]", "test/core_tests/exceptions_test.py::test_exceptions[base2-equal2-diff2]", "test/core_tests/exceptions_test.py::test_exceptions[base3-equal3-diff3]", "test/core_tests/exceptions_test.py::test_exceptions[base4-equal4-diff4]", "test/core_tests/exceptions_test.py::test_exceptions[base5-equal5-diff5]", "test/devices_tests/light_test.py::TestLight::test_process_color_rgbw", "test/devices_tests/light_test.py::TestLight::test_set_color_rgbw", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_from_knx", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_process", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_set", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_to_knx", "test/knxip_tests/cemi_frame_test.py::test_invalid_tpci_apci", "test/knxip_tests/cemi_frame_test.py::test_invalid_invalid_code" ]

[ "test/devices_tests/light_test.py::TestLight::test_do", "test/devices_tests/light_test.py::TestLight::test_has_group_address", "test/devices_tests/light_test.py::TestLight::test_process_color", "test/devices_tests/light_test.py::TestLight::test_process_color_temperature", "test/devices_tests/light_test.py::TestLight::test_process_color_temperature_payload_invalid_length", "test/devices_tests/light_test.py::TestLight::test_process_color_temperature_wrong_payload", "test/devices_tests/light_test.py::TestLight::test_process_dimm", "test/devices_tests/light_test.py::TestLight::test_process_dimm_payload_invalid_length", "test/devices_tests/light_test.py::TestLight::test_process_dimm_wrong_payload", "test/devices_tests/light_test.py::TestLight::test_process_switch", "test/devices_tests/light_test.py::TestLight::test_process_switch_callback", "test/devices_tests/light_test.py::TestLight::test_process_tunable_white", "test/devices_tests/light_test.py::TestLight::test_process_tunable_white_payload_invalid_length", "test/devices_tests/light_test.py::TestLight::test_process_tunable_white_wrong_payload", "test/devices_tests/light_test.py::TestLight::test_set_brightness", "test/devices_tests/light_test.py::TestLight::test_set_brightness_not_dimmable", "test/devices_tests/light_test.py::TestLight::test_set_color", "test/devices_tests/light_test.py::TestLight::test_set_color_not_possible", "test/devices_tests/light_test.py::TestLight::test_set_color_rgbw_not_possible", "test/devices_tests/light_test.py::TestLight::test_set_color_temp", "test/devices_tests/light_test.py::TestLight::test_set_color_temp_unsupported", "test/devices_tests/light_test.py::TestLight::test_set_off", "test/devices_tests/light_test.py::TestLight::test_set_on", "test/devices_tests/light_test.py::TestLight::test_set_tw", "test/devices_tests/light_test.py::TestLight::test_set_tw_unsupported", "test/devices_tests/light_test.py::TestLight::test_supports_color_false", "test/devices_tests/light_test.py::TestLight::test_supports_color_temp_false", "test/devices_tests/light_test.py::TestLight::test_supports_color_temp_true", "test/devices_tests/light_test.py::TestLight::test_supports_color_true", "test/devices_tests/light_test.py::TestLight::test_supports_dimm_no", "test/devices_tests/light_test.py::TestLight::test_supports_dimm_yes", "test/devices_tests/light_test.py::TestLight::test_supports_rgbw_false", "test/devices_tests/light_test.py::TestLight::test_supports_rgbw_true", "test/devices_tests/light_test.py::TestLight::test_supports_tw_no", "test/devices_tests/light_test.py::TestLight::test_supports_tw_yes", "test/devices_tests/light_test.py::TestLight::test_sync", "test/devices_tests/light_test.py::TestLight::test_sync_state_address", "test/devices_tests/light_test.py::TestLight::test_wrong_do", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_to_knx_error", "test/devices_tests/remote_value_color_rgbw_test.py::TestRemoteValueColorRGBW::test_to_process_error", "test/knxip_tests/cemi_frame_test.py::test_valid_command", "test/knxip_tests/cemi_frame_test.py::test_invalid_apdu_len", "test/knxip_tests/cemi_frame_test.py::test_invalid_invalid_len" ]

{ "failed_lite_validators": [ "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2019-09-10 16:47:37+00:00

mit

843

XKNX__xknx-271

diff --git a/xknx/exceptions/__init__.py b/xknx/exceptions/__init__.py index 0875fb6f..95609fa0 100644 --- a/xknx/exceptions/__init__.py +++ b/xknx/exceptions/__init__.py @@ -2,4 +2,5 @@ # flake8: noqa from .exception import ( ConversionError, CouldNotParseAddress, CouldNotParseKNXIP, - CouldNotParseTelegram, DeviceIllegalValue, XKNXException) + CouldNotParseTelegram, DeviceIllegalValue, UnsupportedCEMIMessage, + XKNXException) diff --git a/xknx/exceptions/exception.py b/xknx/exceptions/exception.py index 626299bd..18702952 100644 --- a/xknx/exceptions/exception.py +++ b/xknx/exceptions/exception.py @@ -39,7 +39,7 @@ class CouldNotParseKNXIP(XKNXException): """Exception class for wrong KNXIP data.""" def __init__(self, description=""): - """Initialize CouldNotParseTelegram class.""" + """Initialize CouldNotParseKNXIP class.""" super().__init__() self.description = description @@ -49,6 +49,20 @@ class CouldNotParseKNXIP(XKNXException): .format(self.description) +class UnsupportedCEMIMessage(XKNXException): + """Exception class for unsupported CEMI Messages.""" + + def __init__(self, description=""): + """Initialize UnsupportedCEMIMessage class.""" + super().__init__() + self.description = description + + def __str__(self): + """Return object as readable string.""" + return '<UnsupportedCEMIMessage description="{0}" />' \ + .format(self.description) + + class ConversionError(XKNXException): """Exception class for error while converting one type to another.""" diff --git a/xknx/knxip/cemi_frame.py b/xknx/knxip/cemi_frame.py index 1fc80ead..dffa5064 100644 --- a/xknx/knxip/cemi_frame.py +++ b/xknx/knxip/cemi_frame.py @@ -12,7 +12,8 @@ Documentation within: File: AN117 v02.01 KNX IP Communication Medium DV.pdf """ from xknx.dpt import DPTArray, DPTBinary -from xknx.exceptions import ConversionError, CouldNotParseKNXIP +from xknx.exceptions import ( + ConversionError, CouldNotParseKNXIP, UnsupportedCEMIMessage) from xknx.telegram import GroupAddress, PhysicalAddress, Telegram, TelegramType from .body import KNXIPBody @@ -106,20 +107,25 @@ class CEMIFrame(KNXIPBody): def from_knx(self, raw): """Parse/deserialize from KNX/IP raw data.""" try: - self.code = CEMIMessageCode(raw[0]) - except ValueError: - raise CouldNotParseKNXIP("Could not understand CEMIMessageCode: {0} ".format(raw[0])) - - if self.code == CEMIMessageCode.L_DATA_IND or \ - self.code == CEMIMessageCode.L_Data_REQ or \ - self.code == CEMIMessageCode.L_DATA_CON: - return self.from_knx_data_link_layer(raw) - raise CouldNotParseKNXIP("Could not understand CEMIMessageCode: {0} / {1}".format(self.code, raw[0])) + try: + self.code = CEMIMessageCode(raw[0]) + except ValueError: + raise UnsupportedCEMIMessage("CEMIMessageCode not implemented: {0} ".format(raw[0])) + + if self.code == CEMIMessageCode.L_DATA_IND or \ + self.code == CEMIMessageCode.L_Data_REQ or \ + self.code == CEMIMessageCode.L_DATA_CON: + return self.from_knx_data_link_layer(raw) + raise UnsupportedCEMIMessage("Could not handle CEMIMessageCode: {0} / {1}".format(self.code, raw[0])) + except UnsupportedCEMIMessage as unsupported_cemi_err: + self.xknx.logger.warning("Ignoring not implemented CEMI: %s", unsupported_cemi_err) + return len(raw) def from_knx_data_link_layer(self, cemi): """Parse L_DATA_IND, CEMIMessageCode.L_Data_REQ, CEMIMessageCode.L_DATA_CON.""" if len(cemi) < 11: - raise CouldNotParseKNXIP("CEMI too small") + # eg. ETS Line-Scan issues L_DATA_IND with length 10 + raise UnsupportedCEMIMessage("CEMI too small. Length: {0}; CEMI: {1}".format(len(cemi), cemi)) # AddIL (Additional Info Length), as specified within # KNX Chapter 3.6.3/4.1.4.3 "Additional information." @@ -146,7 +152,7 @@ class CEMIFrame(KNXIPBody): try: self.cmd = APCICommand(tpci_apci & 0xFFC0) except ValueError: - raise CouldNotParseKNXIP( + raise UnsupportedCEMIMessage( "APCI not supported: {0:#012b}".format(tpci_apci & 0xFFC0)) apdu = cemi[10 + addil:]

XKNX/xknx

9790cdb696285b5700ec06c571193a7feeb96a39

diff --git a/test/knxip_tests/cemi_frame_test.py b/test/knxip_tests/cemi_frame_test.py index b305a3b3..711762ec 100644 --- a/test/knxip_tests/cemi_frame_test.py +++ b/test/knxip_tests/cemi_frame_test.py @@ -5,7 +5,7 @@ from unittest.mock import MagicMock from pytest import fixture, raises from xknx.dpt import DPTBinary -from xknx.exceptions import CouldNotParseKNXIP +from xknx.exceptions import CouldNotParseKNXIP, UnsupportedCEMIMessage from xknx.knxip.cemi_frame import CEMIFrame from xknx.knxip.knxip_enum import APCICommand, CEMIMessageCode from xknx.telegram import PhysicalAddress @@ -50,8 +50,8 @@ def test_valid_command(frame): def test_invalid_tpci_apci(frame): """Test for invalid APCICommand""" - with raises(CouldNotParseKNXIP, match=r".*APCI not supported: .*"): - frame.from_knx(get_data(0x29, 0, 0, 0, 0, 1, 0xFFC0, [])) + with raises(UnsupportedCEMIMessage, match=r".*APCI not supported: .*"): + frame.from_knx_data_link_layer(get_data(0x29, 0, 0, 0, 0, 1, 0xFFC0, [])) def test_invalid_apdu_len(frame): @@ -62,11 +62,5 @@ def test_invalid_apdu_len(frame): def test_invalid_invalid_len(frame): """Test for invalid cemi len""" - with raises(CouldNotParseKNXIP, match=r".*CEMI too small"): - frame.from_knx(get_data(0x29, 0, 0, 0, 0, 2, 0, [])[:5]) - - -def test_invalid_invalid_code(frame): - """Test for invalid cemi code""" - with raises(CouldNotParseKNXIP, match=r".*Could not understand CEMIMessageCode"): - frame.from_knx(get_data(0x0, 0, 0, 0, 0, 2, 0, [])) + with raises(UnsupportedCEMIMessage, match=r".*CEMI too small.*"): + frame.from_knx_data_link_layer(get_data(0x29, 0, 0, 0, 0, 2, 0, [])[:5])

Error when reading group addresses with timers I have an extensive KNX installation with all kinds of actors, sensors, switches, etc. My integration with Home Assistant works perfect, but I do get the following error in the logs when input is detected on an object linked to a timer: > Error doing job: Exception in callback UDPTransport._on_read_ready Traceback (most recent call last): File "uvloop/cbhandles.pyx", line 69, in uvloop.loop.Handle._run File "uvloop/handles/udp.pyx", line 64, in uvloop.loop.UDPTransport._on_read_ready File "/usr/local/lib/python3.6/site-packages/xknx/io/udp_client.py", line 55, in datagram_received self.data_received_callback(data) File "/usr/local/lib/python3.6/site-packages/xknx/io/udp_client.py", line 85, in data_received_callback knxipframe.from_knx(raw) File "/usr/local/lib/python3.6/site-packages/xknx/knxip/knxip.py", line 78, in from_knx pos += self.body.from_knx(data[pos:]) File "/usr/local/lib/python3.6/site-packages/xknx/knxip/tunnelling_request.py", line 48, in from_knx pos += self.cemi.from_knx(raw[pos:]) File "/usr/local/lib/python3.6/site-packages/xknx/knxip/cemi_frame.py", line 116, in from_knx return self.from_knx_data_link_layer(raw) File "/usr/local/lib/python3.6/site-packages/xknx/knxip/cemi_frame.py", line 147, in from_knx_data_link_layer self.cmd = APCICommand(tpci_apci & 0xFFC0) File "/usr/local/lib/python3.6/enum.py", line 291, in __call__ return cls.__new__(cls, value) File "/usr/local/lib/python3.6/enum.py", line 533, in __new__ return cls._missing_(value) File "/usr/local/lib/python3.6/enum.py", line 546, in _missing_ raise ValueError("%r is not a valid %s" % (value, cls.__name__)) ValueError: 960 is not a valid APCICommand Two minutes after this error I then receive: `Error: reading rading group address from KNX bus failed: ErrorCode.E_CONNECTION_ID`

0.0

9790cdb696285b5700ec06c571193a7feeb96a39

[ "test/knxip_tests/cemi_frame_test.py::test_valid_command", "test/knxip_tests/cemi_frame_test.py::test_invalid_tpci_apci", "test/knxip_tests/cemi_frame_test.py::test_invalid_apdu_len", "test/knxip_tests/cemi_frame_test.py::test_invalid_invalid_len" ]

[]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2020-03-22 23:56:49+00:00

mit

844

XKNX__xknx-406

diff --git a/xknx/devices/weather.py b/xknx/devices/weather.py index 8b155818..48791d01 100644 --- a/xknx/devices/weather.py +++ b/xknx/devices/weather.py @@ -189,7 +189,7 @@ class Weather(Device): xknx, group_address_state=group_address_air_pressure, sync_state=sync_state, - value_type="pressure", + value_type="pressure_2byte", device_name=self.name, feature_name="Air pressure", after_update_cb=self.after_update,

XKNX/xknx

5a3bbc5c493fd18761b3d0b3b383d3a35b3efa54

diff --git a/test/devices_tests/weather_test.py b/test/devices_tests/weather_test.py index b3956b46..02312d17 100644 --- a/test/devices_tests/weather_test.py +++ b/test/devices_tests/weather_test.py @@ -79,16 +79,9 @@ class TestWeather(unittest.TestCase): """Test resolve state with pressure.""" xknx = XKNX(loop=self.loop) weather = Weather(name="weather", xknx=xknx, group_address_air_pressure="1/3/4") - weather._air_pressure.payload = DPTArray( - ( - 0xC5, - 0xE6, - 0xE6, - 0x63, - ) - ) + weather._air_pressure.payload = DPTArray((0x6C, 0xAD)) - self.assertEqual(weather.air_pressure, -7388.79833984375) + self.assertEqual(weather.air_pressure, 98058.24) self.assertEqual(weather._air_pressure.unit_of_measurement, "Pa") self.assertEqual(weather._air_pressure.ha_device_class, "pressure")

KNX Weather entity payload error for air pressure **Description of problem:** I set up the new weather entity. For the air pressure the HA log shows an error due to an invalid payload. - [ ] using xknx standalone - [X] using Home-Assistant knx plugin **Version information:** - xknx / Home-Assistant release with the issue: 0.13.0 **KNX installation:** Jung Weather Station 2225 WSU - communication object: Air Pressure DPT 9.006 ![image](https://user-images.githubusercontent.com/53949754/93705737-df789100-fb1f-11ea-8c3a-058d1cefed00.png) **Problem-relevant `xknx.yaml` or `configuration.yaml` entries (fill out even if it seems unimportant):** ```` - name: 'Dach' address_temperature: '6/5/11' address_brightness_south: '6/5/6' address_brightness_west: '6/5/7' address_brightness_east: '6/5/5' address_wind_speed: '6/5/0' address_rain_alarm: '6/5/37' # address_frost_alarm: "7/0/6" address_wind_alarm: '6/5/29' # address_day_night: "7/0/8" address_air_pressure: '6/5/13' address_humidity: '6/5/12' expose_sensors: False sync_state: True ```` **Traceback (if applicable):** ``` 2020-09-19 10:35:51 ERROR (MainThread) [homeassistant] Error doing job: Task exception was never retrieved Traceback (most recent call last): File "/usr/local/lib/python3.8/site-packages/xknx/remote_value/remote_value.py", line 151, in read_state await self.process(telegram) File "/usr/local/lib/python3.8/site-packages/xknx/remote_value/remote_value.py", line 92, in process raise CouldNotParseTelegram("payload invalid", xknx.exceptions.exception.CouldNotParseTelegram: <CouldNotParseTelegram description="payload invalid" device_name="Dach" feature_name="Value" group_address="6/5/13" payload="<DPTArray value="[0x6c,0xad]" />"/> ```

0.0

5a3bbc5c493fd18761b3d0b3b383d3a35b3efa54

[ "test/devices_tests/weather_test.py::TestWeather::test_pressure" ]

[ "test/devices_tests/weather_test.py::TestWeather::test_brightness", "test/devices_tests/weather_test.py::TestWeather::test_cloudy_summer", "test/devices_tests/weather_test.py::TestWeather::test_cloudy_winter", "test/devices_tests/weather_test.py::TestWeather::test_day_night", "test/devices_tests/weather_test.py::TestWeather::test_expose_sensor", "test/devices_tests/weather_test.py::TestWeather::test_has_group_address", "test/devices_tests/weather_test.py::TestWeather::test_humidity", "test/devices_tests/weather_test.py::TestWeather::test_iter_remote_values", "test/devices_tests/weather_test.py::TestWeather::test_rain_alarm", "test/devices_tests/weather_test.py::TestWeather::test_state_lightning", "test/devices_tests/weather_test.py::TestWeather::test_state_snowy_rainy", "test/devices_tests/weather_test.py::TestWeather::test_sunny_summer", "test/devices_tests/weather_test.py::TestWeather::test_sunny_winter", "test/devices_tests/weather_test.py::TestWeather::test_temperature", "test/devices_tests/weather_test.py::TestWeather::test_weather_default", "test/devices_tests/weather_test.py::TestWeather::test_weather_state_attributes", "test/devices_tests/weather_test.py::TestWeather::test_wind_alarm", "test/devices_tests/weather_test.py::TestWeather::test_wind_speed" ]

{ "failed_lite_validators": [ "has_hyperlinks", "has_media" ], "has_test_patch": true, "is_lite": false }

2020-09-20 12:20:12+00:00

mit

845

XKNX__xknx-454

diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index f470c332..29b7fbe0 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -2,33 +2,33 @@ You are awesome! Thanks for contributing to our project! Please, DO NOT DELETE ANY TEXT from this template!. --> - +## Description  -## Description - Fixes # (issue) +## Type of change  -## Type of change - [ ] Bug fix (non-breaking change which fixes an issue) - [ ] New feature (non-breaking change which adds functionality) - [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected) - [ ] This change requires a documentation update -# Checklist: +## Checklist: - [ ] I have performed a self-review of my own code -- [ ] I have made corresponding changes to the documentation -- [ ] My changes generate no new warnings -- [ ] I have added tests that prove my fix is effective or that my feature works +- [ ] The documentation has been adjusted accordingly +- [ ] The changes generate no new warnings +- [ ] Tests have been added that prove the fix is effective or that the feature works +- [ ] The changes are documented in the changelog +- [ ] The Homeassistant plugin has been adjusted in case of new config options diff --git a/home-assistant-plugin/custom_components/xknx/const.py b/home-assistant-plugin/custom_components/xknx/const.py index 8bb99529..b5bdd447 100644 --- a/home-assistant-plugin/custom_components/xknx/const.py +++ b/home-assistant-plugin/custom_components/xknx/const.py @@ -18,6 +18,7 @@ DOMAIN = "xknx" CONF_STATE_ADDRESS = "state_address" CONF_SYNC_STATE = "sync_state" +CONF_RESET_AFTER = "reset_after" class ColorTempModes(Enum): diff --git a/home-assistant-plugin/custom_components/xknx/factory.py b/home-assistant-plugin/custom_components/xknx/factory.py index 157565c4..9e721817 100644 --- a/home-assistant-plugin/custom_components/xknx/factory.py +++ b/home-assistant-plugin/custom_components/xknx/factory.py @@ -202,6 +202,7 @@ def _create_switch(knx_module: XKNX, config: ConfigType) -> XknxSwitch: name=config[CONF_NAME], group_address=config[CONF_ADDRESS], group_address_state=config.get(SwitchSchema.CONF_STATE_ADDRESS), + reset_after=config.get(SwitchSchema.CONF_RESET_AFTER), ) diff --git a/home-assistant-plugin/custom_components/xknx/schema.py b/home-assistant-plugin/custom_components/xknx/schema.py index a224d9cb..89a6fac7 100644 --- a/home-assistant-plugin/custom_components/xknx/schema.py +++ b/home-assistant-plugin/custom_components/xknx/schema.py @@ -15,6 +15,7 @@ from homeassistant.const import ( import homeassistant.helpers.config_validation as cv from .const import ( + CONF_RESET_AFTER, CONF_STATE_ADDRESS, CONF_SYNC_STATE, OPERATION_MODES, @@ -86,7 +87,7 @@ class BinarySensorSchema: CONF_SYNC_STATE = CONF_SYNC_STATE CONF_IGNORE_INTERNAL_STATE = "ignore_internal_state" CONF_CONTEXT_TIMEOUT = "context_timeout" - CONF_RESET_AFTER = "reset_after" + CONF_RESET_AFTER = CONF_RESET_AFTER DEFAULT_NAME = "KNX Binary Sensor" @@ -253,6 +254,7 @@ class SwitchSchema: """Voluptuous schema for KNX switches.""" CONF_STATE_ADDRESS = CONF_STATE_ADDRESS + CONF_RESET_AFTER = CONF_RESET_AFTER DEFAULT_NAME = "KNX Switch" SCHEMA = vol.Schema( @@ -260,6 +262,7 @@ class SwitchSchema: vol.Required(CONF_ADDRESS): cv.string, vol.Optional(CONF_NAME, default=DEFAULT_NAME): cv.string, vol.Optional(CONF_STATE_ADDRESS): cv.string, + vol.Optional(CONF_RESET_AFTER): cv.positive_float, } ) diff --git a/xknx/devices/switch.py b/xknx/devices/switch.py index 670eb569..0a9dab20 100644 --- a/xknx/devices/switch.py +++ b/xknx/devices/switch.py @@ -6,6 +6,7 @@ It provides functionality for * switching 'on' and 'off'. * reading the current state from KNX bus. """ +import asyncio import logging from xknx.remote_value import RemoteValueSwitch @@ -22,6 +23,7 @@ class Switch(Device): self, xknx, name, + reset_after=None, group_address=None, group_address_state=None, device_updated_cb=None, @@ -30,6 +32,10 @@ class Switch(Device): # pylint: disable=too-many-arguments super().__init__(xknx, name, device_updated_cb) + self.reset_after = reset_after + self._reset_task = None + self.state = False + self.switch = RemoteValueSwitch( xknx, group_address, @@ -42,6 +48,11 @@ class Switch(Device): """Iterate the devices RemoteValue classes.""" yield self.switch + def __del__(self): + """Destructor. Cleaning up if this was not done before.""" + if self._reset_task: + self._reset_task.cancel() + @classmethod def from_config(cls, xknx, name, config): """Initialize object from configuration structure.""" @@ -55,12 +66,6 @@ class Switch(Device): group_address_state=group_address_state, ) - @property - def state(self): - """Return the current switch state of the device.""" - # None will return False - return bool(self.switch.value) - async def set_on(self): """Switch on switch.""" await self.switch.on() @@ -82,7 +87,18 @@ class Switch(Device): async def process_group_write(self, telegram): """Process incoming and outgoing GROUP WRITE telegram.""" - await self.switch.process(telegram) + if await self.switch.process(telegram): + self.state = self.switch.value + if self.reset_after is not None and self.state: + if self._reset_task: + self._reset_task.cancel() + self._reset_task = asyncio.create_task( + self._reset_state(self.reset_after) + ) + + async def _reset_state(self, wait_seconds: float): + await asyncio.sleep(wait_seconds) + await self.set_off() def __str__(self): """Return object as readable string."""

XKNX/xknx

5b6766ed6f83b863e53b6b6b7d608930ea80718f

diff --git a/requirements/testing.txt b/requirements/testing.txt index 3c8a67ce..71727a7d 100644 --- a/requirements/testing.txt +++ b/requirements/testing.txt @@ -1,6 +1,6 @@ -r production.txt pre-commit==2.7.1 -isort==5.5.4 +isort==5.5.5 coveralls==2.1.2 flake8==3.8.4 flake8-isort==4.0.0 diff --git a/test/devices_tests/switch_test.py b/test/devices_tests/switch_test.py index 42f651b2..a9520431 100644 --- a/test/devices_tests/switch_test.py +++ b/test/devices_tests/switch_test.py @@ -76,6 +76,47 @@ class TestSwitch(unittest.TestCase): self.assertEqual(switch.state, False) + def test_process_reset_after(self): + """Test process reset_after.""" + xknx = XKNX() + reset_after_sec = 0.001 + switch = Switch( + xknx, "TestInput", group_address="1/2/3", reset_after=reset_after_sec + ) + telegram_on = Telegram( + group_address=GroupAddress("1/2/3"), payload=DPTBinary(1) + ) + + self.loop.run_until_complete(switch.process(telegram_on)) + self.assertTrue(switch.state) + self.assertEqual(xknx.telegrams.qsize(), 0) + self.loop.run_until_complete(asyncio.sleep(reset_after_sec * 2)) + self.assertEqual(xknx.telegrams.qsize(), 1) + self.loop.run_until_complete(switch.process(xknx.telegrams.get_nowait())) + self.assertFalse(switch.state) + + def test_process_reset_after_cancel_existing(self): + """Test process reset_after cancels existing reset tasks.""" + xknx = XKNX() + reset_after_sec = 0.01 + switch = Switch( + xknx, "TestInput", group_address="1/2/3", reset_after=reset_after_sec + ) + telegram_on = Telegram( + group_address=GroupAddress("1/2/3"), payload=DPTBinary(1) + ) + + self.loop.run_until_complete(switch.process(telegram_on)) + self.assertTrue(switch.state) + self.assertEqual(xknx.telegrams.qsize(), 0) + self.loop.run_until_complete(asyncio.sleep(reset_after_sec / 2)) + # half way through the reset timer + self.loop.run_until_complete(switch.process(telegram_on)) + self.assertTrue(switch.state) + + self.loop.run_until_complete(asyncio.sleep(reset_after_sec / 2)) + self.assertEqual(xknx.telegrams.qsize(), 0) + def test_process_callback(self): """Test process / reading telegrams from telegram queue. Test if callback was called.""" # pylint: disable=no-self-use

Switch: add auto-off function Sometimes it is required to s always send a "OFF" right after sending a "ON" eg. for door openers. I suggest to add a `reset_after` option to Switch, just like BinarySensor, to send the "OFF" telegram after a timer is finished.

0.0

5b6766ed6f83b863e53b6b6b7d608930ea80718f

[ "test/devices_tests/switch_test.py::TestSwitch::test_process_reset_after", "test/devices_tests/switch_test.py::TestSwitch::test_process_reset_after_cancel_existing" ]

[ "test/devices_tests/switch_test.py::TestSwitch::test_do", "test/devices_tests/switch_test.py::TestSwitch::test_has_group_address", "test/devices_tests/switch_test.py::TestSwitch::test_process", "test/devices_tests/switch_test.py::TestSwitch::test_process_callback", "test/devices_tests/switch_test.py::TestSwitch::test_set_off", "test/devices_tests/switch_test.py::TestSwitch::test_set_on", "test/devices_tests/switch_test.py::TestSwitch::test_sync", "test/devices_tests/switch_test.py::TestSwitch::test_sync_state_address", "test/devices_tests/switch_test.py::TestSwitch::test_wrong_do" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2020-10-07 19:40:38+00:00

mit

846

XKNX__xknx-469

diff --git a/changelog.md b/changelog.md index 97c850a5..7fdd1b95 100644 --- a/changelog.md +++ b/changelog.md @@ -4,6 +4,7 @@ ### Devices +- Sensor: add `always_callback` option - ClimateMode: Refactor climate modes in operation_mode and controller_mode, also fixes a bug for binary operation modes where the mode would be set to AWAY no matter what value was sent to the bus. ### Internals diff --git a/docs/sensor.md b/docs/sensor.md index c741e111..22ae2581 100644 --- a/docs/sensor.md +++ b/docs/sensor.md @@ -15,6 +15,7 @@ Sensors are monitoring temperature, air humidity, pressure etc. from KNX bus. sensor = Sensor( xknx=xknx, name='DiningRoom.Temperature.Sensor', + always_callback=False, group_address_state='6/2/1', sync_state=True, value_type='temperature' @@ -25,6 +26,7 @@ Sensors are monitoring temperature, air humidity, pressure etc. from KNX bus. * `xknx` is the XKNX object. * `name` is the name of the object. +* `always_callback` defines if a callback/update should always be triggered no matter if the previous and the new state are identical. * `group_address_state` is the KNX group address of the sensor device. * `sync_state` defines if the value should be actively read from the bus. If `False` no GroupValueRead telegrams will be sent to its group address. Defaults to `True` * `value_type` controls how the value should be rendered in a human readable representation. The attribut may have may have the values `percent`, `temperature`, `illuminance`, `speed_ms` or `current`. diff --git a/home-assistant-plugin/custom_components/xknx/factory.py b/home-assistant-plugin/custom_components/xknx/factory.py index de552ff2..005d24d5 100644 --- a/home-assistant-plugin/custom_components/xknx/factory.py +++ b/home-assistant-plugin/custom_components/xknx/factory.py @@ -214,6 +214,7 @@ def _create_sensor(knx_module: XKNX, config: ConfigType) -> XknxSensor: name=config[CONF_NAME], group_address_state=config[SensorSchema.CONF_STATE_ADDRESS], sync_state=config[SensorSchema.CONF_SYNC_STATE], + always_callback=config[SensorSchema.CONF_ALWAYS_CALLBACK], value_type=config[CONF_TYPE], ) diff --git a/home-assistant-plugin/custom_components/xknx/schema.py b/home-assistant-plugin/custom_components/xknx/schema.py index 9c628bed..d97a532a 100644 --- a/home-assistant-plugin/custom_components/xknx/schema.py +++ b/home-assistant-plugin/custom_components/xknx/schema.py @@ -306,6 +306,7 @@ class NotifySchema: class SensorSchema: """Voluptuous schema for KNX sensors.""" + CONF_ALWAYS_CALLBACK = "always_callback" CONF_STATE_ADDRESS = CONF_STATE_ADDRESS CONF_SYNC_STATE = CONF_SYNC_STATE DEFAULT_NAME = "KNX Sensor" @@ -318,6 +319,7 @@ class SensorSchema: cv.boolean, cv.string, ), + vol.Optional(CONF_ALWAYS_CALLBACK, default=False): cv.boolean, vol.Required(CONF_STATE_ADDRESS): cv.string, vol.Required(CONF_TYPE): vol.Any(int, float, str), } diff --git a/xknx/devices/sensor.py b/xknx/devices/sensor.py index 1ac1471e..de62ec95 100644 --- a/xknx/devices/sensor.py +++ b/xknx/devices/sensor.py @@ -19,14 +19,15 @@ class Sensor(Device): xknx, name, group_address_state=None, - sync_state=True, - value_type=None, + sync_state: bool = True, + always_callback: bool = False, + value_type: str = None, device_updated_cb=None, ): """Initialize Sensor class.""" # pylint: disable=too-many-arguments super().__init__(xknx, name, device_updated_cb) - + self.always_callback = always_callback self.sensor_value = RemoteValueSensor( xknx, group_address_state=group_address_state, @@ -45,6 +46,7 @@ class Sensor(Device): """Initialize object from configuration structure.""" group_address_state = config.get("group_address_state") sync_state = config.get("sync_state", True) + always_callback = config.get("always_callback", False) value_type = config.get("value_type") return cls( @@ -52,11 +54,16 @@ class Sensor(Device): name, group_address_state=group_address_state, sync_state=sync_state, + always_callback=always_callback, value_type=value_type, ) async def process_group_write(self, telegram): """Process incoming and outgoing GROUP WRITE telegram.""" + await self.sensor_value.process(telegram, always_callback=self.always_callback) + + async def process_group_response(self, telegram): + """Process incoming GroupValueResponse telegrams.""" await self.sensor_value.process(telegram) def unit_of_measurement(self):

XKNX/xknx

715856fdb69deceba4d54afe4ccf3f7ad304c5ec

diff --git a/test/devices_tests/sensor_test.py b/test/devices_tests/sensor_test.py index 2043eb3c..5875ea4e 100644 --- a/test/devices_tests/sensor_test.py +++ b/test/devices_tests/sensor_test.py @@ -47,6 +47,55 @@ class TestSensor(unittest.TestCase): self.assertEqual(sensor.unit_of_measurement(), "K") self.assertEqual(sensor.ha_device_class(), None) + def test_always_callback_sensor(self): + """Test always callback sensor.""" + xknx = XKNX() + sensor = Sensor( + xknx, + "TestSensor", + group_address_state="1/2/3", + always_callback=False, + value_type="volume_liquid_litre", + ) + + after_update_callback = Mock() + + async def async_after_update_callback(device): + """Async callback.""" + after_update_callback(device) + + sensor.register_device_updated_cb(async_after_update_callback) + + payload = DPTArray( + ( + 0x00, + 0x00, + 0x01, + 0x00, + ) + ) + + # set initial payload of sensor + sensor.sensor_value.payload = payload + + telegram = Telegram(group_address=GroupAddress("1/2/3"), payload=payload) + + # verify not called when always_callback is False + self.loop.run_until_complete(sensor.process(telegram)) + after_update_callback.assert_not_called() + after_update_callback.reset_mock() + + sensor.always_callback = True + + # verify called when always_callback is True + self.loop.run_until_complete(sensor.process(telegram)) + after_update_callback.assert_called_once() + after_update_callback.reset_mock() + + # verify not called when processing read responses + self.loop.run_until_complete(sensor.process_group_response(telegram)) + after_update_callback.assert_not_called() + def test_str_acceleration(self): """Test resolve state with acceleration sensor.""" xknx = XKNX()

Feature request: add the "ignore_internal_state" property to "Sensors" the same way it works already for "Binary Sensors" Hi, In the last release the property "ignore_internal_state" was added to the knx "binary sensor", and it would be great to have this property for knx "sensors" as well. For example I am using a sensor with type "scene_number" together with an automation in order to execute some actions within HA when a knx scene number is called, but if the same scene is called two times without any other scene number in between, the value of the HA sensor state is not changed and the automation is not called again. Note : the KNX scene entity is no help in this case as its state in HA does not change when triggered (it stays on "scening") and is only used the other way around (make HA to trigger a KNX scene). Thank you very much in advance !

0.0

715856fdb69deceba4d54afe4ccf3f7ad304c5ec

[ "test/devices_tests/sensor_test.py::TestSensor::test_always_callback_sensor" ]

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"test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_hrs", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_min", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_msec", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_sec", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_seconds", "test/devices_tests/sensor_test.py::TestSensor::test_str_torque", "test/devices_tests/sensor_test.py::TestSensor::test_str_voltage", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_flow", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_liquid_litre", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_m3", "test/devices_tests/sensor_test.py::TestSensor::test_str_weight", "test/devices_tests/sensor_test.py::TestSensor::test_str_wind_speed_kmh", "test/devices_tests/sensor_test.py::TestSensor::test_str_wind_speed_ms", "test/devices_tests/sensor_test.py::TestSensor::test_str_work", "test/devices_tests/sensor_test.py::TestSensor::test_sync" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2020-10-17 20:17:34+00:00

mit

847

XKNX__xknx-470

diff --git a/changelog.md b/changelog.md index 97c850a5..26bbe12a 100644 --- a/changelog.md +++ b/changelog.md @@ -4,11 +4,12 @@ ### Devices +- Sensor: add `always_callback` option - ClimateMode: Refactor climate modes in operation_mode and controller_mode, also fixes a bug for binary operation modes where the mode would be set to AWAY no matter what value was sent to the bus. ### Internals -- StateUpdater: Only request one GA at a time. +- StateUpdater: Only request 3 GAs at a time. ## 0.15.1 bugfix for binary sensors diff --git a/docs/sensor.md b/docs/sensor.md index c741e111..22ae2581 100644 --- a/docs/sensor.md +++ b/docs/sensor.md @@ -15,6 +15,7 @@ Sensors are monitoring temperature, air humidity, pressure etc. from KNX bus. sensor = Sensor( xknx=xknx, name='DiningRoom.Temperature.Sensor', + always_callback=False, group_address_state='6/2/1', sync_state=True, value_type='temperature' @@ -25,6 +26,7 @@ Sensors are monitoring temperature, air humidity, pressure etc. from KNX bus. * `xknx` is the XKNX object. * `name` is the name of the object. +* `always_callback` defines if a callback/update should always be triggered no matter if the previous and the new state are identical. * `group_address_state` is the KNX group address of the sensor device. * `sync_state` defines if the value should be actively read from the bus. If `False` no GroupValueRead telegrams will be sent to its group address. Defaults to `True` * `value_type` controls how the value should be rendered in a human readable representation. The attribut may have may have the values `percent`, `temperature`, `illuminance`, `speed_ms` or `current`. diff --git a/home-assistant-plugin/custom_components/xknx/factory.py b/home-assistant-plugin/custom_components/xknx/factory.py index de552ff2..005d24d5 100644 --- a/home-assistant-plugin/custom_components/xknx/factory.py +++ b/home-assistant-plugin/custom_components/xknx/factory.py @@ -214,6 +214,7 @@ def _create_sensor(knx_module: XKNX, config: ConfigType) -> XknxSensor: name=config[CONF_NAME], group_address_state=config[SensorSchema.CONF_STATE_ADDRESS], sync_state=config[SensorSchema.CONF_SYNC_STATE], + always_callback=config[SensorSchema.CONF_ALWAYS_CALLBACK], value_type=config[CONF_TYPE], ) diff --git a/home-assistant-plugin/custom_components/xknx/schema.py b/home-assistant-plugin/custom_components/xknx/schema.py index 9c628bed..d97a532a 100644 --- a/home-assistant-plugin/custom_components/xknx/schema.py +++ b/home-assistant-plugin/custom_components/xknx/schema.py @@ -306,6 +306,7 @@ class NotifySchema: class SensorSchema: """Voluptuous schema for KNX sensors.""" + CONF_ALWAYS_CALLBACK = "always_callback" CONF_STATE_ADDRESS = CONF_STATE_ADDRESS CONF_SYNC_STATE = CONF_SYNC_STATE DEFAULT_NAME = "KNX Sensor" @@ -318,6 +319,7 @@ class SensorSchema: cv.boolean, cv.string, ), + vol.Optional(CONF_ALWAYS_CALLBACK, default=False): cv.boolean, vol.Required(CONF_STATE_ADDRESS): cv.string, vol.Required(CONF_TYPE): vol.Any(int, float, str), } diff --git a/xknx/core/state_updater.py b/xknx/core/state_updater.py index 268730df..db7df306 100644 --- a/xknx/core/state_updater.py +++ b/xknx/core/state_updater.py @@ -14,12 +14,12 @@ logger = logging.getLogger("xknx.state_updater") class StateUpdater: """Class for keeping the states of RemoteValues up to date.""" - def __init__(self, xknx): + def __init__(self, xknx, parallel_reads: int = 3): """Initialize StateUpdater class.""" self.xknx = xknx self.started = False self._workers = {} - self._one_by_one = asyncio.Lock() + self._semaphore = asyncio.Semaphore(value=parallel_reads) def register_remote_value(self, remote_value: RemoteValue, tracker_options=True): """Register a RemoteValue to initialize its state and/or track for expiration.""" @@ -77,7 +77,7 @@ class StateUpdater: async def read_state_mutex(): """Schedule to read the state from the KNX bus - one at a time.""" - async with self._one_by_one: + async with self._semaphore: # wait until there is nothing else to send to the bus await self.xknx.telegram_queue.outgoing_queue.join() logger.debug( diff --git a/xknx/devices/sensor.py b/xknx/devices/sensor.py index 1ac1471e..de62ec95 100644 --- a/xknx/devices/sensor.py +++ b/xknx/devices/sensor.py @@ -19,14 +19,15 @@ class Sensor(Device): xknx, name, group_address_state=None, - sync_state=True, - value_type=None, + sync_state: bool = True, + always_callback: bool = False, + value_type: str = None, device_updated_cb=None, ): """Initialize Sensor class.""" # pylint: disable=too-many-arguments super().__init__(xknx, name, device_updated_cb) - + self.always_callback = always_callback self.sensor_value = RemoteValueSensor( xknx, group_address_state=group_address_state, @@ -45,6 +46,7 @@ class Sensor(Device): """Initialize object from configuration structure.""" group_address_state = config.get("group_address_state") sync_state = config.get("sync_state", True) + always_callback = config.get("always_callback", False) value_type = config.get("value_type") return cls( @@ -52,11 +54,16 @@ class Sensor(Device): name, group_address_state=group_address_state, sync_state=sync_state, + always_callback=always_callback, value_type=value_type, ) async def process_group_write(self, telegram): """Process incoming and outgoing GROUP WRITE telegram.""" + await self.sensor_value.process(telegram, always_callback=self.always_callback) + + async def process_group_response(self, telegram): + """Process incoming GroupValueResponse telegrams.""" await self.sensor_value.process(telegram) def unit_of_measurement(self):

XKNX/xknx

715856fdb69deceba4d54afe4ccf3f7ad304c5ec

diff --git a/test/devices_tests/sensor_test.py b/test/devices_tests/sensor_test.py index 2043eb3c..5875ea4e 100644 --- a/test/devices_tests/sensor_test.py +++ b/test/devices_tests/sensor_test.py @@ -47,6 +47,55 @@ class TestSensor(unittest.TestCase): self.assertEqual(sensor.unit_of_measurement(), "K") self.assertEqual(sensor.ha_device_class(), None) + def test_always_callback_sensor(self): + """Test always callback sensor.""" + xknx = XKNX() + sensor = Sensor( + xknx, + "TestSensor", + group_address_state="1/2/3", + always_callback=False, + value_type="volume_liquid_litre", + ) + + after_update_callback = Mock() + + async def async_after_update_callback(device): + """Async callback.""" + after_update_callback(device) + + sensor.register_device_updated_cb(async_after_update_callback) + + payload = DPTArray( + ( + 0x00, + 0x00, + 0x01, + 0x00, + ) + ) + + # set initial payload of sensor + sensor.sensor_value.payload = payload + + telegram = Telegram(group_address=GroupAddress("1/2/3"), payload=payload) + + # verify not called when always_callback is False + self.loop.run_until_complete(sensor.process(telegram)) + after_update_callback.assert_not_called() + after_update_callback.reset_mock() + + sensor.always_callback = True + + # verify called when always_callback is True + self.loop.run_until_complete(sensor.process(telegram)) + after_update_callback.assert_called_once() + after_update_callback.reset_mock() + + # verify not called when processing read responses + self.loop.run_until_complete(sensor.process_group_response(telegram)) + after_update_callback.assert_not_called() + def test_str_acceleration(self): """Test resolve state with acceleration sensor.""" xknx = XKNX()

Use Semaphores in StateUpdater In https://github.com/XKNX/xknx/pull/457 we adjusted the state updater to update each value one by one. However, we should leverage the power of semaphores to update more than one state concurrently as the bus can handle more than one telegram per second. A value between 3 and 5 should be fine imho. But this would need further testing.

0.0

715856fdb69deceba4d54afe4ccf3f7ad304c5ec

[ "test/devices_tests/sensor_test.py::TestSensor::test_always_callback_sensor" ]

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"test/devices_tests/sensor_test.py::TestSensor::test_str_electric_displacement", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_field_strength", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_flux_density", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_polarization", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_potential", "test/devices_tests/sensor_test.py::TestSensor::test_str_electric_potential_difference", "test/devices_tests/sensor_test.py::TestSensor::test_str_electrical_conductivity", "test/devices_tests/sensor_test.py::TestSensor::test_str_electromagnetic_moment", "test/devices_tests/sensor_test.py::TestSensor::test_str_electromotive_force", "test/devices_tests/sensor_test.py::TestSensor::test_str_energy", "test/devices_tests/sensor_test.py::TestSensor::test_str_enthalpy", "test/devices_tests/sensor_test.py::TestSensor::test_str_flow_rate_m3h", "test/devices_tests/sensor_test.py::TestSensor::test_str_force", "test/devices_tests/sensor_test.py::TestSensor::test_str_frequency", "test/devices_tests/sensor_test.py::TestSensor::test_str_heat_quantity", "test/devices_tests/sensor_test.py::TestSensor::test_str_heatcapacity", "test/devices_tests/sensor_test.py::TestSensor::test_str_heatflowrate", "test/devices_tests/sensor_test.py::TestSensor::test_str_humidity", "test/devices_tests/sensor_test.py::TestSensor::test_str_illuminance", "test/devices_tests/sensor_test.py::TestSensor::test_str_impedance", "test/devices_tests/sensor_test.py::TestSensor::test_str_kelvin_per_percent", "test/devices_tests/sensor_test.py::TestSensor::test_str_length", "test/devices_tests/sensor_test.py::TestSensor::test_str_length_mm", "test/devices_tests/sensor_test.py::TestSensor::test_str_light_quantity", "test/devices_tests/sensor_test.py::TestSensor::test_str_long_delta_timesec", "test/devices_tests/sensor_test.py::TestSensor::test_str_luminance", "test/devices_tests/sensor_test.py::TestSensor::test_str_luminous_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_luminous_intensity", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetic_field_strength", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetic_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetic_flux_density", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetic_moment", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetic_polarization", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetization", "test/devices_tests/sensor_test.py::TestSensor::test_str_magnetomotive_force", "test/devices_tests/sensor_test.py::TestSensor::test_str_mass", "test/devices_tests/sensor_test.py::TestSensor::test_str_mass_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_mol", "test/devices_tests/sensor_test.py::TestSensor::test_str_momentum", "test/devices_tests/sensor_test.py::TestSensor::test_str_percent", "test/devices_tests/sensor_test.py::TestSensor::test_str_percent_u8", "test/devices_tests/sensor_test.py::TestSensor::test_str_percent_v16", "test/devices_tests/sensor_test.py::TestSensor::test_str_percent_v8", "test/devices_tests/sensor_test.py::TestSensor::test_str_phaseangledeg", "test/devices_tests/sensor_test.py::TestSensor::test_str_phaseanglerad", "test/devices_tests/sensor_test.py::TestSensor::test_str_power", "test/devices_tests/sensor_test.py::TestSensor::test_str_power_2byte", "test/devices_tests/sensor_test.py::TestSensor::test_str_power_density", "test/devices_tests/sensor_test.py::TestSensor::test_str_powerfactor", "test/devices_tests/sensor_test.py::TestSensor::test_str_ppm", "test/devices_tests/sensor_test.py::TestSensor::test_str_pressure", "test/devices_tests/sensor_test.py::TestSensor::test_str_pressure_2byte", "test/devices_tests/sensor_test.py::TestSensor::test_str_pulse", "test/devices_tests/sensor_test.py::TestSensor::test_str_rain_amount", "test/devices_tests/sensor_test.py::TestSensor::test_str_reactance", "test/devices_tests/sensor_test.py::TestSensor::test_str_reactive_energy", "test/devices_tests/sensor_test.py::TestSensor::test_str_reactive_energy_kvarh", "test/devices_tests/sensor_test.py::TestSensor::test_str_resistance", "test/devices_tests/sensor_test.py::TestSensor::test_str_resistivity", "test/devices_tests/sensor_test.py::TestSensor::test_str_rotation_angle", "test/devices_tests/sensor_test.py::TestSensor::test_str_scene_number", "test/devices_tests/sensor_test.py::TestSensor::test_str_self_inductance", "test/devices_tests/sensor_test.py::TestSensor::test_str_solid_angle", "test/devices_tests/sensor_test.py::TestSensor::test_str_sound_intensity", "test/devices_tests/sensor_test.py::TestSensor::test_str_speed", "test/devices_tests/sensor_test.py::TestSensor::test_str_stress", "test/devices_tests/sensor_test.py::TestSensor::test_str_surface_tension", "test/devices_tests/sensor_test.py::TestSensor::test_str_temperature", "test/devices_tests/sensor_test.py::TestSensor::test_str_temperature_a", "test/devices_tests/sensor_test.py::TestSensor::test_str_temperature_difference", "test/devices_tests/sensor_test.py::TestSensor::test_str_temperature_difference_2byte", "test/devices_tests/sensor_test.py::TestSensor::test_str_temperature_f", "test/devices_tests/sensor_test.py::TestSensor::test_str_thermal_capacity", "test/devices_tests/sensor_test.py::TestSensor::test_str_thermal_conductivity", "test/devices_tests/sensor_test.py::TestSensor::test_str_thermoelectric_power", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_1", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_2", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_100msec", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_10msec", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_hrs", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_min", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_msec", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_period_sec", "test/devices_tests/sensor_test.py::TestSensor::test_str_time_seconds", "test/devices_tests/sensor_test.py::TestSensor::test_str_torque", "test/devices_tests/sensor_test.py::TestSensor::test_str_voltage", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_flow", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_flux", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_liquid_litre", "test/devices_tests/sensor_test.py::TestSensor::test_str_volume_m3", "test/devices_tests/sensor_test.py::TestSensor::test_str_weight", "test/devices_tests/sensor_test.py::TestSensor::test_str_wind_speed_kmh", "test/devices_tests/sensor_test.py::TestSensor::test_str_wind_speed_ms", "test/devices_tests/sensor_test.py::TestSensor::test_str_work", "test/devices_tests/sensor_test.py::TestSensor::test_sync" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2020-10-17 20:40:35+00:00

mit

848

XKNX__xknx-482

diff --git a/changelog.md b/changelog.md index b3ef0a15..5ed77445 100644 --- a/changelog.md +++ b/changelog.md @@ -12,6 +12,7 @@ ### Bugfixes - HA Switch entity: keep state without state_address +- Cover: fix `set_position` without writable position / auto_stop_if_necessary ## 0.15.2 Winter is coming diff --git a/xknx/devices/cover.py b/xknx/devices/cover.py index 4ff53c1a..7596c1e5 100644 --- a/xknx/devices/cover.py +++ b/xknx/devices/cover.py @@ -270,13 +270,20 @@ class Cover(Device): async def process_group_write(self, telegram): """Process incoming and outgoing GROUP WRITE telegram.""" + # call after_update to account for travelcalculator changes if await self.updown.process(telegram): - if self.updown.value == RemoteValueUpDown.Direction.UP: + if ( + not self.is_opening() + and self.updown.value == RemoteValueUpDown.Direction.UP + ): self.travelcalculator.start_travel_up() - else: + await self.after_update() + elif ( + not self.is_closing() + and self.updown.value == RemoteValueUpDown.Direction.DOWN + ): self.travelcalculator.start_travel_down() - # call after_update to account for travelcalculator changes - await self.after_update() + await self.after_update() # stop from bus if await self.stop_.process(telegram) or await self.step.process(telegram): if self.is_traveling():

XKNX/xknx

785d73b850a97a688a3b1a5e8baf34e82685d1b6

diff --git a/test/devices_tests/cover_test.py b/test/devices_tests/cover_test.py index 16e4547c..0865454c 100644 --- a/test/devices_tests/cover_test.py +++ b/test/devices_tests/cover_test.py @@ -397,6 +397,10 @@ class TestCover(unittest.TestCase): telegram, Telegram(GroupAddress("1/2/1"), payload=DPTBinary(0)) ) self.assertEqual(cover.travelcalculator.travel_to_position, 50) + self.assertTrue(cover.is_opening()) + # process the outgoing telegram to make sure it doesn't overwrite the target position + self.loop.run_until_complete(cover.process(telegram)) + self.assertEqual(cover.travelcalculator.travel_to_position, 50) def test_position_without_position_address_down(self): """Test moving cover down - with no absolute positioning supported.""" @@ -416,6 +420,10 @@ class TestCover(unittest.TestCase): telegram, Telegram(GroupAddress("1/2/1"), payload=DPTBinary(1)) ) self.assertEqual(cover.travelcalculator.travel_to_position, 80) + self.assertTrue(cover.is_closing()) + # process the outgoing telegram to make sure it doesn't overwrite the target position + self.loop.run_until_complete(cover.process(telegram)) + self.assertEqual(cover.travelcalculator.travel_to_position, 80) def test_position_without_position_address_uninitialized_up(self): """Test moving uninitialized cover to absolute position - with no absolute positioning supported."""

cover.set_cover_position not stopping with no position_address **Description of problem:** Dear xknx team, covers with **no position_address** do not longer stop when moving the slider in the ha frontpanel to a position e.g. 30%. I attached my according HA config as well as some debug log from HA. This was working in precious versions of Home Assistant for me ( version 0.111). The **service cover.set_cover_position ist not stopping at this value**. The services cover.close_cover; service cover.open_cover; cover.stop_cover are working currently. Maybe a bug to the reworked travelcalculator / cover.py? It seems to me, that there is no stop movement send to actor when the calculated position is reached. Remark: My covers do not have a positional feedback. But this applies not only to my knx config, this reproducible to other knx hardware setup with HA as well (a friend of mine reproduces this bug with his knx covers (which have a position_address). When deleting the position address in his config, this bug occurs as well. It would be great, to have this feature back / working again! Let me know, if i can assist you reproducing this bug. All the best Jan - [x ] using Home-Assistant knx plugin **Version information:** - xknx / Home-Assistant release with the issue: 0.116.4 - last working xknx / Home-Assistant release (if known): 0.111 **KNX installation:**  **Problem-relevant `xknx.yaml` or `configuration.yaml` entries (fill out even if it seems unimportant):** [LOG_ha.txt](https://github.com/XKNX/xknx/files/5434327/LOG_ha.txt) [knx_cover.yaml.txt](https://github.com/XKNX/xknx/files/5434337/knx_cover.yaml.txt) [knx.yaml.txt](https://github.com/XKNX/xknx/files/5434338/knx.yaml.txt) ![Log](https://user-images.githubusercontent.com/19536666/97102778-98466880-16a8-11eb-93fd-f1ca839db2ed.JPG)

0.0

785d73b850a97a688a3b1a5e8baf34e82685d1b6

[ "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_down", "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_up" ]

[ "test/devices_tests/cover_test.py::TestCover::test_angle", "test/devices_tests/cover_test.py::TestCover::test_angle_not_supported", "test/devices_tests/cover_test.py::TestCover::test_auto_stop", "test/devices_tests/cover_test.py::TestCover::test_do", "test/devices_tests/cover_test.py::TestCover::test_has_group_address", "test/devices_tests/cover_test.py::TestCover::test_is_traveling", "test/devices_tests/cover_test.py::TestCover::test_position", "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_uninitialized_down", "test/devices_tests/cover_test.py::TestCover::test_position_without_position_address_uninitialized_up", "test/devices_tests/cover_test.py::TestCover::test_process_angle", "test/devices_tests/cover_test.py::TestCover::test_process_callback", "test/devices_tests/cover_test.py::TestCover::test_process_down", "test/devices_tests/cover_test.py::TestCover::test_process_position", "test/devices_tests/cover_test.py::TestCover::test_process_short_stop", "test/devices_tests/cover_test.py::TestCover::test_process_stop", "test/devices_tests/cover_test.py::TestCover::test_process_up", "test/devices_tests/cover_test.py::TestCover::test_set_down", "test/devices_tests/cover_test.py::TestCover::test_set_down_inverted", "test/devices_tests/cover_test.py::TestCover::test_set_short_down", "test/devices_tests/cover_test.py::TestCover::test_set_short_up", "test/devices_tests/cover_test.py::TestCover::test_set_up", "test/devices_tests/cover_test.py::TestCover::test_set_up_inverted", "test/devices_tests/cover_test.py::TestCover::test_stop", "test/devices_tests/cover_test.py::TestCover::test_support_angle_false", "test/devices_tests/cover_test.py::TestCover::test_supports_angle_true", "test/devices_tests/cover_test.py::TestCover::test_supports_position_false", "test/devices_tests/cover_test.py::TestCover::test_supports_position_true", "test/devices_tests/cover_test.py::TestCover::test_supports_stop_false", "test/devices_tests/cover_test.py::TestCover::test_supports_stop_true", "test/devices_tests/cover_test.py::TestCover::test_sync", "test/devices_tests/cover_test.py::TestCover::test_sync_angle", "test/devices_tests/cover_test.py::TestCover::test_sync_angle_state", "test/devices_tests/cover_test.py::TestCover::test_sync_state", "test/devices_tests/cover_test.py::TestCover::test_wrong_do" ]

{ "failed_lite_validators": [ "has_hyperlinks", "has_media", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2020-10-25 20:45:25+00:00

mit

849

XKNX__xknx-572

diff --git a/changelog.md b/changelog.md index 8692b1d2..b8648063 100644 --- a/changelog.md +++ b/changelog.md @@ -2,6 +2,10 @@ ## Unreleased changes +### HA integration + +- knx_event: fire also for outgoing telegrams + ### Devices - BinarySensor: return `None` for `BinarySensor.counter` when context timeout is not used (and don't calculate it) diff --git a/home-assistant-plugin/custom_components/xknx/__init__.py b/home-assistant-plugin/custom_components/xknx/__init__.py index fab7ec68..f7f63d8d 100644 --- a/home-assistant-plugin/custom_components/xknx/__init__.py +++ b/home-assistant-plugin/custom_components/xknx/__init__.py @@ -368,6 +368,7 @@ class KNXModule: self.telegram_received_cb, address_filters=address_filters, group_addresses=[], + match_for_outgoing_telegrams=True, ) async def service_event_register_modify(self, call): diff --git a/xknx/core/telegram_queue.py b/xknx/core/telegram_queue.py index c793ebc4..ea68f572 100644 --- a/xknx/core/telegram_queue.py +++ b/xknx/core/telegram_queue.py @@ -37,15 +37,22 @@ class TelegramQueue: callback: "AsyncTelegramCallback", address_filters: Optional[List[AddressFilter]] = None, group_addresses: Optional[List[GroupAddress]] = None, + match_for_outgoing_telegrams: bool = False, ): """Initialize Callback class.""" self.callback = callback self._match_all = address_filters is None and group_addresses is None + self._match_outgoing = match_for_outgoing_telegrams self.address_filters = [] if address_filters is None else address_filters self.group_addresses = [] if group_addresses is None else group_addresses def is_within_filter(self, telegram: Telegram) -> bool: """Test if callback is filtering for group address.""" + if ( + not self._match_outgoing + and telegram.direction == TelegramDirection.OUTGOING + ): + return False if self._match_all: return True if isinstance(telegram.destination_address, GroupAddress): @@ -69,12 +76,14 @@ class TelegramQueue: telegram_received_cb: "AsyncTelegramCallback", address_filters: Optional[List[AddressFilter]] = None, group_addresses: Optional[List[GroupAddress]] = None, + match_for_outgoing: bool = False, ) -> Callback: - """Register callback for a telegram beeing received from KNX bus.""" + """Register callback for a telegram being received from KNX bus.""" callback = TelegramQueue.Callback( telegram_received_cb, address_filters=address_filters, group_addresses=group_addresses, + match_for_outgoing_telegrams=match_for_outgoing, ) self.telegram_received_cbs.append(callback) return callback @@ -165,6 +174,10 @@ class TelegramQueue: await self.xknx.knxip_interface.send_telegram(telegram) if isinstance(telegram.payload, GroupValueWrite): await self.xknx.devices.process(telegram) + + for telegram_received_cb in self.telegram_received_cbs: + if telegram_received_cb.is_within_filter(telegram): + await telegram_received_cb.callback(telegram) else: raise CommunicationError("No KNXIP interface defined")

XKNX/xknx

afa30c7e0acfa91ad68390eb89120e9f50e35b92

diff --git a/test/core_tests/telegram_queue_test.py b/test/core_tests/telegram_queue_test.py index 9543f66b..6ef23d1b 100644 --- a/test/core_tests/telegram_queue_test.py +++ b/test/core_tests/telegram_queue_test.py @@ -117,10 +117,62 @@ class TestTelegramQueue(unittest.TestCase): payload=GroupValueWrite(DPTBinary(1)), ) self.loop.run_until_complete( - xknx.telegram_queue.process_telegram_incoming(telegram) + xknx.telegram_queue.process_telegram_incoming(telegram), ) async_telegram_received_cb.assert_called_once_with(telegram) + @patch("xknx.io.KNXIPInterface") + def test_register_with_outgoing_telegrams(self, if_mock): + """Test telegram_received_callback with outgoing telegrams.""" + # pylint: disable=no-self-use + xknx = XKNX() + async_telegram_received_cb = AsyncMock() + + async_if_send_telegram = asyncio.Future() + async_if_send_telegram.set_result(None) + if_mock.send_telegram.return_value = async_if_send_telegram + + xknx.telegram_queue.register_telegram_received_cb( + async_telegram_received_cb, None, None, True + ) + + telegram = Telegram( + destination_address=GroupAddress("1/2/3"), + direction=TelegramDirection.OUTGOING, + payload=GroupValueWrite(DPTBinary(1)), + ) + + xknx.knxip_interface = if_mock + self.loop.run_until_complete( + xknx.telegram_queue.process_telegram_outgoing(telegram) + ) + async_telegram_received_cb.assert_called_once_with(telegram) + + @patch("xknx.io.KNXIPInterface") + def test_register_with_outgoing_telegrams_does_not_trigger(self, if_mock): + """Test telegram_received_callback with outgoing telegrams.""" + # pylint: disable=no-self-use + xknx = XKNX() + async_telegram_received_cb = AsyncMock() + + async_if_send_telegram = asyncio.Future() + async_if_send_telegram.set_result(None) + if_mock.send_telegram.return_value = async_if_send_telegram + + xknx.telegram_queue.register_telegram_received_cb(async_telegram_received_cb) + + telegram = Telegram( + destination_address=GroupAddress("1/2/3"), + direction=TelegramDirection.OUTGOING, + payload=GroupValueWrite(DPTBinary(1)), + ) + + xknx.knxip_interface = if_mock + self.loop.run_until_complete( + xknx.telegram_queue.process_telegram_outgoing(telegram) + ) + async_telegram_received_cb.assert_not_called() + # # TEST UNREGISTER #

Enhance HA knx_event There are some requests about updating the HA knx_event. Eg. https://github.com/home-assistant/core/issues/43256 Currently we just fire the `knx_event` for incoming telegrams, as stated in the documentation. We could - [ ] fire on outgoing telegrams too, not only on incoming - [x] add a parameter "direction" for incoming/outgoing - [x] add a parameter "source" for IA (eg. to identify which wall switch was used) - [x] add a parameter "type" for write or response (maybe also read) I'm still not very convinced about using the `knx_event` at all since we can't really decode the payload and dealing with raw payloads should not be a user-facing task in HA (besides maybe for DPT 1/2/3).

0.0

afa30c7e0acfa91ad68390eb89120e9f50e35b92

[ "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_register_with_outgoing_telegrams" ]

[ "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_callback_group_addresses", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_callback_negative_address_filters", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_callback_no_filters", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_callback_positive_address_filters", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_outgoing", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_process_all_telegrams", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_process_exception", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_process_to_callback", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_process_to_device", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_rate_limit", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_register", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_register_with_outgoing_telegrams_does_not_trigger", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_start", "test/core_tests/telegram_queue_test.py::TestTelegramQueue::test_unregister" ]

{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-01-24 14:07:32+00:00

mit

850

XKNX__xknx-832

diff --git a/changelog.md b/changelog.md index e312e426..35e3c87c 100644 --- a/changelog.md +++ b/changelog.md @@ -4,7 +4,8 @@ ### Connection -- Fix rate limiter wait time. Don't add time waiting for ACK or L_DATA.con frames to the rate_limit. +- Handle separate Tunneling control and data endpoints +- Fix rate limiter wait time: don't add time waiting for ACK or L_DATA.con frames to the rate_limit ## Internals diff --git a/xknx/io/request_response/connect.py b/xknx/io/request_response/connect.py index ec97d58a..b5ae8696 100644 --- a/xknx/io/request_response/connect.py +++ b/xknx/io/request_response/connect.py @@ -27,6 +27,7 @@ class Connect(RequestResponse): self.route_back = route_back super().__init__(xknx, self.udp_client, ConnectResponse) self.communication_channel = 0 + self.data_endpoint = HPAI() self.identifier = 0 def create_knxipframe(self) -> KNXIPFrame: @@ -48,6 +49,6 @@ class Connect(RequestResponse): def on_success_hook(self, knxipframe: KNXIPFrame) -> None: """Set communication channel and identifier after having received a valid answer.""" assert isinstance(knxipframe.body, ConnectResponse) - assert isinstance(knxipframe.body.identifier, int) self.communication_channel = knxipframe.body.communication_channel + self.data_endpoint = knxipframe.body.data_endpoint self.identifier = knxipframe.body.identifier diff --git a/xknx/io/request_response/tunnelling.py b/xknx/io/request_response/tunnelling.py index 6a295bea..f7fc0e60 100644 --- a/xknx/io/request_response/tunnelling.py +++ b/xknx/io/request_response/tunnelling.py @@ -26,6 +26,7 @@ class Tunnelling(RequestResponse): self, xknx: XKNX, udp_client: UDPClient, + data_endpoint: tuple[str, int] | None, telegram: Telegram, src_address: IndividualAddress, sequence_counter: int, @@ -34,6 +35,7 @@ class Tunnelling(RequestResponse): """Initialize Tunnelling class.""" self.xknx = xknx self.udp_client = udp_client + self.data_endpoint_addr = data_endpoint self.src_address = src_address super().__init__(xknx, self.udp_client, TunnellingAck) @@ -42,6 +44,10 @@ class Tunnelling(RequestResponse): self.sequence_counter = sequence_counter self.communication_channel_id = communication_channel_id + async def send_request(self) -> None: + """Build knxipframe (within derived class) and send via UDP.""" + self.udpclient.send(self.create_knxipframe(), addr=self.data_endpoint_addr) + def create_knxipframe(self) -> KNXIPFrame: """Create KNX/IP Frame object to be sent to device.""" cemi = CEMIFrame.init_from_telegram( diff --git a/xknx/io/tunnel.py b/xknx/io/tunnel.py index 65752e0a..cd555a13 100644 --- a/xknx/io/tunnel.py +++ b/xknx/io/tunnel.py @@ -69,6 +69,7 @@ class Tunnel(Interface): self.init_udp_client() self._src_address = xknx.own_address + self._data_endpoint_addr: tuple[str, int] | None = None self.sequence_number = 0 self.communication_channel: int | None = None self.number_heartbeat_failed = 0 @@ -144,6 +145,7 @@ class Tunnel(Interface): ) ) self.stop_heartbeat() + self._data_endpoint_addr = None if self.auto_reconnect: self._reconnect_task = asyncio.create_task(self._reconnect()) else: @@ -172,6 +174,7 @@ class Tunnel(Interface): XknxConnectionState.DISCONNECTED ) self.stop_heartbeat() + self._data_endpoint_addr = None self._stop_reconnect() await self._disconnect_request(False) await self.udp_client.stop() @@ -188,6 +191,11 @@ class Tunnel(Interface): await connect.start() if connect.success: self.communication_channel = connect.communication_channel + # assign data_endpoint received from server + self._data_endpoint_addr = ( + connect.data_endpoint.ip_addr, + connect.data_endpoint.port, + ) # Use the individual address provided by the tunnelling server self._src_address = IndividualAddress(connect.identifier) self.xknx.current_address = self._src_address @@ -274,6 +282,7 @@ class Tunnel(Interface): tunnelling = Tunnelling( self.xknx, self.udp_client, + self._data_endpoint_addr, telegram, self._src_address, self.sequence_number, @@ -355,7 +364,9 @@ class Tunnel(Interface): communication_channel_id=communication_channel_id, sequence_counter=sequence_counter, ) - self.udp_client.send(KNXIPFrame.init_from_body(ack)) + self.udp_client.send( + KNXIPFrame.init_from_body(ack), addr=self._data_endpoint_addr + ) def _disconnect_request_received( self, disconnect_request: DisconnectRequest diff --git a/xknx/io/udp_client.py b/xknx/io/udp_client.py index 2637a73f..1aeee391 100644 --- a/xknx/io/udp_client.py +++ b/xknx/io/udp_client.py @@ -116,7 +116,7 @@ class UDPClient: ) else: knx_logger.debug( - "Received from %s:%s at %s:\n%s", + "Received from %s:%s at %s:\n %s", source[0], source[1], time.time(), @@ -213,27 +213,28 @@ class UDPClient: (transport, _) = await loop.create_datagram_endpoint( lambda: udp_client_factory, local_addr=self.local_addr, - remote_addr=self.remote_addr, ) # TODO: typing - remove cast - loop.create_datagram_endpoint should return a DatagramTransport self.transport = cast(asyncio.DatagramTransport, transport) - def send(self, knxipframe: KNXIPFrame) -> None: + def send(self, knxipframe: KNXIPFrame, addr: tuple[str, int] | None = None) -> None: """Send KNXIPFrame to socket.""" + _addr = addr or self.remote_addr knx_logger.debug( - "Sending to %s:%s at %s:\n%s", - self.remote_addr[0], - self.remote_addr[1], - time.time(), - knxipframe, + "Sending to %s:%s at %s:\n %s", _addr[0], _addr[1], time.time(), knxipframe ) if self.transport is None: raise XKNXException("Transport not connected") if self.multicast: + if addr is not None: + logger.warning( + "Multicast send to specific address is invalid. %s", + knxipframe, + ) self.transport.sendto(bytes(knxipframe.to_knx()), self.remote_addr) else: - self.transport.sendto(bytes(knxipframe.to_knx())) + self.transport.sendto(bytes(knxipframe.to_knx()), addr=_addr) def getsockname(self) -> tuple[str, int]: """Return socket IP and port.""" diff --git a/xknx/knxip/connect_response.py b/xknx/knxip/connect_response.py index 3f9c3835..865923ef 100644 --- a/xknx/knxip/connect_response.py +++ b/xknx/knxip/connect_response.py @@ -32,8 +32,8 @@ class ConnectResponse(KNXIPBodyResponse): communication_channel: int = 0, status_code: ErrorCode = ErrorCode.E_NO_ERROR, request_type: ConnectRequestType = ConnectRequestType.TUNNEL_CONNECTION, - control_endpoint: HPAI = HPAI(), - identifier: int | None = None, + data_endpoint: HPAI = HPAI(), + identifier: int = 0, ): """Initialize ConnectResponse class.""" super().__init__(xknx) @@ -41,7 +41,7 @@ class ConnectResponse(KNXIPBodyResponse): self.communication_channel = communication_channel self.status_code = status_code self.request_type = request_type - self.control_endpoint = control_endpoint + self.data_endpoint = data_endpoint # identifier shall contain KNX Individual Address assigned to this KNXnet/IP Tunnelling connection self.identifier = identifier @@ -67,11 +67,11 @@ class ConnectResponse(KNXIPBodyResponse): pos = 2 if self.status_code == ErrorCode.E_NO_ERROR: - pos += self.control_endpoint.from_knx(raw[pos:]) + pos += self.data_endpoint.from_knx(raw[pos:]) pos += crd_from_knx(raw[pos:]) else: # do not parse HPAI and CRD in case of errors - just check length - pos += len(raw[pos:]) + pos = len(raw) return pos def to_knx(self) -> list[int]: @@ -91,7 +91,7 @@ class ConnectResponse(KNXIPBodyResponse): data = [] data.append(self.communication_channel) data.append(self.status_code.value) - data.extend(self.control_endpoint.to_knx()) + data.extend(self.data_endpoint.to_knx()) data.extend(crd_to_knx()) return data @@ -102,7 +102,7 @@ class ConnectResponse(KNXIPBodyResponse): "<ConnectResponse " f'communication_channel="{self.communication_channel}" ' f'status_code="{self.status_code}" ' - f'control_endpoint="{self.control_endpoint}" ' + f'data_endpoint="{self.data_endpoint}" ' f'request_type="{self.request_type}" ' f'identifier="{self.identifier}" />' ) diff --git a/xknx/knxip/knxip.py b/xknx/knxip/knxip.py index b5425a86..ed333e0a 100644 --- a/xknx/knxip/knxip.py +++ b/xknx/knxip/knxip.py @@ -101,7 +101,7 @@ class KNXIPFrame: data.extend(self.body.to_knx()) return data - def __str__(self) -> str: + def __repr__(self) -> str: """Return object as readable string.""" return f'<KNXIPFrame {self.header}\n body="{self.body}" />'

XKNX/xknx

e2f84405a5a62492c4cbf86de9e32abef043cecb

diff --git a/test/io_tests/tunnel_test.py b/test/io_tests/tunnel_test.py index 3615b9cd..d9d8aa48 100644 --- a/test/io_tests/tunnel_test.py +++ b/test/io_tests/tunnel_test.py @@ -1,14 +1,24 @@ """Unit test for KNX/IP Tunnelling Request/Response.""" import asyncio -from unittest.mock import Mock, patch +from unittest.mock import AsyncMock, Mock, patch import pytest from xknx import XKNX from xknx.dpt import DPTArray from xknx.io import Tunnel -from xknx.knxip import HPAI, CEMIFrame, KNXIPFrame, TunnellingAck, TunnellingRequest +from xknx.knxip import ( + HPAI, + CEMIFrame, + ConnectRequest, + ConnectResponse, + DisconnectRequest, + DisconnectResponse, + KNXIPFrame, + TunnellingAck, + TunnellingRequest, +) from xknx.knxip.knxip_enum import CEMIMessageCode -from xknx.telegram import Telegram, TelegramDirection +from xknx.telegram import IndividualAddress, Telegram, TelegramDirection from xknx.telegram.apci import GroupValueWrite @@ -103,3 +113,88 @@ class TestTunnel: # one call for the outgoing request and one for the ACK for the confirmation assert self.tunnel.udp_client.send.call_count == 2 await task + + async def test_tunnel_connect_send_disconnect(self, time_travel): + """Test initiating a tunnelling connection.""" + local_addr = ("192.168.1.1", 12345) + gateway_control_addr = ("192.168.1.2", 3671) + gateway_data_addr = ("192.168.1.2", 56789) + self.tunnel.udp_client.connect = AsyncMock() + self.tunnel.udp_client.getsockname = Mock(return_value=local_addr) + self.tunnel.udp_client.send = Mock() + self.tunnel.udp_client.stop = AsyncMock() + + # Connect + connect_request = ConnectRequest( + self.xknx, + control_endpoint=HPAI(*local_addr), + data_endpoint=HPAI(*local_addr), + ) + connect_frame = KNXIPFrame.init_from_body(connect_request) + + connection_task = asyncio.create_task(self.tunnel.connect()) + await time_travel(0) + self.tunnel.udp_client.connect.assert_called_once() + self.tunnel.udp_client.send.assert_called_once_with(connect_frame) + + connect_response_frame = KNXIPFrame.init_from_body( + ConnectResponse( + self.xknx, + communication_channel=23, + data_endpoint=HPAI(*gateway_data_addr), + identifier=7, + ) + ) + self.tunnel.udp_client.handle_knxipframe( + connect_response_frame, gateway_control_addr + ) + await connection_task + assert self.tunnel._data_endpoint_addr == gateway_data_addr + assert self.tunnel._src_address == IndividualAddress(7) + + # Send - use data endpoint + self.tunnel.udp_client.send.reset_mock() + test_telegram = Telegram(payload=GroupValueWrite(DPTArray((1,)))) + test_telegram_frame = KNXIPFrame.init_from_body( + TunnellingRequest( + self.xknx, + communication_channel_id=23, + sequence_counter=0, + cemi=CEMIFrame.init_from_telegram( + self.xknx, + test_telegram, + code=CEMIMessageCode.L_DATA_REQ, + src_addr=IndividualAddress(7), + ), + ) + ) + asyncio.create_task(self.tunnel.send_telegram(test_telegram)) + await time_travel(0) + self.tunnel.udp_client.send.assert_called_once_with( + test_telegram_frame, addr=gateway_data_addr + ) + # skip ack and confirmation + + # Disconnect + self.tunnel.udp_client.send.reset_mock() + disconnect_request = DisconnectRequest( + self.xknx, communication_channel_id=23, control_endpoint=HPAI(*local_addr) + ) + disconnect_frame = KNXIPFrame.init_from_body(disconnect_request) + + disconnection_task = asyncio.create_task(self.tunnel.disconnect()) + await time_travel(0) + self.tunnel.udp_client.send.assert_called_once_with(disconnect_frame) + + disconnect_response_frame = KNXIPFrame.init_from_body( + DisconnectResponse( + self.xknx, + communication_channel_id=23, + ) + ) + self.tunnel.udp_client.handle_knxipframe( + disconnect_response_frame, gateway_control_addr + ) + await disconnection_task + assert self.tunnel._data_endpoint_addr is None + self.tunnel.udp_client.stop.assert_called_once() diff --git a/test/io_tests/tunnelling_test.py b/test/io_tests/tunnelling_test.py index bfb4142c..b893e3cc 100644 --- a/test/io_tests/tunnelling_test.py +++ b/test/io_tests/tunnelling_test.py @@ -26,6 +26,7 @@ class TestTunnelling: """Test tunnelling from KNX bus.""" xknx = XKNX() communication_channel_id = 23 + data_endpoint = ("192.168.1.2", 4567) udp_client = UDPClient(xknx, ("192.168.1.1", 0), ("192.168.1.2", 1234)) telegram = Telegram( destination_address=GroupAddress("1/2/3"), @@ -36,6 +37,7 @@ class TestTunnelling: tunnelling = Tunnelling( xknx, udp_client, + data_endpoint, telegram, src_address, sequence_counter, @@ -60,7 +62,7 @@ class TestTunnelling: ) as mock_udp_getsockname: mock_udp_getsockname.return_value = ("192.168.1.3", 4321) await tunnelling.start() - mock_udp_send.assert_called_with(exp_knxipframe) + mock_udp_send.assert_called_with(exp_knxipframe, addr=data_endpoint) # Response KNX/IP-Frame with wrong type wrong_knxipframe = KNXIPFrame(xknx) diff --git a/test/knxip_tests/connect_response_test.py b/test/knxip_tests/connect_response_test.py index 71f61a4c..3bd85054 100644 --- a/test/knxip_tests/connect_response_test.py +++ b/test/knxip_tests/connect_response_test.py @@ -38,9 +38,7 @@ class TestKNXIPConnectResponse: assert isinstance(knxipframe.body, ConnectResponse) assert knxipframe.body.communication_channel == 1 assert knxipframe.body.status_code == ErrorCode.E_NO_ERROR - assert knxipframe.body.control_endpoint == HPAI( - ip_addr="192.168.42.10", port=3671 - ) + assert knxipframe.body.data_endpoint == HPAI(ip_addr="192.168.42.10", port=3671) assert knxipframe.body.request_type == ConnectRequestType.TUNNEL_CONNECTION assert knxipframe.body.identifier == 4607 @@ -49,7 +47,7 @@ class TestKNXIPConnectResponse: communication_channel=1, status_code=ErrorCode.E_NO_ERROR, request_type=ConnectRequestType.TUNNEL_CONNECTION, - control_endpoint=HPAI(ip_addr="192.168.42.10", port=3671), + data_endpoint=HPAI(ip_addr="192.168.42.10", port=3671), identifier=4607, ) knxipframe2 = KNXIPFrame.init_from_body(connect_response) @@ -151,7 +149,7 @@ class TestKNXIPConnectResponse: communication_channel=192, status_code=ErrorCode.E_NO_MORE_CONNECTIONS, request_type=ConnectRequestType.TUNNEL_CONNECTION, - control_endpoint=HPAI(ip_addr="10.1.0.41", port=3671), + data_endpoint=HPAI(ip_addr="10.1.0.41", port=3671), identifier=0, ) knxipframe2 = KNXIPFrame.init_from_body(connect_response) diff --git a/test/str_test.py b/test/str_test.py index 72c9ef56..3d34719f 100644 --- a/test/str_test.py +++ b/test/str_test.py @@ -526,12 +526,12 @@ class TestStringRepresentations: connect_response = ConnectResponse(xknx) connect_response.communication_channel = 13 connect_response.request_type = ConnectRequestType.TUNNEL_CONNECTION - connect_response.control_endpoint = HPAI(ip_addr="192.168.42.1", port=33941) + connect_response.data_endpoint = HPAI(ip_addr="192.168.42.1", port=33941) connect_response.identifier = 42 assert ( str(connect_response) == '<ConnectResponse communication_channel="13" status_code="ErrorCode.E_NO_ERROR" ' - 'control_endpoint="192.168.42.1:33941" ' + 'data_endpoint="192.168.42.1:33941" ' 'request_type="ConnectRequestType.TUNNEL_CONNECTION" identifier="42" />' )

Handle different Tunneling data and control endpoints correctly KNX tunneling servers can have different data and control endpoints (eg. Calimero does). `DisconnectRequest`s should be sent to the other device’s control endpoint instead of to the data endpoint. (see KNX specification 03_08_04 Tunneling §2.6 Frame confirmation) I have not found an other usecase for the control endpoint for us yet.

0.0

e2f84405a5a62492c4cbf86de9e32abef043cecb

[ "test/io_tests/tunnel_test.py::TestTunnel::test_tunnel_connect_send_disconnect", "test/io_tests/tunnelling_test.py::TestTunnelling::test_tunnelling", "test/knxip_tests/connect_response_test.py::TestKNXIPConnectResponse::test_connect_response", "test/knxip_tests/connect_response_test.py::TestKNXIPConnectResponse::test_connect_response_connection_error_gira", "test/str_test.py::TestStringRepresentations::test_connect_response" ]

[ "test/io_tests/tunnel_test.py::TestTunnel::test_tunnel_request_received", "test/io_tests/tunnel_test.py::TestTunnel::test_tunnel_request_received_cemi_too_small", "test/io_tests/tunnel_test.py::TestTunnel::test_tunnel_request_received_apci_unsupported", "test/knxip_tests/connect_response_test.py::TestKNXIPConnectResponse::test_from_knx_wrong_crd", "test/knxip_tests/connect_response_test.py::TestKNXIPConnectResponse::test_from_knx_wrong_crd2", "test/knxip_tests/connect_response_test.py::TestKNXIPConnectResponse::test_connect_response_connection_error_lox", "test/knxip_tests/connect_response_test.py::TestKNXIPConnectResponse::test_connect_response_connection_error_mdt", "test/str_test.py::TestStringRepresentations::test_remote_value", "test/str_test.py::TestStringRepresentations::test_binary_sensor", "test/str_test.py::TestStringRepresentations::test_climate", "test/str_test.py::TestStringRepresentations::test_climate_mode", "test/str_test.py::TestStringRepresentations::test_cover", "test/str_test.py::TestStringRepresentations::test_fan", "test/str_test.py::TestStringRepresentations::test_light", "test/str_test.py::TestStringRepresentations::test_light_dimmable", "test/str_test.py::TestStringRepresentations::test_light_color", "test/str_test.py::TestStringRepresentations::test_notification", "test/str_test.py::TestStringRepresentations::test_scene", "test/str_test.py::TestStringRepresentations::test_sensor", "test/str_test.py::TestStringRepresentations::test_expose_sensor", "test/str_test.py::TestStringRepresentations::test_switch", "test/str_test.py::TestStringRepresentations::test_weather", "test/str_test.py::TestStringRepresentations::test_datetime", "test/str_test.py::TestStringRepresentations::test_could_not_parse_telegramn_exception", "test/str_test.py::TestStringRepresentations::test_could_not_parse_telegramn_exception_parameter", "test/str_test.py::TestStringRepresentations::test_could_not_parse_knxip_exception", "test/str_test.py::TestStringRepresentations::test_conversion_error_exception", "test/str_test.py::TestStringRepresentations::test_conversion_error_exception_parameter", "test/str_test.py::TestStringRepresentations::test_could_not_parse_address_exception", "test/str_test.py::TestStringRepresentations::test_device_illegal_value_exception", "test/str_test.py::TestStringRepresentations::test_address", "test/str_test.py::TestStringRepresentations::test_dpt_array", "test/str_test.py::TestStringRepresentations::test_dpt_binary", "test/str_test.py::TestStringRepresentations::test_telegram", "test/str_test.py::TestStringRepresentations::test_dib_generic", "test/str_test.py::TestStringRepresentations::test_dib_supp_svc_families", "test/str_test.py::TestStringRepresentations::test_dib_device_informatio", "test/str_test.py::TestStringRepresentations::test_hpai", "test/str_test.py::TestStringRepresentations::test_header", "test/str_test.py::TestStringRepresentations::test_connect_request", "test/str_test.py::TestStringRepresentations::test_disconnect_request", "test/str_test.py::TestStringRepresentations::test_disconnect_response", "test/str_test.py::TestStringRepresentations::test_connectionstate_request", "test/str_test.py::TestStringRepresentations::test_connectionstate_response", "test/str_test.py::TestStringRepresentations::test_search_reqeust", "test/str_test.py::TestStringRepresentations::test_search_response", "test/str_test.py::TestStringRepresentations::test_tunnelling_request", "test/str_test.py::TestStringRepresentations::test_tunnelling_ack", "test/str_test.py::TestStringRepresentations::test_cemi_frame", "test/str_test.py::TestStringRepresentations::test_knxip_frame", "test/str_test.py::TestStringRepresentations::test_gateway_descriptor", "test/str_test.py::TestStringRepresentations::test_routing_indication_str" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-12-27 10:18:03+00:00

mit

851

XKNX__xknx-910

diff --git a/changelog.md b/changelog.md index aef5dcc2..b7f15948 100644 --- a/changelog.md +++ b/changelog.md @@ -6,10 +6,12 @@ - Add support for SearchRequestExtended to find interfaces that allow IP Secure - Use XKNX `state_updater` argument to set default method for StateUpdater. StateUpdater is always started - Device / RemoteValue can always opt in to use it, even if default is `False`. +- Add support for DPT 16.001 (DPT_String_8859_1) as `DPTLatin1` with value_type "latin_1". ### Bug fixes - Stop SecureSession keepalive_task when session is stopped (and don't restart it from sending STATUS_CLOSE) +- Fix encoding invalid characters for DPTString (value_type "string") ## 0.20.0 IP Secure 2022-03-29 diff --git a/xknx/dpt/__init__.py b/xknx/dpt/__init__.py index 669c6993..cea33e90 100644 --- a/xknx/dpt/__init__.py +++ b/xknx/dpt/__init__.py @@ -172,7 +172,7 @@ from .dpt_date import DPTDate from .dpt_datetime import DPTDateTime from .dpt_hvac_mode import DPTControllerStatus, DPTHVACContrMode, DPTHVACMode from .dpt_scaling import DPTAngle, DPTScaling -from .dpt_string import DPTString +from .dpt_string import DPTLatin1, DPTString from .dpt_time import DPTTime __all__ = [ @@ -249,6 +249,7 @@ __all__ = [ "DPTHVACMode", "DPTImpedance", "DPTKelvinPerPercent", + "DPTLatin1", "DPTLength", "DPTLengthMm", "DPTLightQuantity", diff --git a/xknx/dpt/dpt_string.py b/xknx/dpt/dpt_string.py index 0788bc33..faf33207 100644 --- a/xknx/dpt/dpt_string.py +++ b/xknx/dpt/dpt_string.py @@ -8,7 +8,7 @@ from .dpt import DPTBase class DPTString(DPTBase): """ - Abstraction for KNX 14 Octet ASCII String. + Abstraction for KNX 14 Octet ASCII string. DPT 16.000 """ @@ -19,15 +19,15 @@ class DPTString(DPTBase): value_type = "string" unit = "" + _encoding = "ascii" + @classmethod def from_knx(cls, raw: tuple[int, ...]) -> str: """Parse/deserialize from KNX/IP raw data.""" cls.test_bytesarray(raw) - value = "" - for byte in raw: - if byte != 0x00: - value += chr(byte) - return value + return bytes(byte for byte in raw if byte != 0x00).decode( + cls._encoding, errors="replace" + ) @classmethod def to_knx(cls, value: str) -> tuple[int, ...]: @@ -36,15 +36,26 @@ class DPTString(DPTBase): knx_value = str(value) if not cls._test_boundaries(knx_value): raise ValueError - raw = [ord(character) for character in knx_value] - raw.extend([0] * (cls.payload_length - len(raw))) - # replace invalid characters with question marks - # bytes(knx_value, 'ascii') would raise UnicodeEncodeError - return tuple(map(lambda char: char if char <= 0xFF else ord("?"), raw)) except ValueError: raise ConversionError(f"Could not serialize {cls.__name__}", value=value) + # replace invalid characters with question marks + raw_bytes = knx_value.encode(cls._encoding, errors="replace") + padding = bytes(cls.payload_length - len(raw_bytes)) + return tuple(raw_bytes + padding) @classmethod def _test_boundaries(cls, value: str) -> bool: """Test if value is within defined range for this object.""" return len(value) <= cls.payload_length + + +class DPTLatin1(DPTString): + """ + Abstraction for KNX 14 Octet Latin-1 (ISO 8859-1) string. + + DPT 16.001 + """ + + dpt_sub_number = 1 + value_type = "latin_1" + _encoding = "latin_1"

XKNX/xknx

cf242d29979d21f5433b3e9e36b35ea8b1d14356

diff --git a/test/dpt_tests/dpt_string_test.py b/test/dpt_tests/dpt_string_test.py index b73065ae..0cf820e5 100644 --- a/test/dpt_tests/dpt_string_test.py +++ b/test/dpt_tests/dpt_string_test.py @@ -1,167 +1,91 @@ """Unit test for KNX string object.""" import pytest -from xknx.dpt import DPTString +from xknx.dpt import DPTLatin1, DPTString from xknx.exceptions import ConversionError class TestDPTString: - """Test class for KNX float object.""" + """Test class for KNX ASCII string object.""" - def test_value_from_documentation(self): - """Test parsing and streaming Example from documentation.""" - raw = ( - 0x4B, - 0x4E, - 0x58, - 0x20, - 0x69, - 0x73, - 0x20, - 0x4F, - 0x4B, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - ) - string = "KNX is OK" - assert DPTString.to_knx(string) == raw - assert DPTString.from_knx(raw) == string - - def test_value_empty_string(self): - """Test parsing and streaming empty string.""" - raw = ( - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - ) - string = "" - assert DPTString.to_knx(string) == raw - assert DPTString.from_knx(raw) == string + @pytest.mark.parametrize( + "string,raw", + [ + ( + "KNX is OK", + (75, 78, 88, 32, 105, 115, 32, 79, 75, 0, 0, 0, 0, 0), + ), + ( + "", + (0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), + ), + ( + "AbCdEfGhIjKlMn", + (65, 98, 67, 100, 69, 102, 71, 104, 73, 106, 75, 108, 77, 110), + ), + ( + ".,:;-_!?$@&#%/", + (46, 44, 58, 59, 45, 95, 33, 63, 36, 64, 38, 35, 37, 47), + ), + ], + ) + @pytest.mark.parametrize("test_dpt", [DPTString, DPTLatin1]) + def test_values(self, string, raw, test_dpt): + """Test parsing and streaming strings.""" + assert test_dpt.to_knx(string) == raw + assert test_dpt.from_knx(raw) == string - def test_value_max_string(self): - """Test parsing and streaming large string.""" - raw = ( - 0x41, - 0x41, - 0x41, - 0x41, - 0x41, - 0x42, - 0x42, - 0x42, - 0x42, - 0x42, - 0x43, - 0x43, - 0x43, - 0x43, - ) - string = "AAAAABBBBBCCCC" - assert DPTString.to_knx(string) == raw - assert DPTString.from_knx(raw) == string - - def test_value_special_chars(self): - """Test parsing and streaming string with special chars.""" - raw = ( - 0x48, - 0x65, - 0x79, - 0x21, - 0x3F, - 0x24, - 0x20, - 0xC4, - 0xD6, - 0xDC, - 0xE4, - 0xF6, - 0xFC, - 0xDF, - ) - string = "Hey!?$ ÄÖÜäöüß" - assert DPTString.to_knx(string) == raw - assert DPTString.from_knx(raw) == string - - def test_to_knx_invalid_chars(self): - """Test streaming string with invalid chars.""" - raw = ( - 0x4D, - 0x61, - 0x74, - 0x6F, - 0x75, - 0x3F, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - ) - string = "Matouš" - knx_string = "Matou?" + @pytest.mark.parametrize( + "string,knx_string,raw", + [ + ( + "Matouš", + "Matou?", + (77, 97, 116, 111, 117, 63, 0, 0, 0, 0, 0, 0, 0, 0), + ), + ( + "Gänsefüßchen", + "G?nsef??chen", + (71, 63, 110, 115, 101, 102, 63, 63, 99, 104, 101, 110, 0, 0), + ), + ], + ) + def test_to_knx_ascii_invalid_chars(self, string, knx_string, raw): + """Test streaming ASCII string with invalid chars.""" assert DPTString.to_knx(string) == raw assert DPTString.from_knx(raw) == knx_string + @pytest.mark.parametrize( + "string,raw", + [ + ( + "Gänsefüßchen", + (71, 228, 110, 115, 101, 102, 252, 223, 99, 104, 101, 110, 0, 0), + ), + ( + "àáâãåæçèéêëìíî", + (224, 225, 226, 227, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238), + ), + ], + ) + def test_to_knx_latin_1(self, string, raw): + """Test streaming Latin-1 strings.""" + assert DPTLatin1.to_knx(string) == raw + assert DPTLatin1.from_knx(raw) == string + def test_to_knx_too_long(self): """Test serializing DPTString to KNX with wrong value (to long).""" with pytest.raises(ConversionError): DPTString.to_knx("AAAAABBBBBCCCCx") - def test_from_knx_wrong_parameter_too_large(self): - """Test parsing of KNX string with too many elements.""" - raw = ( - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - ) - with pytest.raises(ConversionError): - DPTString.from_knx(raw) - - def test_from_knx_wrong_parameter_too_small(self): - """Test parsing of KNX string with too less elements.""" - raw = ( - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - 0x00, - ) + @pytest.mark.parametrize( + "raw", + [ + ((0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),), + ((0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),), + ], + ) + def test_from_knx_wrong_parameter_length(self, raw): + """Test parsing of KNX string with wrong elements length.""" with pytest.raises(ConversionError): DPTString.from_knx(raw)

ISO 8859-1 String support (Latin-1) - support DPT 16.001 ISO 8859-1 strings currently we only support DPT 16.000 but I think we encode/decode it as Unicode (`char()`) instead of just ASCII.

0.0

cf242d29979d21f5433b3e9e36b35ea8b1d14356

[ "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTString-KNX", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTString--raw1]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTString-AbCdEfGhIjKlMn-raw2]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTString-.,:;-_!?$@&#%/-raw3]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTLatin1-KNX", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTLatin1--raw1]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTLatin1-AbCdEfGhIjKlMn-raw2]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_values[DPTLatin1-.,:;-_!?$@&#%/-raw3]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_to_knx_ascii_invalid_chars[Matou\\u0161-Matou?-raw0]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_to_knx_ascii_invalid_chars[G\\xe4nsef\\xfc\\xdfchen-G?nsef??chen-raw1]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_to_knx_latin_1[G\\xe4nsef\\xfc\\xdfchen-raw0]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_to_knx_latin_1[\\xe0\\xe1\\xe2\\xe3\\xe5\\xe6\\xe7\\xe8\\xe9\\xea\\xeb\\xec\\xed\\xee-raw1]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_to_knx_too_long", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_from_knx_wrong_parameter_length[raw0]", "test/dpt_tests/dpt_string_test.py::TestDPTString::test_from_knx_wrong_parameter_length[raw1]" ]

[]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2022-04-05 14:17:08+00:00

mit

852

Yelp__pyramid-hypernova-15

diff --git a/pyramid_hypernova/batch.py b/pyramid_hypernova/batch.py index e4592f1..869b5ea 100644 --- a/pyramid_hypernova/batch.py +++ b/pyramid_hypernova/batch.py @@ -131,9 +131,9 @@ class BatchRequest(object): __, __, exc_traceback = sys.exc_info() error = HypernovaError( - repr(type(e)), + type(e).__name__, str(e), - traceback.format_tb(exc_traceback), + [line.rstrip('\n') for line in traceback.format_tb(exc_traceback)], ) self.plugin_controller.on_error(error, jobs) response = create_fallback_response(jobs, True, self.json_encoder, error)

Yelp/pyramid-hypernova

573e13042412461fa31bf046473c0033f9dc3fec

diff --git a/tests/batch_test.py b/tests/batch_test.py index 6a9dcf3..1b9f790 100644 --- a/tests/batch_test.py +++ b/tests/batch_test.py @@ -331,7 +331,7 @@ class TestBatchRequest(object): assert response == { token.identifier: JobResult( error=HypernovaError( - name="<class 'fido.exceptions.NetworkError'>", + name='NetworkError', message='oh no', stack=mock.ANY, ), @@ -475,16 +475,20 @@ class TestBatchRequestLifecycleMethods(object): with mock.patch( 'fido.fetch' ) as mock_fetch, mock.patch( - 'traceback.format_tb' - ) as mock_format_tb: + 'traceback.format_tb', + return_value=[ + 'Traceback:\n', + ' foo:\n', + ], + ): mock_fetch.return_value.wait.return_value.json.side_effect = NetworkError('oh no') batch_request.submit() spy_plugin_controller.on_error.assert_called_once_with( HypernovaError( - name="<class 'fido.exceptions.NetworkError'>", + name='NetworkError', message='oh no', - stack=mock_format_tb.return_value, + stack=['Traceback:', ' foo:'], ), batch_request.jobs, )

"stack" property on HypernovaError is formatted inconsistently When the error is a Python traceback, each element in the list has a trailing newline: ```python [' File "/nail/home/ckuehl/pg/yelp-main/virtualenv_run/lib/python2.7/site-packages/pyramid_hypernova/batch.py", line 116, in process_responses\n response_json = r.json()\n', ' File "/nail/home/ckuehl/pg/yelp-main/virtualenv_run/lib/python2.7/site-packages/fido/fido.py", line 98, in json\n return json.loads(self.body.decode(\'utf-8\'))\n', ' File "/usr/lib/python2.7/json/__init__.py", line 339, in loads\n return _default_decoder.decode(s)\n', [...] ``` When the error comes from the Hypernova server (a JS traceback), each element has no trailing newline: ```python [u'ReferenceError: Component "yelp_main__DEV__yelp_main__SearchApp__dynamic" not registered', u'at YOUR-COMPONENT-DID-NOT-REGISTER_yelp_main__DEV__yelp_main__SearchApp__dynamic:1:1', u'at notFound (/nail/home/ckuehl/proj/react_component_renderer/node_modules/hypernova/lib/utils/BatchManager.js:36:15)', u'at /nail/home/ckuehl/proj/react_component_renderer/node_modules/hypernova/lib/utils/BatchManager.js:186:35', u'at tryCatcher (/nail/home/ckuehl/proj/react_component_renderer/node_modules/bluebird/js/release/util.js:16:23)', u'at Promise._settlePromiseFromHandler (/nail/home/ckuehl/proj/react_component_renderer/node_modules/bluebird/js/release/promise.js:512:31)', [...] ``` Could we normalize these so that it's easier to print these out in a human-readable way?

0.0

573e13042412461fa31bf046473c0033f9dc3fec

[ "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data0-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data2-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data2-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data1-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data0-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data0-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data1-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data1-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_unhealthy_service[test_data2-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data2-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data0-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data1-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data2-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data1-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data0-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data1-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data2-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error_on_unhealthy_service[test_data0-1]" ]

[ "tests/batch_test.py::TestBatchRequest::test_batch_request_with_component_errors[test_data0-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_component_errors[test_data1-2]", "tests/batch_test.py::TestBatchRequest::test_successful_batch_request[test_data0-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[2-test_data0]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data1-None]", "tests/batch_test.py::TestBatchRequest::test_successful_batch_request[test_data0-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data2-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data2-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_component_errors[test_data0-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data0-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[None-test_data0]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_component_errors[test_data2-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[None-test_data1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[1-test_data2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[1-test_data0]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data1-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_component_errors[test_data1-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data0-1]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[None-test_data2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[1-test_data1]", "tests/batch_test.py::TestBatchRequest::test_successful_batch_request[test_data1-1]", "tests/batch_test.py::TestBatchRequest::test_successful_batch_request[test_data1-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data0-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data1-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_component_errors[test_data2-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[2-test_data2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_no_jobs_doesnt_post[2-test_data1]", "tests/batch_test.py::TestBatchRequest::test_successful_batch_request[test_data2-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_component_errors[test_data0-2]", "tests/batch_test.py::TestBatchRequest::test_successful_batch_request[test_data0-None]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_component_errors[test_data1-None]", "tests/batch_test.py::TestBatchRequest::test_successful_batch_request[test_data1-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_component_errors[test_data2-2]", "tests/batch_test.py::TestBatchRequest::test_batch_request_with_application_error[test_data2-None]", "tests/batch_test.py::TestBatchRequest::test_successful_batch_request[test_data2-1]", "tests/batch_test.py::TestBatchRequest::test_successful_batch_request[test_data2-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_after_response[test_data1-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_after_response[test_data0-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_get_view_data[test_data0-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error[test_data1-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data2-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_prepare_request[test_data0-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_will_send_request[test_data0-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data0-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_get_view_data[test_data0-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data1-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data0-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_after_response[test_data2-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_after_response[test_data2-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error[test_data0-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_get_view_data[test_data1-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_will_send_request[test_data2-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_will_send_request[test_data0-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_will_send_request[test_data1-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_prepare_request[test_data1-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_prepare_request[test_data2-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_get_view_data[test_data2-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error[test_data2-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_prepare_request[test_data2-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data1-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_get_view_data[test_data1-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_prepare_request[test_data2-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error[test_data0-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error[test_data0-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_after_response[test_data0-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_after_response[test_data2-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_get_view_data[test_data1-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_after_response[test_data1-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data0-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_get_view_data[test_data0-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data2-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data2-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error[test_data1-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_prepare_request[test_data1-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_will_send_request[test_data1-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_prepare_request[test_data0-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error[test_data1-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_get_view_data[test_data2-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_after_response[test_data1-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error[test_data2-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_will_send_request[test_data1-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_will_send_request[test_data2-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_error[test_data2-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_after_response[test_data0-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_get_view_data[test_data2-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_on_success[test_data1-1]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_will_send_request[test_data2-2]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_will_send_request[test_data0-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_prepare_request[test_data1-None]", "tests/batch_test.py::TestBatchRequestLifecycleMethods::test_calls_prepare_request[test_data0-1]", "tests/batch_test.py::test_create_fallback_response[jobs2-True-json_encoder2]", "tests/batch_test.py::test_create_fallback_response[jobs5-False-json_encoder5]", "tests/batch_test.py::test_create_job_groups[5-expected5]", "tests/batch_test.py::test_create_job_groups[1-expected1]", "tests/batch_test.py::test_create_jobs_payload", "tests/batch_test.py::test_create_job_groups[2-expected2]", "tests/batch_test.py::test_create_fallback_response[jobs1-False-json_encoder1]", "tests/batch_test.py::test_create_job_groups[None-expected0]", "tests/batch_test.py::test_create_fallback_response[jobs0-True-json_encoder0]", "tests/batch_test.py::test_create_job_groups[6-expected6]", "tests/batch_test.py::test_create_fallback_response[jobs3-False-json_encoder3]", "tests/batch_test.py::test_create_fallback_response[jobs4-True-json_encoder4]", "tests/batch_test.py::test_create_job_groups[4-expected4]", "tests/batch_test.py::test_create_job_groups[3-expected3]" ]

{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }

2019-01-18 00:11:18+00:00

mit

853

Yelp__virtualenv-tools-22

diff --git a/tox.ini b/tox.ini index 43f5f76..fceab09 100644 --- a/tox.ini +++ b/tox.ini @@ -16,4 +16,4 @@ envdir = venv-{[tox]project} commands = [pep8] -ignore = E265,E501 +ignore = E265,E501,W504 diff --git a/virtualenv_tools.py b/virtualenv_tools.py index 2b3cfae..2f76a24 100644 --- a/virtualenv_tools.py +++ b/virtualenv_tools.py @@ -31,7 +31,7 @@ ACTIVATION_SCRIPTS = [ _pybin_match = re.compile(r'^python\d+\.\d+$') _pypy_match = re.compile(r'^\d+.\d+$') _activation_path_re = re.compile( - r'^(?:set -gx |setenv |)VIRTUAL_ENV[ =]"(.*?)"\s*$', + r'^(?:set -gx |setenv |)VIRTUAL_ENV[ =][\'"](.*?)[\'"]\s*$', ) VERBOSE = False MAGIC_LENGTH = 4 + 4 # magic length + 4 byte timestamp @@ -169,7 +169,11 @@ def update_pycs(lib_dir, new_path): for dirname, dirnames, filenames in os.walk(lib_dir): for filename in filenames: - if filename.endswith(('.pyc', '.pyo')): + if ( + filename.endswith(('.pyc', '.pyo')) and + # python 2, virtualenv 20.x symlinks os.pyc + not os.path.islink(os.path.join(dirname, filename)) + ): filename = os.path.join(dirname, filename) local_path = get_new_path(filename) update_pyc(filename, local_path) @@ -236,11 +240,13 @@ def get_orig_path(venv_path): with open(activate_path) as activate: for line in activate: - if line.startswith('VIRTUAL_ENV="'): - return line.split('"', 2)[1] + # virtualenv 20 changes the position + for possible in ('VIRTUAL_ENV="', "VIRTUAL_ENV='"): + if line.startswith(possible): + return line.split(possible[-1], 2)[1] else: raise AssertionError( - 'Could not find VIRTUAL_ENV=" in activation script: %s' % + 'Could not find VIRTUAL_ENV= in activation script: %s' % activate_path )

Yelp/virtualenv-tools

5247e0c8c39a584b217ae7de82bc9051903f863f

diff --git a/tests/virtualenv_tools_test.py b/tests/virtualenv_tools_test.py index e34d596..44fdc27 100644 --- a/tests/virtualenv_tools_test.py +++ b/tests/virtualenv_tools_test.py @@ -185,7 +185,7 @@ def test_verbose(venv, capsys): run(venv.before, venv.after, args=('--verbose',)) out, _ = capsys.readouterr() # Lots of output - assert len(out.splitlines()) > 25 + assert len(out.splitlines()) > 10 def test_non_absolute_error(capsys):

Unable to find the VIRTUAL_ENV variable in activate.sh for recent virtualenv versions. Starting in `virtualenv==20.0.0`, the `VIRTUAL_ENV` variable is now defined using single quotes instead of double quotes. This breaks `virtualenv-tools3` as it specifically searches for the string `VIRTUAL_ENV="` in `activate.sh`.

0.0

5247e0c8c39a584b217ae7de82bc9051903f863f

[ "tests/virtualenv_tools_test.py::test_bad_pyc", "tests/virtualenv_tools_test.py::test_already_up_to_date" ]

[ "tests/virtualenv_tools_test.py::test_help[helpargs1]", "tests/virtualenv_tools_test.py::test_not_a_virtualenv_missing_bindir", "tests/virtualenv_tools_test.py::test_help[helpargs0]", "tests/virtualenv_tools_test.py::test_not_a_virtualenv_missing_site_packages", "tests/virtualenv_tools_test.py::test_not_a_virtualenv_missing_activate_file", "tests/virtualenv_tools_test.py::test_not_a_virtualenv_missing_versioned_lib_directory", "tests/virtualenv_tools_test.py::test_non_absolute_error" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2020-02-12 00:45:18+00:00

bsd-3-clause

854

Zepmanbc__creopyson-2

diff --git a/creopyson/creo.py b/creopyson/creo.py index 890f29d..1d86c48 100755 --- a/creopyson/creo.py +++ b/creopyson/creo.py @@ -1,4 +1,5 @@ """Creo module.""" +from creopyson.exceptions import MissingKey def cd(client, dirname): @@ -108,7 +109,11 @@ def list_dirs(client, dirname=None): data = {"dirname": "*"} if dirname: data["dirname"] = dirname - return client._creoson_post("creo", "list_dirs", data, "dirlist") + try: + result = client._creoson_post("creo", "list_dirs", data, "dirlist") + except MissingKey: + result = [] + return result def list_files(client, filename=None):

Zepmanbc/creopyson

4a214ea618fba75d4200cc3dcbc6371d924765e6

diff --git a/tests/fixtures.py b/tests/fixtures.py index 8919eca..6d2ff6e 100644 --- a/tests/fixtures.py +++ b/tests/fixtures.py @@ -55,7 +55,7 @@ def mk_creoson_post_dict(monkeypatch): @pytest.fixture def mk_creoson_post_None(monkeypatch): """Mock _creoson_post return None.""" - def fake_func(client, command, function, data=None): + def fake_func(client, command, function, data=None, key_data=None): return None monkeypatch.setattr( creopyson.connection.Client, '_creoson_post', fake_func) @@ -64,7 +64,7 @@ def mk_creoson_post_None(monkeypatch): @pytest.fixture def mk_creoson_post_list(monkeypatch): """Mock _creoson_post return list.""" - def fake_func(client, command, function, data=None): + def fake_func(client, command, function, data=None, key_data=None): return ['information'] monkeypatch.setattr( creopyson.connection.Client, '_creoson_post', fake_func) diff --git a/tests/test_creo.py b/tests/test_creo.py index ccdb9fe..1398006 100644 --- a/tests/test_creo.py +++ b/tests/test_creo.py @@ -1,5 +1,6 @@ """Creo testing.""" import creopyson +from creopyson.exceptions import MissingKey from .fixtures import mk_creoson_post_dict, mk_creoson_post_None @@ -43,6 +44,23 @@ def test_creo_list_dirs(mk_creoson_post_dict): c = creopyson.Client() result = c.creo_list_dirs("filter_*") assert isinstance(result, (list)) + result = c.creo_list_dirs() + assert isinstance(result, (list)) + + +def test_creo_list_dirs_empty(monkeypatch): + """Correction issue #1. + + if there is no folder in directory, creoson does not return `data`. + Need to return an empty list. + """ + def fake_func(client, command, function, data=None, key_data=None): + raise MissingKey("Missing `data` in creoson return") + monkeypatch.setattr( + creopyson.connection.Client, '_creoson_post', fake_func) + c = creopyson.Client() + result = c.creo_list_dirs() + assert result == [] def test_creo_list_files(mk_creoson_post_dict):

Exception thrown in creo_list_dirs * Creopyson version: 0.3.1 * Python version: 3.6 * Operating System: Windows ### Description I tried to list the directories in the current session with `creo_list_dirs()` but I received an exception telling that Creoson did not return the right data. ### What I Did ``` >>> c.creo_list_dirs() Traceback (most recent call last): File "<stdin>", line 1, in <module> File "C:\Users\Tim\.virtualenvs\creopyson_test-yJfFsqNW\lib\site-packages\creopyson\creo.py", line 111, in list_dirs return client._creoson_post("creo", "list_dirs", data, "dirlist") File "C:\Users\Tim\.virtualenvs\creopyson_test-yJfFsqNW\lib\site-packages\creopyson\connection.py", line 81, in _creoson_post raise MissingKey("Missing `data` in creoson return") creopyson.exceptions.MissingKey: Missing `data` in creoson return ```

0.0

4a214ea618fba75d4200cc3dcbc6371d924765e6

[ "tests/test_creo.py::test_creo_list_dirs_empty" ]

[ "tests/test_creo.py::test_creo_cd", "tests/test_creo.py::test_creo_delete_files", "tests/test_creo.py::test_creo_get_config", "tests/test_creo.py::test_creo_get_std_color", "tests/test_creo.py::test_creo_list_dirs", "tests/test_creo.py::test_creo_list_files", "tests/test_creo.py::test_creo_mkdir", "tests/test_creo.py::test_creo_pwd", "tests/test_creo.py::test_creo_rmdir_ok", "tests/test_creo.py::test_creo_set_config_ok", "tests/test_creo.py::test_creo_set_std_color_ok" ]

{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }

2019-07-03 19:45:24+00:00

mit

855

a2i2__surround-106

diff --git a/surround/cli.py b/surround/cli.py index e8922cb..f57dc50 100644 --- a/surround/cli.py +++ b/surround/cli.py @@ -93,6 +93,16 @@ def is_valid_dir(aparser, arg): else: return arg +def allowed_to_access_dir(path): + try: + os.makedirs(path, exist_ok=True) + except OSError: + print("error: can't write to " + path) + + if os.access(path, os.R_OK | os.W_OK | os.F_OK | os.X_OK): + return True + return False + def is_valid_name(aparser, arg): if not arg.isalpha() or not arg.islower(): aparser.error("Name %s must be lowercase letters" % arg) @@ -229,26 +239,29 @@ def parse_tutorial_args(args): def parse_init_args(args): - if args.project_name: - project_name = args.project_name - else: - while True: - project_name = input("Name of project: ") - if not project_name.isalpha() or not project_name.islower(): - print("Project name requires lowercase letters only") - else: - break - - if args.description: - project_description = args.description - else: - project_description = input("What is the purpose of this project?: ") + if allowed_to_access_dir(args.path): + if args.project_name: + project_name = args.project_name + else: + while True: + project_name = input("Name of project: ") + if not project_name.isalpha() or not project_name.islower(): + print("error: project name requires lowercase letters only") + else: + break + + if args.description: + project_description = args.description + else: + project_description = input("What is the purpose of this project?: ") - new_dir = os.path.join(args.path, project_name) - if process(new_dir, PROJECTS["new"], project_name, project_description, "new"): - print("Project created at %s" % os.path.join(os.path.abspath(args.path), project_name)) + new_dir = os.path.join(args.path, project_name) + if process(new_dir, PROJECTS["new"], project_name, project_description, "new"): + print("info: project created at %s" % os.path.join(os.path.abspath(args.path), project_name)) + else: + print("error: directory %s already exists" % new_dir) else: - print("Directory %s already exists" % new_dir) + print("error: permission denied") def parse_tool_args(parsed_args, remote_parser, tool): if tool == "tutorial": @@ -278,10 +291,10 @@ def main(): tutorial_parser = sub_parser.add_parser('tutorial', help="Create the tutorial project") tutorial_parser.add_argument('tutorial', help="Create the Surround tutorial project", action='store_true') - tutorial_parser.add_argument('path', type=lambda x: is_valid_dir(parser, x), help="Path for creating the tutorial project", nargs='?', default="./") + tutorial_parser.add_argument('path', help="Path for creating the tutorial project", nargs='?', default="./") init_parser = sub_parser.add_parser('init', help="Initialise a new Surround project") - init_parser.add_argument('path', type=lambda x: is_valid_dir(parser, x), help="Path for creating a Surround project", nargs='?', default="./") + init_parser.add_argument('path', help="Path for creating a Surround project", nargs='?', default="./") init_parser.add_argument('-p', '--project-name', help="Name of the project", type=lambda x: is_valid_name(parser, x)) init_parser.add_argument('-d', '--description', help="A description for the project")

a2i2/surround

6e5a32dafc6ba858edc1b21cf6644fb2c6b77815

diff --git a/surround/tests/cli/project_cli/init_test.py b/surround/tests/cli/project_cli/init_test.py index 24d0f53..1bbce4e 100644 --- a/surround/tests/cli/project_cli/init_test.py +++ b/surround/tests/cli/project_cli/init_test.py @@ -9,13 +9,13 @@ class InitTest(unittest.TestCase): def test_happy_path(self): process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Project created at " + os.getcwd() + "/temp\n") + self.assertEqual(process.stdout, "info: project created at " + os.getcwd() + "/temp\n") is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp")) self.assertEqual(is_temp, True) process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Directory ./temp already exists\n") + self.assertEqual(process.stdout, "error: directory ./temp already exists\n") def tearDown(self): # Remove residual files diff --git a/surround/tests/cli/remote_cli/add_test.py b/surround/tests/cli/remote_cli/add_test.py index 07c9ea4..537a8d8 100644 --- a/surround/tests/cli/remote_cli/add_test.py +++ b/surround/tests/cli/remote_cli/add_test.py @@ -9,7 +9,7 @@ class AddTest(unittest.TestCase): def test_rejecting_path(self): process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Project created at " + os.getcwd() + "/temp\n") + self.assertEqual(process.stdout, "info: project created at " + os.getcwd() + "/temp\n") is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp")) self.assertEqual(is_temp, True) @@ -24,7 +24,7 @@ class AddTest(unittest.TestCase): def test_happy_path(self): process = subprocess.run(['surround', 'init', os.getcwd(), '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Project created at " + os.getcwd() + "/temp\n") + self.assertEqual(process.stdout, "info: project created at " + os.getcwd() + "/temp\n") is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp")) self.assertEqual(is_temp, True) diff --git a/surround/tests/cli/remote_cli/list_test.py b/surround/tests/cli/remote_cli/list_test.py index 71970eb..d993284 100644 --- a/surround/tests/cli/remote_cli/list_test.py +++ b/surround/tests/cli/remote_cli/list_test.py @@ -9,7 +9,7 @@ class ListTest(unittest.TestCase): def test_rejecting_path(self): process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Project created at " + os.getcwd() + "/temp\n") + self.assertEqual(process.stdout, "info: project created at " + os.getcwd() + "/temp\n") is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp")) self.assertEqual(is_temp, True) @@ -19,7 +19,7 @@ class ListTest(unittest.TestCase): def test_happy_path(self): process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Project created at " + os.getcwd() + "/temp\n") + self.assertEqual(process.stdout, "info: project created at " + os.getcwd() + "/temp\n") is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp")) self.assertEqual(is_temp, True) diff --git a/surround/tests/cli/remote_cli/remote_test.py b/surround/tests/cli/remote_cli/remote_test.py index e8ed4cd..7236530 100644 --- a/surround/tests/cli/remote_cli/remote_test.py +++ b/surround/tests/cli/remote_cli/remote_test.py @@ -12,7 +12,7 @@ class RemoteTest(unittest.TestCase): self.assertEqual(process.stdout, "error: not a surround project\nerror: goto project root directory\n") process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Project created at " + os.getcwd() + "/temp\n") + self.assertEqual(process.stdout, "info: project created at " + os.getcwd() + "/temp\n") is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp")) self.assertEqual(is_temp, True) @@ -22,7 +22,7 @@ class RemoteTest(unittest.TestCase): def test_remote_add(self): process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp'], encoding='utf-8', stdout=subprocess.PIPE) - self.assertEqual(process.stdout, "Project created at " + os.getcwd() + "/temp\n") + self.assertEqual(process.stdout, "info: project created at " + os.getcwd() + "/temp\n") is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp")) self.assertEqual(is_temp, True)

`surround tutorial` doesn't work if destination directory doesn't exist `surround tutorial <path>` doesn't work if the path doesn't exist. Not sure if this is intended behaviour, but it might be nice to follow what Git does, i.e. * Create the directory if it doesn't exist * Print error if the directory exists but isn't empty My experience below: ``` ➜ surround tutorial usage: surround tutorial [-h] path surround tutorial: error: the following arguments are required: path ➜ surround tutorial my-first-surround-app usage: surround [-h] {tutorial,init} ... surround: error: Invalid directory or can't write to my-first-surround-app ➜ mkdir surround-tutorial ➜ surround tutorial my-first-surround-app The tutorial project has been created. Start by reading the README.md file at: /home/rohan/Development/sandbox/my-first-surround-app/README.md ``` After doing the above, I ended up with all the files in `my-first-surround-app/tutorial`, instead of just in `my-first-surround-app` as I expected.

0.0

6e5a32dafc6ba858edc1b21cf6644fb2c6b77815

[ "surround/tests/cli/project_cli/init_test.py::InitTest::test_happy_path", "surround/tests/cli/remote_cli/add_test.py::AddTest::test_happy_path", "surround/tests/cli/remote_cli/add_test.py::AddTest::test_rejecting_path", "surround/tests/cli/remote_cli/list_test.py::ListTest::test_happy_path", "surround/tests/cli/remote_cli/list_test.py::ListTest::test_rejecting_path", "surround/tests/cli/remote_cli/remote_test.py::RemoteTest::test_remote", "surround/tests/cli/remote_cli/remote_test.py::RemoteTest::test_remote_add" ]

[]

{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }

2019-04-04 06:46:13+00:00

bsd-3-clause

856

abantos__bolt-88

diff --git a/bolt/about.py b/bolt/about.py index 3c285ba..9b6ae95 100644 --- a/bolt/about.py +++ b/bolt/about.py @@ -8,4 +8,4 @@ A task runner written in Python copyright = u'2016 Abantos' author = u'Isaac Rodriguez' version = u'0.2' -release = u'0.2.2' +release = u'0.2.3' diff --git a/bolt/tasks/bolt_setup.py b/bolt/tasks/bolt_setup.py index 6190eb5..e10aa8b 100644 --- a/bolt/tasks/bolt_setup.py +++ b/bolt/tasks/bolt_setup.py @@ -26,8 +26,12 @@ configure the task. :: import distutils.core as dcore import logging +import bolt.errors as errors import bolt.utils as utilities + +class BuildSetupError(errors.TaskError): pass + DEFAULT_ARGUMENTS = ['build'] DEFAULT_SETUP_SCRIPT = 'setup.py' @@ -50,11 +54,13 @@ class ExecuteSetupTask(object): self.setup_script = DEFAULT_SETUP_SCRIPT generator = _SetupArgumentGenerator() self.args = generator.generate_from(config) - self._execute_setup() + result = self._execute_setup() + if not result.dist_files: + raise BuildSetupError() def _execute_setup(self): - dcore.run_setup(self.setup_script, self.args) + return dcore.run_setup(self.setup_script, self.args)

abantos/bolt

39a5db9fa29ec6c13dceb51480fb3e56574aa2a7

diff --git a/test/test_tasks/test_bolt_setup.py b/test/test_tasks/test_bolt_setup.py index d9a03b9..9e874cc 100644 --- a/test/test_tasks/test_bolt_setup.py +++ b/test/test_tasks/test_bolt_setup.py @@ -7,7 +7,7 @@ import _mocks as mck class TestExecuteSetupTask(unittest.TestCase): def setUp(self): - self. subject = ExecuteSetupTaskSpy() + self.subject = ExecuteSetupTaskSpy() return super(TestExecuteSetupTask, self).setUp() @@ -25,6 +25,12 @@ class TestExecuteSetupTask(unittest.TestCase): self.assertEqual(self.subject.setup_script, script) + def test_raises_exception_if_building_setup_fails(self): + self.subject.dist_files = [] + with self.assertRaises(bsetup.BuildSetupError): + self.given({}) + + def given(self, config): self.subject(config=config) @@ -36,9 +42,13 @@ class TestExecuteSetupTask(unittest.TestCase): class ExecuteSetupTaskSpy(bsetup.ExecuteSetupTask): + + def __init__(self): + super(ExecuteSetupTaskSpy, self).__init__() + self.dist_files = [('bdist_wheel', '3.5', '/some/colation/the.whl')] def _execute_setup(self): - pass + return self

Setup Task Swallows Errors Building Distribution ### Description The current implementation of the Setup task does not evaluate the return object from `distutils.core.run_setup()` and it just assumes it works. Unfortunately, some environments will not have the right tools to build a distribution; therefore, the task will silently fail. I found this problem in another project's pipeline where building a `wheel` inside the official Python 2.7 Docker container silently failed because the `wheel` package is not installed by default like when creating a virtual environment. ### Steps to Reproduce - Create a setup task that builds a simple distribution wheel. - Create a virtual environment, activate it, and uninstall the `wheel` package. - Run the setup task within the environment. - Check the dist folder, which will be empty. The current behavior shows that the return code from `distutils.core.run_setup()` invoked by the task is not evaluated, and the task seems to succeed; however, the `.whl` file has not been created. An exception is expected to be raised if the wheel doesn't succeed. ### Fix Analysis Looking at the implementation of `distutils.core.run_setup()`, you can see the function returns a `Distribution` instance. The instance exposes a `dist_files` property, which is empty if the distribution failed to build. If it succeeds, the return value is a list of tuples containing information about each distribution. This allow us to fix the problem, or at list report an error if no distribution was built, by checking the contents of `dist_files`; something like the following code: ```python # dcore is an alias to distutils.core. dist_info = dcore.run_setup(self.setup_script, self.args) if not dist_info.dist_files: raise DistributionBuildError() ``` > NOTE:I need to think on how to handle multiple distributions; although, I believe right now the task only supports one distribution per configuration. The following is an example of the contents of the `dist_files` property: ``` [('bdist_wheel', '3.5', 'D:\\Projects\\Abantos\\bolt\\dist\\bolt_ta-0.2.1-py2.py3-none-any.whl')] ``` ### Acceptance Criteria Raises exception if building the distribution fails.

0.0

39a5db9fa29ec6c13dceb51480fb3e56574aa2a7

[ "test/test_tasks/test_bolt_setup.py::TestExecuteSetupTask::test_raises_exception_if_building_setup_fails" ]

[ "test/test_tasks/test_bolt_setup.py::TestExecuteSetupTask::test_uses_default_if_empty_configuration", "test/test_tasks/test_bolt_setup.py::TestExecuteSetupTask::test_uses_specified_script", "test/test_tasks/test_bolt_setup.py::TestRegisterTasks::test_registers_setup" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }

2017-03-07 16:19:15+00:00

mit

857

abdullahselek__HerePy-25

diff --git a/README.rst b/README.rst index b6bd1b8..78d2e19 100644 --- a/README.rst +++ b/README.rst @@ -224,6 +224,14 @@ Calculate an MxN cost matrix for M start points and N destinations departure='2013-07-04T17:00:00+02', modes=[herepy.RouteMode.fastest, herepy.RouteMode.car]) +Calculate route providing names instead of coordinates + +.. code:: python + + response = routingApi.car_route([11.0, 12.0], + '200 S Mathilda Sunnyvale CA', + [herepy.RouteMode.car, herepy.RouteMode.fastest]) + GeocoderAutoCompleteApi ----------------------- diff --git a/herepy/routing_api.py b/herepy/routing_api.py index d188aaf..9a9fd52 100644 --- a/herepy/routing_api.py +++ b/herepy/routing_api.py @@ -5,12 +5,13 @@ import sys import json import requests +from herepy.geocoder_api import GeocoderApi from herepy.here_api import HEREApi from herepy.utils import Utils from herepy.error import HEREError from herepy.models import RoutingResponse, RoutingMatrixResponse from herepy.here_enum import RouteMode, MatrixSummaryAttribute -from typing import List +from typing import List, Union class RoutingApi(HEREApi): """A python interface into the HERE Routing API""" @@ -53,6 +54,10 @@ class RoutingApi(HEREApi): return str.format('geo!{0},{1}', waypoint_a[0], waypoint_a[1]) def _route(self, waypoint_a, waypoint_b, modes=None, departure=None, arrival=None): + if isinstance(waypoint_a, str): + waypoint_a = self._get_coordinates_for_location_name(waypoint_a) + if isinstance(waypoint_b, str): + waypoint_b = self._get_coordinates_for_location_name(waypoint_b) data = {'waypoint0': self.__array_to_waypoint(waypoint_a), 'waypoint1': self.__array_to_waypoint(waypoint_b), 'mode': self.__prepare_mode_values(modes), @@ -84,16 +89,18 @@ class RoutingApi(HEREApi): return response def bicycle_route(self, - waypoint_a: List[float], - waypoint_b: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], modes: List[RouteMode]=None, departure: str='now'): """Request a bicycle route between two points Args: - waypoint_a (array): - array including latitude and longitude in order. - waypoint_b (array): - array including latitude and longitude in order. + waypoint_a: + array including latitude and longitude in order + or string with the location name + waypoint_b: + array including latitude and longitude in order + or string with the location name. modes (array): array including RouteMode enums. departure (str): @@ -108,16 +115,18 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure) def car_route(self, - waypoint_a: List[float], - waypoint_b: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], modes: List[RouteMode]=None, departure: str='now'): """Request a driving route between two points Args: waypoint_a (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. waypoint_b (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. modes (array): array including RouteMode enums. departure (str): @@ -132,16 +141,18 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure) def pedastrian_route(self, - waypoint_a: List[float], - waypoint_b: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], modes: List[RouteMode]=None, departure: str='now'): """Request a pedastrian route between two points Args: waypoint_a (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. waypoint_b (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. modes (array): array including RouteMode enums. departure (str): @@ -156,19 +167,22 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure) def intermediate_route(self, - waypoint_a: List[float], - waypoint_b: List[float], - waypoint_c: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], + waypoint_c: Union[List[float], str], modes: List[RouteMode]=None, departure: str='now'): """Request a intermediate route from three points Args: waypoint_a (array): - Starting array including latitude and longitude in order. + Starting array including latitude and longitude in order + or string with the location name. waypoint_b (array): - Intermediate array including latitude and longitude in order. + Intermediate array including latitude and longitude in order + or string with the location name. waypoint_c (array): - Last array including latitude and longitude in order. + Last array including latitude and longitude in order + or string with the location name. modes (array): array including RouteMode enums. departure (str): @@ -183,17 +197,19 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure) def public_transport(self, - waypoint_a: List[float], - waypoint_b: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], combine_change: bool, modes: List[RouteMode]=None, departure='now'): """Request a public transport route between two points Args: waypoint_a (array): - Starting array including latitude and longitude in order. + Starting array including latitude and longitude in order + or string with the location name. waypoint_b (array): - Intermediate array including latitude and longitude in order. + Intermediate array including latitude and longitude in order + or string with the location name. combine_change (bool): Enables the change manuever in the route response, which indicates a public transit line change. @@ -211,8 +227,8 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure) def public_transport_timetable(self, - waypoint_a: List[float], - waypoint_b: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], combine_change: bool, modes: List[RouteMode]=None, departure: str=None, @@ -220,9 +236,11 @@ class RoutingApi(HEREApi): """Request a public transport route between two points based on timetables Args: waypoint_a (array): - Starting array including latitude and longitude in order. + Starting array including latitude and longitude in order + or string with the location name. waypoint_b (array): - Intermediate array including latitude and longitude in order. + Intermediate array including latitude and longitude in order + or string with the location name. combine_change (bool): Enables the change manuever in the route response, which indicates a public transit line change. @@ -242,16 +260,18 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure, arrival) def location_near_motorway(self, - waypoint_a: List[float], - waypoint_b: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], modes: List[RouteMode]=None, departure: str='now'): """Calculates the fastest car route between two location Args: waypoint_a (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. waypoint_b (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. modes (array): array including RouteMode enums. departure (str): @@ -266,16 +286,18 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure) def truck_route(self, - waypoint_a: List[float], - waypoint_b: List[float], + waypoint_a: Union[List[float], str], + waypoint_b: Union[List[float], str], modes: List[RouteMode]=None, departure: str='now'): """Calculates the fastest truck route between two location Args: waypoint_a (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. waypoint_b (array): - array including latitude and longitude in order. + array including latitude and longitude in order + or string with the location name. modes (array): array including RouteMode enums. departure (str): @@ -290,8 +312,8 @@ class RoutingApi(HEREApi): return self._route(waypoint_a, waypoint_b, modes, departure) def matrix(self, - start_waypoints: List[float], - destination_waypoints: List[float], + start_waypoints: Union[List[float], str], + destination_waypoints: Union[List[float], str], departure: str='now', modes: List[RouteMode]=[], summary_attributes: List[MatrixSummaryAttribute]=[]): @@ -299,8 +321,10 @@ class RoutingApi(HEREApi): Args: start_waypoints (array): array of arrays of coordinates [lat,long] of start waypoints. + or array of string with the location names. destination_waypoints (array): array of arrays of coordinates [lat,long] of destination waypoints. + or array of string with the location names. departure (str): time when travel is expected to start, e.g.: '2013-07-04T17:00:00+02' modes (array): @@ -320,12 +344,27 @@ class RoutingApi(HEREApi): 'summaryAttributes': ','.join([attribute.__str__() for attribute in summary_attributes]) } for i, start_waypoint in enumerate(start_waypoints): + if isinstance(start_waypoint, str): + start_waypoint = self._get_coordinates_for_location_name(start_waypoint) data['start' + str(i)] = self.__array_to_waypoint(start_waypoint) for i, destination_waypoint in enumerate(destination_waypoints): + if isinstance(destination_waypoint, str): + destination_waypoint = self._get_coordinates_for_location_name(destination_waypoint) data['destination' + str(i)] = self.__array_to_waypoint(destination_waypoint) response = self.__get(self.URL_CALCULATE_MATRIX, data, RoutingMatrixResponse) return response + def _get_coordinates_for_location_name(self, location_name: str) -> List[float]: + """Use the Geocoder API to resolve a location name to a set of coordinates.""" + + geocoder_api = GeocoderApi(self._api_key) + try: + geocoder_response = geocoder_api.free_form(location_name) + coordinates = geocoder_response.Response["View"][0]["Result"][0]["Location"]["NavigationPosition"][0] + return [coordinates["Latitude"], coordinates["Longitude"]] + except (HEREError) as here_error: + raise WaypointNotFoundError(here_error.message) + @staticmethod def _convert_datetime_to_isoformat(datetime_object): """Convert a datetime.datetime object to an ISO8601 string."""

abdullahselek/HerePy

8691e147549141dc8287ba16a4396a63ed09b73b

diff --git a/tests/test_routing_api.py b/tests/test_routing_api.py index db150bd..9239be6 100644 --- a/tests/test_routing_api.py +++ b/tests/test_routing_api.py @@ -455,6 +455,22 @@ class RoutingApiTest(unittest.TestCase): self.assertTrue(response) self.assertIsInstance(response, herepy.RoutingMatrixResponse) + @responses.activate + def test_matrix_multiple_start_names(self): + with codecs.open('testdata/models/routing_matrix_multiple_starts.json', mode='r', encoding='utf-8') as f: + server_response = f.read() + responses.add(responses.GET, 'https://matrix.route.ls.hereapi.com/routing/7.2/calculatematrix.json', + server_response, status=200) + with open('testdata/models/geocoder.json', 'r') as f: + expectedGeocoderResponse = f.read() + responses.add(responses.GET, 'https://geocoder.ls.hereapi.com/6.2/geocode.json', + expectedGeocoderResponse, status=200) + response = self._api.matrix( + start_waypoints=['Seattle', 'Kentucky'], + destination_waypoints=[[9.934574, -84.065544]]) + self.assertTrue(response) + self.assertIsInstance(response, herepy.RoutingMatrixResponse) + @responses.activate def test_matrix_multiple_destinations(self): with codecs.open('testdata/models/routing_matrix_multiple_destinations.json', mode='r', encoding='utf-8') as f: @@ -467,6 +483,22 @@ class RoutingApiTest(unittest.TestCase): self.assertTrue(response) self.assertIsInstance(response, herepy.RoutingMatrixResponse) + @responses.activate + def test_matrix_multiple_destinations(self): + with codecs.open('testdata/models/routing_matrix_multiple_destinations.json', mode='r', encoding='utf-8') as f: + server_response = f.read() + responses.add(responses.GET, 'https://matrix.route.ls.hereapi.com/routing/7.2/calculatematrix.json', + server_response, status=200) + with open('testdata/models/geocoder.json', 'r') as f: + expectedGeocoderResponse = f.read() + responses.add(responses.GET, 'https://geocoder.ls.hereapi.com/6.2/geocode.json', + expectedGeocoderResponse, status=200) + response = self._api.matrix( + start_waypoints=[[9.933231, -84.076831]], + destination_waypoints=['Seattle', 'Kentucky']) + self.assertTrue(response) + self.assertIsInstance(response, herepy.RoutingMatrixResponse) + @responses.activate def test_matrix_bad_request(self): with codecs.open('testdata/models/routing_matrix_bad_request.json', mode='r', encoding='utf-8') as f: @@ -500,4 +532,30 @@ class RoutingApiTest(unittest.TestCase): response = self._api.truck_route([11.0, 12.0], [22.0, 23.0], departure=date) - + + @responses.activate + def test_location_by_name(self): + with codecs.open('testdata/models/routing_truck_route_short.json', mode='r', encoding='utf-8') as f: + expectedRoutingResponse = f.read() + responses.add(responses.GET, 'https://route.ls.hereapi.com/routing/7.2/calculateroute.json', + expectedRoutingResponse, status=200) + with open('testdata/models/geocoder.json', 'r') as f: + expectedGeocoderResponse = f.read() + responses.add(responses.GET, 'https://geocoder.ls.hereapi.com/6.2/geocode.json', + expectedGeocoderResponse, status=200) + response = self._api.truck_route('200 S Mathilda Sunnyvale CA', + '200 S Mathilda Sunnyvale CA') + + @responses.activate + def test_location_by_name_throws_WaypointNotFoundError(self): + with codecs.open('testdata/models/routing_truck_route_short.json', mode='r', encoding='utf-8') as f: + expectedRoutingResponse = f.read() + responses.add(responses.GET, 'https://route.ls.hereapi.com/routing/7.2/calculateroute.json', + expectedRoutingResponse, status=200) + with open('testdata/models/geocoder_error.json', 'r') as f: + expectedGeocoderResponse = f.read() + responses.add(responses.GET, 'https://geocoder.ls.hereapi.com/6.2/geocode.json', + expectedGeocoderResponse, status=200) + with self.assertRaises(herepy.WaypointNotFoundError): + response = self._api.truck_route('200 S Mathilda Sunnyvale CA', + '200 S Mathilda Sunnyvale CA')

Combine routing api and geocoder to allow routing to/from names Add a new function to the routing api that takes names for the origin and destination. Call the geocoder api to resolve these to coordinates. I would be happy to create a PR for this if you would welcome this feature.

0.0

8691e147549141dc8287ba16a4396a63ed09b73b

[ "tests/test_routing_api.py::RoutingApiTest::test_location_by_name_throws_WaypointNotFoundError" ]

[ "tests/test_routing_api.py::RoutingApiTest::test_carroute_route_short", "tests/test_routing_api.py::RoutingApiTest::test_pedastrianroute_when_error_invalid_input_data_occured", "tests/test_routing_api.py::RoutingApiTest::test_matrix_multiple_start_names", "tests/test_routing_api.py::RoutingApiTest::test_pedastrianroute_when_error_no_route_found_occured", "tests/test_routing_api.py::RoutingApiTest::test_publictransport_when_error_invalid_input_data_occured", "tests/test_routing_api.py::RoutingApiTest::test_publictransport_when_error_no_route_found_occured", "tests/test_routing_api.py::RoutingApiTest::test_truckroute_when_error_no_route_found_occured", "tests/test_routing_api.py::RoutingApiTest::test_initiation", "tests/test_routing_api.py::RoutingApiTest::test_matrix_bad_request", "tests/test_routing_api.py::RoutingApiTest::test_location_by_name", "tests/test_routing_api.py::RoutingApiTest::test_publictransport_withdefaultmodes_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_pedastrianroute_when_error_invalid_credentials_occured", "tests/test_routing_api.py::RoutingApiTest::test_carroute_when_error_invalid_input_data_occured", "tests/test_routing_api.py::RoutingApiTest::test_departure_as_datetime", "tests/test_routing_api.py::RoutingApiTest::test_locationnearmotorway_when_error_no_route_found_occured", "tests/test_routing_api.py::RoutingApiTest::test_publictransport_route_short", "tests/test_routing_api.py::RoutingApiTest::test_departure_as_string", "tests/test_routing_api.py::RoutingApiTest::test_matrix_multiple_destinations", "tests/test_routing_api.py::RoutingApiTest::test_locationnearmotorway_withdefaultmodes_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_pedastrianroute_route_short", "tests/test_routing_api.py::RoutingApiTest::test_truckroute_when_error_invalid_credentials_occured", "tests/test_routing_api.py::RoutingApiTest::test_truckroute_withdefaultmodes_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_publictransport_when_error_invalid_credentials_occured", "tests/test_routing_api.py::RoutingApiTest::test_locationnearmotorway_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_carroute_withdefaultmodes_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_locationnearmotorway_when_error_invalid_credentials_occured", "tests/test_routing_api.py::RoutingApiTest::test_intermediateroute_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_truckroute_route_short", "tests/test_routing_api.py::RoutingApiTest::test_truckroute_when_error_invalid_input_data_occured", "tests/test_routing_api.py::RoutingApiTest::test_truckroute_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_intermediateroute_when_error_invalid_credentials_occured", "tests/test_routing_api.py::RoutingApiTest::test_intermediateroute_when_error_invalid_input_data_occured", "tests/test_routing_api.py::RoutingApiTest::test_carroute_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_locationnearmotorway_when_error_invalid_input_data_occured", "tests/test_routing_api.py::RoutingApiTest::test_matrix_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_intermediateroute_when_error_no_route_found_occured", "tests/test_routing_api.py::RoutingApiTest::test_matrix_multiple_starts", "tests/test_routing_api.py::RoutingApiTest::test_carroute_when_error_no_route_found_occured", "tests/test_routing_api.py::RoutingApiTest::test_bicycleroute_route_short", "tests/test_routing_api.py::RoutingApiTest::test_pedastrianroute_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_intermediateroute_withdefaultmodes_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_carroute_when_error_invalid_credentials_occured", "tests/test_routing_api.py::RoutingApiTest::test_publictransport_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_bicycleroute_withdefaultmodes_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_publictransporttimetable_route_short", "tests/test_routing_api.py::RoutingApiTest::test_pedastrianroute_withdefaultmodes_whensucceed", "tests/test_routing_api.py::RoutingApiTest::test_publictransporttimetable_withdefaultmodes_whensucceed" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }

2020-01-22 08:15:56+00:00

mit

858

abs-tudelft__vhdeps-21

diff --git a/vhdeps/targets/ghdl.py b/vhdeps/targets/ghdl.py index a354670..3e0e2b8 100644 --- a/vhdeps/targets/ghdl.py +++ b/vhdeps/targets/ghdl.py @@ -140,7 +140,7 @@ def _run_test_case(output_file, test_case, vcd_dir, ghdl_elaborate, ghdl_run): exit_code, *_ = run_cmd( output_file, ghdl_elaborate, - '--work=%s' % test_case.lib, + '--work=%s' % test_case.file.lib, test_case.unit) if exit_code != 0: output_file.write('Elaboration for %s failed!\n' % test_case.unit) @@ -151,13 +151,13 @@ def _run_test_case(output_file, test_case, vcd_dir, ghdl_elaborate, ghdl_run): vcd_switch = [] if vcd_dir is not None: vcd_file = '%s/%s.%s.vcd' % ( - vcd_dir, test_case.lib, test_case.unit) + vcd_dir, test_case.file.lib, test_case.unit) vcd_switch.append('--vcd=%s' % vcd_file) exit_code, stdout, *_ = run_cmd( output_file, ghdl_run, - '--work=' + test_case.lib, test_case.unit, - '--stop-time=' + test_case.get_timeout().replace(' ', ''), + '--work=' + test_case.file.lib, test_case.unit, + '--stop-time=' + test_case.file.get_timeout().replace(' ', ''), *vcd_switch) if 'simulation stopped by --stop-time' in stdout: code = 1 diff --git a/vhdeps/targets/shared.py b/vhdeps/targets/shared.py index 6318ff2..7fd85b1 100644 --- a/vhdeps/targets/shared.py +++ b/vhdeps/targets/shared.py @@ -16,6 +16,7 @@ import sys import fnmatch +from collections import namedtuple def add_arguments_for_get_test_cases(parser): """Adds the appropriate command line arguments for the `get_test_cases()` @@ -33,6 +34,8 @@ def add_arguments_for_get_test_cases(parser): 'partial match. If no patterns are specified, the matcher defaults to ' 'a single \'*_tc\' pattern.') +TestCase = namedtuple('TestCase', ('file', 'unit')) + def get_test_cases(vhd_list, pattern=None, **_): """Filters the toplevel entities in `vhd_list` using the given pattern list, returning the resulting list.""" @@ -40,25 +43,21 @@ def get_test_cases(vhd_list, pattern=None, **_): pattern = ['*_tc'] test_cases = [] for top in vhd_list.top: - if top.unit is None: - raise NotImplementedError( - 'vhdeps\' test case runners currently do not support having ' - 'multiple test cases per VHDL file.\nThe offending file is ' - '"%s".' % top.fname) - include = False - for pat in pattern: - target = top.unit - if pat.startswith(':'): - target = top.fname - pat = pat[1:] - invert = False - if pat.startswith('!'): - invert = True - pat = pat[1:] - if fnmatch.fnmatchcase(target, pat): - include = not invert - if include: - test_cases.append(top) + for unit in top.entity_defs: + include = False + for pat in pattern: + target = unit + if pat.startswith(':'): + target = top.fname + pat = pat[1:] + invert = False + if pat.startswith('!'): + invert = True + pat = pat[1:] + if fnmatch.fnmatchcase(target, pat): + include = not invert + if include: + test_cases.append(TestCase(top, unit)) return test_cases def run_cmd(output_file, cmd, *args): diff --git a/vhdeps/targets/vsim.py b/vhdeps/targets/vsim.py index 0e10b0a..a2984e3 100644 --- a/vhdeps/targets/vsim.py +++ b/vhdeps/targets/vsim.py @@ -381,11 +381,11 @@ def _write_tcl(vhd_list, tcl_file, **kwargs): test_cases = get_test_cases(vhd_list, **kwargs) for test_case in test_cases: tcl_file.write('lappend testcases [list %s %s "%s"]\n' % ( - test_case.lib, test_case.unit, test_case.get_timeout())) + test_case.file.lib, test_case.unit, test_case.file.get_timeout())) if len(test_cases) == 1: test_case = test_cases[0] tcl_file.write('simulate %s %s "%s"\n' % ( - test_case.lib, test_case.unit, test_case.get_timeout())) + test_case.file.lib, test_case.unit, test_case.file.get_timeout())) else: tcl_file.write('regression\n')

abs-tudelft/vhdeps

85fb3cccacdfa99132170c6ba8ae58d300b3ebfd

diff --git a/tests/test_ghdl.py b/tests/test_ghdl.py index f37a06d..a02b2a8 100644 --- a/tests/test_ghdl.py +++ b/tests/test_ghdl.py @@ -40,6 +40,16 @@ class TestGhdlSimple(TestCase): self.assertTrue('PASSED test_tc' in out) self.assertTrue('Test suite PASSED' in out) + def test_multiple_per_file(self): + """Test that multiple test cases can exist in one file (GHDL)""" + code, out, _ = run_vhdeps('ghdl', '-i', DIR+'/complex/multi-tc-per-file') + self.assertEqual(code, 0) + self.assertTrue('working!' in out) + self.assertTrue('PASSED foo_tc' in out) + self.assertTrue('PASSED bar_tc' in out) + self.assertFalse('baz' in out) + self.assertTrue('Test suite PASSED' in out) + def test_failure(self): """Test that a single failing test case results in failure (GHDL)""" code, out, _ = run_vhdeps('ghdl', '-i', DIR+'/simple/failure') diff --git a/tests/test_patterns.py b/tests/test_patterns.py index ebe47db..efa34b3 100644 --- a/tests/test_patterns.py +++ b/tests/test_patterns.py @@ -92,9 +92,14 @@ class TestPatterns(TestCase): self.assertFalse(bool(re.search(r'ghdl -r [^\n]*baz', out))) def test_multi_tc_per_file(self): - """Test multiple test cases per file (not supported)""" + """Test multiple test cases per file""" with local.env(PATH=DIR+'/ghdl/fake-ghdl:' + local.env['PATH']): - code, _, err = run_vhdeps('ghdl', '-i', DIR+'/complex/multi-tc-per-file') - self.assertEqual(code, 1) - self.assertTrue('NotImplementedError: vhdeps\' test case runners currently do ' - 'not support having multiple test cases per VHDL file.' in err) + code, out, _ = run_vhdeps('ghdl', '-i', DIR+'/complex/multi-tc-per-file') + self.assertEqual(code, 0) + self.assertTrue(bool(re.search(r'ghdl -a [^\n]*test_tc.vhd', out))) + self.assertTrue(bool(re.search(r'ghdl -e [^\n]*foo_tc', out))) + self.assertTrue(bool(re.search(r'ghdl -e [^\n]*bar_tc', out))) + self.assertFalse(bool(re.search(r'ghdl -e [^\n]*baz', out))) + self.assertTrue(bool(re.search(r'ghdl -r [^\n]*foo_tc', out))) + self.assertTrue(bool(re.search(r'ghdl -r [^\n]*bar_tc', out))) + self.assertFalse(bool(re.search(r'ghdl -r [^\n]*baz', out))) diff --git a/tests/test_vsim.py b/tests/test_vsim.py index 2ab1e48..3228735 100644 --- a/tests/test_vsim.py +++ b/tests/test_vsim.py @@ -27,6 +27,12 @@ class TestVsimReal(TestCase): self.assertEqual(code, 0) self.assertTrue('working!' in out) + def test_multiple_per_file(self): + """Test running vsim on a file with multiple test cases""" + code, out, _ = run_vhdeps('ghdl', '-i', DIR+'/complex/multi-tc-per-file') + self.assertEqual(code, 0) + self.assertTrue('working!' in out) + def test_failure(self): """Test running vsim on a single failing test case""" code, out, _ = run_vhdeps('vsim', '-i', DIR+'/simple/failure')

GHDL and vsim backends cannot handle multiple test cases in one file See title. Individual test cases are represented as `VhdFile` objects everywhere in these backends, making use of the `VhdFile.unit` attribute, which can be `None` when multiple are defined per file. This may be fixable by representing the test cases as two-tuples of the library and entity name.

0.0

85fb3cccacdfa99132170c6ba8ae58d300b3ebfd

[ "tests/test_patterns.py::TestPatterns::test_multi_tc_per_file" ]

[ "tests/test_ghdl.py::TestGhdlSpecific::test_analyze_error", "tests/test_ghdl.py::TestGhdlSpecific::test_elaborate_error", "tests/test_ghdl.py::TestGhdlSpecific::test_multi_version", "tests/test_ghdl.py::TestGhdlSpecific::test_no_ghdl", "tests/test_ghdl.py::TestGhdlSpecific::test_no_plumbum", "tests/test_ghdl.py::TestGhdlSpecific::test_no_wc", "tests/test_ghdl.py::TestGhdlSpecific::test_unknown_version", "tests/test_patterns.py::TestPatterns::test_negative_filename", "tests/test_patterns.py::TestPatterns::test_negative_name", "tests/test_patterns.py::TestPatterns::test_no_patterns", "tests/test_patterns.py::TestPatterns::test_positive_filename", "tests/test_patterns.py::TestPatterns::test_positive_name", "tests/test_vsim.py::TestVsimMocked::test_batch_no_tempdir", "tests/test_vsim.py::TestVsimMocked::test_gui_no_tempdir", "tests/test_vsim.py::TestVsimMocked::test_gui_tempdir", "tests/test_vsim.py::TestVsimMocked::test_no_plumbum", "tests/test_vsim.py::TestVsimMocked::test_no_vsim", "tests/test_vsim.py::TestVsimMocked::test_tcl_multi", "tests/test_vsim.py::TestVsimMocked::test_tcl_single", "tests/test_vsim.py::TestVsimMocked::test_tcl_to_file", "tests/test_vsim.py::TestVsimMocked::test_tcl_versions", "tests/test_vsim.py::TestVsimMocked::test_unsupported_version" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2019-07-12 09:11:14+00:00

apache-2.0

859

abs-tudelft__vhdeps-22

diff --git a/vhdeps/targets/ghdl.py b/vhdeps/targets/ghdl.py index 3e0e2b8..ff426a1 100644 --- a/vhdeps/targets/ghdl.py +++ b/vhdeps/targets/ghdl.py @@ -81,7 +81,22 @@ def add_arguments(parser): 'regardless of whether it passed or not. If there are multiple test ' 'cases, gtkwave is launched for the first failure.') -def _get_ghdl_cmds(vhd_list, ieee='synopsys', no_debug=False, coverage=None, **_): + parser.add_argument( + '-W', action='append', metavar='#{#},<options>', dest='extra_args', + # It'd be great to use [] here ^^^ but Python devs managed to + # sufficiently bork argparse's internals to make that break before + # Python 3.8. Since it's completely asenine to require 3.8 for + # something like this, {} will have to do. + help='Pass comma-separated options to the command specified by #. The ' + 'first # can be \'a\' for the analysis command, \'e\' for the ' + 'elaboration command, and \'r\' for the run command. If a second ' + 'character is specified, <options> are chained to a \'-W#,<options>\' ' + 'option for the command specified by the first letter. For instance, ' + '\'-Wac,-O3\' passes -O3 to the GCC compiler during the analysis ' + 'phase.') + +def _get_ghdl_cmds(vhd_list, ieee='synopsys', no_debug=False, + coverage=None, extra_args=None, **_): """Returns a three-tuple of the analyze, elaborate, and run commands for GHDL in plumbum form.""" @@ -130,6 +145,25 @@ def _get_ghdl_cmds(vhd_list, ieee='synopsys', no_debug=False, coverage=None, **_ ghdl_analyze = ghdl_analyze['-Wc,-fprofile-arcs', '-Wc,-ftest-coverage', '-Wc,-O3'] ghdl_elaborate = ghdl_elaborate['-Wl,-lgcov'] + # Add user-specified extra arguments. + if extra_args: + for extra_arg in extra_args: + if ',' not in extra_arg: + raise ValueError('invalid value for -W') + target, *args = extra_arg.split(',') + if len(target) not in (1, 2): + raise ValueError('invalid value for -W') + if len(target) == 2: + args = ['-W%s,%s' % (target[1], ','.join(args))] + if target[0] == 'a': + ghdl_analyze = ghdl_analyze[args] + elif target[0] == 'e': + ghdl_elaborate = ghdl_elaborate[args] + elif target[0] == 'r': + ghdl_run = ghdl_run[args] + else: + raise ValueError('invalid value for -W') + return ghdl_analyze, ghdl_elaborate, ghdl_run def _run_test_case(output_file, test_case, vcd_dir, ghdl_elaborate, ghdl_run):

abs-tudelft/vhdeps

f2b55a77340e99d13e1adea753c63d10f2b06d79

diff --git a/tests/test_ghdl.py b/tests/test_ghdl.py index a02b2a8..9e16da5 100644 --- a/tests/test_ghdl.py +++ b/tests/test_ghdl.py @@ -2,6 +2,7 @@ from unittest import TestCase, skipIf from unittest.mock import patch +import re import os import tempfile from plumbum import local @@ -254,6 +255,22 @@ class TestGhdlSpecific(TestCase): code, _, _ = run_vhdeps('ghdl', '-i', DIR+'/simple/multiple-ok', '-j') self.assertEqual(code, 1) + def test_extra_options(self): + """Test the -W option for GHDL""" + with local.env(PATH=DIR+'/ghdl/fake-ghdl:' + local.env['PATH']): + self.assertNotEqual(run_vhdeps('ghdl', '-i', DIR+'/simple/all-good', '-W'), 0) + self.assertNotEqual(run_vhdeps('ghdl', '-i', DIR+'/simple/all-good', '-Wx'), 0) + self.assertNotEqual(run_vhdeps('ghdl', '-i', DIR+'/simple/all-good', '-W,x'), 0) + self.assertNotEqual(run_vhdeps('ghdl', '-i', DIR+'/simple/all-good', '-Wx,x'), 0) + code, out, _ = run_vhdeps( + 'ghdl', '-i', DIR+'/simple/all-good', + '-Wa,a,na,lyze', '-We,e,la,bo,rate', '-Wr,run', '-Wrx,a,b,c') + self.assertEqual(code, 0) + self.assertTrue(bool(re.search(r'ghdl -a [^\n]* a na lyze', out))) + self.assertTrue(bool(re.search(r'ghdl -e [^\n]* e la bo rate', out))) + self.assertTrue(bool(re.search(r'ghdl -r [^\n]* run', out))) + self.assertTrue(bool(re.search(r'ghdl -r [^\n]* -Wx,a,b,c', out))) + @skipIf( not coverage_supported(),

Passing arbitrary arguments to GHDL Sometimes one might want to pass some extra arguments to GHDL, especially with the GCC backend to pass additional compiler flags. There is currently no command-line syntax for this.

0.0

f2b55a77340e99d13e1adea753c63d10f2b06d79

[ "tests/test_ghdl.py::TestGhdlSpecific::test_extra_options" ]

[ "tests/test_ghdl.py::TestGhdlSpecific::test_analyze_error", "tests/test_ghdl.py::TestGhdlSpecific::test_elaborate_error", "tests/test_ghdl.py::TestGhdlSpecific::test_multi_version", "tests/test_ghdl.py::TestGhdlSpecific::test_no_ghdl", "tests/test_ghdl.py::TestGhdlSpecific::test_no_plumbum", "tests/test_ghdl.py::TestGhdlSpecific::test_no_wc", "tests/test_ghdl.py::TestGhdlSpecific::test_unknown_version" ]

{ "failed_lite_validators": [ "has_short_problem_statement" ], "has_test_patch": true, "is_lite": false }

2019-07-12 14:41:55+00:00

apache-2.0

860

absent1706__sqlalchemy-mixins-108

diff --git a/sqlalchemy_mixins/inspection.py b/sqlalchemy_mixins/inspection.py index 41d1ea6..bd2584e 100644 --- a/sqlalchemy_mixins/inspection.py +++ b/sqlalchemy_mixins/inspection.py @@ -5,12 +5,7 @@ from sqlalchemy.orm import RelationshipProperty, DeclarativeBase from .utils import classproperty -class Base(DeclarativeBase): - __abstract__ = True - - -class InspectionMixin(Base): - __abstract__ = True +class InspectionMixin: @classproperty def columns(cls): diff --git a/sqlalchemy_mixins/inspection.pyi b/sqlalchemy_mixins/inspection.pyi index ebc9da1..09582d8 100644 --- a/sqlalchemy_mixins/inspection.pyi +++ b/sqlalchemy_mixins/inspection.pyi @@ -1,18 +1,16 @@ from typing import List, Protocol, Dict from sqlalchemy.ext.hybrid import hybrid_method -from sqlalchemy.orm import Mapper, DeclarativeBase +from sqlalchemy.orm import Mapper from sqlalchemy.orm.interfaces import MapperProperty from sqlalchemy_mixins.utils import classproperty -class Base(DeclarativeBase): - __abstract__ = True class MappingProtocol(Protocol): __mapper__: Mapper -class InspectionMixin(Base): +class InspectionMixin: @classproperty def columns(cls) -> List[str]: ...

absent1706/sqlalchemy-mixins

4d4e5d575a3b8b3d72ee12b67b17741579ef26c1

diff --git a/sqlalchemy_mixins/tests/test_activerecord.py b/sqlalchemy_mixins/tests/test_activerecord.py index 901ac73..8284b2a 100644 --- a/sqlalchemy_mixins/tests/test_activerecord.py +++ b/sqlalchemy_mixins/tests/test_activerecord.py @@ -3,13 +3,16 @@ import unittest import sqlalchemy as sa from sqlalchemy import create_engine from sqlalchemy.ext.hybrid import hybrid_property -from sqlalchemy.orm import Query, Session, DeclarativeBase +from sqlalchemy.orm import Query, Session, DeclarativeBase, declarative_base from sqlalchemy_mixins import ActiveRecordMixin from sqlalchemy_mixins.activerecord import ModelNotFoundError class Base(DeclarativeBase): __abstract__ = True + +AlternativeBase = declarative_base() + engine = create_engine('sqlite:///:memory:', echo=False) sess = Session(engine) # sess = scoped_session(sessionmaker(bind=engine)) @@ -20,6 +23,9 @@ class BaseModel(Base, ActiveRecordMixin): pass +class BaseModelAlternative(AlternativeBase, ActiveRecordMixin): + __abstract__ = True + class User(BaseModel): __tablename__ = 'user' __repr_attrs__ = ['name'] @@ -29,6 +35,13 @@ class User(BaseModel): posts_viewonly = sa.orm.relationship('Post', viewonly=True) +class UserAlternative(BaseModelAlternative): + __tablename__ = 'user_alt' + __repr_attrs__ = ['name'] + id = sa.Column(sa.Integer, primary_key=True) + name = sa.Column(sa.String) + + class Post(BaseModel): __tablename__ = 'post' id = sa.Column(sa.Integer, primary_key=True) @@ -204,5 +217,21 @@ class TestActiveRecord(unittest.TestCase): _ = User.find_or_fail(123456789) +class TestActiveRecordAlternative(unittest.TestCase): + def setUp(self): + sess.rollback() + + BaseModelAlternative.set_session(None) + AlternativeBase.metadata.drop_all(engine) + AlternativeBase.metadata.create_all(engine) + + BaseModelAlternative.set_session(sess) + + def test_create(self): + u1 = UserAlternative.create(name='Bill u1') + self.assertEqual(u1, sess.query(UserAlternative).first()) + + + if __name__ == '__main__': # pragma: no cover unittest.main()

sqlalchemy.exc.ArgumentError: Class 'MyClass' already has a primary mapper defined. I have a project with SQLAlchemy 1.4 and sqlalchemy-mixins 1.5.3. I have upgraded SQLAlchemy to 2.0 and made the code work and passes the tests. Then, I tried to upgrade sqlalchemy-mixins to 2.0.3 but I get the error of the title. ``` File "/lib/MyClass.py", line 12, in <module> class MyClass(MyBaseClass): File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/decl_api.py", line 195, in __init__ _as_declarative(reg, cls, dict_) File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/decl_base.py", line 247, in _as_declarative return _MapperConfig.setup_mapping(registry, cls, dict_, None, {}) File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/decl_base.py", line 328, in setup_mapping return _ClassScanMapperConfig( File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/decl_base.py", line 520, in __init__ super().__init__(registry, cls_, mapper_kw) File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/decl_base.py", line 344, in __init__ instrumentation.register_class( File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/instrumentation.py", line 684, in register_class manager._update_state( File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/instrumentation.py", line 209, in _update_state registry._add_manager(self) File "/venv38/lib/python3.8/site-packages/sqlalchemy/orm/decl_api.py", line 1380, in _add_manager raise exc.ArgumentError( sqlalchemy.exc.ArgumentError: Class '<class 'lib.MyClass'>' already has a primary mapper defined. ``` MyBaseClass is defined as: ```python class MyBaseClass(AnotherBaseClass): __abstract__ = True #SOME CODE class AnotherBaseClass(Base, AllFeaturesMixin): __abstract__ = True #SOME OTHER CODE ``` Any idea of what may be happening or how to troubleshoot this?

0.0

4d4e5d575a3b8b3d72ee12b67b17741579ef26c1

[ "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_all", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_create", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_delete", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_destroy", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_fill_and_save", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_fill_wrong_attribute", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_find", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_find_or_fail", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_first", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_settable_attributes", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_update", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecordAlternative::test_create" ]

[]

{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2023-07-25 20:54:25+00:00

mit

861

absent1706__sqlalchemy-mixins-110

diff --git a/sqlalchemy_mixins/activerecord.py b/sqlalchemy_mixins/activerecord.py index 7b082f1..122a60d 100644 --- a/sqlalchemy_mixins/activerecord.py +++ b/sqlalchemy_mixins/activerecord.py @@ -23,50 +23,56 @@ class ActiveRecordMixin(InspectionMixin, SessionMixin): return self - def save(self): + def save(self, commit=True): """Saves the updated model to the current entity db. + :param commit: where to commit the transaction """ - try: - self.session.add(self) - self.session.commit() - return self - except: - self.session.rollback() - raise + self.session.add(self) + if commit: + self._commit_or_fail() + return self @classmethod - def create(cls, **kwargs): + def create(cls, commit=True, **kwargs): """Create and persist a new record for the model + :param commit: where to commit the transaction :param kwargs: attributes for the record :return: the new model instance """ - return cls().fill(**kwargs).save() + return cls().fill(**kwargs).save(commit=commit) - def update(self, **kwargs): + def update(self, commit=True, **kwargs): """Same as :meth:`fill` method but persists changes to database. + :param commit: where to commit the transaction """ - return self.fill(**kwargs).save() + return self.fill(**kwargs).save(commit=commit) - def delete(self): + def delete(self, commit=True): """Removes the model from the current entity session and mark for deletion. + :param commit: where to commit the transaction """ + self.session.delete(self) + if commit: + self._commit_or_fail() + + def _commit_or_fail(self): try: - self.session.delete(self) self.session.commit() except: self.session.rollback() raise @classmethod - def destroy(cls, *ids): + def destroy(cls, *ids, commit=True): """Delete the records with the given ids :type ids: list :param ids: primary key ids of records + :param commit: where to commit the transaction """ for pk in ids: obj = cls.find(pk) if obj: - obj.delete() + obj.delete(commit=commit) cls.session.flush() @classmethod

absent1706/sqlalchemy-mixins

cbd35a6ac4d1ae641b08b5542fa13de22c2b74fb

diff --git a/sqlalchemy_mixins/tests/test_activerecord.py b/sqlalchemy_mixins/tests/test_activerecord.py index 8284b2a..1f8b0df 100644 --- a/sqlalchemy_mixins/tests/test_activerecord.py +++ b/sqlalchemy_mixins/tests/test_activerecord.py @@ -1,5 +1,6 @@ import unittest +import sqlalchemy import sqlalchemy as sa from sqlalchemy import create_engine from sqlalchemy.ext.hybrid import hybrid_property @@ -115,6 +116,30 @@ class TestActiveRecord(unittest.TestCase): self.assertEqual(p11, sess.query(Post).first()) self.assertEqual(p11.archived, True) + def test_save_commits(self): + with self.assertRaises(sqlalchemy.exc.InvalidRequestError): + with sess.begin(): + u1 = User() + u1.fill(name='Bill u1') + u1.save() + u2 = User() + u2.fill(name='Bill u2') + u2.save() + self.assertEqual([u1, u2], sess.query(User).order_by(User.id.asc()).all()) + # The first user is saved even when the block raises a Exception + self.assertEqual([u1], sess.query(User).order_by(User.id.asc()).all()) + + def test_save_do_not_commit(self): + with sess.begin(): + u1 = User() + u1.fill(name='Bill u1') + u1.save(commit=False) + u2 = User() + u2.fill(name='Bill u2') + u2.save(commit=False) + + self.assertEqual([u1,u2], sess.query(User).order_by(User.id.asc()).all()) + def test_create(self): u1 = User.create(name='Bill u1') self.assertEqual(u1, sess.query(User).first()) @@ -158,6 +183,16 @@ class TestActiveRecord(unittest.TestCase): self.assertEqual(sess.query(Post).get(11).public, True) self.assertEqual(sess.query(Post).get(11).user, u2) + def test_update_no_commit(self): + u1 = User(name='Bill', id=1) + u1.save() + u1.update(name='Joe', commit=False) + self.assertEqual('Joe', sess.query(User).where(User.id==1).first().name) + sess.rollback() + self.assertEqual('Bill', sess.query(User).where(User.id==1).first().name) + + + def test_fill_wrong_attribute(self): u1 = User(name='Bill u1') sess.add(u1) @@ -179,6 +214,15 @@ class TestActiveRecord(unittest.TestCase): u1.delete() self.assertEqual(sess.query(User).get(1), None) + def test_delete_without_commit(self): + u1 = User() + u1.save() + u1.delete(commit=False) + self.assertIsNone(sess.query(User).one_or_none()) + sess.rollback() + self.assertIsNotNone(sess.query(User).one_or_none()) + + def test_destroy(self): u1, u2, p11, p12, p13 = self._seed() @@ -186,6 +230,16 @@ class TestActiveRecord(unittest.TestCase): Post.destroy(11, 12) self.assertEqual(set(sess.query(Post).all()), {p13}) + + def test_destroy_no_commit(self): + u1, u2, p11, p12, p13 = self._seed() + sess.commit() + self.assertEqual(set(sess.query(Post).order_by(Post.id).all()), {p11, p12, p13}) + Post.destroy(11, 12, commit=False) + self.assertEqual(set(sess.query(Post).order_by(Post.id).all()), {p13}) + sess.rollback() + self.assertEqual(set(sess.query(Post).order_by(Post.id).all()), {p11, p12, p13}) + def test_all(self): u1, u2, p11, p12, p13 = self._seed() @@ -231,6 +285,12 @@ class TestActiveRecordAlternative(unittest.TestCase): u1 = UserAlternative.create(name='Bill u1') self.assertEqual(u1, sess.query(UserAlternative).first()) + def test_create_no_commit(self): + u1 = UserAlternative.create(name='Bill u1', commit=False) + self.assertEqual(u1, sess.query(UserAlternative).first()) + sess.rollback() + self.assertIsNone(sess.query(UserAlternative).one_or_none()) + if __name__ == '__main__': # pragma: no cover

save from Activerecord can commit external transactions I have some code in a transaction: ```python with session.begin(): an_object.save() another_object.save() ``` both objects have the ActiveRecordMixin. That code used to work, and even after going to sqlalchemy 2, it worked. But now with sqlalchemy-mixins 2.0.3, the save method commits the transaction, even when it wasn't the save method who opened it and that code is broken. I was thinking if it makes sense to check whether there is an active transaction an in that case don't commit. Something like this (of course more tidy): ``` python def save(self): """Saves the updated model to the current entity db. """ # If there is an active transaction, we are not responsible for commit or rollback. if self.session.get_transaction(): self.session.add(self) self.session.flush() return self try: self.session.add(self) self.session.commit() return self except: self.session.rollback() raise ``` I realized the same happens with delete

0.0

cbd35a6ac4d1ae641b08b5542fa13de22c2b74fb

[ "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_delete_without_commit", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_destroy_no_commit", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_save_do_not_commit", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_update_no_commit", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecordAlternative::test_create_no_commit" ]

[ "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_all", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_create", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_delete", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_destroy", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_fill_and_save", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_fill_wrong_attribute", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_find", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_find_or_fail", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_first", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_save_commits", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_settable_attributes", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecord::test_update", "sqlalchemy_mixins/tests/test_activerecord.py::TestActiveRecordAlternative::test_create" ]

{ "failed_lite_validators": [ "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }

2023-07-31 13:01:12+00:00

mit

862

aburrell__ocbpy-111

diff --git a/Changelog.rst b/Changelog.rst index 72966f5..30b8cf1 100644 --- a/Changelog.rst +++ b/Changelog.rst @@ -21,6 +21,7 @@ Summary of all changes made since the first stable release * ENH: Added function to select data along a satellite track * ENH: Changed attributes in VectorData into properties to ensure expected behaviour if altering the class data after initialisation +* ENH: Added IMAGE SI12, SI13, and WIC DMSP corrections to `harmonic` * MAINT: Removed support for Python 2.7, 3.5, and 3.6; added support for 3.10 * MAINT: Improved PEP8 compliance * MAINT: Updated pysat routines to v3.0.0 standards diff --git a/docs/citing.rst b/docs/citing.rst index 9a60f6a..f0da9fd 100644 --- a/docs/citing.rst +++ b/docs/citing.rst @@ -42,8 +42,8 @@ which may also be cited if a description of the package is desired. IMAGE FUV Boundaries -------------------- -Please cite both the papers discussing both the instrument and the boundary -retrieval method. +Please cite both the papers discussing the instrument and the appropriate +boundary retrieval method. * **SI12/SI13**: Mende, S., et al. Space Science Reviews (2000) 91: 287-318. http://doi.org/10.1023/A:1005292301251. @@ -53,6 +53,8 @@ retrieval method. high‐latitude ionospheric climatologies and empirical models, J. Geophys. Res. Space Physics, 122, 932–947, http://doi.org/10.1002/2016JA023235. +* **OCB**: Chisham, G. et al. (2022) Ionospheric Boundaries Derived from Auroral + Images. In Prep. * **OCB**: Chisham, G. (2017) Auroral Boundary Derived from IMAGE Satellite Mission Data (May 2000 - Oct 2002), Version 1.1, Polar Data Centre, Natural Environment Research Council, UK. diff --git a/docs/ocb_datasets.rst b/docs/ocb_datasets.rst index 56fdffb..08138a2 100644 --- a/docs/ocb_datasets.rst +++ b/docs/ocb_datasets.rst @@ -19,16 +19,24 @@ provided in the :py:mod:`ocbpy.boundaries.files` sub-module. IMAGE ----- -Data from three auroral instruments provide northern hemisphere OCB and EAB -locations for 3 May 2000 02:41:43 UT - 31 Oct 2002 20:05:16, though not all of -the times included in these files contain high-quality estimations of the -boundary locations. Recommended selection criteria are included as defaults in -the :py:class:`~ocbpy.OCBoundary` class. There are also boundary -files that combine the information from all instruments to obtain the OCB and -EAB. You can read more about the OCB determination, EAB determination, this -selection criteria, and the three auroral instruments (IMAGE Wideband Imaging -Camera (WIC) and FUV Spectrographic Imagers SI12 and SI13) in the articles -listed in :ref:`cite-image`. +Data from three auroral instruments provide northern hemisphere poleward auroral +boundary (PAB) and EAB locations for 3 May 2000 02:41:43 UT - 31 Oct 2002 +20:05:16, though not all of the times included in these files contain +high-quality estimations of the boundary locations. Recommended selection +criteria are included as defaults in the :py:class:`~ocbpy.OCBoundary` class. +There are also boundary files that combine the information from all instruments +to obtain the OCB and EAB. These combined files are the default boundaries for +the IMAGE time period. You can read more about the OCB determination, EAB +determination, this selection criteria, and the three auroral instruments +(IMAGE Wideband Imaging Camera (WIC) and FUV Spectrographic Imagers SI12 and +SI13) in the articles listed in :ref:`cite-image`. + +The most recent corrects for each instrument that add the DMSP particle +precipitation corrections to the PAB and EAB locations are included in +:py:mod:`ocbpy.ocb_correction`. These corrections should be applied to the +data used to obtain the circle fits included in the instrument files, not the +circle fits themselves. These data sets may be obtained from the British +Antarctic Survey. .. _bound-data-ampere: diff --git a/ocbpy/boundaries/README.md b/ocbpy/boundaries/README.md index ad99f4b..9d42e78 100644 --- a/ocbpy/boundaries/README.md +++ b/ocbpy/boundaries/README.md @@ -1,8 +1,8 @@ This directory contains files with Open Closed field line Boundaries obtained from different instruments -IMAGE (si12/si13/wic) File Format ---------------------------------- +IMAGE (image/si12/si13/wic) File Format +--------------------------------------- YR, SOY, NB, PHICENT, RCENT, R, A, R_ERR, R_MERIT YR : Year @@ -20,7 +20,9 @@ R_MERIT : Radial distance from the most typical pole location in degrees There are certain ranges for NB, RCENT, and R that you shouldn’t use that can be found (and explained) in Chisham (2017), doi:10.1002/2016JA023235. These ranges are the defaults in OCBoundary.get_next_good_ocb_ind. When using these -boundaries, remember to cite Chisham (2017). +boundaries, remember to cite Chisham (2017). From ocbpy version 0.3.0 onward, +the SI12, SI13, and WIC files contain uncorrected auroral boundary fits, while +the IMAGE file contains DMSP corrected average boundaries for the OCB and EAB. AMPERE (amp) File Format ------------------------ diff --git a/ocbpy/ocb_correction.py b/ocbpy/ocb_correction.py index ba7cf8a..b73a0e6 100644 --- a/ocbpy/ocb_correction.py +++ b/ocbpy/ocb_correction.py @@ -9,6 +9,8 @@ References ---------- .. [4] Burrell, A. G. et al.: AMPERE Polar Cap Boundaries, Ann. Geophys., 38, 481-490, doi:10.5194/angeo-38-481-2020, 2020. +.. [6] Chisham, G. et al.: Ionospheric Boundaries Derived from Auroral Images, + in prep, 2022. """ @@ -18,7 +20,7 @@ from ocbpy.ocb_time import hr2rad def circular(mlt, r_add=0.0): - """Return a circular boundary correction + """Return a circular boundary correction. Parameters ---------- @@ -42,7 +44,7 @@ def circular(mlt, r_add=0.0): def elliptical(mlt, instrument='ampere', method='median'): - """Return the results of an elliptical correction to the data boundary [4]_ + """Return the results of an elliptical correction to the data boundary. Parameters ---------- @@ -59,6 +61,10 @@ def elliptical(mlt, instrument='ampere', method='median'): r_corr : float or array-like Radius correction in degrees at this MLT + References + ---------- + Prefered AMPERE boundary correction validated in [4]_. + """ if instrument.lower() != 'ampere': @@ -81,7 +87,7 @@ def elliptical(mlt, instrument='ampere', method='median'): def harmonic(mlt, instrument='ampere', method='median'): - """Return the results of a harmonic fit correction to the data boundary [4]_ + """Return the results of a harmonic fit correction to the data boundary. Parameters ---------- @@ -91,38 +97,67 @@ def harmonic(mlt, instrument='ampere', method='median'): Data set's instrument name (default='ampere') method : str Method used to determine coefficients; accepts 'median' or - 'gaussian' (default='median') + 'gaussian' when `instrument` is 'ampere'. Otherwise, accepts 'eab' or + 'ocb'. (default='median') Returns ------- r_corr : float or array-like Radius correction in degrees at this MLT + References + ---------- + AMPERE boundaries obtained from [4]_. IMAGE boundaries obtained from [6]_. + """ - if instrument.lower() != 'ampere': + # Define the harmonic coefficients for each instrument and method/location + coeff = {'ampere': {'median': [3.31000535, -0.5452934, -1.24389141, + 2.42619653, -0.66677988, -1.03467488, + -0.30763009, 0.52426756, 0.04359299, + 0.60201848, 0.50618522, 1.04360529, + 0.25186405], + 'gaussian': [3.80100827, 0.98555723, -3.43760943, + 1.85084271, -0.36730751, -0.81975654, + -1.02823832, 1.30637288, -0.53599218, + 0.40380183, -1.22462708, -1.2733629, + -0.62743381]}, + 'si12': {'ocb': [0.0405, -1.5078, 1.0, 0.5095, 1.0, 0.9371, 1.0, + 0.0708, 1.0, 0.0, 1.0, 0.0, 1.0], + 'eab': [-0.1447, -1.9779, 1.0, 2.6799, 1.0, 0.5778, 1.0, + -1.2297, 1.0, 0.0, 1.0, 0.0, 1.0]}, + 'si13': {'ocb': [0.5797, -0.6837, 1.0, -0.5020, 1.0, 0.2971, 1.0, + -0.4173, 1.0, 0.0, 1.0, 0.0, 1.0], + 'eab': [0.2500, -2.9931, 1.0, 0.8818, 1.0, 0.8511, 1.0, + -0.6300, 1.0, 0.0, 1.0, 0.0, 1.0]}, + 'wic': {'ocb': [1.0298, -1.1249, 1.0, -0.7380, 1.0, 0.1838, 1.0, + -0.6171, 1.0, 0.0, 1.0, 0.0, 1.0], + 'eab': [-0.4935, -2.1186, 1.0, 0.3188, 1.0, 0.5749, 1.0, + -0.3118, 1.0, 0.0, 1.0, 0.0, 1.0]}} + + # Check the inputs + inst = instrument.lower() + if inst not in coeff.keys(): raise ValueError("no harmonic correction for {:}".format(instrument)) method = method.lower() - coeff = {'median': [3.31000535, -0.5452934, -1.24389141, 2.42619653, - -0.66677988, -1.03467488, -0.30763009, 0.52426756, - 0.04359299, 0.60201848, 0.50618522, 1.04360529, - 0.25186405], - 'gaussian': [3.80100827, 0.98555723, -3.43760943, 1.85084271, - -0.36730751, -0.81975654, -1.02823832, 1.30637288, - -0.53599218, 0.40380183, -1.22462708, -1.2733629, - -0.62743381]} - - if method not in coeff.keys(): - raise ValueError("unknown coefficient computation method") + if method not in coeff[inst].keys(): + raise ValueError("".join(["unknown coefficient computation method, ", + "expects one of: {:}".format( + coeff[inst].keys())])) + # Calculate the offset rad_mlt = hr2rad(mlt) - r_corr = coeff[method][0] \ - + coeff[method][1] * np.cos(rad_mlt + coeff[method][2]) \ - + coeff[method][3] * np.sin(rad_mlt + coeff[method][4]) \ - + coeff[method][5] * np.cos(2.0 * (rad_mlt + coeff[method][6])) \ - + coeff[method][7] * np.sin(2.0 * (rad_mlt + coeff[method][8])) \ - + coeff[method][9] * np.cos(3.0 * (rad_mlt + coeff[method][10])) \ - + coeff[method][11] * np.sin(3.0 * (rad_mlt + coeff[method][12])) + r_corr = coeff[inst][method][0] \ + + coeff[inst][method][1] * np.cos(rad_mlt + coeff[inst][method][2]) \ + + coeff[inst][method][3] * np.sin(rad_mlt + coeff[inst][method][4]) \ + + coeff[inst][method][5] * np.cos(2.0 * ( + rad_mlt + coeff[inst][method][6])) \ + + coeff[inst][method][7] * np.sin(2.0 * ( + rad_mlt + coeff[inst][method][8])) \ + + coeff[inst][method][9] * np.cos(3.0 * ( + rad_mlt + coeff[inst][method][10])) \ + + coeff[inst][method][11] * np.sin(3.0 * ( + rad_mlt + coeff[inst][method][12])) # Because this is a poleward shift, return the negative of the correction return -r_corr

aburrell/ocbpy

ce1ee978f2f1f31e8777bed474750dcef493ee31

diff --git a/ocbpy/tests/test_ocb_correction.py b/ocbpy/tests/test_ocb_correction.py index fc2f648..787cc62 100644 --- a/ocbpy/tests/test_ocb_correction.py +++ b/ocbpy/tests/test_ocb_correction.py @@ -3,8 +3,7 @@ # Copyright (C) 2017, AGB & GC # Full license can be found in License.md # ----------------------------------------------------------------------------- -""" Tests the ocboundary class and functions -""" +"""Tests the ocboundary class and functions.""" import numpy as np import unittest @@ -13,38 +12,48 @@ from ocbpy import ocb_correction as ocb_cor class TestOCBCorrectionFailure(unittest.TestCase): + """Unit tests for correction failure evaluations.""" + def setUp(self): - """ Set up the test runs """ + """Set up the test runs.""" self.mlt = 12.0 self.bad_kwarg = 'bad_kwarg' self.functions = {'elliptical': ocb_cor.elliptical, 'harmonic': ocb_cor.harmonic} self.bound = None + return def tearDown(self): - """ Tear down the test runs """ + """Tear down the test runs.""" del self.mlt, self.bad_kwarg, self.functions, self.bound + return def test_instrument_failure(self): - """ Test failure when an unknown instrument is provided """ + """Test failure when an unknown instrument is provided.""" for self.bound in self.functions.keys(): with self.subTest(bound=self.bound): - with self.assertRaises(ValueError): + msg = "no {:s} correction for".format(self.bound) + with self.assertRaisesRegex(ValueError, msg): self.functions[self.bound](self.mlt, instrument=self.bad_kwarg) + return def test_method_failure(self): - """ Test failure when an unknown method is provided """ + """Test failure when an unknown method is provided.""" + msg = "unknown coefficient computation method" for self.bound in self.functions.keys(): with self.subTest(bound=self.bound): - with self.assertRaises(ValueError): + with self.assertRaisesRegex(ValueError, msg): self.functions[self.bound](self.mlt, method=self.bad_kwarg) + return class TestOCBCorrection(unittest.TestCase): + """Unit tests for the boundary correction functions.""" + def setUp(self): - """ Set up test runs """ + """Set up test runs.""" self.functions = {'circular': ocb_cor.circular, 'elliptical': ocb_cor.elliptical, 'harmonic': ocb_cor.harmonic} @@ -56,36 +65,65 @@ class TestOCBCorrection(unittest.TestCase): -3.4392638193624325])} self.gaus_results = {'elliptical': -2.51643691301747, 'harmonic': -2.293294645880221} + self.image_results = {'si12': {'ocb': np.array([0.67103129, + -0.10084541]), + 'eab': np.array([0.31691853, + 2.68970685])}, + 'si13': {'ocb': np.array([0.71521016, + -0.86843608]), + 'eab': np.array([1.55220967, + -0.19812977])}, + 'wic': {'ocb': np.array([0.83660688, + -1.62097642]), + 'eab': np.array([1.89268527, + 0.13983824])}} self.bound = None + return def tearDown(self): - """ Clean up after each test """ + """Clean up after each test.""" del self.mlt, self.functions, self.def_results, self.gaus_results - del self.bound + del self.bound, self.image_results + return def test_default_float(self): - """ Test the boundary functions using a float and function defaults""" + """Test the boundary functions using a float and function defaults.""" for self.bound in self.functions.keys(): with self.subTest(bound=self.bound): self.assertEqual(self.functions[self.bound](self.mlt[0]), self.def_results[self.bound][0]) + return def test_default_arr(self): - """ Test the boundary functions using an array and function defaults""" + """Test the boundary functions using an array and function defaults.""" for self.bound in self.functions.keys(): with self.subTest(bound=self.bound): self.assertTrue(np.all( abs(self.functions[self.bound](self.mlt) - self.def_results[self.bound]) < 1.0e-7)) + return def test_circular_offset(self): - """ Test the circular boundary function with an offset """ + """Test the circular boundary function with an offset.""" self.assertEqual(ocb_cor.circular(self.mlt[0], r_add=1.0), 1.0) + return def test_gauss_method(self): - """ Test the boundary functions using an array and function defaults""" + """Test the boundary functions using an array and function defaults.""" for self.bound in self.gaus_results.keys(): with self.subTest(bound=self.bound): self.assertAlmostEqual( self.functions[self.bound](self.mlt[0], method='gaussian'), self.gaus_results[self.bound]) + return + + def test_image_harmonic(self): + """Test the IMAGE harmonic correction functions.""" + for self.bound in self.image_results.keys(): + for method in self.image_results[self.bound].keys(): + with self.subTest(bound=self.bound, method=method): + self.assertTrue(np.all( + abs(self.functions["harmonic"]( + self.mlt, instrument=self.bound, method=method) + - self.image_results[self.bound][method]) < 1.0e-7)) + return

BUG: individual IMAGE instrument OCBs **Describe the bug** The new individual IMAGE "ocb" files are actually the poleward edge of the auroral oval w/o the DMSP correction. **Expected behavior** A clear explanation of what they are. **To Fix** - [x] Update documentation

0.0

ce1ee978f2f1f31e8777bed474750dcef493ee31

[ "ocbpy/tests/test_ocb_correction.py::TestOCBCorrection::test_image_harmonic" ]

[ "ocbpy/tests/test_ocb_correction.py::TestOCBCorrectionFailure::test_instrument_failure", "ocbpy/tests/test_ocb_correction.py::TestOCBCorrectionFailure::test_method_failure", "ocbpy/tests/test_ocb_correction.py::TestOCBCorrection::test_circular_offset", "ocbpy/tests/test_ocb_correction.py::TestOCBCorrection::test_default_arr", "ocbpy/tests/test_ocb_correction.py::TestOCBCorrection::test_default_float", "ocbpy/tests/test_ocb_correction.py::TestOCBCorrection::test_gauss_method" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }

2022-04-05 19:29:16+00:00

bsd-3-clause

863

achabotl__popthings-4

diff --git a/popthings.py b/popthings.py index eeda9e6..4310e2d 100644 --- a/popthings.py +++ b/popthings.py @@ -24,7 +24,7 @@ what's possible. They would be added to Things as two separate projects. Note under project 1 - Task 1 @due($start + 1w) @$where A note under task 1 - - Task 2 @start($start) + - Task 2 @start($start - 1) - Checklist item under task 2 - Also a checklist item under task 2 Heading 1: @@ -40,9 +40,11 @@ Attributes ---------- """ +from datetime import datetime, timedelta from io import open import json import logging +import operator import re import sys try: @@ -87,6 +89,65 @@ PATTERN_TAG = re.compile(r"""(?:^|\s+)@ # space and @ before tag # space or EOL """, re.VERBOSE) +# Patterns to match dates and dates with day offsets +ISO_DATE_RE = re.compile(r"^\d{4}-\d{2}-\d{2}$") +DATE_OFFSET_RE = re.compile(r""" + (?P<base_date>\d{4}-\d{2}-\d{2}) + \s* + (?P<op>[+-]) + \s* + (?P<offset_count>\d+) + """, re.X) + + +def compute_date(date_str): + """ + Compute new date string given dates with day offsets. + + Parameters + ========== + date_str : string + Text string representing a date. The format must be a standalone date: + 'YYYY-MM-DD', a date with a day offset: 'YYYY-MM-DD + 1' or 'YYYY-MM-DD + - 10'. Other values as just passed through, assuming Things knows how + to handled them, like 'today', 'tomorrow', 'evening', 'next month', + etc. + + Returns + ======= + new_date_str : string + Date where the offset has been added or subtracted from the date. + + """ + date_str = date_str.strip() + + # Simple ISO date + if ISO_DATE_RE.match(date_str): + return date_str + + elif DATE_OFFSET_RE.match(date_str): + # Precompute dates with offsets of days + m = DATE_OFFSET_RE.match(date_str) + if m is None: + raise ValueError(f"Unable to parse date '{date_str}' as 'YYYY-MM-DD+/-offset' date.") + + try: + op = { + '-': operator.sub, + '+': operator.add, + }.get(m.group('op')) + except KeyError: + raise ValueError(f"Unable to parse date {date_str} as YYYY-MM-DD +/- D date. The operator is wrong.") + + count = int(m.group('offset_count')) + date_delta = timedelta(count) + + date = datetime.strptime(m.group("base_date"), '%Y-%m-%d') + + return op(date, date_delta).strftime('%Y-%m-%d') + + return date_str + class TPNode(object): def __init__(self, line, text, indent, type, line_number=None, tags=None): @@ -442,8 +503,8 @@ class _ThingsRichObject(ThingsObject): """ super(_ThingsRichObject, self).__init__(title) self.notes = notes - self.when = when - self.deadline = deadline + self.when = compute_date(when) if when else when + self.deadline = compute_date(deadline) if deadline else deadline if tags is None: tags = [] self.tags = tags

achabotl/popthings

29523615476639f8e844768ef7730258bd7d13ad

diff --git a/tests/test_date_parsing.py b/tests/test_date_parsing.py new file mode 100644 index 0000000..127090a --- /dev/null +++ b/tests/test_date_parsing.py @@ -0,0 +1,33 @@ +from unittest import TestCase +from popthings import compute_date + + +class TestDateParsing(TestCase): + def test_iso_date(self): + """ ISO formatted dates: YYYY-MM-DD.""" + date = "2018-12-31" + self.assertEqual(date, compute_date(date)) + + def test_iso_date_with_space(self): + date = " 2018-12-31 " + self.assertEqual("2018-12-31", compute_date(date)) + + def test_invalid_date(self): + self.assertEqual("31/12/2018", compute_date("31/12/2018")) + + def test_iso_date_with_positive_offset(self): + date = "2018-12-30 + 1" + self.assertEqual("2018-12-31", compute_date(date)) + + def test_iso_date_with_negative_offset(self): + date = "2018-12-30 - 1" + self.assertEqual("2018-12-29", compute_date(date)) + + def test_iso_date_with_negative_large_offset(self): + date = "2018-12-30 - 10" + self.assertEqual("2018-12-20", compute_date(date)) + + def test_other_values(self): + for word in ('today', 'tomorrow', 'evening', 'anytime', 'someday', 'next month'): + with self.subTest(word=word): + self.assertEqual(word, compute_date(word))

Parse dates in popthings instead of Things.app As of Things 3.8, it still parse dates with a `-` as if it was a `+`, e.g., "Today - 1 day" is actually tomorrow… I could write my own, possible with the help of `dateutil`, or consider using [dateparser](https://dateparser.readthedocs.io/en/latest/) by [Scraping Hub](https://blog.scrapinghub.com/2015/11/09/parse-natural-language-dates-with-dateparser).

0.0

29523615476639f8e844768ef7730258bd7d13ad

[ "tests/test_date_parsing.py::TestDateParsing::test_invalid_date", "tests/test_date_parsing.py::TestDateParsing::test_iso_date", "tests/test_date_parsing.py::TestDateParsing::test_iso_date_with_negative_large_offset", "tests/test_date_parsing.py::TestDateParsing::test_iso_date_with_negative_offset", "tests/test_date_parsing.py::TestDateParsing::test_iso_date_with_positive_offset", "tests/test_date_parsing.py::TestDateParsing::test_iso_date_with_space", "tests/test_date_parsing.py::TestDateParsing::test_other_values" ]

[]

{ "failed_lite_validators": [ "has_hyperlinks", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2022-03-25 13:01:13+00:00

mit

864

acorg__dark-matter-569

diff --git a/CHANGELOG.md b/CHANGELOG.md index 3aac224..4781caa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,20 @@ +## 2.0.4 April 29, 2018 + +* Added `--sampleIndexFilename` and `--pathogenIndexFilename` to + `proteins-to-pathogens.py`. These cause the writing of files containing + lines with an integer index, a space, then a sample or pathogen name. + These can be later used to identify the de-duplicated reads files for a + given sample or pathogen name. + +## 2.0.3 April 28, 2018 + +* Added number of identical and positive amino acid matches to BLAST and + DIAMOND hsps. + +## 2.0.2 April 23, 2018 + +* The protein grouper now de-duplicates read by id, not sequence. + ## 2.0.1 April 23, 2018 * Fixed HTML tiny formatting error in `toHTML` method of `ProteinGrouper` diff --git a/bin/proteins-to-pathogens.py b/bin/proteins-to-pathogens.py index 004263a..3a3ce34 100755 --- a/bin/proteins-to-pathogens.py +++ b/bin/proteins-to-pathogens.py @@ -83,6 +83,22 @@ if __name__ == '__main__': help=('An (optional) filename to write a pathogen-sample panel PNG ' 'image to.')) + parser.add_argument( + '--sampleIndexFilename', + help=('An (optional) filename to write a sample index file to. ' + 'Lines in the file will have an integer index, a space, and ' + 'then the sample name. Only produced if --html is used ' + '(because the pathogen-NNN-sample-MMM.fastq are only written ' + 'in that case).')) + + parser.add_argument( + '--pathogenIndexFilename', + help=('An (optional) filename to write a pathogen index file to. ' + 'Lines in the file will have an integer index, a space, and ' + 'then the pathogen name. Only produced if --html is used ' + '(because the pathogen-NNN-sample-MMM.fastq are only written ' + 'in that case).')) + parser.add_argument( '--html', default=False, action='store_true', help='If specified, output HTML instead of plain text.') @@ -123,6 +139,16 @@ if __name__ == '__main__': args = parser.parse_args() + if not args.html: + if args.sampleIndexFilename: + print('It does not make sense to use --sampleIndexFilename ' + 'without also using --html', file=sys.stderr) + sys.exit(1) + if args.pathogenIndexFilename: + print('It does not make sense to use --pathogenIndexFilename ' + 'without also using --html', file=sys.stderr) + sys.exit(1) + if args.proteinFastaFilename: # Flatten lists of lists that we get from using both nargs='+' and # action='append'. We use both because it allows people to use @@ -153,6 +179,8 @@ if __name__ == '__main__': if args.html: print(grouper.toHTML(args.pathogenPanelFilename, minProteinFraction=args.minProteinFraction, - pathogenType=args.pathogenType)) + pathogenType=args.pathogenType, + sampleIndexFilename=args.sampleIndexFilename, + pathogenIndexFilename=args.pathogenIndexFilename)) else: print(grouper.toStr()) diff --git a/dark/__init__.py b/dark/__init__.py index c8923d7..d0bf4db 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -5,4 +5,6 @@ if sys.version_info < (2, 7): # Note that the version string must have the following format, otherwise it # will not be found by the version() function in ../setup.py -__version__ = '2.0.3' +# +# Remember to update ../CHANGELOG.md describing what's new in each version. +__version__ = '2.0.4' diff --git a/dark/proteins.py b/dark/proteins.py index 6a1270f..8e6a850 100644 --- a/dark/proteins.py +++ b/dark/proteins.py @@ -178,6 +178,28 @@ class PathogenSampleFiles(object): sampleIndex = self._samples[sampleName] return self._readsFilenames[(pathogenIndex, sampleIndex)] + def writeSampleIndex(self, fp): + """ + Write a file of sample indices and names, sorted by index. + + @param fp: A file-like object, opened for writing. + """ + print('\n'.join( + '%d %s' % (index, name) for (index, name) in + sorted((index, name) for (name, index) in self._samples.items()) + ), file=fp) + + def writePathogenIndex(self, fp): + """ + Write a file of pathogen indices and names, sorted by index. + + @param fp: A file-like object, opened for writing. + """ + print('\n'.join( + '%d %s' % (index, name) for (index, name) in + sorted((index, name) for (name, index) in self._pathogens.items()) + ), file=fp) + class ProteinGrouper(object): """ @@ -387,7 +409,8 @@ class ProteinGrouper(object): return '\n'.join(result) def toHTML(self, pathogenPanelFilename=None, minProteinFraction=0.0, - pathogenType='viral'): + pathogenType='viral', sampleIndexFilename=None, + pathogenIndexFilename=None): """ Produce an HTML string representation of the pathogen summary. @@ -398,6 +421,12 @@ class ProteinGrouper(object): for that pathogen to be displayed. @param pathogenType: A C{str} giving the type of the pathogen involved, either 'bacterial' or 'viral'. + @param sampleIndexFilename: A C{str} filename to write a sample index + file to. Lines in the file will have an integer index, a space, and + then the sample name. + @param pathogenIndexFilename: A C{str} filename to write a pathogen + index file to. Lines in the file will have an integer index, a + space, and then the pathogen name. @return: An HTML C{str} suitable for printing. """ if pathogenType not in ('bacterial', 'viral'): @@ -411,6 +440,14 @@ class ProteinGrouper(object): if pathogenPanelFilename: self.pathogenPanel(pathogenPanelFilename) + if sampleIndexFilename: + with open(sampleIndexFilename, 'w') as fp: + self.pathogenSampleFiles.writeSampleIndex(fp) + + if pathogenIndexFilename: + with open(pathogenIndexFilename, 'w') as fp: + self.pathogenSampleFiles.writePathogenIndex(fp) + pathogenNames = sorted( pathogenName for pathogenName in self.pathogenNames if self.maxProteinFraction(pathogenName) >= minProteinFraction) @@ -494,7 +531,8 @@ class ProteinGrouper(object): proteinFieldsDescription = [ '', - 'In all bullet point protein lists below, there are eight fields:', + 'In all bullet point protein lists below, there are the following ' + 'fields:', '<ol>', '<li>Coverage fraction.</li>', '<li>Median bit score.</li>',

acorg/dark-matter

bb55d862e66a923688c1f4db4fdfc9467c8210f4

diff --git a/test/test_proteins.py b/test/test_proteins.py index ed8c49f..81bcccb 100644 --- a/test/test_proteins.py +++ b/test/test_proteins.py @@ -917,3 +917,35 @@ class TestPathogenSampleFiles(TestCase): proteins['gi|327410| protein 77']['readLengths']) self.assertEqual((2, 7), proteins['gi|327409| ubiquitin']['readLengths']) + + def testWriteSampleIndex(self): + """ + The writeSampleIndex function must write a file with the expected + content. + """ + pathogenSampleFiles = PathogenSampleFiles(None) + pathogenSampleFiles._samples = { + 'NEO11': 500, + 'NEO33': 24, + 'NEO66': 333, + } + + fp = StringIO() + pathogenSampleFiles.writeSampleIndex(fp) + self.assertEqual('24 NEO33\n333 NEO66\n500 NEO11\n', fp.getvalue()) + + def testWritePathogenIndex(self): + """ + The writePatogenIndex function must write a file with the expected + content. + """ + pathogenSampleFiles = PathogenSampleFiles(None) + pathogenSampleFiles._pathogens = { + 'virus b': 4, + 'virus a': 3, + 'virus c': 9, + } + + fp = StringIO() + pathogenSampleFiles.writePathogenIndex(fp) + self.assertEqual('3 virus a\n4 virus b\n9 virus c\n', fp.getvalue())

The protein grouper should write a plain text index of pathogen index and name Right now after running `proteins-to-pathogens.py` we are left with files with names like `pathogen-219-sample-228.fastq` but there is no simple way to match a pathogen name with its index. That information is in the `index.html` file but should also be in a text file so we can know which file to look in to get reads when we just have a pathogen name (e.g., from a different pipeline run). The `toStr` method could perhaps print it?

0.0

bb55d862e66a923688c1f4db4fdfc9467c8210f4

[ "test/test_proteins.py::TestPathogenSampleFiles::testWritePathogenIndex", "test/test_proteins.py::TestPathogenSampleFiles::testWriteSampleIndex" ]

[ "test/test_proteins.py::TestSplitNames::testNestedBrackets", "test/test_proteins.py::TestSplitNames::testNoBrackets", "test/test_proteins.py::TestSplitNames::testNormalCase", "test/test_proteins.py::TestSplitNames::testTwoSetsOfBrackets", "test/test_proteins.py::TestSplitNames::testWhitespaceStripping", "test/test_proteins.py::TestGetPathogenProteinCounts::testNone", "test/test_proteins.py::TestProteinGrouper::testAssetDir", "test/test_proteins.py::TestProteinGrouper::testDuplicatePathogenProteinSample", "test/test_proteins.py::TestProteinGrouper::testNoAssetDir", "test/test_proteins.py::TestProteinGrouper::testNoFiles", "test/test_proteins.py::TestProteinGrouper::testNoFilesToStr", "test/test_proteins.py::TestProteinGrouper::testNoRegex", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesDifferentPathogens", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesDifferentPathogensTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogen", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogenTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFile", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileFASTQ", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileToStr", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileDifferentPathogens", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileSamePathogen", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testUnknownFormat", "test/test_proteins.py::TestProteinGrouper::testUnknownPathogenType", "test/test_proteins.py::TestPathogenSampleFiles::testUnknownFormat" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2018-04-29 11:55:47+00:00

mit

865

acorg__dark-matter-576

diff --git a/Makefile b/Makefile index 8bf842a..afdcfe8 100644 --- a/Makefile +++ b/Makefile @@ -1,10 +1,10 @@ .PHONY: check, pycodestyle, pyflakes, lint check: - python -m discover -v + env PYTHONPATH=. python -m discover -v tcheck: - trial --rterrors test + env PYTHONPATH=. trial --rterrors test pycodestyle: find . -path './.tox' -prune -o -path './build' -prune -o -path './dist' -prune -o -name '*.py' -print0 | xargs -0 pycodestyle diff --git a/bin/proteins-to-pathogens.py b/bin/proteins-to-pathogens.py index 3a3ce34..726d4a9 100755 --- a/bin/proteins-to-pathogens.py +++ b/bin/proteins-to-pathogens.py @@ -137,6 +137,12 @@ if __name__ == '__main__': 'contain the lengths of all reads that match proteins for a ' 'pathogen.')) + parser.add_argument( + '--assetDir', default='out', + help=('The output directory where noninteractive-alignment-panel.py ' + 'puts its HTML, plots and FASTA or FASTQ files, needed for ' + 'using --html')) + args = parser.parse_args() if not args.html: @@ -162,7 +168,8 @@ if __name__ == '__main__': else: proteinFastaFilenames = None - grouper = ProteinGrouper(sampleNameRegex=args.sampleNameRegex, + grouper = ProteinGrouper(assetDir=args.assetDir, + sampleNameRegex=args.sampleNameRegex, format_=args.format, proteinFastaFilenames=proteinFastaFilenames, saveReadLengths=args.showReadLengths) diff --git a/dark/__init__.py b/dark/__init__.py index 0246a07..6a59296 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.5' +__version__ = '3.0.6' diff --git a/dark/filter.py b/dark/filter.py index 0665ffc..b0daa76 100644 --- a/dark/filter.py +++ b/dark/filter.py @@ -279,6 +279,23 @@ def addFASTAFilteringCommandLineOptions(parser): help=('A file of (1-based) sequence numbers to retain. Numbers must ' 'be one per line.')) + parser.add_argument( + '--idLambda', metavar='LAMBDA-FUNCTION', + help=('A one-argument function taking and returning a read id. ' + 'E.g., --idLambda "lambda id: id.split(\'_\')[0]" or ' + '--idLambda "lambda id: id[:10]". If the function returns None, ' + 'the read will be filtered out.')) + + parser.add_argument( + '--readLambda', metavar='LAMBDA-FUNCTION', + help=('A one-argument function taking and returning a read. ' + 'E.g., --readLambda "lambda r: Read(r.id.split(\'_\')[0], ' + 'r.sequence.strip(\'-\')". Make sure to also modify the quality ' + 'string if you change the length of a FASTQ sequence. If the ' + 'function returns None, the read will be filtered out. The ' + 'function will be passed to eval with the dark.reads classes ' + 'Read, DNARead, AARead, etc. all in scope.')) + # A mutually exclusive group for --keepSites, --keepSitesFile, # --removeSites, and --removeSitesFile. group = parser.add_mutually_exclusive_group() @@ -381,4 +398,5 @@ def parseFASTAFilteringCommandLineOptions(args, reads): randomSubset=args.randomSubset, trueLength=args.trueLength, sampleFraction=args.sampleFraction, sequenceNumbersFile=args.sequenceNumbersFile, + idLambda=args.idLambda, readLambda=args.readLambda, keepSites=keepSites, removeSites=removeSites) diff --git a/dark/proteins.py b/dark/proteins.py index 8e6a850..33e53eb 100644 --- a/dark/proteins.py +++ b/dark/proteins.py @@ -9,19 +9,9 @@ import numpy as np from textwrap import fill from collections import Counter -try: - import matplotlib - if not os.environ.get('DISPLAY'): - # Use non-interactive Agg backend - matplotlib.use('Agg') - import matplotlib.pyplot as plt -except ImportError: - import platform - if platform.python_implementation() == 'PyPy': - raise NotImplementedError( - 'matplotlib is not supported under pypy') - else: - raise +import matplotlib +matplotlib.use('PDF') +import matplotlib.pyplot as plt from dark.dimension import dimensionalIterator from dark.fasta import FastaReads diff --git a/dark/reads.py b/dark/reads.py index 42390e4..1074f78 100644 --- a/dark/reads.py +++ b/dark/reads.py @@ -740,8 +740,9 @@ class ReadFilter(object): sequence identity. @param removeDuplicatesById: If C{True} remove duplicated reads based only on read id. - @param removeDescriptions: If C{True} remove the description part of read - ids (i.e., the part following the first whitespace). + @param removeDescriptions: If C{True} remove the description (the part + following the first whitespace) from read ids. The description is + removed after applying the function specified by --idLambda (if any). @param modifier: If not C{None}, a function that is passed a read and which either returns a read or C{None}. If it returns a read, that read is passed through the filter. If it returns C{None}, @@ -791,6 +792,14 @@ class ReadFilter(object): file containing (1-based) sequence numbers, in ascending order, one per line. Only those sequences matching the given numbers will be kept. + @param idLambda: If not C{None}, a C{str} Python lambda function + specification to use to modify read ids. The function is applied + before removing the description (if --removeDescriptions is also + specified). + @param readLambda: If not C{None}, a C{str} Python lambda function + specification to use to modify reads. The function will be passed, + and must return, a single Read (or one of its subclasses). This + function is called after the --idLambda function, if any. @param keepSites: A set of C{int} 0-based sites (i.e., indices) in sequences that should be kept. If C{None} (the default), all sites are kept. @@ -819,7 +828,8 @@ class ReadFilter(object): removeDuplicates=False, removeDuplicatesById=False, removeDescriptions=False, modifier=None, randomSubset=None, trueLength=None, sampleFraction=None, - sequenceNumbersFile=None, keepSites=None, removeSites=None): + sequenceNumbersFile=None, idLambda=None, readLambda=None, + keepSites=None, removeSites=None): if randomSubset is not None: if sampleFraction is not None: @@ -929,6 +939,9 @@ class ReadFilter(object): sampleFraction = None self.sampleFraction = sampleFraction + self.idLambda = eval(idLambda) if idLambda else None + self.readLambda = eval(readLambda) if readLambda else None + def filter(self, read): """ Check if a read passes the filter. @@ -1038,6 +1051,20 @@ class ReadFilter(object): elif self.removeSites is not None: read = read.newFromSites(self.removeSites, exclude=True) + if self.idLambda: + newId = self.idLambda(read.id) + if newId is None: + return False + else: + read.id = newId + + if self.readLambda: + newRead = self.readLambda(read) + if newRead is None: + return False + else: + read = newRead + if self.removeDescriptions: read.id = read.id.split()[0] diff --git a/doc/mac.md b/doc/mac.md index ae0d13f..15b1c08 100644 --- a/doc/mac.md +++ b/doc/mac.md @@ -59,3 +59,24 @@ and follow the instructions in that file to install `numpy`. Then run the # Install a taxonomy database (optional) See [taxonomy.md](taxonomy.md) for details. + +# Running the tests + +If you run the tests using `make tcheck` you may encounter the following +error: + +``` +RuntimeError: Python is not installed as a framework. The Mac OS X backend +will not be able to function correctly if Python is not installed as a +framework. See the Python documentation for more information on installing +Python as a framework on Mac OS X. Please either reinstall Python as a +framework, or try one of the other backends. If you are using (Ana)Conda +please install python.app and replace the use of 'python' with 'pythonw'. See + 'Working with Matplotlib on OSX' in the Matplotlib FAQ for more information. +``` + +You can solve this by editing ~/.matplotlib/matplotlibrc (you may have to create the ~/.matplotlib directory) and inserting the following line: + +``` +backend: TkAgg +```

acorg/dark-matter

66f246ba9417430e3f00e94ca0abc88de59a92d4

diff --git a/test/test_proteins.py b/test/test_proteins.py index 81bcccb..5b0d5e9 100644 --- a/test/test_proteins.py +++ b/test/test_proteins.py @@ -255,6 +255,42 @@ class TestProteinGrouper(TestCase): }, pg.pathogenNames) + def testOneLineInOneFileWithDifferentAssetDir(self): + """ + If a protein grouper is given a different assetDir name, + the outDir needs to have that same name, as expected. + """ + fp = StringIO( + '0.77 46.6 48.1 5 6 74 gi|327|X|I44.6 ubiquitin [Lausannevirus]\n') + pg = ProteinGrouper(assetDir='differentname') + pg.addFile('sample-filename', fp) + self.assertEqual( + { + 'Lausannevirus': { + 'sample-filename': { + 'proteins': { + 'gi|327|X|I44.6 ubiquitin': { + 'bestScore': 48.1, + 'bluePlotFilename': 'differentname/0.png', + 'coverage': 0.77, + 'readsFilename': 'differentname/0.fasta', + 'hspCount': 6, + 'index': 0, + 'medianScore': 46.6, + 'outDir': 'differentname', + 'proteinLength': 74, + 'proteinName': 'gi|327|X|I44.6 ubiquitin', + 'proteinURL': ( + 'http://www.ncbi.nlm.nih.gov/nuccore/I44'), + 'readCount': 5, + }, + }, + 'uniqueReadCount': None, + }, + } + }, + pg.pathogenNames) + def testOneLineInOneFileFASTQ(self): """ If a protein grouper is given one file with one line, its pathogenNames diff --git a/test/test_reads.py b/test/test_reads.py index 4e51442..5d9cd3e 100644 --- a/test/test_reads.py +++ b/test/test_reads.py @@ -3126,6 +3126,52 @@ class TestReadsFiltering(TestCase): six.assertRaisesRegex(self, ValueError, error, Reads().filter, keepSites={4}, removeSites={5}) + def testIdLambda(self): + """ + A passed idLambda function should produce the expected read ids. + """ + read = Read('id1', 'ATCGCC') + reads = Reads(initialReads=[read]) + result = reads.filter(idLambda='lambda id: "x-" + id.upper()') + self.assertEqual('x-ID1', list(result)[0].id) + + def testIdLambdaReturningNone(self): + """ + A passed idLambda function should produce the expected read ids, + including when it returns None. + """ + read1 = Read('id1', 'ATCGCC') + read2 = Read('id2', 'GGATCG') + reads = Reads(initialReads=[read1, read2]) + result = reads.filter( + idLambda='lambda id: "aa" if id.find("1") > -1 else None') + (result,) = list(result) + self.assertEqual('aa', result.id) + + def testReadLambda(self): + """ + A passed readLambda function should produce the expected reads. + """ + read = Read('id1', 'ATCGCC') + reads = Reads(initialReads=[read]) + result = reads.filter(readLambda='lambda r: Read("hey", "AAA")') + (result,) = list(result) + self.assertEqual(Read('hey', 'AAA'), result) + + def testReadLambdaReturningNone(self): + """ + A passed readLambda function should produce the expected reads, + including when it returns None. + """ + read1 = Read('xid1', 'ATCGCC') + read2 = Read('yid2', 'GGATCG') + reads = Reads(initialReads=[read1, read2]) + result = reads.filter( + readLambda=('lambda r: Read(r.id + "-x", r.sequence[:2]) ' + 'if r.id.startswith("x") else None')) + (result,) = list(result) + self.assertEqual(Read('xid1-x', 'AT'), result) + class TestReadsInRAM(TestCase): """

Add ability to give an anonymous Python function for read id conversion when filtering FASTA

0.0

66f246ba9417430e3f00e94ca0abc88de59a92d4

[ "test/test_reads.py::TestReadsFiltering::testIdLambda", "test/test_reads.py::TestReadsFiltering::testIdLambdaReturningNone", "test/test_reads.py::TestReadsFiltering::testReadLambda", "test/test_reads.py::TestReadsFiltering::testReadLambdaReturningNone" ]

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"test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogen", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogenTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFile", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileFASTQ", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileToStr", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileWithDifferentAssetDir", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileDifferentPathogens", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileSamePathogen", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testUnknownFormat", "test/test_proteins.py::TestProteinGrouper::testUnknownPathogenType", "test/test_proteins.py::TestPathogenSampleFiles::testUnknownFormat", "test/test_proteins.py::TestPathogenSampleFiles::testWritePathogenIndex", "test/test_proteins.py::TestPathogenSampleFiles::testWriteSampleIndex", "test/test_reads.py::TestRead::testCasePreservation", "test/test_reads.py::TestRead::testCheckAlphabetAAReadMatchingReturnTrue", "test/test_reads.py::TestRead::testCheckAlphabetAAReadNotMatchingRaise", "test/test_reads.py::TestRead::testCheckAlphabetDNAReadMatchingReturnTrue", "test/test_reads.py::TestRead::testCheckAlphabetDNAReadNotMatchingRaise", "test/test_reads.py::TestRead::testCheckAlphabetwithReadMustBePermissive", "test/test_reads.py::TestRead::testEquality", "test/test_reads.py::TestRead::testEqualityWithDifferingIds", "test/test_reads.py::TestRead::testEqualityWithDifferingQuality", "test/test_reads.py::TestRead::testEqualityWithDifferingSequences", "test/test_reads.py::TestRead::testEqualityWithNoQuality", "test/test_reads.py::TestRead::testEqualityWithOneOmittedQuality", "test/test_reads.py::TestRead::testExpectedAttributes", "test/test_reads.py::TestRead::testFromDict", "test/test_reads.py::TestRead::testFromDictNoQuality", "test/test_reads.py::TestRead::testGetitemFullCopy", "test/test_reads.py::TestRead::testGetitemId", "test/test_reads.py::TestRead::testGetitemLength", "test/test_reads.py::TestRead::testGetitemQuality", "test/test_reads.py::TestRead::testGetitemReturnsNewRead", "test/test_reads.py::TestRead::testGetitemReversed", "test/test_reads.py::TestRead::testGetitemSequence", "test/test_reads.py::TestRead::testGetitemSingleIndex", "test/test_reads.py::TestRead::testGetitemWithStep", "test/test_reads.py::TestRead::testHashDiffersIfIdDiffers", "test/test_reads.py::TestRead::testHashDiffersIfQualityDiffers", "test/test_reads.py::TestRead::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestRead::testHashIdenticalNoQuality", "test/test_reads.py::TestRead::testHashIdenticalWithQuality", "test/test_reads.py::TestRead::testHashViaDict", "test/test_reads.py::TestRead::testHashViaSet", 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"test/test_reads.py::TestRead::testToFASTA", "test/test_reads.py::TestRead::testToFASTAWithQuality", "test/test_reads.py::TestRead::testToFASTQ", "test/test_reads.py::TestRead::testToFASTQWithNoQuality", "test/test_reads.py::TestRead::testToUnknownFormat", "test/test_reads.py::TestRead::testUnequalLengths", "test/test_reads.py::TestRead::testWalkHSPExactMatch", "test/test_reads.py::TestRead::testWalkHSPExactMatchWithGap", "test/test_reads.py::TestRead::testWalkHSPLeftAndRightOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPLeftAndRightOverhangingMatchNoWhiskers", "test/test_reads.py::TestRead::testWalkHSPLeftOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPLeftOverhangingMatchNoWhiskers", "test/test_reads.py::TestRead::testWalkHSPRightOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPRightOverhangingMatchNoWhiskers", "test/test_reads.py::TestDNARead::testGetitemReturnsNewDNARead", "test/test_reads.py::TestDNARead::testReverseComplement", "test/test_reads.py::TestDNARead::testReverseComplementAmbiguous", "test/test_reads.py::TestDNARead::testReverseComplementReversesQuality", "test/test_reads.py::TestDNARead::testTranslationOfMultipleStopCodons", "test/test_reads.py::TestDNARead::testTranslationOfStartCodonATG", "test/test_reads.py::TestDNARead::testTranslationOfStopCodonTAG", "test/test_reads.py::TestDNARead::testTranslationOfStopCodonTGA", "test/test_reads.py::TestDNARead::testTranslations", "test/test_reads.py::TestDNARead::testTranslationsOfEmptySequence", "test/test_reads.py::TestDNARead::testTranslationsOfOneBaseSequence", "test/test_reads.py::TestDNARead::testTranslationsOfTwoBaseSequence", "test/test_reads.py::TestRNARead::testGetitemReturnsNewRNARead", "test/test_reads.py::TestRNARead::testReverseComplement", "test/test_reads.py::TestRNARead::testReverseComplementAmbiguous", "test/test_reads.py::TestRNARead::testTranslationOfStopCodonUAA", "test/test_reads.py::TestAARead::testCloseCloseORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseCloseORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseCloseORFWithJunk", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseOpenORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseOpenORFWithJunk", "test/test_reads.py::TestAARead::testCloseCloseThenCloseOpenORF", "test/test_reads.py::TestAARead::testCloseOpenORF", "test/test_reads.py::TestAARead::testCloseOpenORFWithMultipleStarts", "test/test_reads.py::TestAARead::testGetitemReturnsNewAARead", "test/test_reads.py::TestAARead::testNoStartCodon_GithubIssue239", "test/test_reads.py::TestAARead::testORFsEmptySequence", "test/test_reads.py::TestAARead::testORFsEmptySequenceWithStart", "test/test_reads.py::TestAARead::testORFsEmptySequenceWithStartStop", "test/test_reads.py::TestAARead::testORFsWithJustStartsAndStops", "test/test_reads.py::TestAARead::testORFsWithOneStopCodon", "test/test_reads.py::TestAARead::testORFsWithTwoStopCodons", "test/test_reads.py::TestAARead::testOpenCloseORF", "test/test_reads.py::TestAARead::testOpenCloseORFWithMultipleStops", "test/test_reads.py::TestAARead::testOpenCloseThenCloseCloseThenCloseOpenORF", "test/test_reads.py::TestAARead::testOpenCloseThenCloseCloseThenCloseOpenORFWithJunk", "test/test_reads.py::TestAARead::testOpenCloseThenCloseOpenORF", "test/test_reads.py::TestAARead::testOpenOpenORF", "test/test_reads.py::TestAARead::testPropertiesCorrectTranslation", "test/test_reads.py::TestAARead::testPropertyDetailsCorrectTranslation", "test/test_reads.py::TestAAReadWithX::testAlphabet", "test/test_reads.py::TestAAReadWithX::testAlphabetChecking", "test/test_reads.py::TestAAReadWithX::testGetitemReturnsNewAAReadWithX", "test/test_reads.py::TestAAReadORF::testClosedClosedId", "test/test_reads.py::TestAAReadORF::testClosedOpenId", "test/test_reads.py::TestAAReadORF::testFromDict", "test/test_reads.py::TestAAReadORF::testOpenClosedId", "test/test_reads.py::TestAAReadORF::testOpenLeft", "test/test_reads.py::TestAAReadORF::testOpenOpenId", "test/test_reads.py::TestAAReadORF::testOpenRight", "test/test_reads.py::TestAAReadORF::testSequence", "test/test_reads.py::TestAAReadORF::testStart", "test/test_reads.py::TestAAReadORF::testStartGreaterThanStop", "test/test_reads.py::TestAAReadORF::testStartNegative", "test/test_reads.py::TestAAReadORF::testStop", "test/test_reads.py::TestAAReadORF::testStopGreaterThanOriginalSequenceLength", "test/test_reads.py::TestAAReadORF::testToDict", "test/test_reads.py::TestSSAARead::testCorrectAttributes", "test/test_reads.py::TestSSAARead::testFromDict", "test/test_reads.py::TestSSAARead::testGetitemFullCopy", "test/test_reads.py::TestSSAARead::testGetitemId", "test/test_reads.py::TestSSAARead::testGetitemLength", "test/test_reads.py::TestSSAARead::testGetitemReturnsNewRead", "test/test_reads.py::TestSSAARead::testGetitemReversed", "test/test_reads.py::TestSSAARead::testGetitemSequence", "test/test_reads.py::TestSSAARead::testGetitemSingleIndex", "test/test_reads.py::TestSSAARead::testGetitemStructure", "test/test_reads.py::TestSSAARead::testGetitemWithStep", "test/test_reads.py::TestSSAARead::testHashDiffersIfIdDiffers", "test/test_reads.py::TestSSAARead::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestSSAARead::testHashDiffersIfStructureDiffers", "test/test_reads.py::TestSSAARead::testHashViaDict", "test/test_reads.py::TestSSAARead::testHashViaSet", "test/test_reads.py::TestSSAARead::testKeepSites", "test/test_reads.py::TestSSAARead::testKeepSitesAllSites", "test/test_reads.py::TestSSAARead::testKeepSitesNoSites", "test/test_reads.py::TestSSAARead::testKeepSitesOutOfRange", "test/test_reads.py::TestSSAARead::testReads", "test/test_reads.py::TestSSAARead::testRemoveSites", "test/test_reads.py::TestSSAARead::testRemoveSitesAllSites", "test/test_reads.py::TestSSAARead::testRemoveSitesNoSites", "test/test_reads.py::TestSSAARead::testRemoveSitesOutOfRange", "test/test_reads.py::TestSSAARead::testSequenceLengthMatchesStructureLength", "test/test_reads.py::TestSSAARead::testToDict", "test/test_reads.py::TestSSAARead::testToString", "test/test_reads.py::TestSSAARead::testToStringWithExplicitFastaFormat", "test/test_reads.py::TestSSAARead::testToStringWithExplicitFastaSSFormat", "test/test_reads.py::TestSSAARead::testToStringWithStructureSuffix", "test/test_reads.py::TestSSAARead::testToStringWithUnknownFormat", "test/test_reads.py::TestSSAAReadWithX::testCorrectAttributes", "test/test_reads.py::TestSSAAReadWithX::testFromDict", "test/test_reads.py::TestSSAAReadWithX::testGetitemFullCopy", "test/test_reads.py::TestSSAAReadWithX::testGetitemId", "test/test_reads.py::TestSSAAReadWithX::testGetitemLength", "test/test_reads.py::TestSSAAReadWithX::testGetitemReturnsNewRead", "test/test_reads.py::TestSSAAReadWithX::testGetitemReversed", "test/test_reads.py::TestSSAAReadWithX::testGetitemSequence", "test/test_reads.py::TestSSAAReadWithX::testGetitemSingleIndex", "test/test_reads.py::TestSSAAReadWithX::testGetitemStructure", "test/test_reads.py::TestSSAAReadWithX::testGetitemWithStep", "test/test_reads.py::TestSSAAReadWithX::testHashDiffersIfIdDiffers", "test/test_reads.py::TestSSAAReadWithX::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestSSAAReadWithX::testHashDiffersIfStructureDiffers", "test/test_reads.py::TestSSAAReadWithX::testHashViaDict", "test/test_reads.py::TestSSAAReadWithX::testHashViaSet", "test/test_reads.py::TestSSAAReadWithX::testKeepSites", "test/test_reads.py::TestSSAAReadWithX::testKeepSitesAllSites", "test/test_reads.py::TestSSAAReadWithX::testKeepSitesNoSites", "test/test_reads.py::TestSSAAReadWithX::testKeepSitesOutOfRange", "test/test_reads.py::TestSSAAReadWithX::testReads", "test/test_reads.py::TestSSAAReadWithX::testRemoveSites", "test/test_reads.py::TestSSAAReadWithX::testRemoveSitesAllSites", "test/test_reads.py::TestSSAAReadWithX::testRemoveSitesNoSites", "test/test_reads.py::TestSSAAReadWithX::testRemoveSitesOutOfRange", "test/test_reads.py::TestSSAAReadWithX::testSequenceContainingX", "test/test_reads.py::TestSSAAReadWithX::testSequenceLengthMatchesStructureLength", "test/test_reads.py::TestSSAAReadWithX::testToDict", "test/test_reads.py::TestSSAAReadWithX::testToString", "test/test_reads.py::TestSSAAReadWithX::testToStringWithExplicitFastaFormat", "test/test_reads.py::TestSSAAReadWithX::testToStringWithExplicitFastaSSFormat", "test/test_reads.py::TestSSAAReadWithX::testToStringWithStructureSuffix", "test/test_reads.py::TestSSAAReadWithX::testToStringWithUnknownFormat", "test/test_reads.py::TestTranslatedRead::testExpectedAttributes", "test/test_reads.py::TestTranslatedRead::testExpectedFrame", "test/test_reads.py::TestTranslatedRead::testFromDict", "test/test_reads.py::TestTranslatedRead::testId", "test/test_reads.py::TestTranslatedRead::testIdReverseComplemented", "test/test_reads.py::TestTranslatedRead::testMaximumORFLength", "test/test_reads.py::TestTranslatedRead::testMaximumORFLengthNoStops", "test/test_reads.py::TestTranslatedRead::testOutOfRangeFrame", "test/test_reads.py::TestTranslatedRead::testReverseComplemented", "test/test_reads.py::TestTranslatedRead::testSequence", "test/test_reads.py::TestTranslatedRead::testToDict", "test/test_reads.py::TestReadClassNameToClass::testNames", "test/test_reads.py::TestReads::testEmptyInitialReads", "test/test_reads.py::TestReads::testInitialReads", "test/test_reads.py::TestReads::testManuallyAddedReads", "test/test_reads.py::TestReads::testManuallyAddedReadsLength", "test/test_reads.py::TestReads::testNoReads", "test/test_reads.py::TestReads::testNoReadsLength", "test/test_reads.py::TestReads::testRepeatedIter", "test/test_reads.py::TestReads::testSaveAsFASTA", "test/test_reads.py::TestReads::testSaveAsFASTQ", "test/test_reads.py::TestReads::testSaveAsFASTQFailsOnReadWithNoQuality", "test/test_reads.py::TestReads::testSaveFASTAIsDefault", "test/test_reads.py::TestReads::testSaveReturnsReadCount", "test/test_reads.py::TestReads::testSaveToFileDescriptor", "test/test_reads.py::TestReads::testSaveWithUnknownFormat", "test/test_reads.py::TestReads::testSaveWithUppercaseFormat", "test/test_reads.py::TestReads::testSubclass", "test/test_reads.py::TestReads::testSubclassLength", "test/test_reads.py::TestReads::testSubclassWithAdditionalReads", "test/test_reads.py::TestReads::testUnfilteredLengthAdditionalReads", "test/test_reads.py::TestReads::testUnfilteredLengthAdditionalReadsAfterFiltering", "test/test_reads.py::TestReads::testUnfilteredLengthBeforeIterating", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReads", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReadsAfterFiltering", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReadsIsReads", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReadsIsReadsWithAdditional", "test/test_reads.py::TestReads::testUnfilteredLengthInitialSubclassThenFiltered", "test/test_reads.py::TestReads::testUnfilteredLengthInitialSubclassWithAdditionalThenFiltered", "test/test_reads.py::TestReads::testUnfilteredLengthInitialSubclassWithNoLen", "test/test_reads.py::TestReads::testUnfilteredLengthNoReads", "test/test_reads.py::TestReadsFiltering::testAddFiltersThenClearFilters", "test/test_reads.py::TestReadsFiltering::testFilterBlacklist", "test/test_reads.py::TestReadsFiltering::testFilterDoNotRemoveDescriptions", "test/test_reads.py::TestReadsFiltering::testFilterDuplicates", "test/test_reads.py::TestReadsFiltering::testFilterDuplicatesById", "test/test_reads.py::TestReadsFiltering::testFilterHead", "test/test_reads.py::TestReadsFiltering::testFilterHeadZero", "test/test_reads.py::TestReadsFiltering::testFilterKeepSequences", "test/test_reads.py::TestReadsFiltering::testFilterKeepSequencesNoSequences", "test/test_reads.py::TestReadsFiltering::testFilterNegativeRegex", "test/test_reads.py::TestReadsFiltering::testFilterNoArgs", "test/test_reads.py::TestReadsFiltering::testFilterOnLengthEverythingMatches", "test/test_reads.py::TestReadsFiltering::testFilterOnLengthNothingMatches", "test/test_reads.py::TestReadsFiltering::testFilterOnMaxLength", "test/test_reads.py::TestReadsFiltering::testFilterOnMinLength", "test/test_reads.py::TestReadsFiltering::testFilterPositiveRegex", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfFiveFromFiveReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfFiveFromOneRead", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfOneFromOneRead", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfTwoFromFiveReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfZeroReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetSizeZeroNoReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetSizeZeroTwoReads", "test/test_reads.py::TestReadsFiltering::testFilterRemoveDescriptions", "test/test_reads.py::TestReadsFiltering::testFilterRemoveGaps", "test/test_reads.py::TestReadsFiltering::testFilterRemoveGapsWithQuality", "test/test_reads.py::TestReadsFiltering::testFilterRemoveSequences", "test/test_reads.py::TestReadsFiltering::testFilterRemoveSequencesNoSequences", "test/test_reads.py::TestReadsFiltering::testFilterReturnsReadInstance", "test/test_reads.py::TestReadsFiltering::testFilterTruncateTitles", "test/test_reads.py::TestReadsFiltering::testFilterWhitelist", "test/test_reads.py::TestReadsFiltering::testFilterWithMinLengthEqualToMaxLength", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatChangesIds", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatOmits", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatOmitsAndChangesIds", "test/test_reads.py::TestReadsFiltering::testFilteredReadsInstanceHasExpectedLength", "test/test_reads.py::TestReadsFiltering::testKeepSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesAllSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesNoSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesOutOfRange", "test/test_reads.py::TestReadsFiltering::testKeepSitesWithQuality", "test/test_reads.py::TestReadsFiltering::testLineNumberFile", "test/test_reads.py::TestReadsFiltering::testLineNumberFileEmpty", "test/test_reads.py::TestReadsFiltering::testLineNumberFileFirstLineTooSmall", "test/test_reads.py::TestReadsFiltering::testLineNumberFileNonAscending", "test/test_reads.py::TestReadsFiltering::testLineNumberFileRunOutOfSequences", "test/test_reads.py::TestReadsFiltering::testRemoveAndKeepSites", "test/test_reads.py::TestReadsFiltering::testRemoveSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesAllSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesNoSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesOutOfRange", "test/test_reads.py::TestReadsFiltering::testRemoveSitesWithQuality", "test/test_reads.py::TestReadsFiltering::testSampleFractionAndNoTrueLengthRaisesValueError", "test/test_reads.py::TestReadsFiltering::testSampleFractionAndRandomSubsetRaisesValueError", "test/test_reads.py::TestReadsFiltering::testSampleFractionOne", "test/test_reads.py::TestReadsFiltering::testSampleFractionPointOne", "test/test_reads.py::TestReadsFiltering::testSampleFractionZero", "test/test_reads.py::TestReadsInRAM::testAdd", "test/test_reads.py::TestReadsInRAM::testFromReads", "test/test_reads.py::TestReadsInRAM::testNoReads", "test/test_reads.py::TestReadsInRAM::testOneReadIndex", "test/test_reads.py::TestReadsInRAM::testOneReadLength", "test/test_reads.py::TestReadsInRAM::testOneReadList", "test/test_reads.py::TestReadsInRAM::testSetItem", "test/test_reads.py::TestReadsInRAM::testTwoReadsIndex", "test/test_reads.py::TestReadsInRAM::testTwoReadsLength", "test/test_reads.py::TestReadsInRAM::testTwoReadsList", "test/test_reads.py::TestSummarizePosition::testCorrectFrequencies", "test/test_reads.py::TestSummarizePosition::testExcludeShortSequences", "test/test_reads.py::TestSummarizePosition::testFrequenciesNoReads", "test/test_reads.py::TestSummarizePosition::testIndexLargerThanSequenceLength", "test/test_reads.py::TestSummarizePosition::testNumberOfExclusionsNoReads", "test/test_reads.py::TestSitesMatching::testAllMatches", "test/test_reads.py::TestSitesMatching::testIgnoreCase", "test/test_reads.py::TestSitesMatching::testMatchCase", "test/test_reads.py::TestSitesMatching::testMultipleReadsAll", "test/test_reads.py::TestSitesMatching::testMultipleReadsAllWithDifferingLengths", "test/test_reads.py::TestSitesMatching::testMultipleReadsAny", "test/test_reads.py::TestSitesMatching::testMultipleReadsAnyWithDifferingLengths", "test/test_reads.py::TestSitesMatching::testNoMatches", "test/test_reads.py::TestSitesMatching::testPartialMatch" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }

2018-05-27 14:07:28+00:00

mit

866

acorg__dark-matter-610

diff --git a/CHANGELOG.md b/CHANGELOG.md index d7f91b4..add466a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +## 3.0.23 June 22, 2018 + +Changed the way reference sequence insertions are stored in a +`dark.sam.PaddedSAM` instance to make it possible to tell which query +sequences caused reference insertions. + ## 3.0.22 June 21, 2018 Made `dark/sam.py` properly deal with secondary alignments that are missing diff --git a/dark/__init__.py b/dark/__init__.py index db6691a..e3d166b 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.22' +__version__ = '3.0.23' diff --git a/dark/sam.py b/dark/sam.py index f0ffa19..2165ea6 100644 --- a/dark/sam.py +++ b/dark/sam.py @@ -29,12 +29,12 @@ class PaddedSAM(object): """ def __init__(self, filename): self.samfile = AlignmentFile(filename) - # self.referenceInsertions will be keyed by offset into the reference - # sequence. The inserted bases would need to begin at this offset. The - # value will be a Counter whose keys are the nucleotides proposed for - # insertion, with a value indicating how many times the nucleotide was - # proposed for insertion at that offset. - self.referenceInsertions = defaultdict(Counter) + # self.referenceInsertions will be keyed by query id (the query + # that would cause a reference insertion). The values will be lists + # of 2-tuples, with each 2-tuple containing an offset into the + # reference sequence and the C{str} of nucleotide that would be + # inserted starting at that offset. + self.referenceInsertions = defaultdict(list) def close(self): """ @@ -182,6 +182,16 @@ class PaddedSAM(object): if rcSuffix: read.query_name += rcSuffix + # Adjust the query id if it's a duplicate and we're not + # allowing duplicates. + if allowDuplicateIds: + queryId = read.query_name + else: + count = idCount[read.query_name] + idCount[read.query_name] += 1 + queryId = read.query_name + ( + '' if count == 0 else '/%d' % count) + referenceStart = read.reference_start atStart = True queryIndex = 0 @@ -205,9 +215,9 @@ class PaddedSAM(object): # query but record what would have been inserted into the # reference. atStart = False - for i in range(length): - self.referenceInsertions[referenceIndex + i][ - query[queryIndex + i]] += 1 + self.referenceInsertions[queryId].append( + (referenceIndex, + query[queryIndex:queryIndex + length])) elif operation == CDEL: # Delete from the reference. Some bases from the reference # would need to be deleted to continue the match. So we put @@ -293,14 +303,7 @@ class PaddedSAM(object): padChar * (referenceLength - (referenceStart + len(alignedSequence)))) - if allowDuplicateIds: - suffix = '' - else: - count = idCount[read.query_name] - idCount[read.query_name] += 1 - suffix = '' if count == 0 else '/%d' % count - - yield Read('%s%s' % (read.query_name, suffix), paddedSequence) + yield Read(queryId, paddedSequence) @contextmanager

acorg/dark-matter

d75630ac7a4f6f99bd0c4e87737290ff971b92d5

diff --git a/test/test_sam.py b/test/test_sam.py index e31f801..f8fd7e9 100644 --- a/test/test_sam.py +++ b/test/test_sam.py @@ -347,8 +347,32 @@ class TestPaddedSAM(TestCase): self.assertEqual(Read('query1', '-TCGG-----'), read) self.assertEqual( { - 3: {'T': 1}, - 4: {'A': 1}, + 'query1': [(3, 'TA')], + }, + ps.referenceInsertions) + ps.close() + + def testPrimaryAndSecondaryReferenceInsertion(self): + """ + A primary and secondary insertion into the reference (of the same + query) must result in the expected padded sequences and the expected + value in the referenceInsertions dictionary. + """ + data = '\n'.join([ + '@SQ SN:ref1 LN:10', + 'query1 0 ref1 2 60 2M2I2M * 0 0 TCTAGG ZZZZZZ', + 'query1 256 ref1 4 60 2M3I1M * 0 0 * *', + ]).replace(' ', '\t') + + with dataFile(data) as filename: + ps = PaddedSAM(filename) + (read1, read2) = list(ps.queries()) + self.assertEqual(Read('query1', '-TCGG-----'), read1) + self.assertEqual(Read('query1/1', '---TCG----'), read2) + self.assertEqual( + { + 'query1': [(3, 'TA')], + 'query1/1': [(5, 'TAG')], }, ps.referenceInsertions) ps.close()

SAM referenceInsertion should record what reads cause reference insertions The code currently records all reference insertions but doesn't keep track of which reads caused insertions. That makes it impossible to ignore insertions according to which read created it.

0.0

d75630ac7a4f6f99bd0c4e87737290ff971b92d5

[ "test/test_sam.py::TestPaddedSAM::testPrimaryAndSecondaryReferenceInsertion", "test/test_sam.py::TestPaddedSAM::testReferenceInsertion" ]

[ "test/test_sam.py::TestPaddedSAM::testAllMMatch", "test/test_sam.py::TestPaddedSAM::testAllowDuplicateIds", "test/test_sam.py::TestPaddedSAM::testDropDuplicates", "test/test_sam.py::TestPaddedSAM::testDropSecondary", "test/test_sam.py::TestPaddedSAM::testDropSupplementary", "test/test_sam.py::TestPaddedSAM::testDuplicateIdDisambiguation", "test/test_sam.py::TestPaddedSAM::testHardClipLeft", "test/test_sam.py::TestPaddedSAM::testHardClipRight", "test/test_sam.py::TestPaddedSAM::testKF414679SoftClipLeft", "test/test_sam.py::TestPaddedSAM::testKeepQualityControlFailures", "test/test_sam.py::TestPaddedSAM::testMinLength", "test/test_sam.py::TestPaddedSAM::testMinLengthWithReferenceDeletion", "test/test_sam.py::TestPaddedSAM::testMixedMatch", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReference", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReferenceButNoMatches", "test/test_sam.py::TestPaddedSAM::testNotSecondaryAndNotSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testQueryHardClipAndSoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesRight", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesLeftEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesRightEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipRight", "test/test_sam.py::TestPaddedSAM::testRcNeeded", "test/test_sam.py::TestPaddedSAM::testRcSuffix", "test/test_sam.py::TestPaddedSAM::testReferenceDeletion", "test/test_sam.py::TestPaddedSAM::testReferenceDeletionAlternateChar", "test/test_sam.py::TestPaddedSAM::testReferenceSkip", "test/test_sam.py::TestPaddedSAM::testReferenceSkipAlternateChar", "test/test_sam.py::TestPaddedSAM::testReferencesToStr", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testUnequalReferenceLengths", "test/test_sam.py::TestPaddedSAM::testUnknownReferences" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2018-06-22 17:31:59+00:00

mit

867

acorg__dark-matter-617

diff --git a/CHANGELOG.md b/CHANGELOG.md index 67af944..2065375 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,11 @@ +## 3.0.28 July 3, 2018 + +Added `alsoYieldAlignments` option to `PaddedSAM.queries` method to have +the returned generator also yield the `pysam.AlignedSegment` instance with +the gap-padded query sequence. This makes it possible to retrieve padded +queries from SAM/BAM and generate SAM/BAM (or FASTQ) of some subset of the +queries. + ## 3.0.27 June 30, 2018 Added `bin/filter-sam.py` script. diff --git a/bin/filter-sam.py b/bin/filter-sam.py index 18b5b47..363fed1 100755 --- a/bin/filter-sam.py +++ b/bin/filter-sam.py @@ -38,26 +38,26 @@ if __name__ == '__main__': 'error message is printed unless --quiet is used).')) parser.add_argument( - '--dropUnmapped', default=False, action='store_true', - help='If given, unmapped matches will not be output.') + '--dropUnmapped', default=False, action='store_true', + help='If given, unmapped matches will not be output.') parser.add_argument( - '--dropSecondary', default=False, action='store_true', - help='If given, secondary matches will not be output.') + '--dropSecondary', default=False, action='store_true', + help='If given, secondary matches will not be output.') parser.add_argument( - '--dropSupplementary', default=False, action='store_true', - help='If given, supplementary matches will not be output.') + '--dropSupplementary', default=False, action='store_true', + help='If given, supplementary matches will not be output.') parser.add_argument( - '--dropDuplicates', default=False, action='store_true', - help=('If given, matches flagged as optical or PCR duplicates will ' - 'not be output.')) + '--dropDuplicates', default=False, action='store_true', + help=('If given, matches flagged as optical or PCR duplicates will ' + 'not be output.')) parser.add_argument( - '--keepQCFailures', default=False, action='store_true', - help=('If given, reads that are considered quality control failures ' - 'will be included in the output.')) + '--keepQCFailures', default=False, action='store_true', + help=('If given, reads that are considered quality control failures ' + 'will be included in the output.')) parser.add_argument( '--referenceWhitelist', metavar='NAME', action='append', @@ -106,17 +106,17 @@ if __name__ == '__main__': if (filterRead(Read(alignment.query_name, alignment.query_sequence, - alignment.qual)) - and not ( - (alignment.is_unmapped and dropUnmapped) or - (alignment.is_secondary and dropSecondary) or - (alignment.is_supplementary and dropSupplementary) or - (alignment.is_duplicate and dropDuplicates) or - (alignment.is_qcfail and not keepQCFailures) or - (referenceWhitelist is not None and - alignment.reference_name not in referenceWhitelist) or - (referenceBlacklist is not None and - alignment.reference_name in referenceBlacklist))): + alignment.qual)) and + not ( + (alignment.is_unmapped and dropUnmapped) or + (alignment.is_secondary and dropSecondary) or + (alignment.is_supplementary and dropSupplementary) or + (alignment.is_duplicate and dropDuplicates) or + (alignment.is_qcfail and not keepQCFailures) or + (referenceWhitelist is not None and + alignment.reference_name not in referenceWhitelist) or + (referenceBlacklist is not None and + alignment.reference_name in referenceBlacklist))): kept += 1 save(alignment) out.close() diff --git a/dark/__init__.py b/dark/__init__.py index dabfdd7..2f8e41d 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.27' +__version__ = '3.0.28' diff --git a/dark/sam.py b/dark/sam.py index f2bb28b..a5d9363 100644 --- a/dark/sam.py +++ b/dark/sam.py @@ -61,7 +61,7 @@ class PaddedSAM(object): dropSecondary=False, dropSupplementary=False, dropDuplicates=False, allowDuplicateIds=False, keepQCFailures=False, rcNeeded=False, padChar='-', - queryInsertionChar='N'): + queryInsertionChar='N', alsoYieldAlignments=False): """ Produce padded (with gaps) queries according to the CIGAR string and reference sequence length for each matching query sequence. @@ -107,13 +107,18 @@ class PaddedSAM(object): is inserted as a 'missing' query character (i.e., a base that can be assumed to have been lost due to an error) whose existence is necessary for the match to continue. + @param alsoYieldAlignments: If C{True} the returned generator will + yield 2-tuples containing a padded query and the + C{pysam.AlignedSegment} for each query. @raises UnequalReferenceLengthError: If C{referenceName} is C{None} and the reference sequence lengths in the SAM/BAM file are not all identical. @raises UnknownReference: If C{referenceName} does not exist. @return: A generator that yields C{Read} instances that are padded with gap characters to align them to the length of the reference - sequence. + sequence. See C{alsoYieldAlignments}, above, to have the generator + yield tuples also containing the corresponding + C{pysam.AlignedSegment}. """ samfile = self.samfile @@ -142,24 +147,24 @@ class PaddedSAM(object): MATCH_OPERATIONS = {CMATCH, CEQUAL, CDIFF} lastQuery = None - for lineNumber, read in enumerate(samfile.fetch(), start=1): - if (read.is_unmapped or - (read.is_secondary and dropSecondary) or - (read.is_supplementary and dropSupplementary) or - (read.is_duplicate and dropDuplicates) or - (read.is_qcfail and not keepQCFailures) or + for lineNumber, alignment in enumerate(samfile.fetch(), start=1): + if (alignment.is_unmapped or + (alignment.is_secondary and dropSecondary) or + (alignment.is_supplementary and dropSupplementary) or + (alignment.is_duplicate and dropDuplicates) or + (alignment.is_qcfail and not keepQCFailures) or (referenceId is not None and - read.reference_id != referenceId)): + alignment.reference_id != referenceId)): continue - query = read.query_sequence + query = alignment.query_sequence # Secondary (and presumably supplementary) alignments may have # a '*' (None in pysam) SEQ field, indicating that the previous # sequence should be used. This is best practice according to # section 2.5.2 of https://samtools.github.io/hts-specs/SAMv1.pdf if query is None: - if read.is_secondary or read.is_supplementary: + if alignment.is_secondary or alignment.is_supplementary: if lastQuery is None: raise ValueError( 'Query line %d has an empty SEQ field, but no ' @@ -176,29 +181,29 @@ class PaddedSAM(object): # due to it being reverse complimented for the alignment). lastQuery = query - if read.is_reverse: + if alignment.is_reverse: if rcNeeded: query = DNARead('id', query).reverseComplement().sequence if rcSuffix: - read.query_name += rcSuffix + alignment.query_name += rcSuffix # Adjust the query id if it's a duplicate and we're not # allowing duplicates. if allowDuplicateIds: - queryId = read.query_name + queryId = alignment.query_name else: - count = idCount[read.query_name] - idCount[read.query_name] += 1 - queryId = read.query_name + ( + count = idCount[alignment.query_name] + idCount[alignment.query_name] += 1 + queryId = alignment.query_name + ( '' if count == 0 else '/%d' % count) - referenceStart = read.reference_start + referenceStart = alignment.reference_start atStart = True queryIndex = 0 referenceIndex = referenceStart alignedSequence = '' - for operation, length in read.cigartuples: + for operation, length in alignment.cigartuples: # The operations are tested in the order they appear in # https://samtools.github.io/hts-specs/SAMv1.pdf It would be @@ -303,7 +308,11 @@ class PaddedSAM(object): padChar * (referenceLength - (referenceStart + len(alignedSequence)))) - yield Read(queryId, paddedSequence) + read = Read(queryId, paddedSequence) + if alsoYieldAlignments: + yield (read, alignment) + else: + yield read @contextmanager

acorg/dark-matter

252de3e0a17525dde6a5f4167ea1e54a70ba91ee

diff --git a/test/test_sam.py b/test/test_sam.py index f8fd7e9..a6ee95a 100644 --- a/test/test_sam.py +++ b/test/test_sam.py @@ -706,3 +706,31 @@ class TestPaddedSAM(TestCase): queries = ps.queries() assertRaisesRegex(self, ValueError, error, list, queries) ps.close() + + def testAlsoYieldAlignments(self): + """ + A request for queries and their pysam alignments should have the + expected result. + """ + data = '\n'.join([ + '@SQ SN:ref1 LN:10', + 'query1 0 ref1 2 60 2=2X2M * 0 0 TCTAGG 123456', + 'query2 0 ref1 2 60 2= * 0 0 TC XY', + ]).replace(' ', '\t') + + with dataFile(data) as filename: + ps = PaddedSAM(filename) + ((read1, alignment1), + (read2, alignment2)) = list(ps.queries(alsoYieldAlignments=True)) + + self.assertEqual(Read('query1', '-TCTAGG---'), read1) + self.assertEqual('TCTAGG', alignment1.query_sequence) + self.assertEqual('123456', ''.join( + map(lambda x: chr(x + 33), alignment1.query_qualities))) + + self.assertEqual(Read('query2', '-TC-------'), read2) + self.assertEqual('TC', alignment2.query_sequence) + self.assertEqual('XY', ''.join( + map(lambda x: chr(x + 33), alignment2.query_qualities))) + + ps.close()

Add an option to the `PaddedSAM.queries` method to have it also return the pysam.AlignedSegment

0.0

252de3e0a17525dde6a5f4167ea1e54a70ba91ee

[ "test/test_sam.py::TestPaddedSAM::testAlsoYieldAlignments" ]

[ "test/test_sam.py::TestPaddedSAM::testAllMMatch", "test/test_sam.py::TestPaddedSAM::testAllowDuplicateIds", "test/test_sam.py::TestPaddedSAM::testDropDuplicates", "test/test_sam.py::TestPaddedSAM::testDropSecondary", "test/test_sam.py::TestPaddedSAM::testDropSupplementary", "test/test_sam.py::TestPaddedSAM::testDuplicateIdDisambiguation", "test/test_sam.py::TestPaddedSAM::testHardClipLeft", "test/test_sam.py::TestPaddedSAM::testHardClipRight", "test/test_sam.py::TestPaddedSAM::testKF414679SoftClipLeft", "test/test_sam.py::TestPaddedSAM::testKeepQualityControlFailures", "test/test_sam.py::TestPaddedSAM::testMinLength", "test/test_sam.py::TestPaddedSAM::testMinLengthWithReferenceDeletion", "test/test_sam.py::TestPaddedSAM::testMixedMatch", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReference", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReferenceButNoMatches", "test/test_sam.py::TestPaddedSAM::testNotSecondaryAndNotSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testPrimaryAndSecondaryReferenceInsertion", "test/test_sam.py::TestPaddedSAM::testQueryHardClipAndSoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesRight", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesLeftEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesRightEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipRight", "test/test_sam.py::TestPaddedSAM::testRcNeeded", "test/test_sam.py::TestPaddedSAM::testRcSuffix", "test/test_sam.py::TestPaddedSAM::testReferenceDeletion", "test/test_sam.py::TestPaddedSAM::testReferenceDeletionAlternateChar", "test/test_sam.py::TestPaddedSAM::testReferenceInsertion", "test/test_sam.py::TestPaddedSAM::testReferenceSkip", "test/test_sam.py::TestPaddedSAM::testReferenceSkipAlternateChar", "test/test_sam.py::TestPaddedSAM::testReferencesToStr", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testUnequalReferenceLengths", "test/test_sam.py::TestPaddedSAM::testUnknownReferences" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }

2018-07-03 11:07:54+00:00

mit

868

acorg__dark-matter-631

diff --git a/CHANGELOG.md b/CHANGELOG.md index 2468b6e..d82fc9b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +## 3.0.38 October 5, 2018 + +Fixed [#630](https://github.com/acorg/dark-matter/issues/630) to deal with +non-hard-clipped queries that have a CIGAR string that indicates they have +been clipped. + ## 3.0.37 October 1, 2018 Add a `--titlesJSONFile` option to `noninteractive-alignment-panel.py`. diff --git a/dark/__init__.py b/dark/__init__.py index 0c505ca..7513e6e 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.37' +__version__ = '3.0.38' diff --git a/dark/sam.py b/dark/sam.py index eef7854..0167fdc 100644 --- a/dark/sam.py +++ b/dark/sam.py @@ -65,6 +65,63 @@ def samReferencesToStr(filenameOrSamfile, indent=0): return _references(sam) +def _hardClip(sequence, cigartuples): + """ + Hard clip (if necessary) a sequence. + + @param sequence: A C{str} nucleotide sequence. + @param cigartuples: An iterable of (operation, length) tuples, specifying + matching as per the SAM specification. + @return: A hard-clipped C{str} sequence if hard-clipping is indicated by + the CIGAR operations and has not already been performed (as indicated + by the lengths of the sequence and the sum of the CIGAR operation + lengths). + """ + hardClipCount = cigarLength = 0 + for (operation, length) in cigartuples: + hardClipCount += operation == CHARD_CLIP + cigarLength += length + + sequenceLength = len(sequence) + clipLeft = clipRight = 0 + + if hardClipCount == 0: + pass + elif hardClipCount == 1: + # Hard clip either at the start or the end. + if cigartuples[0][0] == CHARD_CLIP: + clipLeft = cigartuples[0][1] + if sequenceLength == cigarLength: + # The LHS hard clipping has not been done. + sequence = sequence[clipLeft:] + elif cigartuples[-1][0] == CHARD_CLIP: + clipRight = cigartuples[-1][1] + if sequenceLength == cigarLength: + # The RHS hard clipping has not been done. + sequence = sequence[:-clipRight] + else: + raise ValueError( + 'Invalid CIGAR tuples (%s) contains hard-clipping operation ' + 'that is neither at the start nor the end of the sequence.' % + (cigartuples,)) + elif hardClipCount == 2: + # Hard clip at both the start and end. + assert cigartuples[0][0] == cigartuples[-1][0] == CHARD_CLIP + clipLeft, clipRight = cigartuples[0][1], cigartuples[-1][1] + if sequenceLength == cigarLength: + # The hard clipping has not been done. + sequence = sequence[clipLeft:-clipRight] + else: + raise ValueError( + 'Invalid CIGAR tuples (%s) specifies hard-clipping %d times (2 ' + 'is the maximum).' % (cigartuples, hardClipCount)) + + assert len(sequence) + clipLeft + clipRight == cigarLength, ( + '%d + %d + %d != %d' % (len(sequence), clipLeft, clipRight, + cigarLength)) + return sequence + + class SAMFilter(object): """ Filter a SAM/BAM file. @@ -378,16 +435,16 @@ class PaddedSAM(object): 'Query line %d has an empty SEQ field, but no ' 'previous alignment is present.' % lineNumber) else: - query = lastQuery + query = _hardClip(lastQuery, alignment.cigartuples) else: raise InvalidSAM( 'Query line %d has an empty SEQ field, but the ' 'alignment is not marked as secondary or ' 'supplementary.' % lineNumber) - - # Remember the last query here (before we potentially modify it - # due to it being reverse complimented for the alignment). - lastQuery = query + else: + # Remember the last query here (before we potentially modify + # it due to it being reverse complimented for the alignment). + lastQuery = query if alignment.is_reverse: if rcNeeded: @@ -495,8 +552,13 @@ class PaddedSAM(object): if operation in _CONSUMES_REFERENCE: referenceIndex += length - # Sanity check that we consumed the entire query. - assert queryIndex == len(query) + if queryIndex != len(query): + # Oops, we did not consume the entire query. + raise ValueError( + 'Query %s not fully consumed when parsing CIGAR string. ' + 'Query %s (len %d), final query index %d, CIGAR: %r' % + (alignment.query_name, query, len(query), queryIndex, + alignment.cigartuples)) # We cannot test we consumed the entire reference. The CIGAR # string applies to (and exhausts) the query but is silent

acorg/dark-matter

845ae82628e8ca00f8a1a1abbe07b07c1ca26677

diff --git a/test/test_sam.py b/test/test_sam.py index 28c640b..35acba8 100644 --- a/test/test_sam.py +++ b/test/test_sam.py @@ -4,10 +4,12 @@ from tempfile import mkstemp from os import close, unlink, write from contextlib import contextmanager +from pysam import CHARD_CLIP, CMATCH + from dark.reads import Read, ReadFilter from dark.sam import ( PaddedSAM, SAMFilter, UnequalReferenceLengthError, UnknownReference, - InvalidSAM, samReferencesToStr) + InvalidSAM, samReferencesToStr, _hardClip) # These tests actually use the filesystem to read files. That's due to the API @@ -273,6 +275,32 @@ class TestPaddedSAM(TestCase): assertRaisesRegex(self, UnequalReferenceLengthError, error, PaddedSAM, SAMFilter(filename)) + def testQueryTooLong(self): + """ + If the query sequence is longer than the total of the lengths in the + CIGAR operations, a ValueError must be raised. + """ + # This test just returns. It used to be possible to reach the + # "Query ... not fully consumed when parsing CIGAR string." + # ValueError in sam.py, prior to the fix of + # https://github.com/acorg/dark-matter/issues/630 but it is not + # possible to get a CIGAR string that has a different total length + # from the sequence length through to our code in sam.py because + # pysam catches the error. I'm leaving this test here because it + # documents that the error checked for in sam.py cannot currently + # be reached and the test may become useful. For now it just returns. + return + data = '\n'.join([ + '@SQ SN:ref1 LN:90', + 'query1 0 ref1 1 60 4M * 0 0 TCTAGG ZZZZZZ', + ]).replace(' ', '\t') + + with dataFile(data) as filename: + ps = PaddedSAM(SAMFilter(filename)) + error = ('^Query TCTAGG not fully consumed when parsing CIGAR ' + 'string\\.') + assertRaisesRegex(self, ValueError, error, list, ps.queries()) + def testAllMMatch(self): """ A simple all-'M' match must result in the expected padded sequence. @@ -866,6 +894,33 @@ class TestPaddedSAM(TestCase): self.assertEqual('XY', ''.join( map(lambda x: chr(x + 33), read2.alignment.query_qualities))) + def testHardClippingInCIGARButQueryNotHardClipped(self): + """ + As documented in https://github.com/acorg/dark-matter/issues/630 we + have to deal correctly with a case in which the CIGAR string says a + query should be hard clipped but the query sequence in the SAM file + actually isn't. This can be due to a prior alignment with a soft clip, + in which case the full query sequence has to be given before the + secondary alignment with the hard clip. + """ + data = '\n'.join([ + '@SQ SN:Chimp-D00220 LN:8', + '@SQ SN:D-AM494716 LN:8', + 'query1 0 Chimp-D00220 1 0 3S5M * 0 0 TTTTGGTT 12345678', + 'query1 256 D-AM494716 1 0 3H5M * 0 0 * *', + ]).replace(' ', '\t') + + with dataFile(data) as filename: + ps = PaddedSAM(SAMFilter(filename)) + (read1, read2) = list(ps.queries(addAlignment=True)) + + self.assertEqual(Read('query1', 'TGGTT---'), read1) + self.assertEqual('TTTTGGTT', read1.alignment.query_sequence) + + self.assertEqual(Read('query1/1', 'TGGTT---'), read2) + # pysam uses None for the query sequence on a secondary alignment. + self.assertIs(None, read2.alignment.query_sequence) + class TestSamReferencesToStr(TestCase): """ @@ -897,3 +952,104 @@ class TestSamReferencesToStr(TestCase): with dataFile(data) as filename: self.assertEqual(' id1 (length 90)\n id2 (length 91)', samReferencesToStr(filename, indent=2)) + + +class TestHardClip(TestCase): + """ + Test the _hardClip function. + """ + def testCIGARLengthTooHigh(self): + """ + If the total length of the CIGAR operations exceeds the length of the + sequence, an AssertionError must be raised. + """ + self.assertRaises(AssertionError, _hardClip, 'CGT', ((CMATCH, 5),)) + + def testCIGARLengthTooLow(self): + """ + If the total length of the CIGAR operations is less than the length of + the sequence, an AssertionError must be raised. + """ + self.assertRaises(AssertionError, _hardClip, 'CGT', ((CMATCH, 2),)) + + def testHardClipInMiddle(self): + """ + If hard clipping is given as an operation not at the beginning or end + of the sequence, a ValueError must be raised. + """ + error = ('^Invalid CIGAR tuples .* contains hard-clipping operation ' + 'that is neither at the start nor the end of the sequence\.$') + self.assertRaisesRegex( + ValueError, error, + _hardClip, 'CGT', ((CMATCH, 1), (CHARD_CLIP, 1), (CMATCH, 1),)) + + def testThreeHardClips(self): + """ + If hard clipping is specified more than twice, a ValueError must be + raised. + """ + error = ('^Invalid CIGAR tuples .* specifies hard-clipping 3 times ' + '$2 is the maximum$.$') + self.assertRaisesRegex( + ValueError, error, + _hardClip, 'CGT', + ((CHARD_CLIP, 1), (CHARD_CLIP, 1), (CHARD_CLIP, 1),)) + + def testNoClip(self): + """ + If no hard clipping is indicated, the function must return the + original sequence. + """ + self.assertEqual('CGT', _hardClip('CGT', ((CMATCH, 3),))) + + def testClipLeft(self): + """ + If hard clipping on the left is indicated, and has not been done, + the function must return the expected sequence. + """ + self.assertEqual('CGT', + _hardClip('CAACGT', ((CHARD_CLIP, 3), (CMATCH, 3),))) + + def testClipRight(self): + """ + If hard clipping on the right is indicated, and has not been done, + the function must return the expected sequence. + """ + self.assertEqual('CA', + _hardClip('CAACGT', ((CMATCH, 2), (CHARD_CLIP, 4),))) + + def testClipBoth(self): + """ + If hard clipping on the left and right is indicated, and has not been + done, the function must return the expected sequence. + """ + self.assertEqual( + 'AA', + _hardClip('CAACGT', + ((CHARD_CLIP, 1), (CMATCH, 2), (CHARD_CLIP, 3),))) + + def testClipLeftAlreadyDone(self): + """ + If hard clipping on the left is indicated, and has already been done, + the function must return the expected sequence. + """ + self.assertEqual('CGT', + _hardClip('CGT', ((CHARD_CLIP, 3), (CMATCH, 3),))) + + def testClipRightAlreadyDone(self): + """ + If hard clipping on the right is indicated, and has already been done, + the function must return the expected sequence. + """ + self.assertEqual('CA', + _hardClip('CA', ((CMATCH, 2), (CHARD_CLIP, 4),))) + + def testClipBothAlreadyDone(self): + """ + If hard clipping on the left and right is indicated, and has already + been done, the function must return the expected sequence. + """ + self.assertEqual( + 'AA', + _hardClip('AA', + ((CHARD_CLIP, 1), (CMATCH, 2), (CHARD_CLIP, 3),)))

Change SAM filtering to allow for CIGAR strings that indicate hard clipping but that have sequences that are not clipped It can happen that an aligner (`bwa mem -a` does this) can generate SAM lines like these two: ``` K00234:90:HTWVHBBXX:6:1101:1844:10493 0 Chimp-D00220 364 0 3S78M * 0 0 TTTTGGTTATCGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGCCTCATCTTATTGTTGGT AAFFFJAJJJJJFJJJ7JJJJFJFJJFJFJAFJJJJAAF<FFFAF<JJ-FF<JF-AF7F<AJF--<-F7-AA-7JFJJFJ< NM:i:1 MD:Z:69C8 AS:i:73 XS:i:73 K00234:90:HTWVHBBXX:6:1101:1844:10493 256 D-AM494716 364 0 3H78M * 0 0 * * NM:i:1 MD:Z:69C8 AS:i:73 ``` those are actually just 2 lines in the SAM file, giving alignments for the same read. The issue here is that the first alignment has a CIGAR string of `3S78M` (3 soft clipped nts, 78 matches) and because it's a soft clip the bases are still in the query string. On the next line we have `*` and `*` for the query and quality (because this is a secondary match (flag = 256)) and a CIGAR string of `3H78M` (3 hard clipped, 78 match). Normally with hard clipping the bases are removed from the sequence, but in this case because the query is first given with a soft clip the bases are retained. So code that assumes hard -clipped bases will be removed will break. You might think `bwa mem -a -H` would cause hard clipping to always be done (perhaps by repeating the (clipped) query sequence in secondary matches) but that's not what happens - bwa reverts to the non- `-a` option behaviour. So our code in `dark/sam.py` will need to be smarter. It should figure out in advance if the query has actually been hard clipped and use that to decide whether a hard clip indicator in the CIGAR string should consume query bases or not.

0.0

845ae82628e8ca00f8a1a1abbe07b07c1ca26677

[ "test/test_sam.py::TestSAMFilter::testAlignmentCount", "test/test_sam.py::TestSAMFilter::testDropDuplicates", "test/test_sam.py::TestSAMFilter::testDropSecondary", "test/test_sam.py::TestSAMFilter::testDropSupplementary", "test/test_sam.py::TestSAMFilter::testKeepQualityControlFailures", "test/test_sam.py::TestSAMFilter::testMaxScore", "test/test_sam.py::TestSAMFilter::testMaxScoreNoScores", "test/test_sam.py::TestSAMFilter::testMinAndMaxScore", "test/test_sam.py::TestSAMFilter::testMinLength", "test/test_sam.py::TestSAMFilter::testMinScore", "test/test_sam.py::TestSAMFilter::testMinScoreNoScores", "test/test_sam.py::TestSAMFilter::testStoreQueryIds", "test/test_sam.py::TestSAMFilter::testUnknownReferences", "test/test_sam.py::TestPaddedSAM::testAllMMatch", "test/test_sam.py::TestPaddedSAM::testAllowDuplicateIds", "test/test_sam.py::TestPaddedSAM::testAlsoYieldAlignments", "test/test_sam.py::TestPaddedSAM::testDropDuplicates", "test/test_sam.py::TestPaddedSAM::testDropSecondary", "test/test_sam.py::TestPaddedSAM::testDropSupplementary", "test/test_sam.py::TestPaddedSAM::testDuplicateIdDisambiguation", "test/test_sam.py::TestPaddedSAM::testHardClipLeft", "test/test_sam.py::TestPaddedSAM::testHardClipRight", "test/test_sam.py::TestPaddedSAM::testHardClippingInCIGARButQueryNotHardClipped", "test/test_sam.py::TestPaddedSAM::testKF414679SoftClipLeft", "test/test_sam.py::TestPaddedSAM::testKeepQualityControlFailures", "test/test_sam.py::TestPaddedSAM::testMinLength", "test/test_sam.py::TestPaddedSAM::testMixedMatch", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReference", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReferenceButNoMatches", "test/test_sam.py::TestPaddedSAM::testNotSecondaryAndNotSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testPrimaryAndSecondaryReferenceInsertion", "test/test_sam.py::TestPaddedSAM::testQueryHardClipAndSoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesRight", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesLeftEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesRightEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipRight", "test/test_sam.py::TestPaddedSAM::testQueryTooLong", "test/test_sam.py::TestPaddedSAM::testRcNeeded", "test/test_sam.py::TestPaddedSAM::testRcSuffix", "test/test_sam.py::TestPaddedSAM::testReferenceDeletion", "test/test_sam.py::TestPaddedSAM::testReferenceDeletionAlternateChar", "test/test_sam.py::TestPaddedSAM::testReferenceInsertion", "test/test_sam.py::TestPaddedSAM::testReferenceSkip", "test/test_sam.py::TestPaddedSAM::testReferenceSkipAlternateChar", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testUnequalReferenceLengths", "test/test_sam.py::TestSamReferencesToStr::testIndent", "test/test_sam.py::TestSamReferencesToStr::testSimple", "test/test_sam.py::TestHardClip::testCIGARLengthTooHigh", "test/test_sam.py::TestHardClip::testCIGARLengthTooLow", "test/test_sam.py::TestHardClip::testClipBoth", "test/test_sam.py::TestHardClip::testClipBothAlreadyDone", "test/test_sam.py::TestHardClip::testClipLeft", "test/test_sam.py::TestHardClip::testClipLeftAlreadyDone", "test/test_sam.py::TestHardClip::testClipRight", "test/test_sam.py::TestHardClip::testClipRightAlreadyDone", "test/test_sam.py::TestHardClip::testHardClipInMiddle", "test/test_sam.py::TestHardClip::testNoClip", "test/test_sam.py::TestHardClip::testThreeHardClips" ]

[]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }

2018-10-05 08:26:07+00:00

mit

869

acorg__dark-matter-637

diff --git a/CHANGELOG.md b/CHANGELOG.md index a68180a..77e9eb6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +## 3.0.44 Nov 1, 2018 + +Fix [636](https://github.com/acorg/dark-matter/issues/636) in which SAM file +parsing threw an exception when an unmapped sequence with no CIGAR string +occurred in a SAM file (this can happen when running `bowtie2 --all`). + ## 3.0.43 Nov 1, 2018 Fixed thinko in 3.0.42. diff --git a/dark/__init__.py b/dark/__init__.py index f10e319..e8e1c5a 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.43' +__version__ = '3.0.44' diff --git a/dark/sam.py b/dark/sam.py index a4f2c1a..f6052ca 100644 --- a/dark/sam.py +++ b/dark/sam.py @@ -332,14 +332,24 @@ class SAMFilter(object): # the previous sequence should be used. This is best # practice according to section 2.5.2 of # https://samtools.github.io/hts-specs/SAMv1.pdf So we use - # the last alignment if we get None as a query sequence. + # the last alignment query and quality strings if we get + # None as a query sequence. if alignment.query_sequence is None: if lastAlignment is None: raise InvalidSAM( 'pysam produced an alignment (number %d) with no ' 'query sequence without previously giving an ' 'alignment with a sequence.' % count) - # Use the previous query sequence and quality. + # Use the previous query sequence and quality. I'm not + # making the call to _hardClip dependent on + # alignment.cigartuples (as in the else clause below) + # because I don't think it's possible for + # alignment.cigartuples to be None in this case. If we + # have a second match on a query, then it must be + # aligned to something (i.e., it cannot be unmapped + # with no CIGAR string). The assertion will tell us if + # this is ever not the case. + assert alignment.cigartuples (alignment.query_sequence, alignment.query_qualities, _) = _hardClip( lastAlignment.query_sequence, @@ -347,11 +357,12 @@ class SAMFilter(object): alignment.cigartuples) else: lastAlignment = alignment - (alignment.query_sequence, - alignment.query_qualities, _) = _hardClip( - alignment.query_sequence, - alignment.query_qualities, - alignment.cigartuples) + if alignment.cigartuples: + (alignment.query_sequence, + alignment.query_qualities, _) = _hardClip( + alignment.query_sequence, + alignment.query_qualities, + alignment.cigartuples) if ((filterRead is None or filterRead(Read(alignment.query_name,

acorg/dark-matter

7fc47a737e687f6b0f0bfe7414c7f8947bb16bea

diff --git a/test/test_sam.py b/test/test_sam.py index 524f8a2..ab4bf4c 100644 --- a/test/test_sam.py +++ b/test/test_sam.py @@ -247,6 +247,24 @@ class TestSAMFilter(TestCase): self.assertEqual('query1', alignment1.query_name) self.assertEqual('query4', alignment2.query_name) + def testCloseButNoCIGAR(self): + """ + An unmapped query with no CIGAR string must be passed through + unchanged if dropUnmapped is not specified. + """ + data = '\n'.join([ + '@SQ SN:ref LN:10', + 'query1 4 * 0 0 * * 0 0 TCTAGG ZZZZZZ', + ]).replace(' ', '\t') + + with dataFile(data) as filename: + sf = SAMFilter(filename) + (alignment,) = list(sf.alignments()) + self.assertEqual('query1', alignment.query_name) + self.assertEqual('TCTAGG', alignment.query_sequence) + self.assertEqual('ZZZZZZ', ''.join( + map(lambda x: chr(x + 33), alignment.query_qualities))) + class TestPaddedSAM(TestCase): """

SAM parsing throws an exception Fix this: ```sh $ filter-sam.py --referenceId Sorsum_high_freq --dropSecond --dropSupp --samfile sorsum-assortedGenotypesDieter-bowtie2.sam >/dev/null Traceback (most recent call last): File "/Users/terry/.virtualenvs/lm36/bin/filter-sam.py", line 90, in <module> for kept, alignment in enumerate(samFilter.alignments(), start=1): File "/Users/terry/.virtualenvs/lm36/lib/python3.6/site-packages/dark/sam.py", line 354, in alignments alignment.cigartuples) File "/Users/terry/.virtualenvs/lm36/lib/python3.6/site-packages/dark/sam.py", line 88, in _hardClip for (operation, length) in cigartuples: TypeError: 'NoneType' object is not iterable ```

0.0

7fc47a737e687f6b0f0bfe7414c7f8947bb16bea

[ "test/test_sam.py::TestSAMFilter::testCloseButNoCIGAR" ]

[ "test/test_sam.py::TestSAMFilter::testAlignmentCount", "test/test_sam.py::TestSAMFilter::testDropDuplicates", "test/test_sam.py::TestSAMFilter::testDropSecondary", "test/test_sam.py::TestSAMFilter::testDropSupplementary", "test/test_sam.py::TestSAMFilter::testKeepQualityControlFailures", "test/test_sam.py::TestSAMFilter::testMaxScore", "test/test_sam.py::TestSAMFilter::testMaxScoreNoScores", "test/test_sam.py::TestSAMFilter::testMinAndMaxScore", "test/test_sam.py::TestSAMFilter::testMinLength", "test/test_sam.py::TestSAMFilter::testMinScore", "test/test_sam.py::TestSAMFilter::testMinScoreNoScores", "test/test_sam.py::TestSAMFilter::testStoreQueryIds", "test/test_sam.py::TestSAMFilter::testUnknownReferences", "test/test_sam.py::TestPaddedSAM::testAllMMatch", "test/test_sam.py::TestPaddedSAM::testAllowDuplicateIds", "test/test_sam.py::TestPaddedSAM::testAlsoYieldAlignments", "test/test_sam.py::TestPaddedSAM::testDropDuplicates", "test/test_sam.py::TestPaddedSAM::testDropSecondary", "test/test_sam.py::TestPaddedSAM::testDropSupplementary", "test/test_sam.py::TestPaddedSAM::testDuplicateIdDisambiguation", "test/test_sam.py::TestPaddedSAM::testHardClipLeft", "test/test_sam.py::TestPaddedSAM::testHardClipRight", "test/test_sam.py::TestPaddedSAM::testHardClippingInCIGARButQueryNotHardClipped", "test/test_sam.py::TestPaddedSAM::testKF414679SoftClipLeft", "test/test_sam.py::TestPaddedSAM::testKeepQualityControlFailures", "test/test_sam.py::TestPaddedSAM::testMinLength", "test/test_sam.py::TestPaddedSAM::testMixedMatch", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReference", "test/test_sam.py::TestPaddedSAM::testMixedMatchSpecificReferenceButNoMatches", "test/test_sam.py::TestPaddedSAM::testNotSecondaryAndNotSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testPrimaryAndSecondaryReferenceInsertion", "test/test_sam.py::TestPaddedSAM::testQueryHardClipAndSoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesBothSides", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesLeft", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipProtrudesRight", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesLeftEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipReachesRightEdge", "test/test_sam.py::TestPaddedSAM::testQuerySoftClipRight", "test/test_sam.py::TestPaddedSAM::testQueryTooLong", "test/test_sam.py::TestPaddedSAM::testRcNeeded", "test/test_sam.py::TestPaddedSAM::testRcSuffix", "test/test_sam.py::TestPaddedSAM::testReferenceDeletion", "test/test_sam.py::TestPaddedSAM::testReferenceDeletionAlternateChars", "test/test_sam.py::TestPaddedSAM::testReferenceInsertion", "test/test_sam.py::TestPaddedSAM::testReferenceSkip", "test/test_sam.py::TestPaddedSAM::testReferenceSkipAlternateChars", "test/test_sam.py::TestPaddedSAM::testSecondaryAlignmentHasQuery", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSecondaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryAlignmentHasQuery", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoPreviousSequence", "test/test_sam.py::TestPaddedSAM::testSupplementaryWithNoSequence", "test/test_sam.py::TestPaddedSAM::testUnequalReferenceLengths", "test/test_sam.py::TestSamReferencesToStr::testIndent", "test/test_sam.py::TestSamReferencesToStr::testSimple", "test/test_sam.py::TestHardClip::testClipBoth", "test/test_sam.py::TestHardClip::testClipBothAlreadyDone", "test/test_sam.py::TestHardClip::testClipLeft", "test/test_sam.py::TestHardClip::testClipLeftAlreadyDone", "test/test_sam.py::TestHardClip::testClipRight", "test/test_sam.py::TestHardClip::testClipRightAlreadyDone", "test/test_sam.py::TestHardClip::testHardClipInMiddle", "test/test_sam.py::TestHardClip::testNoClip", "test/test_sam.py::TestHardClip::testThreeHardClips" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2018-11-01 19:19:21+00:00

mit

870

acorg__dark-matter-647

diff --git a/CHANGELOG.md b/CHANGELOG.md index 2ce0779..3931a9b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,8 @@ +## 3.0.50 Nov 23, 2018 + +Added `bin/convert-diamond-to-sam.py` script to convert DIAMOND output +format 6 to SAM. + ## 3.0.49 Nov 22, 2018 Added `btop2cigar` to `dark.btop` to convert BTOP strings to CIGAR strings. diff --git a/bin/convert-diamond-to-sam.py b/bin/convert-diamond-to-sam.py new file mode 100755 index 0000000..38e3365 --- /dev/null +++ b/bin/convert-diamond-to-sam.py @@ -0,0 +1,145 @@ +#!/usr/bin/env python + +# See https://samtools.github.io/hts-specs/SAMv1.pdf for the SAM file +# format specification. + +from __future__ import print_function, division + +import sys +import argparse +from os.path import basename +from tempfile import TemporaryFile +from functools import partial + +from dark import __version__ as VERSION +from dark.btop import btop2cigar +from dark.diamond.conversion import diamondTabularFormatToDicts +from dark.reads import DNARead + +FIELDS = 'bitscore btop qframe qqual qseq qseqid slen sstart stitle' + +parser = argparse.ArgumentParser( + formatter_class=argparse.ArgumentDefaultsHelpFormatter, + description=('Convert DIAMOND tabular format to SAM. The DIAMOND ' + 'invocation *must* include --outfmt 6 %s' % FIELDS)) + +parser.add_argument( + '--printFields', default=False, action='store_true', + help=('Print the field names in the order that they must be given to ' + 'diamond --outfmt 6 to produce correct input for this script, ' + 'then exit.')) + +parser.add_argument( + '--mappingQuality', type=int, default=255, + help=('The mapping quality to use for MAPQ (field 5). The default (255) ' + 'indicates that mapping quality information is not available.')) + +parser.add_argument( + '--ram', action='store_true', default=False, + help=('Do not use a temporary file to hold the non-header SAM output. ' + 'This will run faster but use more memory since all non-header SAM ' + 'output will be stored in RAM and only written out when the full ' + 'header can be determined.')) + +parser.add_argument( + '--keepDescriptions', action='store_true', default=False, + help=('Do not discard text after the first space in query or subject ' + 'sequence ids. Note that. Note that this violates the SAM ' + 'specification, but since SAM files are TAB-separated there ' + 'is probably only a small chance this will cause any problems ' + 'downstream.')) + +args = parser.parse_args() + +if args.printFields: + print(FIELDS) + sys.exit(0) + +idOnly = not args.keepDescriptions +mappingQuality = args.mappingQuality +ram = args.ram + +if 0 > mappingQuality > 255: + raise ValueError('Mapping quality must be between 0 and 255 (inclusive)') + +referenceLengths = {} + +if ram: + nonHeaderLines = [] + emit = nonHeaderLines.append +else: + tf = TemporaryFile(mode='w+t', encoding='utf-8') + emit = partial(print, file=tf) + +for match in diamondTabularFormatToDicts(sys.stdin, FIELDS.split()): + qseqid = match['qseqid'].split()[0] if idOnly else match['qseqid'] + stitle = match['stitle'].split()[0] if idOnly else match['stitle'] + + referenceLengths[stitle] = match['slen'] + + # If the query frame is less than zero, the match was with a reverse + # complemented translation of the query. Put the reverse compliment + # into the SAM output, which seems to be standard / accepted practice + # based on my web searches. See e.g., https://www.biostars.org/p/131891/ + # for what Bowtie2 does and for some comments on this issue for SAM/BAM + # files in general. + if match['qframe'] > 0: + flag = 0 + qseq = match['qseq'] + qqual = match['qqual'] or '*' + else: + flag = 16 + qseq = DNARead('id', match['qseq']).reverseComplement().sequence + qqual = match['qqual'][::-1] if match['qqual'] else '*' + + emit('\t'.join(map(str, [ + # 1. QNAME + qseqid, + # 2. FLAG + flag, + # 3. RNAME + stitle, + # 4. POS + match['sstart'], + # 5. MAPQ + mappingQuality, + # 6. CIGAR + btop2cigar(match['btop']), + # 7. RNEXT + '*', + # 8. PNEXT + 0, + # 9. TLEN + 0, + # 10. SEQ + qseq, + # 11. QUAL + qqual, + # 12. Alignment score + 'AS:i:%d' % int(match['bitscore'])]))) + + +progName = basename(sys.argv[0]) + +# Print SAM headers. +print('\n'.join( + [ + '@PG\tID:DIAMOND\tPN:DIAMOND', + '@PG\tID:%s\tPN:%s (version %s)\tCL:%s %s\tPP:DIAMOND' % + (progName, progName, VERSION, progName, ' '.join(sys.argv[1:])), + '@CO\t%s is from the dark-matter package ' + '(https://github.com/acorg/dark-matter/)' % progName, + ] + + [ + '@SQ\tSN:%s\tLN:%d' % (name, referenceLengths[name]) + for name in sorted(referenceLengths) + ])) + +# Print non-header lines. +if ram: + print('\n'.join(nonHeaderLines)) +else: + tf.seek(0) + for line in tf: + print(line, end='') + tf.close() diff --git a/dark/__init__.py b/dark/__init__.py index e37701e..a768585 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.49' +__version__ = '3.0.50' diff --git a/dark/diamond/conversion.py b/dark/diamond/conversion.py index 29c2694..42c2a8d 100644 --- a/dark/diamond/conversion.py +++ b/dark/diamond/conversion.py @@ -4,6 +4,7 @@ import six import bz2 from json import dumps, loads from operator import itemgetter +from collections import Counter from Bio.File import as_handle @@ -13,6 +14,85 @@ from dark.alignments import Alignment, ReadAlignments from dark.diamond.hsp import normalizeHSP +# The keys in the following are DIAMOND format 6 field names. The values +# are one-argument functions that take a string and return an appropriately +# converted field value. +# +# The following fields are taken from the DIAMOND manual v0.9.22 2018-05-11. +# Fields whose name doesn't appear here will be left as strings. +DIAMOND_FIELD_CONVERTER = { + 'bitscore': float, + 'evalue': float, + 'frame': int, + 'gapopen': int, + 'gaps': int, + 'identicalCount': lambda nident: None if nident is None else int(nident), + 'length': int, + 'mismatch': int, + 'nident': int, + 'pident': float, + 'positive': int, + 'positiveCount': lambda pos: None if pos is None else int(pos), + 'ppos': float, + 'qcovhsp': float, + 'qend': int, + 'qframe': int, + 'qlen': int, + 'qstart': int, + 'score': float, + 'send': int, + 'slen': int, + 'sstart': int, +} + + +def diamondTabularFormatToDicts(filename, fieldNames): + """ + Read DIAMOND tabular (--outfmt 6) output and convert lines to dictionaries. + + @param filename: Either a C{str} file name or an open file pointer. + @param fieldNames: A C{list} or C{tuple} of C{str} DIAMOND field names. + Run 'diamond -help' to see the full list. + @raise ValueError: If a line of C{filename} does not have the expected + number of TAB-separated fields (i.e., len(fieldNames)). Or if + C{fieldNames} is empty or contains duplicates. + @return: A generator that yields C{dict}s with keys that are the DIAMOND + field names and values as converted by DIAMOND_FIELD_CONVERTER. + """ + nFields = len(fieldNames) + if not nFields: + raise ValueError('fieldNames cannot be empty.') + + c = Counter(fieldNames) + if c.most_common(1)[0][1] > 1: + raise ValueError( + 'fieldNames contains duplicated names: %s.' % + (', '.join(sorted(x[0] for x in c.most_common() if x[1] > 1)))) + + def identity(x): + return x + + convertFunc = DIAMOND_FIELD_CONVERTER.get + + with as_handle(filename) as fp: + for count, line in enumerate(fp, start=1): + result = {} + line = line[:-1] + values = line.split('\t') + if len(values) != nFields: + raise ValueError( + 'Line %d of %s had %d field values (expected %d). ' + 'Line was %r.' % + (count, + (filename if isinstance(filename, six.string_types) + else 'input'), + len(values), nFields, line)) + for fieldName, value in zip(fieldNames, values): + value = convertFunc(fieldName, identity)(value) + result[fieldName] = value + yield result + + class DiamondTabularFormatReader(object): """ Provide a method that yields parsed tabular records from a file. Store and diff --git a/dark/reads.py b/dark/reads.py index b2a4bcc..18171d0 100644 --- a/dark/reads.py +++ b/dark/reads.py @@ -766,7 +766,7 @@ class ReadFilter(object): only return those that have length <= 100, so your result may have less than 20 reads. The former version extracts reads of the desired length and then takes 20 reads at random from that set, so - you'll always get 20 raeds in your result, assuming there are at + you'll always get 20 reads in your result, assuming there are at least that many reads satisfying the length filter. @param trueLength: The C{int} number of reads in this C{Reads} instance. Under normal circumstances it will not be necessary to pass this diff --git a/setup.py b/setup.py index fef9e17..bc089e7 100644 --- a/setup.py +++ b/setup.py @@ -35,6 +35,7 @@ scripts = [ 'bin/compare-sequences.py', 'bin/convert-blast-xml-to-json.py', 'bin/convert-diamond-to-json.py', + 'bin/convert-diamond-to-sam.py', 'bin/convert-sam-to-fastq.sh', 'bin/dark-matter-version.py', 'bin/dna-to-aa.py',

acorg/dark-matter

b36a743b85c8a5b2b8b6d21d337deb70cff193d5

diff --git a/test/diamond/test_conversion.py b/test/diamond/test_conversion.py index 9f80670..fbc6e3f 100644 --- a/test/diamond/test_conversion.py +++ b/test/diamond/test_conversion.py @@ -3,6 +3,7 @@ from unittest import TestCase from io import BytesIO, StringIO import bz2file from bz2 import compress +from six import assertRaisesRegex try: from unittest.mock import patch @@ -13,8 +14,8 @@ from ..mocking import mockOpen from json import dumps -from dark.diamond.conversion import (JSONRecordsReader, - DiamondTabularFormatReader) +from dark.diamond.conversion import ( + JSONRecordsReader, DiamondTabularFormatReader, diamondTabularFormatToDicts) from dark.reads import Reads, AARead @@ -1137,3 +1138,113 @@ class TestJSONRecordsReader(TestCase): reader = JSONRecordsReader('file.json') alignment = list(reader.readAlignments(reads))[0] self.assertEqual('id1 1', alignment.read.id) + + +class TestDiamondTabularFormatToDicts(TestCase): + """ + Tests for the diamondTabularFormatToDicts function. + """ + + def testEmptyFieldNameList(self): + """ + If an empty field name list is passed, the function must raise a + ValueError. + """ + error = '^fieldNames cannot be empty\\.$' + assertRaisesRegex(self, ValueError, error, list, + diamondTabularFormatToDicts(None, [])) + + def testDuplicatesInFieldNameList(self): + """ + If a field name list that contains duplicates is passed, the function + must raise a ValueError. + """ + error = '^fieldNames contains duplicated names: a, b\\.$' + assertRaisesRegex( + self, ValueError, error, list, + diamondTabularFormatToDicts(None, ['a', 'b', 'a', 'c', 'b'])) + + def testTooFewFields(self): + """ + If an input line does not have enough fields, a ValueError must be + raised. + """ + data = StringIO('a\tb\n') + error = (r"^Line 1 of input had 2 field values $expected 3$\. " + r"Line was 'a\\tb'\.") + assertRaisesRegex( + self, ValueError, error, list, + diamondTabularFormatToDicts(data, ['a', 'b', 'c'])) + + def testTooManyFields(self): + """ + If an input line has too many fields, a ValueError must be raised. + """ + data = StringIO('a\tb\tc\n') + error = (r"^Line 1 of input had 3 field values $expected 2$\. " + r"Line was 'a\\tb\\tc'\.") + assertRaisesRegex( + self, ValueError, error, list, + diamondTabularFormatToDicts(data, ['a', 'b'])) + + def testUnknownField(self): + """ + An unknown field name must result in a returned field name and value + that are identical to those in the function call and its input string. + """ + data = StringIO('3.5\n') + (result,) = list(diamondTabularFormatToDicts(data, ['__blah__'])) + self.assertEqual({'__blah__': '3.5'}, result) + + def testConversions(self): + """ + The fields in input lines must be recognized and converted to their + correct types. + """ + fields = [ + 'bitscore', + 'evalue', + 'frame', + 'identicalCount', + 'positiveCount', + 'qstart', + 'qend', + 'sstart', + 'send', + 'qseq', + ] + data = StringIO( + ('3.5 1.7 1 7 4 10 12 1 2 ACGT\n' + '3.6 1.8 2 8 5 11 13 2 3 TGCA').replace(' ', '\t') + '\n' + ) + (result1, result2) = list(diamondTabularFormatToDicts(data, fields)) + + self.assertEqual( + { + 'bitscore': 3.5, + 'evalue': 1.7, + 'frame': 1, + 'identicalCount': 7, + 'positiveCount': 4, + 'qstart': 10, + 'qend': 12, + 'sstart': 1, + 'send': 2, + 'qseq': 'ACGT', + }, + result1) + + self.assertEqual( + { + 'bitscore': 3.6, + 'evalue': 1.8, + 'frame': 2, + 'identicalCount': 8, + 'positiveCount': 5, + 'qstart': 11, + 'qend': 13, + 'sstart': 2, + 'send': 3, + 'qseq': 'TGCA', + }, + result2)

Add a script to convert DIAMOND output to SAM

0.0

b36a743b85c8a5b2b8b6d21d337deb70cff193d5

[ "test/diamond/test_conversion.py::TestDiamondTabularFormatReader::testDiamondInput", "test/diamond/test_conversion.py::TestDiamondTabularFormatReader::testDiamondInputWithoutNidentOrPositives", "test/diamond/test_conversion.py::TestDiamondTabularFormatReader::testDiamondParams", "test/diamond/test_conversion.py::TestDiamondTabularFormatReader::testSaveAsJSON", "test/diamond/test_conversion.py::TestDiamondTabularFormatReader::testSaveAsJSONBzip2", "test/diamond/test_conversion.py::TestDiamondTabularFormatReader::testSpacesMustBePreserved", "test/diamond/test_conversion.py::TestJSONRecordsReader::testCorrectNumberOfAlignments", "test/diamond/test_conversion.py::TestJSONRecordsReader::testCorrectNumberOfAlignmentsMatchMissingEnd", "test/diamond/test_conversion.py::TestJSONRecordsReader::testCorrectNumberOfAlignmentsMatchMissingMiddle", "test/diamond/test_conversion.py::TestJSONRecordsReader::testCorrectNumberOfAlignmentsMatchMissingStart", "test/diamond/test_conversion.py::TestJSONRecordsReader::testCorrectNumberOfAlignmentsTwoMatchesMissingEnd", "test/diamond/test_conversion.py::TestJSONRecordsReader::testSpaceInReadIdNotInJSONRecord", "test/diamond/test_conversion.py::TestJSONRecordsReader::testSpacesMustBePreserved", "test/diamond/test_conversion.py::TestDiamondTabularFormatToDicts::testConversions", "test/diamond/test_conversion.py::TestDiamondTabularFormatToDicts::testDuplicatesInFieldNameList", "test/diamond/test_conversion.py::TestDiamondTabularFormatToDicts::testEmptyFieldNameList", "test/diamond/test_conversion.py::TestDiamondTabularFormatToDicts::testTooFewFields", "test/diamond/test_conversion.py::TestDiamondTabularFormatToDicts::testTooManyFields", "test/diamond/test_conversion.py::TestDiamondTabularFormatToDicts::testUnknownField" ]

[]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_added_files", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }

2018-11-23 14:15:52+00:00

mit

871

acorg__dark-matter-649

diff --git a/CHANGELOG.md b/CHANGELOG.md index 271f053..588c254 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,7 @@ +## 3.0.52 Nov 23, 2018 + +Added hard-clipping to CIGAR in SAM created by `convert-diamond-to-sam.py`. + ## 3.0.51 Nov 23, 2018 Use `from six import StringIO` to avoid a PY2/3 incompatibility. diff --git a/bin/convert-diamond-to-sam.py b/bin/convert-diamond-to-sam.py index 38e3365..0b3484f 100755 --- a/bin/convert-diamond-to-sam.py +++ b/bin/convert-diamond-to-sam.py @@ -16,7 +16,8 @@ from dark.btop import btop2cigar from dark.diamond.conversion import diamondTabularFormatToDicts from dark.reads import DNARead -FIELDS = 'bitscore btop qframe qqual qseq qseqid slen sstart stitle' +FIELDS = ('bitscore btop qframe qend qqual qlen qseq qseqid qstart slen ' + 'sstart stitle') parser = argparse.ArgumentParser( formatter_class=argparse.ArgumentDefaultsHelpFormatter, @@ -92,6 +93,21 @@ for match in diamondTabularFormatToDicts(sys.stdin, FIELDS.split()): qseq = DNARead('id', match['qseq']).reverseComplement().sequence qqual = match['qqual'][::-1] if match['qqual'] else '*' + # Make a CIGAR string, including hard-clipped bases at the start and + # end of the query (DIAMOND outputs a hard-clipped query sequence). + startClipCount = match['qstart'] - 1 + endClipCount = match['qlen'] - match['qend'] + + assert startClipCount >= 0 + assert endClipCount >= 0, ( + 'Query sequence %s has length %d but the qend value is %d' % + (qseq, len(match['qseq']), match['qend'])) + + cigar = ( + ('%dH' % startClipCount if startClipCount else '') + + btop2cigar(match['btop'], concise=False, aa=True) + + ('%dH' % endClipCount if endClipCount else '')) + emit('\t'.join(map(str, [ # 1. QNAME qseqid, @@ -104,7 +120,7 @@ for match in diamondTabularFormatToDicts(sys.stdin, FIELDS.split()): # 5. MAPQ mappingQuality, # 6. CIGAR - btop2cigar(match['btop']), + cigar, # 7. RNEXT '*', # 8. PNEXT diff --git a/dark/__init__.py b/dark/__init__.py index 3e72b1a..147b204 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.51' +__version__ = '3.0.52' diff --git a/dark/btop.py b/dark/btop.py index 9855734..aa338da 100644 --- a/dark/btop.py +++ b/dark/btop.py @@ -73,24 +73,34 @@ def countGaps(btopString): return (queryGaps, subjectGaps) -def btop2cigar(btopString, concise=False): +def btop2cigar(btopString, concise=False, aa=False): """ Convert a BTOP string to a CIGAR string. @param btopString: A C{str} BTOP sequence. @param concise: If C{True}, use 'M' for matches and mismatches instead of the more specific 'X' and '='. - - @raise ValueError: If L{parseBtop} finds an error in C{btopString}. + @param aa: If C{True}, C{btopString} will be interpreted as though it + refers to amino acids (as in the BTOP string produced by DIAMOND). + In that case, it is not possible to use the 'precise' CIGAR characters + because amino acids have multiple codons so we cannot know whether + an amino acid match is due to an exact nucleotide matches or not. + Also, the numbers in the BTOP string will be multiplied by 3 since + they refer to a number of amino acids matching. + @raise ValueError: If L{parseBtop} finds an error in C{btopString} or + if C{aa} and C{concise} are both C{True}. @return: A C{str} CIGAR string. """ + if aa and concise: + raise ValueError('aa and concise cannot both be True') + result = [] thisLength = thisOperation = currentLength = currentOperation = None for item in parseBtop(btopString): if isinstance(item, int): thisLength = item - thisOperation = CMATCH if concise else CEQUAL + thisOperation = CEQUAL if concise else CMATCH else: thisLength = 1 query, reference = item @@ -108,13 +118,16 @@ def btop2cigar(btopString, concise=False): else: # A substitution was needed. assert query != reference - thisOperation = CMATCH if concise else CDIFF + thisOperation = CDIFF if concise else CMATCH if thisOperation == currentOperation: currentLength += thisLength else: if currentOperation: - result.append('%d%s' % (currentLength, currentOperation)) + result.append( + '%d%s' % + ((3 * currentLength) if aa else currentLength, + currentOperation)) currentLength, currentOperation = thisLength, thisOperation # We reached the end of the BTOP string. If there was an operation @@ -122,6 +135,8 @@ def btop2cigar(btopString, concise=False): # case where btopString was empty. assert currentOperation or btopString == '' if currentOperation: - result.append('%d%s' % (currentLength, currentOperation)) + result.append( + '%d%s' % + ((3 * currentLength) if aa else currentLength, currentOperation)) return ''.join(result)

acorg/dark-matter

3d48d201d41d8cabaa1f31d5dd7987e882a68af3

diff --git a/test/test_btop.py b/test/test_btop.py index 9f1f22a..e019563 100644 --- a/test/test_btop.py +++ b/test/test_btop.py @@ -164,15 +164,15 @@ class TestCountGaps(TestCase): self.assertEqual((3, 2), countGaps('-GG-34-T-T39F-')) -class TestBtop2CigarConcise(TestCase): +class TestBtop2CigarPrecise(TestCase): """ - Tests for the btop2cigar function when concise is True. + Tests for the btop2cigar function when concise is False. """ def testEmpty(self): """ An empty BTOP string must result in an empty CIGAR string. """ - self.assertEqual('', btop2cigar('', concise=True)) + self.assertEqual('', btop2cigar('', concise=False)) def testMixedMatch(self): """ @@ -180,7 +180,7 @@ class TestBtop2CigarConcise(TestCase): CIGAR sense where M could be identical characters or not), the CIGAR string must be all Ms. """ - self.assertEqual('7M', btop2cigar('2GC3AT', concise=True)) + self.assertEqual('7M', btop2cigar('2GC3AT', concise=False)) def testRefenceInsertion(self): """ @@ -188,7 +188,7 @@ class TestBtop2CigarConcise(TestCase): subject (reference) does not, the CIGAR string must indicate an insertion to the reference. """ - self.assertEqual('1I', btop2cigar('A-', concise=True)) + self.assertEqual('1I', btop2cigar('A-', concise=False)) def testQueryInsertion(self): """ @@ -196,7 +196,7 @@ class TestBtop2CigarConcise(TestCase): but the query does not, the CIGAR string must indicate an deletion in the reference. """ - self.assertEqual('1D', btop2cigar('-A', concise=True)) + self.assertEqual('1D', btop2cigar('-A', concise=False)) def testAll(self): """ @@ -204,25 +204,36 @@ class TestBtop2CigarConcise(TestCase): string must be correct. """ self.assertEqual('7M2I4M2D5M', - btop2cigar('2GC3ATC-G-4-T-A5', concise=True)) + btop2cigar('2GC3ATC-G-4-T-A5', concise=False)) + def testAllAA(self): + """ + If a BTOP string specifies all possible variations, and we indicate + that the BTOP string refers to amino acids, the CIGAR string must be + correct (i.e., all counts must be tripled). + """ + self.assertEqual( + '21M6I12M6D15M', + btop2cigar('2GC3ATC-G-4-T-A5', concise=False, aa=True)) -class TestBtop2CigarPrecise(TestCase): + +class TestBtop2CigarConcise(TestCase): """ - Tests for the btop2cigar function when concise is False. + Tests for the btop2cigar function when concise is True. """ + def testEmpty(self): """ An empty BTOP string must result in an empty CIGAR string. """ - self.assertEqual('', btop2cigar('', concise=False)) + self.assertEqual('', btop2cigar('', concise=True)) def testMixedMatch(self): """ If a BTOP string specifies that some characters match and some do not, the CIGAR string must be specific about the matches / mismatches. """ - self.assertEqual('2=1X3=1X', btop2cigar('2GC3AT', concise=False)) + self.assertEqual('2=1X3=1X', btop2cigar('2GC3AT', concise=True)) def testRefenceInsertion(self): """ @@ -230,7 +241,7 @@ class TestBtop2CigarPrecise(TestCase): subject (reference) does not, the CIGAR string must indicate an insertion to the reference. """ - self.assertEqual('1I', btop2cigar('A-', concise=False)) + self.assertEqual('1I', btop2cigar('A-', concise=True)) def testQueryInsertion(self): """ @@ -238,7 +249,7 @@ class TestBtop2CigarPrecise(TestCase): but the query does not, the CIGAR string must indicate an deletion in the reference. """ - self.assertEqual('1D', btop2cigar('-A', concise=False)) + self.assertEqual('1D', btop2cigar('-A', concise=True)) def testAll(self): """ @@ -246,4 +257,12 @@ class TestBtop2CigarPrecise(TestCase): string must be correct. """ self.assertEqual('2=1X3=1X2I4=2D5=', - btop2cigar('2GC3ATC-G-4-T-A5', concise=False)) + btop2cigar('2GC3ATC-G-4-T-A5', concise=True)) + + def testWithAATrue(self): + """ + If concise and aa are both set to True, a ValueError must be raised. + """ + error = '^aa and concise cannot both be True$' + assertRaisesRegex(self, ValueError, error, btop2cigar, '', + concise=True, aa=True)

Add soft-clipping to CIGAR string in convert-diamond-to-sam.py

0.0

3d48d201d41d8cabaa1f31d5dd7987e882a68af3

[ "test/test_btop.py::TestBtop2CigarPrecise::testAll", "test/test_btop.py::TestBtop2CigarPrecise::testAllAA", "test/test_btop.py::TestBtop2CigarPrecise::testMixedMatch", "test/test_btop.py::TestBtop2CigarConcise::testAll", "test/test_btop.py::TestBtop2CigarConcise::testMixedMatch", "test/test_btop.py::TestBtop2CigarConcise::testWithAATrue" ]

[ "test/test_btop.py::TestParseBtop::testConsecutiveGaps", "test/test_btop.py::TestParseBtop::testConsecutiveIdentical", "test/test_btop.py::TestParseBtop::testEmpty", "test/test_btop.py::TestParseBtop::testOneLetter", "test/test_btop.py::TestParseBtop::testOneLetterThenANumber", "test/test_btop.py::TestParseBtop::testOneNumber", "test/test_btop.py::TestParseBtop::testOneNumberThatIsZero", "test/test_btop.py::TestParseBtop::testOneNumberWithLeadingZeroes", "test/test_btop.py::TestParseBtop::testOneNumberWithTrailingOneLetter", "test/test_btop.py::TestParseBtop::testOneQuerySubjectPair", "test/test_btop.py::TestParseBtop::testOneQuerySubjectPairAndANumber", "test/test_btop.py::TestParseBtop::testThreeLetters", "test/test_btop.py::TestParseBtop::testTwoNumbersWithOneLetterBetween", "test/test_btop.py::TestParseBtop::testTwoQuerySubjectPairs", "test/test_btop.py::TestCountGaps::testEmpty", "test/test_btop.py::TestCountGaps::testLettersButNoGaps", "test/test_btop.py::TestCountGaps::testMultipleQueryAndSubjectGaps", "test/test_btop.py::TestCountGaps::testNumberOnly", "test/test_btop.py::TestCountGaps::testOneQueryAndOneSubjectGap", "test/test_btop.py::TestCountGaps::testOneQueryGap", "test/test_btop.py::TestCountGaps::testOneSubjectGap", "test/test_btop.py::TestBtop2CigarPrecise::testEmpty", "test/test_btop.py::TestBtop2CigarPrecise::testQueryInsertion", "test/test_btop.py::TestBtop2CigarPrecise::testRefenceInsertion", "test/test_btop.py::TestBtop2CigarConcise::testEmpty", "test/test_btop.py::TestBtop2CigarConcise::testQueryInsertion", "test/test_btop.py::TestBtop2CigarConcise::testRefenceInsertion" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }

2018-11-23 16:46:53+00:00

mit

872

acorg__dark-matter-663

diff --git a/CHANGELOG.md b/CHANGELOG.md index fa389b6..e329501 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,10 @@ +## 3.0.60 Dec 13, 2018 + +In `reads.py`, changed the `_makeComplementTable` function so that +uppercase and lowercase bases are correctly reverse complemented into their +respective uppercase and lowercase complementary letters. Added a test to +`test/reads.py` to confirm that `reverseComplement` does this. + ## 3.0.59 Dec 11, 2018 Added `--sampleName` option to `proteins-to-pathogens`. diff --git a/dark/__init__.py b/dark/__init__.py index 278f52a..ffb465c 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -8,4 +8,4 @@ if sys.version_info < (2, 7): # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.59' +__version__ = '3.0.60' diff --git a/dark/reads.py b/dark/reads.py index 18171d0..df381e0 100644 --- a/dark/reads.py +++ b/dark/reads.py @@ -27,7 +27,8 @@ def _makeComplementTable(complementData): """ table = list(range(256)) for _from, to in complementData.items(): - table[ord(_from[0])] = ord(to[0]) + table[ord(_from[0].lower())] = ord(to[0].lower()) + table[ord(_from[0].upper())] = ord(to[0].upper()) return ''.join(map(chr, table))

acorg/dark-matter

31c6f64ccf9e55821a250a5a4324860c29782a0e

diff --git a/test/test_reads.py b/test/test_reads.py index d586ab1..4663234 100644 --- a/test/test_reads.py +++ b/test/test_reads.py @@ -652,6 +652,16 @@ class TestDNARead(TestCase): read = DNARead('id', 'ATCGMRWSVHXN') self.assertEqual('NXDBSWYKCGAT', read.reverseComplement().sequence) + def testReverseComplementLowercaseLetters(self): + """ + The reverseComplement function must correctly reverse complement + lowercase letters. The issue is described here: + https://github.com/acorg/dark-matter/issues/662 + """ + read = DNARead('id', 'CAGCAGctgcagcaccagcaccagcagcttcCACAT') + expected = ('ATGTGgaagctgctggtgctggtgctgcagCTGCTG') + self.assertEqual(expected, read.reverseComplement().sequence) + def testTranslationsOfEmptySequence(self): """ The translations function must correctly return all six (empty)

Extract-ORFs.py mistranslates lowercase letters In a sequence with mixed uppercase and lowercase letters, extract-ORFs.py output has incorrect translations only for the sites of lowercase letters. (Even though the `translations` function of `dark/reads.py` translate a sequence with mixed upper and lower case letters correctly)

0.0

31c6f64ccf9e55821a250a5a4324860c29782a0e

[ "test/test_reads.py::TestDNARead::testReverseComplementLowercaseLetters" ]

[ "test/test_reads.py::TestRead::testCasePreservation", "test/test_reads.py::TestRead::testCheckAlphabetAAReadMatchingReturnTrue", "test/test_reads.py::TestRead::testCheckAlphabetAAReadNotMatchingRaise", "test/test_reads.py::TestRead::testCheckAlphabetDNAReadMatchingReturnTrue", "test/test_reads.py::TestRead::testCheckAlphabetDNAReadNotMatchingRaise", "test/test_reads.py::TestRead::testCheckAlphabetwithReadMustBePermissive", "test/test_reads.py::TestRead::testEquality", "test/test_reads.py::TestRead::testEqualityWithDifferingIds", "test/test_reads.py::TestRead::testEqualityWithDifferingQuality", "test/test_reads.py::TestRead::testEqualityWithDifferingSequences", "test/test_reads.py::TestRead::testEqualityWithNoQuality", "test/test_reads.py::TestRead::testEqualityWithOneOmittedQuality", "test/test_reads.py::TestRead::testExpectedAttributes", "test/test_reads.py::TestRead::testFromDict", "test/test_reads.py::TestRead::testFromDictNoQuality", "test/test_reads.py::TestRead::testGetitemFullCopy", "test/test_reads.py::TestRead::testGetitemId", "test/test_reads.py::TestRead::testGetitemLength", "test/test_reads.py::TestRead::testGetitemQuality", "test/test_reads.py::TestRead::testGetitemReturnsNewRead", "test/test_reads.py::TestRead::testGetitemReversed", "test/test_reads.py::TestRead::testGetitemSequence", "test/test_reads.py::TestRead::testGetitemSingleIndex", "test/test_reads.py::TestRead::testGetitemWithStep", "test/test_reads.py::TestRead::testHashDiffersIfIdDiffers", "test/test_reads.py::TestRead::testHashDiffersIfQualityDiffers", "test/test_reads.py::TestRead::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestRead::testHashIdenticalNoQuality", "test/test_reads.py::TestRead::testHashIdenticalWithQuality", "test/test_reads.py::TestRead::testHashViaDict", "test/test_reads.py::TestRead::testHashViaSet", "test/test_reads.py::TestRead::testKeepSites", "test/test_reads.py::TestRead::testKeepSitesAllSites", "test/test_reads.py::TestRead::testKeepSitesNoSites", "test/test_reads.py::TestRead::testKeepSitesOutOfRange", "test/test_reads.py::TestRead::testKeepSitesWithQuality", "test/test_reads.py::TestRead::testLength", "test/test_reads.py::TestRead::testLowComplexityFraction", "test/test_reads.py::TestRead::testLowComplexityFractionEmptySequence", "test/test_reads.py::TestRead::testLowComplexityFractionOne", "test/test_reads.py::TestRead::testLowComplexityFractionZero", "test/test_reads.py::TestRead::testNoQuality", "test/test_reads.py::TestRead::testRemoveSites", "test/test_reads.py::TestRead::testRemoveSitesAllSites", "test/test_reads.py::TestRead::testRemoveSitesNoSites", "test/test_reads.py::TestRead::testRemoveSitesOutOfRange", "test/test_reads.py::TestRead::testRemoveSitesWithQuality", "test/test_reads.py::TestRead::testToDict", "test/test_reads.py::TestRead::testToDictNoQuality", "test/test_reads.py::TestRead::testToFASTA", "test/test_reads.py::TestRead::testToFASTAWithQuality", "test/test_reads.py::TestRead::testToFASTQ", "test/test_reads.py::TestRead::testToFASTQWithNoQuality", "test/test_reads.py::TestRead::testToUnknownFormat", "test/test_reads.py::TestRead::testUnequalLengths", "test/test_reads.py::TestRead::testWalkHSPExactMatch", "test/test_reads.py::TestRead::testWalkHSPExactMatchWithGap", "test/test_reads.py::TestRead::testWalkHSPLeftAndRightOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPLeftAndRightOverhangingMatchNoWhiskers", "test/test_reads.py::TestRead::testWalkHSPLeftOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPLeftOverhangingMatchNoWhiskers", "test/test_reads.py::TestRead::testWalkHSPRightOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPRightOverhangingMatchNoWhiskers", "test/test_reads.py::TestDNARead::testGetitemReturnsNewDNARead", "test/test_reads.py::TestDNARead::testReverseComplement", "test/test_reads.py::TestDNARead::testReverseComplementAmbiguous", "test/test_reads.py::TestDNARead::testReverseComplementReversesQuality", "test/test_reads.py::TestDNARead::testTranslationOfMultipleStopCodons", "test/test_reads.py::TestDNARead::testTranslationOfStartCodonATG", "test/test_reads.py::TestDNARead::testTranslationOfStopCodonTAG", "test/test_reads.py::TestDNARead::testTranslationOfStopCodonTGA", "test/test_reads.py::TestDNARead::testTranslations", "test/test_reads.py::TestDNARead::testTranslationsOfEmptySequence", "test/test_reads.py::TestDNARead::testTranslationsOfOneBaseSequence", "test/test_reads.py::TestDNARead::testTranslationsOfTwoBaseSequence", "test/test_reads.py::TestRNARead::testGetitemReturnsNewRNARead", "test/test_reads.py::TestRNARead::testReverseComplement", "test/test_reads.py::TestRNARead::testReverseComplementAmbiguous", "test/test_reads.py::TestRNARead::testTranslationOfStopCodonUAA", "test/test_reads.py::TestAARead::testCloseCloseORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseCloseORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseCloseORFWithJunk", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseOpenORF", "test/test_reads.py::TestAARead::testCloseCloseThenCloseCloseThenCloseOpenORFWithJunk", "test/test_reads.py::TestAARead::testCloseCloseThenCloseOpenORF", "test/test_reads.py::TestAARead::testCloseOpenORF", "test/test_reads.py::TestAARead::testCloseOpenORFWithMultipleStarts", "test/test_reads.py::TestAARead::testGetitemReturnsNewAARead", "test/test_reads.py::TestAARead::testNoStartCodon_GithubIssue239", "test/test_reads.py::TestAARead::testORFsEmptySequence", "test/test_reads.py::TestAARead::testORFsEmptySequenceWithStart", "test/test_reads.py::TestAARead::testORFsEmptySequenceWithStartStop", "test/test_reads.py::TestAARead::testORFsWithJustStartsAndStops", "test/test_reads.py::TestAARead::testORFsWithOneStopCodon", "test/test_reads.py::TestAARead::testORFsWithTwoStopCodons", "test/test_reads.py::TestAARead::testOpenCloseORF", "test/test_reads.py::TestAARead::testOpenCloseORFWithMultipleStops", "test/test_reads.py::TestAARead::testOpenCloseThenCloseCloseThenCloseOpenORF", "test/test_reads.py::TestAARead::testOpenCloseThenCloseCloseThenCloseOpenORFWithJunk", "test/test_reads.py::TestAARead::testOpenCloseThenCloseOpenORF", "test/test_reads.py::TestAARead::testOpenOpenORF", "test/test_reads.py::TestAARead::testPropertiesCorrectTranslation", "test/test_reads.py::TestAARead::testPropertyDetailsCorrectTranslation", "test/test_reads.py::TestAAReadWithX::testAlphabet", "test/test_reads.py::TestAAReadWithX::testAlphabetChecking", "test/test_reads.py::TestAAReadWithX::testGetitemReturnsNewAAReadWithX", "test/test_reads.py::TestAAReadORF::testClosedClosedId", "test/test_reads.py::TestAAReadORF::testClosedOpenId", "test/test_reads.py::TestAAReadORF::testFromDict", "test/test_reads.py::TestAAReadORF::testOpenClosedId", "test/test_reads.py::TestAAReadORF::testOpenLeft", "test/test_reads.py::TestAAReadORF::testOpenOpenId", "test/test_reads.py::TestAAReadORF::testOpenRight", "test/test_reads.py::TestAAReadORF::testSequence", "test/test_reads.py::TestAAReadORF::testStart", "test/test_reads.py::TestAAReadORF::testStartGreaterThanStop", "test/test_reads.py::TestAAReadORF::testStartNegative", "test/test_reads.py::TestAAReadORF::testStop", "test/test_reads.py::TestAAReadORF::testStopGreaterThanOriginalSequenceLength", "test/test_reads.py::TestAAReadORF::testToDict", "test/test_reads.py::TestSSAARead::testCorrectAttributes", "test/test_reads.py::TestSSAARead::testFromDict", "test/test_reads.py::TestSSAARead::testGetitemFullCopy", "test/test_reads.py::TestSSAARead::testGetitemId", "test/test_reads.py::TestSSAARead::testGetitemLength", "test/test_reads.py::TestSSAARead::testGetitemReturnsNewRead", "test/test_reads.py::TestSSAARead::testGetitemReversed", "test/test_reads.py::TestSSAARead::testGetitemSequence", "test/test_reads.py::TestSSAARead::testGetitemSingleIndex", "test/test_reads.py::TestSSAARead::testGetitemStructure", "test/test_reads.py::TestSSAARead::testGetitemWithStep", "test/test_reads.py::TestSSAARead::testHashDiffersIfIdDiffers", "test/test_reads.py::TestSSAARead::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestSSAARead::testHashDiffersIfStructureDiffers", "test/test_reads.py::TestSSAARead::testHashViaDict", "test/test_reads.py::TestSSAARead::testHashViaSet", "test/test_reads.py::TestSSAARead::testKeepSites", "test/test_reads.py::TestSSAARead::testKeepSitesAllSites", "test/test_reads.py::TestSSAARead::testKeepSitesNoSites", "test/test_reads.py::TestSSAARead::testKeepSitesOutOfRange", "test/test_reads.py::TestSSAARead::testReads", "test/test_reads.py::TestSSAARead::testRemoveSites", "test/test_reads.py::TestSSAARead::testRemoveSitesAllSites", "test/test_reads.py::TestSSAARead::testRemoveSitesNoSites", "test/test_reads.py::TestSSAARead::testRemoveSitesOutOfRange", "test/test_reads.py::TestSSAARead::testSequenceLengthMatchesStructureLength", "test/test_reads.py::TestSSAARead::testToDict", "test/test_reads.py::TestSSAARead::testToString", "test/test_reads.py::TestSSAARead::testToStringWithExplicitFastaFormat", "test/test_reads.py::TestSSAARead::testToStringWithExplicitFastaSSFormat", "test/test_reads.py::TestSSAARead::testToStringWithStructureSuffix", "test/test_reads.py::TestSSAARead::testToStringWithUnknownFormat", "test/test_reads.py::TestSSAAReadWithX::testCorrectAttributes", "test/test_reads.py::TestSSAAReadWithX::testFromDict", "test/test_reads.py::TestSSAAReadWithX::testGetitemFullCopy", "test/test_reads.py::TestSSAAReadWithX::testGetitemId", "test/test_reads.py::TestSSAAReadWithX::testGetitemLength", "test/test_reads.py::TestSSAAReadWithX::testGetitemReturnsNewRead", "test/test_reads.py::TestSSAAReadWithX::testGetitemReversed", "test/test_reads.py::TestSSAAReadWithX::testGetitemSequence", "test/test_reads.py::TestSSAAReadWithX::testGetitemSingleIndex", "test/test_reads.py::TestSSAAReadWithX::testGetitemStructure", "test/test_reads.py::TestSSAAReadWithX::testGetitemWithStep", "test/test_reads.py::TestSSAAReadWithX::testHashDiffersIfIdDiffers", "test/test_reads.py::TestSSAAReadWithX::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestSSAAReadWithX::testHashDiffersIfStructureDiffers", "test/test_reads.py::TestSSAAReadWithX::testHashViaDict", "test/test_reads.py::TestSSAAReadWithX::testHashViaSet", "test/test_reads.py::TestSSAAReadWithX::testKeepSites", "test/test_reads.py::TestSSAAReadWithX::testKeepSitesAllSites", "test/test_reads.py::TestSSAAReadWithX::testKeepSitesNoSites", "test/test_reads.py::TestSSAAReadWithX::testKeepSitesOutOfRange", "test/test_reads.py::TestSSAAReadWithX::testReads", "test/test_reads.py::TestSSAAReadWithX::testRemoveSites", "test/test_reads.py::TestSSAAReadWithX::testRemoveSitesAllSites", "test/test_reads.py::TestSSAAReadWithX::testRemoveSitesNoSites", "test/test_reads.py::TestSSAAReadWithX::testRemoveSitesOutOfRange", "test/test_reads.py::TestSSAAReadWithX::testSequenceContainingX", "test/test_reads.py::TestSSAAReadWithX::testSequenceLengthMatchesStructureLength", "test/test_reads.py::TestSSAAReadWithX::testToDict", "test/test_reads.py::TestSSAAReadWithX::testToString", "test/test_reads.py::TestSSAAReadWithX::testToStringWithExplicitFastaFormat", "test/test_reads.py::TestSSAAReadWithX::testToStringWithExplicitFastaSSFormat", "test/test_reads.py::TestSSAAReadWithX::testToStringWithStructureSuffix", "test/test_reads.py::TestSSAAReadWithX::testToStringWithUnknownFormat", "test/test_reads.py::TestTranslatedRead::testExpectedAttributes", "test/test_reads.py::TestTranslatedRead::testExpectedFrame", "test/test_reads.py::TestTranslatedRead::testFromDict", "test/test_reads.py::TestTranslatedRead::testId", "test/test_reads.py::TestTranslatedRead::testIdReverseComplemented", "test/test_reads.py::TestTranslatedRead::testMaximumORFLength", "test/test_reads.py::TestTranslatedRead::testMaximumORFLengthNoStops", "test/test_reads.py::TestTranslatedRead::testOutOfRangeFrame", "test/test_reads.py::TestTranslatedRead::testReverseComplemented", "test/test_reads.py::TestTranslatedRead::testSequence", "test/test_reads.py::TestTranslatedRead::testToDict", "test/test_reads.py::TestReadClassNameToClass::testNames", "test/test_reads.py::TestReads::testEmptyInitialReads", "test/test_reads.py::TestReads::testInitialReads", "test/test_reads.py::TestReads::testManuallyAddedReads", "test/test_reads.py::TestReads::testManuallyAddedReadsLength", "test/test_reads.py::TestReads::testNoReads", "test/test_reads.py::TestReads::testNoReadsLength", "test/test_reads.py::TestReads::testRepeatedIter", "test/test_reads.py::TestReads::testSaveAsFASTA", "test/test_reads.py::TestReads::testSaveAsFASTQ", "test/test_reads.py::TestReads::testSaveAsFASTQFailsOnReadWithNoQuality", "test/test_reads.py::TestReads::testSaveFASTAIsDefault", "test/test_reads.py::TestReads::testSaveReturnsReadCount", "test/test_reads.py::TestReads::testSaveToFileDescriptor", "test/test_reads.py::TestReads::testSaveWithUnknownFormat", "test/test_reads.py::TestReads::testSaveWithUppercaseFormat", "test/test_reads.py::TestReads::testSubclass", "test/test_reads.py::TestReads::testSubclassLength", "test/test_reads.py::TestReads::testSubclassWithAdditionalReads", "test/test_reads.py::TestReads::testUnfilteredLengthAdditionalReads", "test/test_reads.py::TestReads::testUnfilteredLengthAdditionalReadsAfterFiltering", "test/test_reads.py::TestReads::testUnfilteredLengthBeforeIterating", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReads", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReadsAfterFiltering", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReadsIsReads", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReadsIsReadsWithAdditional", "test/test_reads.py::TestReads::testUnfilteredLengthInitialSubclassThenFiltered", "test/test_reads.py::TestReads::testUnfilteredLengthInitialSubclassWithAdditionalThenFiltered", "test/test_reads.py::TestReads::testUnfilteredLengthInitialSubclassWithNoLen", "test/test_reads.py::TestReads::testUnfilteredLengthNoReads", "test/test_reads.py::TestReadsFiltering::testAddFiltersThenClearFilters", "test/test_reads.py::TestReadsFiltering::testFilterBlacklist", "test/test_reads.py::TestReadsFiltering::testFilterDoNotRemoveDescriptions", "test/test_reads.py::TestReadsFiltering::testFilterDuplicates", "test/test_reads.py::TestReadsFiltering::testFilterDuplicatesById", "test/test_reads.py::TestReadsFiltering::testFilterHead", "test/test_reads.py::TestReadsFiltering::testFilterHeadZero", "test/test_reads.py::TestReadsFiltering::testFilterKeepSequences", "test/test_reads.py::TestReadsFiltering::testFilterKeepSequencesNoSequences", "test/test_reads.py::TestReadsFiltering::testFilterNegativeRegex", "test/test_reads.py::TestReadsFiltering::testFilterNoArgs", "test/test_reads.py::TestReadsFiltering::testFilterOnLengthEverythingMatches", "test/test_reads.py::TestReadsFiltering::testFilterOnLengthNothingMatches", "test/test_reads.py::TestReadsFiltering::testFilterOnMaxLength", "test/test_reads.py::TestReadsFiltering::testFilterOnMinLength", "test/test_reads.py::TestReadsFiltering::testFilterPositiveRegex", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfFiveFromFiveReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfFiveFromOneRead", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfOneFromOneRead", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfTwoFromFiveReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfZeroReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetSizeZeroNoReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetSizeZeroTwoReads", "test/test_reads.py::TestReadsFiltering::testFilterRemoveDescriptions", "test/test_reads.py::TestReadsFiltering::testFilterRemoveGaps", "test/test_reads.py::TestReadsFiltering::testFilterRemoveGapsWithQuality", "test/test_reads.py::TestReadsFiltering::testFilterRemoveSequences", "test/test_reads.py::TestReadsFiltering::testFilterRemoveSequencesNoSequences", "test/test_reads.py::TestReadsFiltering::testFilterReturnsReadInstance", "test/test_reads.py::TestReadsFiltering::testFilterTruncateTitles", "test/test_reads.py::TestReadsFiltering::testFilterWhitelist", "test/test_reads.py::TestReadsFiltering::testFilterWithMinLengthEqualToMaxLength", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatChangesIds", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatOmits", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatOmitsAndChangesIds", "test/test_reads.py::TestReadsFiltering::testFilteredReadsInstanceHasExpectedLength", "test/test_reads.py::TestReadsFiltering::testIdLambda", "test/test_reads.py::TestReadsFiltering::testIdLambdaReturningNone", "test/test_reads.py::TestReadsFiltering::testKeepSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesAllSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesNoSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesOutOfRange", "test/test_reads.py::TestReadsFiltering::testKeepSitesWithQuality", "test/test_reads.py::TestReadsFiltering::testLineNumberFile", "test/test_reads.py::TestReadsFiltering::testLineNumberFileEmpty", "test/test_reads.py::TestReadsFiltering::testLineNumberFileFirstLineTooSmall", "test/test_reads.py::TestReadsFiltering::testLineNumberFileNonAscending", "test/test_reads.py::TestReadsFiltering::testLineNumberFileRunOutOfSequences", "test/test_reads.py::TestReadsFiltering::testReadLambda", "test/test_reads.py::TestReadsFiltering::testReadLambdaReturningNone", "test/test_reads.py::TestReadsFiltering::testRemoveAndKeepSites", "test/test_reads.py::TestReadsFiltering::testRemoveSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesAllSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesNoSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesOutOfRange", "test/test_reads.py::TestReadsFiltering::testRemoveSitesWithQuality", "test/test_reads.py::TestReadsFiltering::testSampleFractionAndNoTrueLengthRaisesValueError", "test/test_reads.py::TestReadsFiltering::testSampleFractionAndRandomSubsetRaisesValueError", "test/test_reads.py::TestReadsFiltering::testSampleFractionOne", "test/test_reads.py::TestReadsFiltering::testSampleFractionPointOne", "test/test_reads.py::TestReadsFiltering::testSampleFractionZero", "test/test_reads.py::TestReadsInRAM::testAdd", "test/test_reads.py::TestReadsInRAM::testFromReads", "test/test_reads.py::TestReadsInRAM::testNoReads", "test/test_reads.py::TestReadsInRAM::testOneReadIndex", "test/test_reads.py::TestReadsInRAM::testOneReadLength", "test/test_reads.py::TestReadsInRAM::testOneReadList", "test/test_reads.py::TestReadsInRAM::testSetItem", "test/test_reads.py::TestReadsInRAM::testTwoReadsIndex", "test/test_reads.py::TestReadsInRAM::testTwoReadsLength", "test/test_reads.py::TestReadsInRAM::testTwoReadsList", "test/test_reads.py::TestSummarizePosition::testCorrectFrequencies", "test/test_reads.py::TestSummarizePosition::testExcludeShortSequences", "test/test_reads.py::TestSummarizePosition::testFrequenciesNoReads", "test/test_reads.py::TestSummarizePosition::testIndexLargerThanSequenceLength", "test/test_reads.py::TestSummarizePosition::testNumberOfExclusionsNoReads", "test/test_reads.py::TestSitesMatching::testAllMatches", "test/test_reads.py::TestSitesMatching::testIgnoreCase", "test/test_reads.py::TestSitesMatching::testMatchCase", "test/test_reads.py::TestSitesMatching::testMultipleReadsAll", "test/test_reads.py::TestSitesMatching::testMultipleReadsAllWithDifferingLengths", "test/test_reads.py::TestSitesMatching::testMultipleReadsAny", "test/test_reads.py::TestSitesMatching::testMultipleReadsAnyWithDifferingLengths", "test/test_reads.py::TestSitesMatching::testNoMatches", "test/test_reads.py::TestSitesMatching::testPartialMatch" ]

{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2018-12-14 13:22:15+00:00

mit

873

acorg__dark-matter-680

diff --git a/CHANGELOG.md b/CHANGELOG.md index cf03d75..fc519cd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,16 @@ +## 3.0.70 Jul 30, 2019 + +Added `titleRegex` and `negativeTitleRegex` to `ProteinGrouper` class and +`--titleRegex` and `--negativeTitleRegex` arguments to +`proteins-to-pathogens.py`. + +## 3.0.69 Jul 30, 2019 + +Added `--title` and `--preamble` args to output from +`proteins-to-pathogens.py`. Fixed `ProteinGrouper` HTML NCBI protein link +and added genome link. Added positive and negative filtering by regex to +`TitlesAlignments` and tests. Improved NCBI link generation and tests. + ## 3.0.68 Jun 9, 2019 Refactored `SAMFilter` to allow filtering alignments in pileups. Added diff --git a/bin/proteins-to-pathogens.py b/bin/proteins-to-pathogens.py index ed0bbd8..c39670e 100755 --- a/bin/proteins-to-pathogens.py +++ b/bin/proteins-to-pathogens.py @@ -157,6 +157,14 @@ if __name__ == '__main__': '--preamble', help='Optional preamble text to show after the title.') + parser.add_argument( + '--titleRegex', default=None, + Help='A regex that pathogen names must match.') + + parser.add_argument( + '--negativeTitleRegex', default=None, + help='a regex that pathogen names must not match.') + args = parser.parse_args() if args.sampleName and args.sampleNameRegex: @@ -192,7 +200,9 @@ if __name__ == '__main__': sampleNameRegex=args.sampleNameRegex, format_=args.format, proteinFastaFilenames=proteinFastaFilenames, - saveReadLengths=args.showReadLengths) + saveReadLengths=args.showReadLengths, + titleRegex=args.titleRegex, + negativeTitleRegex=args.negativeTitleRegex) if args.filenames: filenames = args.filenames diff --git a/dark/__init__.py b/dark/__init__.py index 8df318a..50781d0 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -8,4 +8,4 @@ if sys.version_info < (2, 7): # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.69' +__version__ = '3.0.70' diff --git a/dark/proteins.py b/dark/proteins.py index 1cef243..1310abd 100644 --- a/dark/proteins.py +++ b/dark/proteins.py @@ -11,6 +11,7 @@ from textwrap import fill from dark.dimension import dimensionalIterator from dark.fasta import FastaReads from dark.fastq import FastqReads +from dark.filter import TitleFilter from dark.html import NCBISequenceLinkURL from dark.reads import Reads @@ -211,6 +212,14 @@ class ProteinGrouper(object): proteins each matched pathogen has. @param saveReadLengths: If C{True}, save the lengths of all reads matching proteins. + @param titleRegex: A regex that pathogen names must match. + Note that this matching is done on the final part of the protein title + in square brackets, according to the convention used by the NCBI viral + refseq database and RVDB. + @param negativeTitleRegex: A regex that pathogen names must not match. + Note that this matching is done on the final part of the protein title + in square brackets, according to the convention used by the NCBI viral + refseq database and RVDB. @raise ValueError: If C{format_} is unknown. """ @@ -218,7 +227,8 @@ class ProteinGrouper(object): def __init__(self, assetDir='out', sampleName=None, sampleNameRegex=None, format_='fasta', proteinFastaFilenames=None, - saveReadLengths=False): + saveReadLengths=False, titleRegex=None, + negativeTitleRegex=None): self._assetDir = assetDir self._sampleName = sampleName self._sampleNameRegex = (re.compile(sampleNameRegex) if sampleNameRegex @@ -229,6 +239,12 @@ class ProteinGrouper(object): raise ValueError("format_ must be either 'fasta' or 'fastq'.") self._saveReadLengths = saveReadLengths + if titleRegex or negativeTitleRegex: + self.titleFilter = TitleFilter( + positiveRegex=titleRegex, negativeRegex=negativeTitleRegex) + else: + self.titleFilter = None + self._pathogenProteinCount = getPathogenProteinCounts( proteinFastaFilenames) @@ -285,6 +301,11 @@ class ProteinGrouper(object): proteinName, pathogenName = splitNames(names) + # Ignore pathogens with names we don't want. + if (self.titleFilter and self.titleFilter.accept( + pathogenName) == TitleFilter.REJECT): + continue + if pathogenName not in self.pathogenNames: self.pathogenNames[pathogenName] = {}

acorg/dark-matter

e76e23cc5230e4db4742c4418b6e5b8ddb0bc8d4

diff --git a/test/test_proteins.py b/test/test_proteins.py index 3cd8d09..f68397a 100644 --- a/test/test_proteins.py +++ b/test/test_proteins.py @@ -744,6 +744,94 @@ class TestProteinGrouper(TestCase): 'GENBANK|I44.6|GENBANK|J77|VP1\n', pg.toStr()) + def testPathogenNameRegex(self): + """ + If a protein grouper is given one file with two lines from different + pathogens, and one pathogen title does not match a passed title regex, + the pathogenNames dict must be as expected. + """ + fp = StringIO( + '0.63 41.3 44.2 9 9 12 acc|GENBANK|I44.6|GENBANK|J77|VP1 ' + '[Lausannevirus]\n' + '0.77 46.6 48.1 5 6 74 acc|GENBANK|I44.7|GENBANK|J78|VP2 ' + '[Hepatitis B virus]\n' + ) + pg = ProteinGrouper(titleRegex='Lausannevirus') + pg.addFile('sample-filename', fp) + self.assertEqual( + { + 'Lausannevirus': { + 'sample-filename': { + 'proteins': { + 'acc|GENBANK|I44.6|GENBANK|J77|VP1': { + 'bestScore': 44.2, + 'bluePlotFilename': 'out/0.png', + 'coverage': 0.63, + 'readsFilename': 'out/0.fasta', + 'hspCount': 9, + 'index': 0, + 'medianScore': 41.3, + 'outDir': 'out', + 'proteinLength': 12, + 'proteinName': ( + 'acc|GENBANK|I44.6|GENBANK|J77|VP1'), + 'proteinURL': ('http://www.ncbi.nlm.nih.gov/' + 'nuccore/I44.6'), + 'genomeURL': ( + 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), + 'readCount': 9, + }, + }, + 'uniqueReadCount': None, + }, + }, + }, + pg.pathogenNames) + + def testPathogenNegativeNameRegex(self): + """ + If a protein grouper is given one file with two lines from different + pathogens, and one pathogen title does not match a passed negative + title regex, the pathogenNames dict must be as expected. + """ + fp = StringIO( + '0.63 41.3 44.2 9 9 12 acc|GENBANK|I44.6|GENBANK|J77|VP1 ' + '[Lausannevirus]\n' + '0.77 46.6 48.1 5 6 74 acc|GENBANK|I44.7|GENBANK|J78|VP2 ' + '[Hepatitis B virus]\n' + ) + pg = ProteinGrouper(negativeTitleRegex='Hepatitis') + pg.addFile('sample-filename', fp) + self.assertEqual( + { + 'Lausannevirus': { + 'sample-filename': { + 'proteins': { + 'acc|GENBANK|I44.6|GENBANK|J77|VP1': { + 'bestScore': 44.2, + 'bluePlotFilename': 'out/0.png', + 'coverage': 0.63, + 'readsFilename': 'out/0.fasta', + 'hspCount': 9, + 'index': 0, + 'medianScore': 41.3, + 'outDir': 'out', + 'proteinLength': 12, + 'proteinName': ( + 'acc|GENBANK|I44.6|GENBANK|J77|VP1'), + 'proteinURL': ('http://www.ncbi.nlm.nih.gov/' + 'nuccore/I44.6'), + 'genomeURL': ( + 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), + 'readCount': 9, + }, + }, + 'uniqueReadCount': None, + }, + }, + }, + pg.pathogenNames) + class TestPathogenSampleFiles(TestCase): """

Add title regex (positive and negative) to protein grouper

0.0

e76e23cc5230e4db4742c4418b6e5b8ddb0bc8d4

[ "test/test_proteins.py::TestProteinGrouper::testPathogenNameRegex", "test/test_proteins.py::TestProteinGrouper::testPathogenNegativeNameRegex" ]

[ "test/test_proteins.py::TestSplitNames::testNestedBrackets", "test/test_proteins.py::TestSplitNames::testNoBrackets", "test/test_proteins.py::TestSplitNames::testNormalCase", "test/test_proteins.py::TestSplitNames::testTwoSetsOfBrackets", "test/test_proteins.py::TestSplitNames::testWhitespaceStripping", "test/test_proteins.py::TestGetPathogenProteinCounts::testExpected", "test/test_proteins.py::TestGetPathogenProteinCounts::testExpectedWithTwoFiles", "test/test_proteins.py::TestGetPathogenProteinCounts::testNone", "test/test_proteins.py::TestProteinGrouper::testAssetDir", "test/test_proteins.py::TestProteinGrouper::testDuplicatePathogenProteinSample", "test/test_proteins.py::TestProteinGrouper::testNoAssetDir", "test/test_proteins.py::TestProteinGrouper::testNoFiles", "test/test_proteins.py::TestProteinGrouper::testNoFilesToStr", "test/test_proteins.py::TestProteinGrouper::testNoFilesToStrWithTitle", "test/test_proteins.py::TestProteinGrouper::testNoFilesToStrWithTitleAndPreamble", "test/test_proteins.py::TestProteinGrouper::testNoRegex", "test/test_proteins.py::TestProteinGrouper::testNoSampleName", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesDifferentPathogens", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesDifferentPathogensTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogen", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogenTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFile", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileFASTQ", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileToStr", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileWithDifferentAssetDir", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileDifferentPathogens", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileSamePathogen", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testUnknownFormat", "test/test_proteins.py::TestProteinGrouper::testUnknownPathogenType", "test/test_proteins.py::TestPathogenSampleFiles::testIdenticalReadsRemoved", "test/test_proteins.py::TestPathogenSampleFiles::testOpenNotCalledOnRepeatedCall", "test/test_proteins.py::TestPathogenSampleFiles::testProteinsSavedCorrectly", "test/test_proteins.py::TestPathogenSampleFiles::testReadLengthsAdded", "test/test_proteins.py::TestPathogenSampleFiles::testUnknownFormat", "test/test_proteins.py::TestPathogenSampleFiles::testWritePathogenIndex", "test/test_proteins.py::TestPathogenSampleFiles::testWriteSampleIndex" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2019-07-30 15:24:11+00:00

mit

874

acorg__dark-matter-686

diff --git a/CHANGELOG.md b/CHANGELOG.md index 6a08922..5f2e8a9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,12 @@ +## 3.0.79 Aug 8, 2019 + +Add `--omitVirusLinks` and `--omitSampleProteinCount` options to +`proteins-to-pathogens.py` to make HTML output less confusing when running +on RVDB or OKIAV databases. Removed highlighting of pathogens with high +protein fraction since that was done in a non-useful way. Removed index +field from HTML output and removed HSP count unless it differs from the +read count. + ## 3.0.78 Aug 2, 2019 Fixed silly import error. diff --git a/bin/proteins-to-pathogens.py b/bin/proteins-to-pathogens.py index 252d025..3daa58e 100755 --- a/bin/proteins-to-pathogens.py +++ b/bin/proteins-to-pathogens.py @@ -170,6 +170,23 @@ if __name__ == '__main__': '--negativeTitleRegex', default=None, help='a regex that pathogen names must not match.') + parser.add_argument( + '--omitVirusLinks', default=False, action='store_true', + help=('If specified, the HTML output (use --html to get this) for ' + 'viruses will not contain links to ICTV and ViralZone. ' + 'This should be used when working with viruses that do not yet ' + 'have names that can be looked up.')) + + parser.add_argument( + '--omitSampleProteinCount', default=False, action='store_true', + help=('If specified, the HTML output (use --html to get this) for ' + 'viruses will not contain counts of the number of proteins ' + 'matched by each sample for a given pathogen. This should be ' + 'used when working with RVDB where there are many sequences ' + 'for some proteins and a sample matches many of them, leading ' + 'to incorrect reporting of the number of proteins of a pathogen ' + 'that are matched by samples.')) + args = parser.parse_args() if args.sampleName and args.sampleNameRegex: @@ -186,6 +203,19 @@ if __name__ == '__main__': print('It does not make sense to use --pathogenIndexFilename ' 'without also using --html', file=sys.stderr) sys.exit(1) + if args.omitVirusLinks: + print('It does not make sense to use --omitVirusLinks ' + 'without also using --html', file=sys.stderr) + sys.exit(1) + if args.omitSampleProteinCount: + print('It does not make sense to use --omitSampleProteinCount ' + 'without also using --html', file=sys.stderr) + sys.exit(1) + + if args.omitVirusLinks and args.pathogenType != 'viral': + print('The --omitVirusLinks option only makes sense with ' + '--pathogenType viral', file=sys.stderr) + sys.exit(1) if args.proteinFastaFilename: # Flatten lists of lists that we get from using both nargs='+' and @@ -220,11 +250,14 @@ if __name__ == '__main__': grouper.addFile(filename, fp) if args.html: - print(grouper.toHTML(args.pathogenPanelFilename, - minProteinFraction=args.minProteinFraction, - pathogenType=args.pathogenType, - title=args.title, preamble=args.preamble, - sampleIndexFilename=args.sampleIndexFilename, - pathogenIndexFilename=args.pathogenIndexFilename)) + print(grouper.toHTML( + args.pathogenPanelFilename, + minProteinFraction=args.minProteinFraction, + pathogenType=args.pathogenType, + title=args.title, preamble=args.preamble, + sampleIndexFilename=args.sampleIndexFilename, + pathogenIndexFilename=args.pathogenIndexFilename, + omitVirusLinks=args.omitVirusLinks, + omitSampleProteinCount=args.omitSampleProteinCount)) else: print(grouper.toStr()) diff --git a/dark/__init__.py b/dark/__init__.py index 15c32b1..6e9c357 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -8,4 +8,4 @@ if sys.version_info < (2, 7): # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.0.78' +__version__ = '3.0.79' diff --git a/dark/proteins.py b/dark/proteins.py index 0449e7e..d6cefee 100644 --- a/dark/proteins.py +++ b/dark/proteins.py @@ -244,6 +244,7 @@ class ProteinGrouper(object): VIRALZONE = 'https://viralzone.expasy.org/search?query=' ICTV = 'https://talk.ictvonline.org/search-124283882/?q=' READCOUNT_MARKER = '*READ-COUNT*' + READ_AND_HSP_COUNT_STR_SEP = '/' def __init__(self, assetDir='out', sampleName=None, sampleNameRegex=None, format_='fasta', proteinFastaFilenames=None, @@ -362,7 +363,7 @@ class ProteinGrouper(object): proteinURL = NCBISequenceLinkURL(proteinName, field=2) genomeURL = NCBISequenceLinkURL(proteinName, field=4) - proteins[proteinName] = { + proteinInfo = proteins[proteinName] = { 'bestScore': float(bestScore), 'bluePlotFilename': join(outDir, '%d.png' % index), 'coverage': float(coverage), @@ -378,6 +379,12 @@ class ProteinGrouper(object): 'readCount': int(readCount), } + if proteinInfo['readCount'] == proteinInfo['hspCount']: + proteinInfo['readAndHspCountStr'] = readCount + else: + proteinInfo['readAndHspCountStr'] = '%s%s%s' % ( + readCount, self.READ_AND_HSP_COUNT_STR_SEP, hspCount) + if self._saveReadLengths: readsClass = (FastaReads if self._format == 'fasta' else FastqReads) @@ -435,8 +442,8 @@ class ProteinGrouper(object): for proteinName in sorted(proteins): append( ' %(coverage).2f\t%(medianScore).2f\t' - '%(bestScore).2f\t%(readCount)4d\t%(hspCount)4d\t' - '%(index)3d\t%(proteinName)s' + '%(bestScore).2f\t%(readAndHspCountStr)11s\t' + '%(proteinName)s' % proteins[proteinName]) append('') @@ -445,7 +452,8 @@ class ProteinGrouper(object): def toHTML(self, pathogenPanelFilename=None, minProteinFraction=0.0, pathogenType='viral', title='Summary of pathogens', preamble=None, sampleIndexFilename=None, - pathogenIndexFilename=None): + pathogenIndexFilename=None, omitVirusLinks=False, + omitSampleProteinCount=False): """ Produce an HTML string representation of the pathogen summary. @@ -465,6 +473,13 @@ class ProteinGrouper(object): @param pathogenIndexFilename: A C{str} filename to write a pathogen index file to. Lines in the file will have an integer index, a space, and then the pathogen name. + @param omitVirusLinks: If C{True}, links to ICTV and ViralZone will be + omitted in output. + @param omitSampleProteinCount: If C{True}, do not display a number of + matched pathogen proteins for a sample. This should be used when + those numbers are inaccurate (e.g., when using the unclustered RVDB + protein database and there are many sequences for the same + protein). @return: An HTML C{str} suitable for printing. """ if pathogenType not in ('bacterial', 'viral'): @@ -475,7 +490,6 @@ class ProteinGrouper(object): if not exists(self._pathogenDataDir): os.mkdir(self._pathogenDataDir) - highlightSymbol = '&starf;' self._computeUniqueReadCounts() if pathogenPanelFilename: @@ -548,10 +562,6 @@ class ProteinGrouper(object): margin-top: 10px; margin-bottom: 3px; } - .significant { - color: red; - margin-right: 2px; - } .sample { margin-top: 5px; margin-bottom: 2px; @@ -599,10 +609,10 @@ class ProteinGrouper(object): '<li>Coverage fraction.</li>', '<li>Median bit score.</li>', '<li>Best bit score.</li>', - '<li>Read count.</li>', - '<li>HSP count (a read can match a protein more than once).</li>', - '<li>Protein length (in AAs).</li>', - '<li>Index (just ignore this).</li>', + '<li>Read count (if the HSP count differs, read and HSP ', + ('counts are both given, separated by "%s").</li>' % + self.READ_AND_HSP_COUNT_STR_SEP), + '<li>Protein length (in amino acids).</li>', ] if self._saveReadLengths: @@ -644,11 +654,6 @@ class ProteinGrouper(object): 'but all pathogens have at least %.2f%% of their ' 'proteins matched by at least one sample.' % percent) - append('Samples that match a pathogen (and pathogens with a ' - 'matching sample) with at least this protein fraction are ' - 'highlighted using %s.' % - highlightSymbol) - append('') if pathogenPanelFilename: @@ -692,7 +697,7 @@ class ProteinGrouper(object): samples = self.pathogenNames[pathogenName] sampleCount = len(samples) pathogenProteinCount = self._pathogenProteinCount[pathogenName] - if pathogenType == 'viral': + if pathogenType == 'viral' and not omitVirusLinks: quoted = quote(pathogenName) pathogenLinksHTML = ( ' (<a href="%s%s">ICTV</a>, <a href="%s%s">ViralZone</a>)' @@ -755,21 +760,19 @@ class ProteinGrouper(object): uniqueReadCount = samples[sampleName]['uniqueReadCount'] pathogenReadCount += uniqueReadCount - if pathogenProteinCount and ( - proteinCount / pathogenProteinCount >= - minProteinFraction): - highlight = ('%s' % - highlightSymbol) + if omitSampleProteinCount: + proteinCountHTML = '' else: - highlight = '' + proteinCountHTML = '%d protein%s, ' % ( + proteinCount, '' if proteinCount == 1 else 's') append( '' - '%sSample <a href="#sample-%s">%s</a> ' - '(%d protein%s, <a href="%s">%d de-duplicated (by id) ' + 'Sample <a href="#sample-%s">%s</a> ' + '(%s<a href="%s">%d de-duplicated (by id) ' 'read%s</a>, <a href="%s">panel</a>):' % - (highlight, sampleName, sampleName, - proteinCount, '' if proteinCount == 1 else 's', + (sampleName, sampleName, + proteinCountHTML, readsFileName, uniqueReadCount, '' if uniqueReadCount == 1 else 's', self.sampleNames[sampleName])) @@ -780,8 +783,7 @@ class ProteinGrouper(object): '<li>' '' '%(coverage).2f %(medianScore)6.2f %(bestScore)6.2f ' - '%(readCount)5d %(hspCount)5d %(proteinLength)4d ' - '%(index)3d ' + '%(readAndHspCountStr)11s %(proteinLength)4d ' % proteinMatch ) @@ -861,7 +863,7 @@ class ProteinGrouper(object): '<a id="sample-%s"></a>' 'Sample ' '%s ' - 'matched proteins from 0 pathogens.' % + 'did not match anything.' % (sampleName, sampleName)) continue @@ -875,24 +877,19 @@ class ProteinGrouper(object): proteinCount = len(proteins) pathogenProteinCount = self._pathogenProteinCount[pathogenName] - highlight = '' if pathogenProteinCount: proteinCountStr = '%d/%d protein%s' % ( proteinCount, pathogenProteinCount, '' if pathogenProteinCount == 1 else 's') - if (proteinCount / pathogenProteinCount >= - minProteinFraction): - highlight = ('%s' % - highlightSymbol) else: proteinCountStr = '%d protein%s' % ( proteinCount, '' if proteinCount == 1 else 's') append( '' - '%s<a href="#pathogen-%s">%s</a> %s, ' + '<a href="#pathogen-%s">%s</a> %s, ' '<a href="%s">%d de-duplicated (by id) read%s</a>:' % - (highlight, pathogenName, pathogenName, + (pathogenName, pathogenName, proteinCountStr, readsFileName, uniqueReadCount, '' if uniqueReadCount == 1 else 's')) append('<ul class="protein-list indented">') @@ -902,8 +899,7 @@ class ProteinGrouper(object): '<li>' '' '%(coverage).2f %(medianScore)6.2f %(bestScore)6.2f ' - '%(readCount)5d %(hspCount)5d %(proteinLength)4d ' - '%(index)3d ' + '%(readAndHspCountStr)11s %(proteinLength)4d ' ' ' '' '%(proteinName)s'

acorg/dark-matter

3398b2f5af3d2fa4dcce840ad04ff605a5221fb9

diff --git a/test/test_proteins.py b/test/test_proteins.py index ba46f58..cf00b38 100644 --- a/test/test_proteins.py +++ b/test/test_proteins.py @@ -259,6 +259,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': None, @@ -298,6 +299,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': None, @@ -337,6 +339,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': None, @@ -411,6 +414,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 9, + 'readAndHspCountStr': '9', }, 'acc|GENBANK|I44.7|GENBANK|J78|VP2': { 'bestScore': 48.1, @@ -429,6 +433,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J78'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': None, @@ -472,6 +477,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 9, + 'readAndHspCountStr': '9', }, }, 'uniqueReadCount': None, @@ -497,6 +503,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J78'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': None, @@ -543,6 +550,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 9, + 'readAndHspCountStr': '9', }, }, 'uniqueReadCount': None, @@ -566,6 +574,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J78'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': None, @@ -633,6 +642,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 9, + 'readAndHspCountStr': '9', }, }, 'uniqueReadCount': None, @@ -658,6 +668,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J78'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': None, @@ -740,7 +751,7 @@ class TestProteinGrouper(TestCase): '\n' 'Lausannevirus (in 1 sample)\n' ' sample-filename (1 protein, 5 reads)\n' - ' 0.77\t46.60\t48.10\t 5\t 6\t 0\tacc|' + ' 0.77\t46.60\t48.10\t 5/6\tacc|' 'GENBANK|I44.6|GENBANK|J77|VP1\n', pg.toStr()) @@ -780,6 +791,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 9, + 'readAndHspCountStr': '9', }, }, 'uniqueReadCount': None, @@ -824,6 +836,7 @@ class TestProteinGrouper(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 9, + 'readAndHspCountStr': '9', }, }, 'uniqueReadCount': None, @@ -1076,6 +1089,7 @@ class TestPathogenSampleFiles(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J77'), 'readCount': 9, + 'readAndHspCountStr': '9', }, 'acc|GENBANK|I44.7|GENBANK|J78|VP2': { 'bestScore': 48.1, @@ -1094,6 +1108,7 @@ class TestPathogenSampleFiles(TestCase): 'genomeURL': ( 'http://www.ncbi.nlm.nih.gov/nuccore/J78'), 'readCount': 5, + 'readAndHspCountStr': '5/6', }, }, 'uniqueReadCount': 3,

Add options to proteins-to-pathogens.py to omit virus links and incorrect virus protein counts

0.0

3398b2f5af3d2fa4dcce840ad04ff605a5221fb9

[ "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesDifferentPathogens", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogen", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFile", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileFASTQ", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileToStr", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileWithDifferentAssetDir", "test/test_proteins.py::TestProteinGrouper::testPathogenNameRegex", "test/test_proteins.py::TestProteinGrouper::testPathogenNegativeNameRegex", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileDifferentPathogens", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileSamePathogen", "test/test_proteins.py::TestPathogenSampleFiles::testProteinsSavedCorrectly" ]

[ "test/test_proteins.py::TestSplitNames::testNestedBrackets", "test/test_proteins.py::TestSplitNames::testNoBrackets", "test/test_proteins.py::TestSplitNames::testNormalCase", "test/test_proteins.py::TestSplitNames::testTwoSetsOfBrackets", "test/test_proteins.py::TestSplitNames::testWhitespaceStripping", "test/test_proteins.py::TestGetPathogenProteinCounts::testExpected", "test/test_proteins.py::TestGetPathogenProteinCounts::testExpectedWithTwoFiles", "test/test_proteins.py::TestGetPathogenProteinCounts::testNone", "test/test_proteins.py::TestProteinGrouper::testAssetDir", "test/test_proteins.py::TestProteinGrouper::testDuplicatePathogenProteinSample", "test/test_proteins.py::TestProteinGrouper::testNoAssetDir", "test/test_proteins.py::TestProteinGrouper::testNoFiles", "test/test_proteins.py::TestProteinGrouper::testNoFilesToStr", "test/test_proteins.py::TestProteinGrouper::testNoFilesToStrWithTitle", "test/test_proteins.py::TestProteinGrouper::testNoFilesToStrWithTitleAndPreamble", "test/test_proteins.py::TestProteinGrouper::testNoRegex", "test/test_proteins.py::TestProteinGrouper::testNoSampleName", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesDifferentPathogensTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInEachOfTwoFilesSamePathogenTitle", "test/test_proteins.py::TestProteinGrouper::testOneLineInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testTwoLinesInOneFileTitle", "test/test_proteins.py::TestProteinGrouper::testUnknownFormat", "test/test_proteins.py::TestProteinGrouper::testUnknownPathogenType", "test/test_proteins.py::TestPathogenSampleFiles::testIdenticalReadsRemoved", "test/test_proteins.py::TestPathogenSampleFiles::testOpenNotCalledOnRepeatedCall", "test/test_proteins.py::TestPathogenSampleFiles::testPathogenIndex", "test/test_proteins.py::TestPathogenSampleFiles::testReadLengthsAdded", "test/test_proteins.py::TestPathogenSampleFiles::testUnknownFormat", "test/test_proteins.py::TestPathogenSampleFiles::testWritePathogenIndex", "test/test_proteins.py::TestPathogenSampleFiles::testWriteSampleIndex" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2019-08-08 13:18:14+00:00

mit

875

acorg__dark-matter-704

diff --git a/CHANGELOG.md b/CHANGELOG.md index ee662c9..9212725 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,7 @@ +## 3.1.31 Jan 13, 2020 + +Added `sam-coverage-depth.py`. + ## 3.1.30 Jan 13, 2020 Added `--minGenomeLength` to `make-protein-database.py`. diff --git a/bin/sam-coverage-depth.py b/bin/sam-coverage-depth.py new file mode 100755 index 0000000..7516f61 --- /dev/null +++ b/bin/sam-coverage-depth.py @@ -0,0 +1,122 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import sys +import argparse +from collections import Counter +from numpy import std + +from dark.filter import ( + addFASTAFilteringCommandLineOptions, parseFASTAFilteringCommandLineOptions) +from dark.reads import Reads +from dark.sam import samfile, SAMFilter, samReferences, UnknownReference +from dark.utils import pct + + +def baseCountsToStr(counts): + """ + Convert base counts to a string. + + @param counts: A C{Counter} instance. + @return: A C{str} representation of nucleotide counts. + """ + return ' '.join([ + ('%s:%d' % (base, counts[base])) for base in sorted(counts)]) + + +parser = argparse.ArgumentParser( + formatter_class=argparse.ArgumentDefaultsHelpFormatter, + description=('Print SAM/BAM file coverage statistics by offset. ' + 'Output lines show the offset.')) + +addFASTAFilteringCommandLineOptions(parser) +SAMFilter.addFilteringOptions(parser, samfileIsPositional=True) + +parser.add_argument( + '--noOffsets', default=False, action='store_true', + help='Do not print per-offset details of base counts.') + +parser.add_argument( + '--noStats', default=False, action='store_true', + help='Do not print final average and standard deviation statistics.') + +args = parser.parse_args() + +if args.noOffsets and args.noStats: + print('You have used both --noOffsets and --noStats, so there is no ' + 'output!', file=sys.stderr) + sys.exit(1) + +# We don't have a file of reads, we just want a read filter that we +# can use to filter the SAM file query sequences. +reads = parseFASTAFilteringCommandLineOptions(args, Reads()) +samFilter = SAMFilter.parseFilteringOptions(args, reads.filterRead) + +printOffsets = not args.noOffsets +printStats = not args.noStats + +if samFilter.referenceIds and len(samFilter.referenceIds) > 1: + print('Only one reference id can be given. To calculate coverage for more ' + 'than one reference, run this script multiple times.', + file=sys.stderr) + sys.exit(1) + +try: + referenceLengths = samFilter.referenceLengths() +except UnknownReference: + referenceId = samFilter.referenceIds.pop() + referenceIds = samReferences(args.samfile) + print('Reference %r does not appear in SAM file %s. Known ' + 'references are: %s.' % ( + referenceId, args.samfile, ', '.join(sorted(referenceIds))), + file=sys.stderr) + sys.exit(1) + +if printStats: + counts = [] + +with samfile(args.samfile) as sam: + + if samFilter.referenceIds: + # No need to check if the given reference id is in referenceLengths + # because the samFilter.referenceLengths call above catched that. + referenceId = samFilter.referenceIds.pop() + else: + if len(referenceLengths) == 1: + referenceId = list(referenceLengths)[0] + else: + print('SAM file %r contains %d references (%s). Only one ' + 'reference id can be analyzed at a time. Please use ' + '--referenceId to specify the one you want examined.' % ( + args.samfile, len(referenceLengths), + ', '.join(sorted(referenceLengths))), file=sys.stderr) + sys.exit(1) + + for column in sam.pileup(reference=referenceId): + bases = Counter() + for read in column.pileups: + if (not read.is_del and not read.is_refskip and + samFilter.filterAlignment(read.alignment)): + base = read.alignment.query_sequence[read.query_position] + bases[base] += 1 + + baseCount = sum(bases.values()) + + if printStats: + counts.append(baseCount) + + if printOffsets: + print('%d: %d %s' % (column.reference_pos + 1, baseCount, + baseCountsToStr(bases))) + +if printStats: + referenceLength = referenceLengths[referenceId] + print('Reference id: %s' % referenceId) + print('Reference length: %d' % referenceLength) + print('Bases covered: %s' % pct(len(counts), referenceLength)) + print('Min coverage depth: %d' % ( + 0 if len(counts) < referenceLength else min(counts))) + print('Max coverage depth: %d' % max(counts)) + print('Mean coverage depth: %.3f' % (sum(counts) / referenceLength)) + print('Coverage depth s.d.: %.3f' % std(counts)) diff --git a/dark/__init__.py b/dark/__init__.py index 324a302..da9777a 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.1.30' +__version__ = '3.1.31' diff --git a/dark/sam.py b/dark/sam.py index b668b4f..07a5e08 100644 --- a/dark/sam.py +++ b/dark/sam.py @@ -334,13 +334,10 @@ class SAMFilter(object): SAM/BAM file is read. @return: A C{SAMFilter} instance. """ - referenceIds = (set(chain.from_iterable(args.referenceId)) - if args.referenceId else None) - return cls( args.samfile, filterRead=filterRead, - referenceIds=referenceIds, + referenceIds=set(args.referenceId) if args.referenceId else None, storeQueryIds=storeQueryIds, dropUnmapped=args.dropUnmapped, dropSecondary=args.dropSecondary, diff --git a/dark/utils.py b/dark/utils.py index 0059330..1ffa57f 100644 --- a/dark/utils.py +++ b/dark/utils.py @@ -259,6 +259,22 @@ def countPrint(mesg, count, len1, len2=None): count, len2, percentage(count, len2))) +def pct(a, b): + """ + Format a string showing two integers and what percentage the first + is of the second. + + @param a: An C{int}, the numerator. + @param b: An C{int}, the denominator. + """ + assert 0 <= a <= b + if b: + return ('%d/%d (%.3f%%)' % + (a, b, (a / b if b else 0.0) * 100.0)) + else: + return '0/0 (0.000%)' + + @contextmanager def cd(newdir): """

acorg/dark-matter

5d785403629c4bd5c2e848219ed0fc4fc896c3cf

diff --git a/test/test_utils.py b/test/test_utils.py index f7d7ed6..5656906 100644 --- a/test/test_utils.py +++ b/test/test_utils.py @@ -14,8 +14,8 @@ except ImportError: from .mocking import mockOpen from dark.utils import ( - numericallySortFilenames, median, asHandle, parseRangeString, StringIO, - baseCountsToStr, nucleotidesToStr, countPrint) + numericallySortFilenames, median, asHandle, parseRangeString, pct, + StringIO, baseCountsToStr, nucleotidesToStr, countPrint) class TestNumericallySortFilenames(TestCase): @@ -382,3 +382,36 @@ class TestCountPrint(TestCase): ' 2/8 (25.00%) of sequence 2', countPrint('Count is', count, len1, len2) ) + + +class TestPct(TestCase): + """ + Test the pct function. + """ + def testZeroNumerator(self): + """ + The pct function must produce the correct result if the numerator is + zero. + """ + self.assertEqual('0/10 (0.000%)', pct(0, 10)) + + def testZeroDenominator(self): + """ + The pct function must produce the correct result if the denominator is + zero. + """ + self.assertEqual('0/0 (0.000%)', pct(0, 0)) + + def testOneHalf(self): + """ + The pct function must produce the correct result if the numerator is + one half of the denominator. + """ + self.assertEqual('5/10 (50.000%)', pct(5, 10)) + + def testOneSeventh(self): + """ + The pct function must produce the correct result if the numerator is + one seventh of the denominator. + """ + self.assertEqual('2/14 (14.286%)', pct(2, 14))

Add a script to print per-offset coverage and overall coverage stats from a SAM/BAM file

0.0

5d785403629c4bd5c2e848219ed0fc4fc896c3cf

[ "test/test_utils.py::TestNumericallySortFilenames::testBasename", "test/test_utils.py::TestNumericallySortFilenames::testNoNames", "test/test_utils.py::TestNumericallySortFilenames::testOneNonNumericName", "test/test_utils.py::TestNumericallySortFilenames::testOneNumericName", "test/test_utils.py::TestNumericallySortFilenames::testSeveralNames", "test/test_utils.py::TestNumericallySortFilenames::testSeveralNamesWithUnequalPrefixLengths", "test/test_utils.py::TestMedian::testEmptyArgRaises", "test/test_utils.py::TestMedian::testMedianOfFive", "test/test_utils.py::TestMedian::testMedianOfFour", "test/test_utils.py::TestMedian::testMedianOfOne", "test/test_utils.py::TestMedian::testMedianOfThree", "test/test_utils.py::TestMedian::testMedianOfTwo", "test/test_utils.py::TestAsHandle::testOpenFile", "test/test_utils.py::TestAsHandle::testStr", "test/test_utils.py::TestParseRangeString::testEmptyString", "test/test_utils.py::TestParseRangeString::testSingleNumber", "test/test_utils.py::TestParseRangeString::testSingleNumberSpaceAfter", "test/test_utils.py::TestParseRangeString::testSingleNumberSpaceBefore", "test/test_utils.py::TestParseRangeString::testSingleNumberSpaceBeforeAndAfter", "test/test_utils.py::TestParseRangeString::testSingleRange", "test/test_utils.py::TestParseRangeString::testSingleRangeWithSpaceAfterHyphen", "test/test_utils.py::TestParseRangeString::testSingleRangeWithSpaceBeforeAfterHyphen", "test/test_utils.py::TestParseRangeString::testSingleRangeWithSpaceBeforeHyphen", "test/test_utils.py::TestParseRangeString::testTwoOverlappingRanges", "test/test_utils.py::TestParseRangeString::testTwoRanges", "test/test_utils.py::TestParseRangeString::testTwoRangesAndANumber", "test/test_utils.py::TestParseRangeString::testTwoRangesAndTwoNumbers", "test/test_utils.py::TestParseRangeString::testZeroConversion", "test/test_utils.py::TestStringIO::testContextManager", "test/test_utils.py::TestStringIO::testInitializedRead", "test/test_utils.py::TestStringIO::testInitiallyEmpty", "test/test_utils.py::TestStringIO::testWriteRead", "test/test_utils.py::TestBaseCountsToStr::testSimple", "test/test_utils.py::TestNucleotidesToStr::testSimple", "test/test_utils.py::TestCountPrint::testSimple", "test/test_utils.py::TestCountPrint::testTwoSequences", "test/test_utils.py::TestPct::testOneHalf", "test/test_utils.py::TestPct::testOneSeventh", "test/test_utils.py::TestPct::testZeroDenominator", "test/test_utils.py::TestPct::testZeroNumerator" ]

[]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2020-01-13 01:04:10+00:00

mit

876

acorg__dark-matter-705

diff --git a/CHANGELOG.md b/CHANGELOG.md index 18dbb93..5a22e5b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,7 @@ +## 3.1.37 Jan 13, 2020 + +Add final `genome-protein-summary.py` script. + ## 3.1.35 Jan 13, 2020 Drop Python 3.8 from Travis and tox checking. diff --git a/bin/genome-protein-summary.py b/bin/genome-protein-summary.py index cb0608d..71ce8b4 100755 --- a/bin/genome-protein-summary.py +++ b/bin/genome-protein-summary.py @@ -14,22 +14,19 @@ from dark.genbank import GenomeRanges from dark.genomes import GenomeProteinInfo from dark.reads import Reads from dark.sam import SAMFilter, samReferences +from dark.utils import pct -def pct(a, b): - assert a <= b - if b: - return ('%d/%d (%.3f%%)' % - (a, b, (a / b if b else 0.0) * 100.0)) - else: - return '0/0 (0.00%)' - - -def summarize(gpi, sortOn): +def summarize(gpi, sortOn, minReadOffsetCount): """ Print a summary of the genome proteins. @param gpi: A C{GenomeProteinInfo} instance. + @param sortOn: How to sort proteins for output. One of 'coverage', + 'depth', 'name', 'offset', or 'readCount'. + @param minReadOffsetCount: The minimum number of reads offsets that must + overlap a protein for the read to be considered as sufficiently + intersecting the protein. """ genome = gpi.genome @@ -48,9 +45,9 @@ def summarize(gpi, sortOn): print(' Whole genome coverage (not just proteins):') print(' Reads matching genome: %d' % len(gpi.readIdsMatchingGenome)) - print(' Covered offsets: %s' % ( + print(' Covered genome offsets: %s' % ( pct(len(gpi.coveredOffsetCount), genome['length']))) - print(' Average depth: %.3f' % ( + print(' Average depth across genome: %.3f' % ( sum(gpi.coveredOffsetCount.values()) / genome['length'])) coveredProteinOffsetCount = coveredProteinBasesCount = 0 @@ -58,16 +55,15 @@ def summarize(gpi, sortOn): coveredProteinOffsetCount += bool(gpi.coveredOffsetCount[offset]) coveredProteinBasesCount += gpi.coveredOffsetCount[offset] - print(' Total protein coverage:') + print(' Total protein coverage (irrespective of minReadOffsetCount):') print(' Reads matching proteins: %d' % len(gpi.readIdsForAllProteins())) - print(' Covered offsets: %s' % ( + print(' Proteins with any coverage: %s' % + pct(len(gpi.coveredProteins), genome['proteinCount'])) + print(' Covered protein offsets: %s' % ( pct(coveredProteinOffsetCount, len(gpi.offsets)))) - print(' Average depth: %.3f' % ( + print(' Average depth across proteins: %.3f' % ( coveredProteinBasesCount / len(gpi.offsets))) - print(' Proteins matched: %s (sorted by %s):' % ( - pct(len(gpi.coveredProteins), genome['proteinCount']), sortOn)) - if sortOn == 'name': def key(proteinAccession): return gpi.proteins[proteinAccession]['name'] @@ -93,25 +89,41 @@ def summarize(gpi, sortOn): return coverage['totalBases'] / coverage['ntLength'] reverse = True - for i, proteinAccession in enumerate( - sorted(gpi.coveredProteins, key=key, reverse=reverse), - start=1): + if minReadOffsetCount is None: + print(' Proteins covered (no minReadOffsetCount):') + else: + print(' Proteins covered (minReadOffsetCount=%d):' % + minReadOffsetCount) + + proteinCount = 0 + for proteinAccession in sorted(gpi.coveredProteins, key=key, + reverse=reverse): protein = gpi.proteins[proteinAccession] - print(' %d: %s (%d AA, %d nt with stop codon, %s)' % - (i, protein['product'], protein['length'], - protein['length'] * 3 + 3, protein['accession'])) - coverage = gpi.proteinCoverageInfo(proteinAccession) + coverage = gpi.proteinCoverageInfo(proteinAccession, + minReadOffsetCount) + + readCount = len(coverage['readIds']) - print(' Read count: %d' % len(coverage['readIds'])) + if readCount: + proteinCount += 1 - print(' Covered offsets: %s' % ( - pct(coverage['coveredOffsets'], coverage['ntLength']))) + print(' %d: %s (%d AA, %d nt with stop codon, %s)' % + (proteinCount, protein['product'], protein['length'], + protein['length'] * 3 + 3, protein['accession'])) - print(' Average depth: %.3f' % ( - coverage['totalBases'] / coverage['ntLength'])) + print(' Read count: %d' % readCount) - print(' Offsets: %s' % protein['offsets']) + print(' Covered offsets: %s' % ( + pct(coverage['coveredOffsets'], coverage['ntLength']))) + + print(' Average depth: %.3f' % ( + coverage['totalBases'] / coverage['ntLength'])) + + print(' Offsets: %s' % protein['offsets']) + + print(' Proteins matched: %s (sorted by %s):' % ( + pct(proteinCount, genome['proteinCount']), sortOn)) if __name__ == '__main__': @@ -124,11 +136,23 @@ if __name__ == '__main__': help=('The filename of an Sqlite3 database holding protein and ' 'genome information, as built by make-protein-database.py')) + parser.add_argument( + '--progress', default=False, action='store_true', + help='Print progress info to standard error.') + parser.add_argument( '--sortOn', default='readCount', choices=('coverage', 'depth', 'name', 'offset', 'readCount'), help='How to sort proteins for output.') + parser.add_argument( + '--minReadOffsetCount', type=int, + help=('The minimum number of reads offsets that must overlap a ' + 'protein for the read to be considered as sufficiently ' + 'intersecting the protein. Use this to prevent reads that ' + 'just overlap the protein in a very small number offsets ' + 'from being counted.')) + parser.add_argument( '--skipTranslationChecks', dest='checkTranslations', action='store_false', default=True, @@ -184,11 +208,13 @@ if __name__ == '__main__': referenceId, file=sys.stderr) else: if samfiles: - print('Processing %d SAM file%s for matches with %r:' % - (len(samfiles), '' if len(samfiles) == 1 else 's', - referenceId), file=sys.stderr) + if args.progress: + print('Processing %d SAM file%s for matches with %r:' % + (len(samfiles), '' if len(samfiles) == 1 else 's', + referenceId), file=sys.stderr) for i, filename in enumerate(samfiles, start=1): - print(' %d: %s' % (i, filename), file=sys.stderr) + if args.progress: + print(' %d: %s' % (i, filename), file=sys.stderr) gpInfo.addSAM(filename, filterAlignment) - summarize(gpInfo, args.sortOn) + summarize(gpInfo, args.sortOn, args.minReadOffsetCount) diff --git a/dark/__init__.py b/dark/__init__.py index 7336433..8aacdfa 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.1.36' +__version__ = '3.1.37' diff --git a/dark/genomes.py b/dark/genomes.py index 63b642b..e920d56 100644 --- a/dark/genomes.py +++ b/dark/genomes.py @@ -24,10 +24,11 @@ class GenomeProteinInfo(object): # self.proteins is keyed by protein accession number. self.proteins = {} self.coveredProteins = set() - # self.offsets is keyed by offset, values are dicts that contain a list - # of protein accession numbers that overlap that offset and a set of - # read ids (if any) that match at that offset. The offsets keys are - # only those that correspond to a protein. + # self.offsets is keyed by genome offset, values are dicts that + # contain a list of protein accession numbers that overlap that + # offset and a set of read ids (if any) that match at that offset. + # The offsets keys are only those that correspond to one or more + # proteins in the genome. self.offsets = {} # self.coveredOffsetCount holds the read counts for all offsets covered # by reads, regardless of whether the offsets correspond to proteins or @@ -123,11 +124,17 @@ class GenomeProteinInfo(object): offsetInfo['proteinAccessions']) offsetInfo['readIds'].add(readId) - def proteinCoverageInfo(self, proteinAccession): + def proteinCoverageInfo(self, proteinAccession, minReadOffsetCount=None): """ Calculate coverage information for a protein. @param proteinAccession: A C{str} accession number. + @param minReadOffsetCount: An C{int}, specifying the minimum number of + reads offsets that must overlap the protein for the read to be + considered as sufficiently intersecting the protein. Use this to + prevent reads that just overlap the protein in a very small number + offsets from being counted. Or C{None} to indicate that no such + filtering should be applied. @raises KeyError: If C{proteinAccession} is not known. @return: A C{dict} containing * the number of covered offsets, @@ -143,6 +150,13 @@ class GenomeProteinInfo(object): offsetsSeen = set() proteinLength = 0 + if minReadOffsetCount is not None and minReadOffsetCount < 2: + # Zero or one is equivalent to not giving a value. + minReadOffsetCount = None + + if minReadOffsetCount: + readOffsetCounts = Counter() + for (start, stop, forward) in GenomeRanges(protein['offsets']).ranges: proteinLength += stop - start for offset in range(start, stop): @@ -153,10 +167,15 @@ class GenomeProteinInfo(object): coveredOffsets += 1 totalBases += len(readIds) allReadIds.update(readIds) - - # The +3 in the following is because the database holds the AA length, - # not including the stop codon. But the database range covers the stop - # codon. + if minReadOffsetCount: + readOffsetCounts.update(readIds) + + # Sanity check that the sum of the range lengths is the same as the + # overall length given in the database. + # + # The +3 in the following is because the database holds the AA + # length, not including the stop codon. But the database range + # covers the stop codon. dbProteinLength = self.proteins[proteinAccession]['length'] * 3 + 3 if proteinLength != dbProteinLength: raise ValueError( @@ -164,6 +183,12 @@ class GenomeProteinInfo(object): 'database protein length (%d) for protein %s!' % (proteinLength, dbProteinLength, proteinAccession)) + # Do not report on reads whose overlapping offset count is too low. + if minReadOffsetCount: + unwanted = set(readId for readId in readOffsetCounts + if readOffsetCounts[readId] < minReadOffsetCount) + allReadIds.symmetric_difference_update(unwanted) + return { 'coveredOffsets': coveredOffsets, 'totalBases': totalBases,

acorg/dark-matter

7e8ca419ef2d6d10287c020e194587a400052ad6

diff --git a/test/test_genomes.py b/test/test_genomes.py index 4819f31..c221136 100644 --- a/test/test_genomes.py +++ b/test/test_genomes.py @@ -172,3 +172,32 @@ class TestGenomeProteinInfo(TestCase): self.assertEqual(750, info['totalBases']) self.assertEqual((3221 - 2306) + (1623 - 0), info['ntLength']) self.assertEqual({'query1', 'query2', 'query3'}, info['readIds']) + + def testTooFewReadOffsetsBAM1(self): + """ + Test that a read is not returned as overlapping a protein unless it + meets the minimum number of required overlapping offsets. + """ + gpi = GenomeProteinInfo('KJ586809.1', DB, True) + gpi.addSAM(BAM1) + + # Look at protein AJF20804.1 coverage (its ranges are 2306-3221 and + # 0-1623). There should be no matching reads because the query + # (query1) is only 200 nt long and so cannot match with at least + # 500 nucleotides. + info = gpi.proteinCoverageInfo('AJF20804.1', 500) + self.assertEqual(set(), info['readIds']) + + def testSufficientReadOffsetsBAM1(self): + """ + Test that a read is returned as overlapping a protein when it meets + the minimum number of required overlapping offsets. + """ + gpi = GenomeProteinInfo('KJ586809.1', DB, True) + gpi.addSAM(BAM1) + + # Look at protein AJF20804.1 coverage (its ranges are 2306-3221 and + # 0-1623). The query (query1) must be returned as it has 200 + # matching nucleotides. + info = gpi.proteinCoverageInfo('AJF20804.1', 199) + self.assertEqual({'query1'}, info['readIds'])

Add tool to summarize protein hits in a SAM/BAM file

0.0

7e8ca419ef2d6d10287c020e194587a400052ad6

[ "test/test_genomes.py::TestGenomeProteinInfo::testSufficientReadOffsetsBAM1", "test/test_genomes.py::TestGenomeProteinInfo::testTooFewReadOffsetsBAM1" ]

[ "test/test_genomes.py::TestGenomeProteinInfo::testLoadBAM1", "test/test_genomes.py::TestGenomeProteinInfo::testLoadBAM12", "test/test_genomes.py::TestGenomeProteinInfo::testLoadBAM123", "test/test_genomes.py::TestGenomeProteinInfo::testLoadReference" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2020-01-13 10:35:47+00:00

mit

877

acorg__dark-matter-726

diff --git a/CHANGELOG.md b/CHANGELOG.md index 66b60e7..17a90c5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,7 @@ +## 3.1.70 March 24, 2020 + +Added `--maxNFraction` arg to `filter-fasta.py`. + ## 3.1.69 March 23, 2020 Added `--md5` arg to `fasta-sequences.py`. @@ -429,9 +433,9 @@ Removed bone-headed use of full path to `fasta-join.sh` from ## 3.0.63 Jan 14, 2019 -Added `compareAaReads` and `matchToString` to `aa.py`. Wrote tests in +Added `compareAaReads` and `matchToString` to `aa.py`. Wrote tests in `test_aa.py` for both. Moved `countPrint` to utils, used by `matchToString` -in `dna.py` and `aa.py`. Added `compare-aa-sequences.py` to the bin. +in `dna.py` and `aa.py`. Added `compare-aa-sequences.py` to the bin. ## 3.0.62 Dec 30, 2018 @@ -444,9 +448,9 @@ and the underlying `ReadFilter` class. ## 3.0.60 Dec 13, 2018 -In `reads.py`, changed the `_makeComplementTable` function so that +In `reads.py`, changed the `_makeComplementTable` function so that uppercase and lowercase bases are correctly reverse complemented into their -respective uppercase and lowercase complementary letters. Added a test to +respective uppercase and lowercase complementary letters. Added a test to `test/reads.py` to confirm that `reverseComplement` does this. ## 3.0.59 Dec 11, 2018 diff --git a/dark/__init__.py b/dark/__init__.py index 52bc094..01d72bb 100644 --- a/dark/__init__.py +++ b/dark/__init__.py @@ -7,4 +7,4 @@ if sys.version_info < (2, 7): # will not be found by the version() function in ../setup.py # # Remember to update ../CHANGELOG.md describing what's new in each version. -__version__ = '3.1.69' +__version__ = '3.1.70' diff --git a/dark/filter.py b/dark/filter.py index 07e00d7..216db82 100644 --- a/dark/filter.py +++ b/dark/filter.py @@ -1,3 +1,5 @@ +from __future__ import division + import re from math import ceil from collections import OrderedDict @@ -187,6 +189,10 @@ def addFASTAFilteringCommandLineOptions(parser): '--maxLength', type=int, metavar='N', help='The maximum sequence length') + parser.add_argument( + '--maxNFraction', type=float, metavar='N', + help='The maximum fraction of Ns that can be present in the sequence') + parser.add_argument( '--whitelist', action='append', metavar='SEQUENCE-ID', help='Sequence titles (ids) that should be whitelisted') @@ -297,6 +303,7 @@ def parseFASTAFilteringCommandLineOptions(args, reads): return reads.filter( minLength=args.minLength, maxLength=args.maxLength, + maxNFraction=args.maxNFraction, whitelist=set(args.whitelist) if args.whitelist else None, blacklist=set(args.blacklist) if args.blacklist else None, whitelistFile=args.whitelistFile, blacklistFile=args.blacklistFile, diff --git a/dark/reads.py b/dark/reads.py index 8da2fef..113ffdd 100644 --- a/dark/reads.py +++ b/dark/reads.py @@ -817,6 +817,8 @@ class ReadFilter(object): @param minLength: The minimum acceptable length. @param maxLength: The maximum acceptable length. + @param maxNFraction: The maximum fraction of Ns that can be present in the + sequence. @param removeGaps: If C{True} remove all gaps ('-' characters) from the read sequences. @param whitelist: If not C{None}, a set of exact read ids that are @@ -935,8 +937,8 @@ class ReadFilter(object): # save and restore the state of the RNG and/or to optionally add # 'seed=XXX' to the end of the id of the first read, etc. - def __init__(self, minLength=None, maxLength=None, removeGaps=False, - whitelist=None, blacklist=None, + def __init__(self, minLength=None, maxLength=None, maxNFraction=None, + removeGaps=False, whitelist=None, blacklist=None, whitelistFile=None, blacklistFile=None, titleRegex=None, negativeTitleRegex=None, truncateTitlesAfter=None, keepSequences=None, @@ -960,6 +962,7 @@ class ReadFilter(object): self.minLength = minLength self.maxLength = maxLength + self.maxNFraction = maxNFraction self.removeGaps = removeGaps self.head = head self.removeDuplicates = removeDuplicates @@ -1126,6 +1129,11 @@ class ReadFilter(object): (self.maxLength is not None and readLen > self.maxLength)): return False + if self.maxNFraction is not None: + nFraction = read.sequence.count('N') / readLen + if self.maxNFraction < nFraction: + return False + if self.removeGaps: if read.quality is None: read = read.__class__(read.id, read.sequence.replace('-', ''))

acorg/dark-matter

4c3115b2c5e585068988dfec0a7330b2d4f2ba37

diff --git a/test/test_reads.py b/test/test_reads.py index 273b87d..ea53b3f 100644 --- a/test/test_reads.py +++ b/test/test_reads.py @@ -2550,6 +2550,46 @@ class TestReads(TestCase): self.assertEqual(sorted([read2, read3]), sorted(reads)) self.assertEqual(3, reads.unfilteredLength()) + def testMaxNFractionAllPassNoNs(self): + """ + Test filtering by maximum fraction of Ns. If there are no Ns in the + sequences, all must pass the filtering. + """ + read1 = Read('id1', 'ATTA') + read2 = Read('id2', 'ATTAAC') + initialReads = Reads([read1, read2]) + initialReads.filter(maxNFraction=0.9) + + reads = Reads(initialReads) + self.assertEqual([read1, read2], list(reads)) + + def testMaxNFractionOnePasses(self): + """ + Test filtering by maximum fraction of Ns. If there are too many Ns in + one of the sequences, only one must pass the filtering. + """ + read1 = Read('id1', 'ATTA') + read2 = Read('id2', 'ATTNNN') + initialReads = Reads([read1, read2]) + initialReads.filter(maxNFraction=0.4) + + reads = Reads(initialReads) + self.assertEqual([read1], list(reads)) + + def testMaxNFractionAllPassNs(self): + """ + Test filtering by maximum fraction of Ns. If there are Ns in the + sequence, but below the threshold, all sequences must pass the + filtering. + """ + read1 = Read('id1', 'ATTA') + read2 = Read('id2', 'ATTNNN') + initialReads = Reads([read1, read2]) + initialReads.filter(maxNFraction=0.6) + + reads = Reads(initialReads) + self.assertEqual([read1, read2], list(reads)) + def testNoVariableSitesConfirm(self): """ If two Reads have no bases that are variable, nothing should be

Add filtering options for maximum number of Ns in a sequence

0.0

4c3115b2c5e585068988dfec0a7330b2d4f2ba37

[ "test/test_reads.py::TestReads::testMaxNFractionAllPassNoNs", "test/test_reads.py::TestReads::testMaxNFractionAllPassNs", "test/test_reads.py::TestReads::testMaxNFractionOnePasses" ]

[ "test/test_reads.py::TestRead::testCasePreservation", "test/test_reads.py::TestRead::testCheckAlphabetAAReadMatchingReturnTrue", "test/test_reads.py::TestRead::testCheckAlphabetAAReadNotMatchingRaise", "test/test_reads.py::TestRead::testCheckAlphabetDNAReadMatchingReturnTrue", "test/test_reads.py::TestRead::testCheckAlphabetDNAReadNotMatchingRaise", "test/test_reads.py::TestRead::testCheckAlphabetwithReadMustBePermissive", "test/test_reads.py::TestRead::testEquality", "test/test_reads.py::TestRead::testEqualityWithDifferingIds", "test/test_reads.py::TestRead::testEqualityWithDifferingQuality", "test/test_reads.py::TestRead::testEqualityWithDifferingSequences", "test/test_reads.py::TestRead::testEqualityWithNoQuality", "test/test_reads.py::TestRead::testEqualityWithOneOmittedQuality", "test/test_reads.py::TestRead::testExpectedAttributes", "test/test_reads.py::TestRead::testFromDict", "test/test_reads.py::TestRead::testFromDictNoQuality", "test/test_reads.py::TestRead::testGetitemFullCopy", "test/test_reads.py::TestRead::testGetitemId", "test/test_reads.py::TestRead::testGetitemLength", "test/test_reads.py::TestRead::testGetitemQuality", "test/test_reads.py::TestRead::testGetitemReturnsNewRead", "test/test_reads.py::TestRead::testGetitemReversed", "test/test_reads.py::TestRead::testGetitemSequence", "test/test_reads.py::TestRead::testGetitemSingleIndex", "test/test_reads.py::TestRead::testGetitemWithStep", "test/test_reads.py::TestRead::testHashDiffersIfIdDiffers", "test/test_reads.py::TestRead::testHashDiffersIfQualityDiffers", "test/test_reads.py::TestRead::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestRead::testHashIdenticalNoQuality", "test/test_reads.py::TestRead::testHashIdenticalWithQuality", "test/test_reads.py::TestRead::testHashViaDict", "test/test_reads.py::TestRead::testHashViaSet", "test/test_reads.py::TestRead::testKeepSites", "test/test_reads.py::TestRead::testKeepSitesAllSites", "test/test_reads.py::TestRead::testKeepSitesNoSites", "test/test_reads.py::TestRead::testKeepSitesOutOfRange", "test/test_reads.py::TestRead::testKeepSitesWithQuality", "test/test_reads.py::TestRead::testLength", "test/test_reads.py::TestRead::testLowComplexityFraction", "test/test_reads.py::TestRead::testLowComplexityFractionEmptySequence", "test/test_reads.py::TestRead::testLowComplexityFractionOne", "test/test_reads.py::TestRead::testLowComplexityFractionZero", "test/test_reads.py::TestRead::testNoQuality", "test/test_reads.py::TestRead::testRemoveSites", "test/test_reads.py::TestRead::testRemoveSitesAllSites", "test/test_reads.py::TestRead::testRemoveSitesNoSites", "test/test_reads.py::TestRead::testRemoveSitesOutOfRange", "test/test_reads.py::TestRead::testRemoveSitesWithQuality", "test/test_reads.py::TestRead::testReverseNoQuality", "test/test_reads.py::TestRead::testReverseWithQuality", "test/test_reads.py::TestRead::testToDict", "test/test_reads.py::TestRead::testToDictNoQuality", "test/test_reads.py::TestRead::testToFASTA", "test/test_reads.py::TestRead::testToFASTAWithQuality", "test/test_reads.py::TestRead::testToFASTQ", "test/test_reads.py::TestRead::testToFASTQWithNoQuality", "test/test_reads.py::TestRead::testToUnknownFormat", "test/test_reads.py::TestRead::testUnequalLengths", "test/test_reads.py::TestRead::testWalkHSPExactMatch", "test/test_reads.py::TestRead::testWalkHSPExactMatchWithGap", "test/test_reads.py::TestRead::testWalkHSPLeftAndRightOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPLeftAndRightOverhangingMatchNoWhiskers", "test/test_reads.py::TestRead::testWalkHSPLeftOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPLeftOverhangingMatchNoWhiskers", "test/test_reads.py::TestRead::testWalkHSPRightOverhangingMatch", "test/test_reads.py::TestRead::testWalkHSPRightOverhangingMatchNoWhiskers", "test/test_reads.py::TestDNARead::testGetitemReturnsNewDNARead", 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"test/test_reads.py::TestSSAARead::testGetitemFullCopy", "test/test_reads.py::TestSSAARead::testGetitemId", "test/test_reads.py::TestSSAARead::testGetitemLength", "test/test_reads.py::TestSSAARead::testGetitemReturnsNewRead", "test/test_reads.py::TestSSAARead::testGetitemReversed", "test/test_reads.py::TestSSAARead::testGetitemSequence", "test/test_reads.py::TestSSAARead::testGetitemSingleIndex", "test/test_reads.py::TestSSAARead::testGetitemStructure", "test/test_reads.py::TestSSAARead::testGetitemWithStep", "test/test_reads.py::TestSSAARead::testHashDiffersIfIdDiffers", "test/test_reads.py::TestSSAARead::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestSSAARead::testHashDiffersIfStructureDiffers", "test/test_reads.py::TestSSAARead::testHashViaDict", "test/test_reads.py::TestSSAARead::testHashViaSet", "test/test_reads.py::TestSSAARead::testKeepSites", "test/test_reads.py::TestSSAARead::testKeepSitesAllSites", "test/test_reads.py::TestSSAARead::testKeepSitesNoSites", "test/test_reads.py::TestSSAARead::testKeepSitesOutOfRange", "test/test_reads.py::TestSSAARead::testReads", "test/test_reads.py::TestSSAARead::testRemoveSites", "test/test_reads.py::TestSSAARead::testRemoveSitesAllSites", "test/test_reads.py::TestSSAARead::testRemoveSitesNoSites", "test/test_reads.py::TestSSAARead::testRemoveSitesOutOfRange", "test/test_reads.py::TestSSAARead::testSequenceLengthMatchesStructureLength", "test/test_reads.py::TestSSAARead::testToDict", "test/test_reads.py::TestSSAARead::testToString", "test/test_reads.py::TestSSAARead::testToStringWithExplicitFastaFormat", "test/test_reads.py::TestSSAARead::testToStringWithExplicitFastaSSFormat", "test/test_reads.py::TestSSAARead::testToStringWithStructureSuffix", "test/test_reads.py::TestSSAARead::testToStringWithUnknownFormat", "test/test_reads.py::TestSSAAReadWithX::testCorrectAttributes", "test/test_reads.py::TestSSAAReadWithX::testFromDict", "test/test_reads.py::TestSSAAReadWithX::testGetitemFullCopy", "test/test_reads.py::TestSSAAReadWithX::testGetitemId", "test/test_reads.py::TestSSAAReadWithX::testGetitemLength", "test/test_reads.py::TestSSAAReadWithX::testGetitemReturnsNewRead", "test/test_reads.py::TestSSAAReadWithX::testGetitemReversed", "test/test_reads.py::TestSSAAReadWithX::testGetitemSequence", "test/test_reads.py::TestSSAAReadWithX::testGetitemSingleIndex", "test/test_reads.py::TestSSAAReadWithX::testGetitemStructure", "test/test_reads.py::TestSSAAReadWithX::testGetitemWithStep", "test/test_reads.py::TestSSAAReadWithX::testHashDiffersIfIdDiffers", "test/test_reads.py::TestSSAAReadWithX::testHashDiffersIfSequenceDiffers", "test/test_reads.py::TestSSAAReadWithX::testHashDiffersIfStructureDiffers", "test/test_reads.py::TestSSAAReadWithX::testHashViaDict", "test/test_reads.py::TestSSAAReadWithX::testHashViaSet", "test/test_reads.py::TestSSAAReadWithX::testKeepSites", "test/test_reads.py::TestSSAAReadWithX::testKeepSitesAllSites", "test/test_reads.py::TestSSAAReadWithX::testKeepSitesNoSites", "test/test_reads.py::TestSSAAReadWithX::testKeepSitesOutOfRange", "test/test_reads.py::TestSSAAReadWithX::testReads", "test/test_reads.py::TestSSAAReadWithX::testRemoveSites", "test/test_reads.py::TestSSAAReadWithX::testRemoveSitesAllSites", "test/test_reads.py::TestSSAAReadWithX::testRemoveSitesNoSites", "test/test_reads.py::TestSSAAReadWithX::testRemoveSitesOutOfRange", "test/test_reads.py::TestSSAAReadWithX::testSequenceContainingX", "test/test_reads.py::TestSSAAReadWithX::testSequenceLengthMatchesStructureLength", "test/test_reads.py::TestSSAAReadWithX::testToDict", "test/test_reads.py::TestSSAAReadWithX::testToString", "test/test_reads.py::TestSSAAReadWithX::testToStringWithExplicitFastaFormat", "test/test_reads.py::TestSSAAReadWithX::testToStringWithExplicitFastaSSFormat", "test/test_reads.py::TestSSAAReadWithX::testToStringWithStructureSuffix", "test/test_reads.py::TestSSAAReadWithX::testToStringWithUnknownFormat", "test/test_reads.py::TestTranslatedRead::testExpectedAttributes", "test/test_reads.py::TestTranslatedRead::testExpectedFrame", "test/test_reads.py::TestTranslatedRead::testFromDict", "test/test_reads.py::TestTranslatedRead::testId", "test/test_reads.py::TestTranslatedRead::testIdReverseComplemented", "test/test_reads.py::TestTranslatedRead::testMaximumORFLength", "test/test_reads.py::TestTranslatedRead::testMaximumORFLengthNoOpenORF", "test/test_reads.py::TestTranslatedRead::testMaximumORFLengthNoStops", "test/test_reads.py::TestTranslatedRead::testOutOfRangeFrame", "test/test_reads.py::TestTranslatedRead::testReverseComplemented", "test/test_reads.py::TestTranslatedRead::testSequence", "test/test_reads.py::TestTranslatedRead::testToDict", "test/test_reads.py::TestReadClassNameToClass::testNames", "test/test_reads.py::TestReads::testEmptyInitialReads", "test/test_reads.py::TestReads::testInitialReads", "test/test_reads.py::TestReads::testManuallyAddedReads", "test/test_reads.py::TestReads::testManuallyAddedReadsLength", "test/test_reads.py::TestReads::testNoReads", "test/test_reads.py::TestReads::testNoReadsLength", "test/test_reads.py::TestReads::testNoVariableSitesConfirm", "test/test_reads.py::TestReads::testNoVariableSitesUnconfirm", "test/test_reads.py::TestReads::testOneAmbiguousCompatibleVariableSitesConfirm", "test/test_reads.py::TestReads::testOneAmbiguousCompatibleVariableSitesUnconfirm", "test/test_reads.py::TestReads::testOneAmbiguousIncompatibleVariableSitesConfirm", "test/test_reads.py::TestReads::testOneAmbiguousIncompatibleVariableSitesUnconfirm", "test/test_reads.py::TestReads::testOneVariableSitesConfirm", "test/test_reads.py::TestReads::testOneVariableSitesUnconfirm", "test/test_reads.py::TestReads::testRepeatedIter", "test/test_reads.py::TestReads::testSaveAsFASTA", "test/test_reads.py::TestReads::testSaveAsFASTQ", "test/test_reads.py::TestReads::testSaveAsFASTQFailsOnReadWithNoQuality", "test/test_reads.py::TestReads::testSaveFASTAIsDefault", "test/test_reads.py::TestReads::testSaveReturnsReadCount", "test/test_reads.py::TestReads::testSaveToFileDescriptor", "test/test_reads.py::TestReads::testSaveWithUnknownFormat", "test/test_reads.py::TestReads::testSaveWithUppercaseFormat", "test/test_reads.py::TestReads::testSubclass", "test/test_reads.py::TestReads::testSubclassLength", "test/test_reads.py::TestReads::testSubclassWithAdditionalReads", "test/test_reads.py::TestReads::testUnfilteredLengthAdditionalReads", "test/test_reads.py::TestReads::testUnfilteredLengthAdditionalReadsAfterFiltering", "test/test_reads.py::TestReads::testUnfilteredLengthBeforeIterating", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReads", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReadsAfterFiltering", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReadsIsReads", "test/test_reads.py::TestReads::testUnfilteredLengthInitialReadsIsReadsWithAdditional", "test/test_reads.py::TestReads::testUnfilteredLengthInitialSubclassThenFiltered", "test/test_reads.py::TestReads::testUnfilteredLengthInitialSubclassWithAdditionalThenFiltered", "test/test_reads.py::TestReads::testUnfilteredLengthInitialSubclassWithNoLen", "test/test_reads.py::TestReads::testUnfilteredLengthNoReads", "test/test_reads.py::TestReads::testVariableSitesHeterogeneous", "test/test_reads.py::TestReads::testVariableSitesHeterogeneousCounts", "test/test_reads.py::TestReads::testVariableSitesTooHomogeneous", "test/test_reads.py::TestReads::testVariableSitesUnequalLengths", "test/test_reads.py::TestReadsFiltering::testAddFiltersThenClearFilters", "test/test_reads.py::TestReadsFiltering::testFilterBlacklist", "test/test_reads.py::TestReadsFiltering::testFilterDoNotRemoveDescriptions", "test/test_reads.py::TestReadsFiltering::testFilterDuplicates", "test/test_reads.py::TestReadsFiltering::testFilterDuplicatesById", "test/test_reads.py::TestReadsFiltering::testFilterDuplicatesByIdMD5", "test/test_reads.py::TestReadsFiltering::testFilterDuplicatesUseMD5", "test/test_reads.py::TestReadsFiltering::testFilterHead", "test/test_reads.py::TestReadsFiltering::testFilterHeadZero", "test/test_reads.py::TestReadsFiltering::testFilterKeepSequences", "test/test_reads.py::TestReadsFiltering::testFilterKeepSequencesNoSequences", "test/test_reads.py::TestReadsFiltering::testFilterNegativeRegex", "test/test_reads.py::TestReadsFiltering::testFilterNoArgs", "test/test_reads.py::TestReadsFiltering::testFilterOnLengthEverythingMatches", "test/test_reads.py::TestReadsFiltering::testFilterOnLengthNothingMatches", "test/test_reads.py::TestReadsFiltering::testFilterOnMaxLength", "test/test_reads.py::TestReadsFiltering::testFilterOnMinLength", "test/test_reads.py::TestReadsFiltering::testFilterPositiveRegex", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfFiveFromFiveReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfFiveFromOneRead", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfOneFromOneRead", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfTwoFromFiveReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetOfZeroReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetSizeZeroNoReads", "test/test_reads.py::TestReadsFiltering::testFilterRandomSubsetSizeZeroTwoReads", "test/test_reads.py::TestReadsFiltering::testFilterRemoveDescriptions", "test/test_reads.py::TestReadsFiltering::testFilterRemoveGaps", "test/test_reads.py::TestReadsFiltering::testFilterRemoveGapsWithQuality", "test/test_reads.py::TestReadsFiltering::testFilterRemoveSequences", "test/test_reads.py::TestReadsFiltering::testFilterRemoveSequencesNoSequences", "test/test_reads.py::TestReadsFiltering::testFilterReturnsReadInstance", "test/test_reads.py::TestReadsFiltering::testFilterTruncateTitles", "test/test_reads.py::TestReadsFiltering::testFilterWhitelist", "test/test_reads.py::TestReadsFiltering::testFilterWithMinLengthEqualToMaxLength", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatChangesIds", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatOmits", "test/test_reads.py::TestReadsFiltering::testFilterWithModifierThatOmitsAndChangesIds", "test/test_reads.py::TestReadsFiltering::testFilteredReadsInstanceHasExpectedLength", "test/test_reads.py::TestReadsFiltering::testIdLambda", "test/test_reads.py::TestReadsFiltering::testIdLambdaReturningNone", "test/test_reads.py::TestReadsFiltering::testKeepSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesAllSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesNoSites", "test/test_reads.py::TestReadsFiltering::testKeepSitesOutOfRange", "test/test_reads.py::TestReadsFiltering::testKeepSitesWithQuality", "test/test_reads.py::TestReadsFiltering::testLineNumberFile", "test/test_reads.py::TestReadsFiltering::testLineNumberFileEmpty", "test/test_reads.py::TestReadsFiltering::testLineNumberFileFirstLineTooSmall", "test/test_reads.py::TestReadsFiltering::testLineNumberFileNonAscending", "test/test_reads.py::TestReadsFiltering::testLineNumberFileRunOutOfSequences", "test/test_reads.py::TestReadsFiltering::testReadLambda", "test/test_reads.py::TestReadsFiltering::testReadLambdaReturningNone", "test/test_reads.py::TestReadsFiltering::testRemoveAndKeepSites", "test/test_reads.py::TestReadsFiltering::testRemoveSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesAllSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesNoSites", "test/test_reads.py::TestReadsFiltering::testRemoveSitesOutOfRange", "test/test_reads.py::TestReadsFiltering::testRemoveSitesWithQuality", "test/test_reads.py::TestReadsFiltering::testReverse", "test/test_reads.py::TestReadsFiltering::testReverseAndReverseComplement", "test/test_reads.py::TestReadsFiltering::testReverseComplement", "test/test_reads.py::TestReadsFiltering::testReverseComplementAARead", "test/test_reads.py::TestReadsFiltering::testReverseComplementNonDNA", "test/test_reads.py::TestReadsFiltering::testSampleFractionAndNoTrueLengthRaisesValueError", "test/test_reads.py::TestReadsFiltering::testSampleFractionAndRandomSubsetRaisesValueError", "test/test_reads.py::TestReadsFiltering::testSampleFractionOne", "test/test_reads.py::TestReadsFiltering::testSampleFractionPointOne", "test/test_reads.py::TestReadsFiltering::testSampleFractionZero", "test/test_reads.py::TestReadsInRAM::testAdd", "test/test_reads.py::TestReadsInRAM::testFastaFile", "test/test_reads.py::TestReadsInRAM::testFromReads", "test/test_reads.py::TestReadsInRAM::testNoReads", "test/test_reads.py::TestReadsInRAM::testOneReadIndex", "test/test_reads.py::TestReadsInRAM::testOneReadLength", "test/test_reads.py::TestReadsInRAM::testOneReadList", "test/test_reads.py::TestReadsInRAM::testSetItem", "test/test_reads.py::TestReadsInRAM::testTwoReadsIndex", "test/test_reads.py::TestReadsInRAM::testTwoReadsLength", "test/test_reads.py::TestReadsInRAM::testTwoReadsList", "test/test_reads.py::TestSummarizePosition::testCorrectFrequencies", "test/test_reads.py::TestSummarizePosition::testExcludeShortSequences", "test/test_reads.py::TestSummarizePosition::testFrequenciesNoReads", "test/test_reads.py::TestSummarizePosition::testIndexLargerThanSequenceLength", "test/test_reads.py::TestSummarizePosition::testNumberOfExclusionsNoReads", "test/test_reads.py::TestSitesMatching::testAllMatches", "test/test_reads.py::TestSitesMatching::testIgnoreCase", "test/test_reads.py::TestSitesMatching::testMatchCase", "test/test_reads.py::TestSitesMatching::testMultipleReadsAll", "test/test_reads.py::TestSitesMatching::testMultipleReadsAllWithDifferingLengths", "test/test_reads.py::TestSitesMatching::testMultipleReadsAny", "test/test_reads.py::TestSitesMatching::testMultipleReadsAnyWithDifferingLengths", "test/test_reads.py::TestSitesMatching::testNoMatches", "test/test_reads.py::TestSitesMatching::testPartialMatch" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2020-03-24 11:35:19+00:00

mit

878

adafruit__Adafruit_CircuitPython_GPS-76

diff --git a/adafruit_gps.py b/adafruit_gps.py index 10bc89c..a28a065 100644 --- a/adafruit_gps.py +++ b/adafruit_gps.py @@ -50,11 +50,11 @@ _ST_MAX = _RMC_4_1 _SENTENCE_PARAMS = ( # 0 - _GLL - "dcdcfcC", + "dcdcscC", # 1 - _RMC - "fcdcdcffiDCC", + "scdcdcffsDCC", # 2 - _GGA - "fdcdciiffsfsIS", + "sdcdciiffsfsIS", # 3 - _GSA "ciIIIIIIIIIIIIfff", # 4 - _GSA_4_11 @@ -68,7 +68,7 @@ _SENTENCE_PARAMS = ( # 8 - _GSV19 "iiiiiiIiiiIiiiIiiiI", # 9 - _RMC_4_1 - "fcdcdcffiDCCC", + "scdcdcffsDCCC", ) @@ -394,9 +394,9 @@ class GPS: return (data_type, sentence[delimiter + 1 :]) def _update_timestamp_utc(self, time_utc, date=None): - hours = time_utc // 10000 - mins = (time_utc // 100) % 100 - secs = time_utc % 100 + hours = int(time_utc[0:2]) + mins = int(time_utc[2:4]) + secs = int(time_utc[4:6]) if date is None: if self.timestamp_utc is None: day, month, year = 0, 0, 0 @@ -405,9 +405,9 @@ class GPS: month = self.timestamp_utc.tm_mon year = self.timestamp_utc.tm_year else: - day = date // 10000 - month = (date // 100) % 100 - year = 2000 + date % 100 + day = int(date[0:2]) + month = int(date[2:4]) + year = 2000 + int(date[4:6]) self.timestamp_utc = time.struct_time( (year, month, day, hours, mins, secs, 0, 0, -1) @@ -429,7 +429,7 @@ class GPS: self.longitude = _read_degrees(data, 2, "w") # UTC time of position - self._update_timestamp_utc(int(data[4])) + self._update_timestamp_utc(data[4]) # Status Valid(A) or Invalid(V) self.isactivedata = data[5] @@ -450,7 +450,7 @@ class GPS: return False # Params didn't parse # UTC time of position and date - self._update_timestamp_utc(int(data[0]), data[8]) + self._update_timestamp_utc(data[0], data[8]) # Status Valid(A) or Invalid(V) self.isactivedata = data[1] @@ -494,7 +494,7 @@ class GPS: return False # Params didn't parse # UTC time of position - self._update_timestamp_utc(int(data[0])) + self._update_timestamp_utc(data[0]) # Latitude self.latitude = _read_degrees(data, 1, "s")

adafruit/Adafruit_CircuitPython_GPS

b9e06e93f258ef3251b8104e19c9cfd435d12d60

diff --git a/tests/adafruit_gps_test.py b/tests/adafruit_gps_test.py index 9e09c85..8a956f3 100644 --- a/tests/adafruit_gps_test.py +++ b/tests/adafruit_gps_test.py @@ -140,14 +140,14 @@ def test_GPS_update_timestamp_UTC_date_None(): assert gps.datetime is None assert gps.timestamp_utc is None exp_struct = time.struct_time((0, 0, 0, 22, 14, 11, 0, 0, -1)) - gps._update_timestamp_utc(time_utc=221411) + gps._update_timestamp_utc(time_utc="221411") assert gps.timestamp_utc == exp_struct def test_GPS_update_timestamp_UTC_date_not_None(): gps = GPS(uart=UartMock()) exp_struct = time.struct_time((2021, 10, 2, 22, 14, 11, 0, 0, -1)) - gps._update_timestamp_utc(time_utc=221411, date=21021) + gps._update_timestamp_utc(time_utc="221411", date="021021") assert gps.timestamp_utc == exp_struct @@ -157,7 +157,7 @@ def test_GPS_update_timestamp_timestamp_utc_was_not_none_new_date_none(): gps.timestamp_utc = time.struct_time((2021, 10, 2, 22, 10, 11, 0, 0, -1)) exp_struct = time.struct_time((2021, 10, 2, 22, 14, 11, 0, 0, -1)) # update the timestamp - gps._update_timestamp_utc(time_utc=221411) + gps._update_timestamp_utc(time_utc="221411") assert gps.timestamp_utc == exp_struct

Usage of float causes timestamp_utc to be imprecise NMEA timestamp is written as HHMMSS.sss, which is stored as float in the module. Later it is converted to int which is inaccurate: See example: ``` >> int(184105.000) 184104 ``` This is then math'ed into the fields in time_struct. Propose storing the NMEA sentence as string instead, and grabbing the sections of the sting directly.

0.0

b9e06e93f258ef3251b8104e19c9cfd435d12d60

[ "tests/adafruit_gps_test.py::test_GPS_update_timestamp_timestamp_utc_was_not_none_new_date_none", "tests/adafruit_gps_test.py::test_GPS_update_timestamp_UTC_date_None", "tests/adafruit_gps_test.py::test_GPS_update_timestamp_UTC_date_not_None" ]

[ "tests/adafruit_gps_test.py::test_parse_talker_regular", "tests/adafruit_gps_test.py::test_GPS_update_empty_sentence", "tests/adafruit_gps_test.py::test_read_degrees[west", "tests/adafruit_gps_test.py::test_GPS_update_from_GSA[greater", "tests/adafruit_gps_test.py::test_parse_float_invalid[None]", "tests/adafruit_gps_test.py::test_parse_degrees[long", "tests/adafruit_gps_test.py::test_parse_float", "tests/adafruit_gps_test.py::test_GPS_update_rmc_has_magnetic_variation[E]", "tests/adafruit_gps_test.py::test_parse_data_unknown_sentence_type[10]", "tests/adafruit_gps_test.py::test_GPS_update_from_GSV_both_parts_sats_are_removed", "tests/adafruit_gps_test.py::test_parse_str_invalid[]", "tests/adafruit_gps_test.py::test_read_sentence_too_few_in_waiting", "tests/adafruit_gps_test.py::test_GPS_update_rmc_fix_is_set", "tests/adafruit_gps_test.py::test_GPS_update_data_type_too_short", "tests/adafruit_gps_test.py::test_GPS_update_sentence_is_None", "tests/adafruit_gps_test.py::test_read_degrees[south", "tests/adafruit_gps_test.py::test_GPS_send_command_without_checksum", "tests/adafruit_gps_test.py::test_parse_degrees[leading", "tests/adafruit_gps_test.py::test_parse_int_invalid[None]", "tests/adafruit_gps_test.py::test_parse_str_invalid[None]", "tests/adafruit_gps_test.py::test_parse_degrees[regular", "tests/adafruit_gps_test.py::test_parse_str_valid", "tests/adafruit_gps_test.py::test_GPS_update_from_GLL", "tests/adafruit_gps_test.py::test_parse_int_invalid[]", "tests/adafruit_gps_test.py::test_GPS_update_with_unknown_talker", "tests/adafruit_gps_test.py::test_read_degrees[north", "tests/adafruit_gps_test.py::test_GPS_update_from_GSV_first_part", "tests/adafruit_gps_test.py::test_GPS_update_rmc_debug_shows_sentence", "tests/adafruit_gps_test.py::test_GPS_update_rmc_no_magnetic_variation", "tests/adafruit_gps_test.py::test_parse_degrees_too_short", "tests/adafruit_gps_test.py::test_GPS_update_from_GSA[smaller", "tests/adafruit_gps_test.py::test_GPS_update_rmc_invalid_checksum", "tests/adafruit_gps_test.py::test_GPS_update_from_GGA", "tests/adafruit_gps_test.py::test_parse_data_unexpected_parameter_type", "tests/adafruit_gps_test.py::test_GPS_update_rmc_has_magnetic_variation[W]", "tests/adafruit_gps_test.py::test_parse_data_unknown_sentence_type[-1]", "tests/adafruit_gps_test.py::test_parse_talker_prop_code", "tests/adafruit_gps_test.py::test_read_degrees[east", "tests/adafruit_gps_test.py::test_GPS_update_rmc_fix_is_set_new", "tests/adafruit_gps_test.py::test_parse_float_invalid[]", "tests/adafruit_gps_test.py::test_GPS_send_command_with_checksum", "tests/adafruit_gps_test.py::test_GPS_update_from_RMC", "tests/adafruit_gps_test.py::test_param_types_does_not_match_data_items", "tests/adafruit_gps_test.py::test_parse_int", "tests/adafruit_gps_test.py::test_parse_sentence_invalid_delimiter" ]

{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-12-08 21:02:48+00:00

mit

879

adafruit__circup-21

diff --git a/circup.py b/circup.py index da2acab..5e9aef8 100644 --- a/circup.py +++ b/circup.py @@ -502,9 +502,21 @@ def ensure_latest_bundle(): logger.exception(ex) if tag > old_tag: logger.info("New version available ({}).".format(tag)) - get_bundle(tag) - with open(BUNDLE_DATA, "w", encoding="utf-8") as data: - json.dump({"tag": tag}, data) + try: + get_bundle(tag) + with open(BUNDLE_DATA, "w", encoding="utf-8") as data: + json.dump({"tag": tag}, data) + except requests.exceptions.HTTPError as ex: + # See #20 for reason this this + click.secho( + ( + "There was a problem downloading the bundle. " + "Please try again in a moment." + ), + fg="red", + ) + logger.exception(ex) + sys.exit(1) else: logger.info("Current library bundle up to date ({}).".format(tag)) @@ -761,10 +773,14 @@ def install(name, py): # pragma: no cover shutil.copyfile(source_path, target_path) else: # Use pre-compiled mpy modules. - module_name = os.path.basename(metadata["path"]).replace(".py", ".mpy") + module_name = os.path.basename(metadata["path"]).replace( + ".py", ".mpy" + ) if not module_name: # Must be a directory based module. - module_name = os.path.basename(os.path.dirname(metadata["path"])) + module_name = os.path.basename( + os.path.dirname(metadata["path"]) + ) major_version = CPY_VERSION.split(".")[0] bundle_platform = "{}mpy".format(major_version) bundle_path = ""

adafruit/circup

024a8bc0cb4555cb122aadd567bd991222fd630a

diff --git a/tests/test_circup.py b/tests/test_circup.py index 32e8ae8..40b87ee 100644 --- a/tests/test_circup.py +++ b/tests/test_circup.py @@ -26,6 +26,7 @@ import circup import ctypes import pytest import json +import requests from unittest import mock @@ -545,8 +546,8 @@ def test_ensure_latest_bundle_bad_bundle_data(): def test_ensure_latest_bundle_to_update(): """ - If the version found in the BUNDLE_DATA is out of date, the cause an update - to the bundle. + If the version found in the BUNDLE_DATA is out of date, then cause an + update to the bundle. """ with mock.patch("circup.get_latest_tag", return_value="54321"), mock.patch( "circup.os.path.isfile", return_value=True @@ -561,6 +562,30 @@ def test_ensure_latest_bundle_to_update(): assert mock_json.dump.call_count == 1 # Current version saved to file. +def test_ensure_latest_bundle_to_update_http_error(): + """ + If an HTTP error happens during a bundle update, print a friendly + error message and exit 1. + """ + with mock.patch("circup.get_latest_tag", return_value="54321"), mock.patch( + "circup.os.path.isfile", return_value=True + ), mock.patch("circup.open"), mock.patch( + "circup.get_bundle", side_effect=requests.exceptions.HTTPError("404") + ) as mock_gb, mock.patch( + "circup.json" + ) as mock_json, mock.patch( + "circup.click.secho" + ) as mock_click, mock.patch( + "circup.sys.exit" + ) as mock_exit: + mock_json.load.return_value = {"tag": "12345"} + circup.ensure_latest_bundle() + mock_gb.assert_called_once_with("54321") + assert mock_json.dump.call_count == 0 # not saved. + mock_click.call_count == 1 # friendly message. + mock_exit.assert_called_once_with(1) # exit 1. + + def test_ensure_latest_bundle_no_update(): """ If the version found in the BUNDLE_DATA is NOT out of date, just log the

Error while running CircUp Show during bundle release I kind of got lucky finding this one. At the time I ran it, the release had been created, but the bundle asset hadn't been finished being generated. ``` bash-3.2$ circup show Found device at /Volumes/CIRCUITPY, running CircuitPython 5.0.0-alpha.4. Downloading latest version information. Traceback (most recent call last): File "/usr/local/bin/circup", line 10, in <module> sys.exit(main()) File "/usr/local/lib/python3.7/site-packages/click/core.py", line 764, in __call__ return self.main(*args, **kwargs) File "/usr/local/lib/python3.7/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/usr/local/lib/python3.7/site-packages/click/core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/usr/local/lib/python3.7/site-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, **ctx.params) File "/usr/local/lib/python3.7/site-packages/click/core.py", line 555, in invoke return callback(*args, **kwargs) File "/usr/local/lib/python3.7/site-packages/circup.py", line 719, in show available_modules = get_bundle_versions() File "/usr/local/lib/python3.7/site-packages/circup.py", line 403, in get_bundle_versions ensure_latest_bundle() File "/usr/local/lib/python3.7/site-packages/circup.py", line 505, in ensure_latest_bundle get_bundle(tag) File "/usr/local/lib/python3.7/site-packages/circup.py", line 547, in get_bundle r.raise_for_status() File "/usr/local/lib/python3.7/site-packages/requests/models.py", line 940, in raise_for_status raise HTTPError(http_error_msg, response=self) requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://github.com/adafruit/Adafruit_CircuitPython_Bundle/releases/download/20191029/adafruit-circuitpython-bundle-py-20191029.zip ```

0.0

024a8bc0cb4555cb122aadd567bd991222fd630a

[ "tests/test_circup.py::test_ensure_latest_bundle_to_update_http_error" ]

[ "tests/test_circup.py::test_Module_init_file_module", "tests/test_circup.py::test_Module_init_directory_module", "tests/test_circup.py::test_Module_outofdate", "tests/test_circup.py::test_Module_outofdate_bad_versions", "tests/test_circup.py::test_Module_row", "tests/test_circup.py::test_Module_update_dir", "tests/test_circup.py::test_Module_update_file", "tests/test_circup.py::test_Module_repr", "tests/test_circup.py::test_find_device_posix_exists", "tests/test_circup.py::test_find_device_posix_no_mount_command", "tests/test_circup.py::test_find_device_posix_missing", "tests/test_circup.py::test_find_device_nt_exists", "tests/test_circup.py::test_find_device_nt_missing", "tests/test_circup.py::test_find_device_unknown_os", "tests/test_circup.py::test_get_latest_tag", "tests/test_circup.py::test_extract_metadata_python", "tests/test_circup.py::test_extract_metadata_byte_code", "tests/test_circup.py::test_find_modules", "tests/test_circup.py::test_find_modules_goes_bang", "tests/test_circup.py::test_get_bundle_versions", "tests/test_circup.py::test_get_circuitpython_version", "tests/test_circup.py::test_get_device_versions", "tests/test_circup.py::test_get_modules_empty_path", "tests/test_circup.py::test_get_modules_that_are_files", "tests/test_circup.py::test_get_modules_that_are_directories", "tests/test_circup.py::test_get_modules_that_are_directories_with_no_metadata", "tests/test_circup.py::test_ensure_latest_bundle_no_bundle_data", "tests/test_circup.py::test_ensure_latest_bundle_bad_bundle_data", "tests/test_circup.py::test_ensure_latest_bundle_to_update", "tests/test_circup.py::test_ensure_latest_bundle_no_update", "tests/test_circup.py::test_get_bundle", "tests/test_circup.py::test_get_bundle_network_error" ]

{ "failed_lite_validators": [ "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }

2019-10-30 08:45:28+00:00

mit

880

adamboche__python-marshmallow-union-29

diff --git a/src/marshmallow_union/__init__.py b/src/marshmallow_union/__init__.py index 69e3099..b3b86e1 100644 --- a/src/marshmallow_union/__init__.py +++ b/src/marshmallow_union/__init__.py @@ -59,9 +59,22 @@ class Union(marshmallow.fields.Field): for candidate_field in fields: try: - return candidate_field.serialize( - attr, obj, error_store=error_store, **kwargs - ) + try: + return candidate_field.serialize( + attr, obj, error_store=error_store, **kwargs + ) + except TypeError: + # When serialising a mapping (eg dict) value item, 'attr' and 'obj' + # is none (as a dict value is not an attribute of anything). This + # causes issues with the attribute-get methods within + # 'marshmallow', but can be bypassed by passing the known 'value' + # directly to '_serialize' + if attr is obj is None: + # pylint: disable=protected-access + return candidate_field._serialize( + value, attr, obj, **kwargs + ) + raise # pylint: disable=broad-except except Exception as exc: pass

adamboche/python-marshmallow-union

49f82a94403b686e56c4509cf75bca40a9dfe23a

diff --git a/tests/test_union.py b/tests/test_union.py index 10e6066..c4ffd4f 100644 --- a/tests/test_union.py +++ b/tests/test_union.py @@ -32,6 +32,19 @@ class OtherSchema(marshmallow.Schema): ) +class MappingSchema(marshmallow.Schema): + """Schema with union inside mapping.""" + items = marshmallow.fields.Dict( + marshmallow.fields.String(), + marshmallow_union.Union( + [ + marshmallow.fields.Integer(), + marshmallow.fields.List(marshmallow.fields.Integer()), + ], + ), + ) + + class StrIntSchema(marshmallow.Schema): """Schema with str and int candidates.""" @@ -46,6 +59,7 @@ class StrIntSchema(marshmallow.Schema): ({"name": "Alice", "number_or_numbers": [25, 50]}, OtherSchema()), ({"x": 5}, StrIntSchema()), ({"x": "hello"}, StrIntSchema()), + ({"items": {"a": 42, "b": [17]}}, MappingSchema()), ], ) def test_round_trip(data, schema): @@ -60,6 +74,7 @@ def test_round_trip(data, schema): [ ({"name": "Alice", "number_or_numbers": "twenty-five"}, PersonSchema()), ({"name": "Alice", "number_or_numbers": {"x": 14}}, PersonSchema()), + ({"items": {"a": 42, "b": "spam"}}, MappingSchema()), ], ) def test_raises(data, schema):

Support union for mapping value When using a union for a mapping value-type, marshmallow-union raises `ExceptionGroup` during serialisation. All candidate fields raise as marshmallow-union calls `schema.serialise(attr, obj, ...)`. However, inside a mapping value-type, marshmallow calls `schema._serialise(value, None, None)`, as the mapping values are not part of the serialised object. ### Reproduction ```python import typing as t import dataclasses import marshmallow import marshmallow_dataclass @marshmallow_dataclass.dataclass class Foo: bar: t.Dict[str, t.Union[int, str]] = dataclasses.field(default_factory=dict) obj = Foo(bar={"spam": "eggs", "ham": 42}) schema = Foo.Schema() schema.dump(obj) ``` ### Expected ```python {'bar': {'spam': 'eggs', 'ham': 42}} ``` ### Actual ```python Traceback (most recent call last): File "<stdin>", line 1, in <module> File "~/env-tmp/lib/python3.7/site-packages/marshmallow/schema.py", line 553, in dump result = self._serialize(processed_obj, many=many) File "~/env-tmp/lib/python3.7/site-packages/marshmallow/schema.py", line 517, in _serialize value = field_obj.serialize(attr_name, obj, accessor=self.get_attribute) File "~/env-tmp/lib/python3.7/site-packages/marshmallow/fields.py", line 325, in serialize return self._serialize(value, attr, obj, **kwargs) File "`/env-tmp/lib/python3.7/site-packages/marshmallow/fields.py", line 1510, in _serialize result[keys[k]] = self.value_field._serialize(v, None, None, **kwargs) File "~/env-tmp/lib/python3.7/site-packages/marshmallow_union/__init__.py", line 69, in _serialize raise ExceptionGroup("All serializers raised exceptions.\n", error_store.errors) marshmallow_union.ExceptionGroup: ('All serializers raised exceptions.\n', {}) ``` ### Environment * OS: Ubuntu 19:10 * Python: 3.7.5 * marshmallow: 3.2.2 * marshmallow-union: 0.1.12 * marshmallow-dataclass: 7.1

0.0

49f82a94403b686e56c4509cf75bca40a9dfe23a

[ "tests/test_union.py::test_round_trip[data5-schema5]" ]

[ "tests/test_union.py::test_round_trip[data0-schema0]", "tests/test_union.py::test_round_trip[data1-schema1]", "tests/test_union.py::test_round_trip[data2-schema2]", "tests/test_union.py::test_round_trip[data3-schema3]", "tests/test_union.py::test_round_trip[data4-schema4]", "tests/test_union.py::test_raises[data0-schema0]", "tests/test_union.py::test_raises[data1-schema1]", "tests/test_union.py::test_raises[data2-schema2]" ]

{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }

2019-12-27 12:40:46+00:00

mit

881

adamboche__python-marshmallow-union-33

diff --git a/src/marshmallow_union/__init__.py b/src/marshmallow_union/__init__.py index 22d5ef4..ee47920 100644 --- a/src/marshmallow_union/__init__.py +++ b/src/marshmallow_union/__init__.py @@ -13,6 +13,7 @@ class MarshmallowUnionException(Exception): class ExceptionGroup(MarshmallowUnionException): """Collection of possibly multiple exceptions.""" + def __init__(self, msg: str, errors): self.msg = msg self.errors = errors @@ -63,8 +64,8 @@ class Union(marshmallow.fields.Field): for candidate_field in fields: try: - return candidate_field.serialize( - attr, obj, error_store=error_store, **kwargs + return candidate_field._serialize( + value, attr, obj, error_store=error_store, **kwargs ) except ValueError as e: error_store.store_error({attr: e})

adamboche/python-marshmallow-union

58bfc9fb069e00478afba87da3e003464cbdaebe

diff --git a/tests/test_union.py b/tests/test_union.py index 6377c06..c93f004 100644 --- a/tests/test_union.py +++ b/tests/test_union.py @@ -52,6 +52,14 @@ class IntStrSchema(marshmallow.Schema): x = marshmallow_union.Union([marshmallow.fields.Int(), marshmallow.fields.String()]) +class ListUnionSchema(marshmallow.Schema): + """Schema with a list of unions.""" + + l = marshmallow.fields.List( + marshmallow_union.Union([marshmallow.fields.Int(), marshmallow.fields.String()]) + ) + + @pytest.mark.parametrize( "data, schema", [ @@ -59,6 +67,7 @@ class IntStrSchema(marshmallow.Schema): ({"name": "Alice", "number_or_numbers": [25, 50]}, PersonSchema()), ({"name": "Alice", "number_or_numbers": [25, 50]}, OtherSchema()), ({"x": 5}, IntStrSchema()), + ({"l": ["h", 5, "n", 1]}, ListUnionSchema()), ({"x": "hello"}, IntStrSchema()), ({"items": {"a": 42, "b": [17]}}, MappingSchema()), ],

_serialize ignores the given value The `_serialize` method of `Union` calls the `serialize` method (instead of `_serialize`) on the underlying fields. This means that it ignores the given `value` parameter, and may try to serialize a completely different value. See: https://github.com/adamboche/python-marshmallow-union/blob/master/src/marshmallow_union/__init__.py#L66-L68 Initially reported in: https://github.com/lovasoa/marshmallow_dataclass/issues/67

0.0

58bfc9fb069e00478afba87da3e003464cbdaebe

[ "tests/test_union.py::test_round_trip[data4-schema4]" ]

[ "tests/test_union.py::test_round_trip[data0-schema0]", "tests/test_union.py::test_round_trip[data1-schema1]", "tests/test_union.py::test_round_trip[data2-schema2]", "tests/test_union.py::test_round_trip[data3-schema3]", "tests/test_union.py::test_round_trip[data5-schema5]", "tests/test_union.py::test_round_trip[data6-schema6]", "tests/test_union.py::test_load_raises[data0-schema0]", "tests/test_union.py::test_load_raises[data1-schema1]", "tests/test_union.py::test_load_raises[data2-schema2]", "tests/test_union.py::test_dump_raises[data0-schema0]", "tests/test_union.py::test_dump_raises[data1-schema1]", "tests/test_union.py::test_dump_raises[data2-schema2]" ]

{ "failed_lite_validators": [ "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }

2020-05-23 13:45:41+00:00

mit

882

adamchainz__apig-wsgi-118

diff --git a/src/apig_wsgi.py b/src/apig_wsgi.py index efb01d2..d5ea0f0 100644 --- a/src/apig_wsgi.py +++ b/src/apig_wsgi.py @@ -94,10 +94,8 @@ def get_environ(event, binary_support): if key == "CONTENT_TYPE": environ["CONTENT_TYPE"] = values[-1] - continue elif key == "HOST": environ["SERVER_NAME"] = values[-1] - continue elif key == "X_FORWARDED_FOR": environ["REMOTE_ADDR"] = values[-1].split(", ")[0] elif key == "X_FORWARDED_PROTO":

adamchainz/apig-wsgi

4f3b043beb5067379a7d1459aea751eb74a27e5e

diff --git a/tests/test_apig_wsgi.py b/tests/test_apig_wsgi.py index 736d859..fff9c37 100644 --- a/tests/test_apig_wsgi.py +++ b/tests/test_apig_wsgi.py @@ -343,10 +343,60 @@ def test_special_headers(simple_app): simple_app.handler(event, None) assert simple_app.environ["CONTENT_TYPE"] == "text/plain" + assert simple_app.environ["HTTP_CONTENT_TYPE"] == "text/plain" assert simple_app.environ["SERVER_NAME"] == "example.com" + assert simple_app.environ["HTTP_HOST"] == "example.com" assert simple_app.environ["REMOTE_ADDR"] == "1.2.3.4" + assert simple_app.environ["HTTP_X_FORWARDED_FOR"] == "1.2.3.4, 5.6.7.8" assert simple_app.environ["wsgi.url_scheme"] == "https" + assert simple_app.environ["HTTP_X_FORWARDED_PROTO"] == "https" assert simple_app.environ["SERVER_PORT"] == "123" + assert simple_app.environ["HTTP_X_FORWARDED_PORT"] == "123" + + +def test_special_content_type(simple_app): + event = make_event(headers={"Content-Type": ["text/plain"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["CONTENT_TYPE"] == "text/plain" + assert simple_app.environ["HTTP_CONTENT_TYPE"] == "text/plain" + + +def test_special_host(simple_app): + event = make_event(headers={"Host": ["example.com"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["SERVER_NAME"] == "example.com" + assert simple_app.environ["HTTP_HOST"] == "example.com" + + +def test_special_x_forwarded_for(simple_app): + event = make_event(headers={"X-Forwarded-For": ["1.2.3.4, 5.6.7.8"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["REMOTE_ADDR"] == "1.2.3.4" + assert simple_app.environ["HTTP_X_FORWARDED_FOR"] == "1.2.3.4, 5.6.7.8" + + +def test_x_forwarded_proto(simple_app): + event = make_event(headers={"X-Forwarded-Proto": ["https"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["wsgi.url_scheme"] == "https" + assert simple_app.environ["HTTP_X_FORWARDED_PROTO"] == "https" + + +def test_x_forwarded_port(simple_app): + event = make_event(headers={"X-Forwarded-Port": ["123"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["SERVER_PORT"] == "123" + assert simple_app.environ["HTTP_X_FORWARDED_PORT"] == "123" def test_no_headers(simple_app):

2.5.0 Multivalue support breaks Host Header support The new update for 2.5.0 broke for us, because we're trying to access the HTTP Host header directly, rather than accessing via the `SERVER_NAME` WSGI variable. Was this intentional, or just a byproduct of trying to also set `SERVER_NAME` for WSGI spec compliance?

0.0

4f3b043beb5067379a7d1459aea751eb74a27e5e

[ "tests/test_apig_wsgi.py::test_special_headers", "tests/test_apig_wsgi.py::test_special_content_type", "tests/test_apig_wsgi.py::test_special_host" ]

[ "tests/test_apig_wsgi.py::test_get", "tests/test_apig_wsgi.py::test_get_missing_content_type", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::test_get_binary_support_binary", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]", "tests/test_apig_wsgi.py::test_get_binary_support_no_content_type", "tests/test_apig_wsgi.py::test_post", "tests/test_apig_wsgi.py::test_post_binary_support", "tests/test_apig_wsgi.py::test_querystring_none", "tests/test_apig_wsgi.py::test_querystring_none_single", "tests/test_apig_wsgi.py::test_querystring_empty", "tests/test_apig_wsgi.py::test_querystring_empty_single", "tests/test_apig_wsgi.py::test_querystring_one", "tests/test_apig_wsgi.py::test_querystring_one_single", "tests/test_apig_wsgi.py::test_querystring_encoding_value", "tests/test_apig_wsgi.py::test_querystring_encoding_key", "tests/test_apig_wsgi.py::test_querystring_multi", "tests/test_apig_wsgi.py::test_plain_header", "tests/test_apig_wsgi.py::test_plain_header_single", "tests/test_apig_wsgi.py::test_plain_header_multi", "tests/test_apig_wsgi.py::test_special_x_forwarded_for", "tests/test_apig_wsgi.py::test_x_forwarded_proto", "tests/test_apig_wsgi.py::test_x_forwarded_port", "tests/test_apig_wsgi.py::test_no_headers", "tests/test_apig_wsgi.py::test_headers_None", "tests/test_apig_wsgi.py::test_exc_info", "tests/test_apig_wsgi.py::test_request_context", "tests/test_apig_wsgi.py::test_full_event" ]

{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }

2020-02-26 12:33:27+00:00

isc

883

adamchainz__apig-wsgi-156

diff --git a/HISTORY.rst b/HISTORY.rst index 048a4ab..8eb3af1 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -1,6 +1,12 @@ History ======= +* Add defaults for ``SERVER_HOST``, ``SERVER_PORT`` and ``wsgi.url_scheme``. + This enables responding to `ELB health check events + <https://docs.aws.amazon.com/elasticloadbalancing/latest/application/lambda-functions.html#enable-health-checks-lambda>`__, + which don't contain the relevant headers + (`Issue #155 <https://github.com/adamchainz/apig-wsgi/pull/155>`__). + 2.6.0 (2020-03-07) ------------------ diff --git a/src/apig_wsgi.py b/src/apig_wsgi.py index 4c7a17a..c12b638 100644 --- a/src/apig_wsgi.py +++ b/src/apig_wsgi.py @@ -62,12 +62,15 @@ def get_environ(event, context, binary_support): "REQUEST_METHOD": method, "SCRIPT_NAME": "", "SERVER_PROTOCOL": "HTTP/1.1", + "SERVER_NAME": "", + "SERVER_PORT": "", "wsgi.errors": sys.stderr, "wsgi.input": BytesIO(body), "wsgi.multiprocess": False, "wsgi.multithread": False, "wsgi.run_once": False, "wsgi.version": (1, 0), + "wsgi.url_scheme": "http", } # Multi-value query strings need explicit activation on ALB

adamchainz/apig-wsgi

d42e72a00409c1ce51011db1d46ecd9a1667984a

diff --git a/tests/test_apig_wsgi.py b/tests/test_apig_wsgi.py index 2e091a8..8339a89 100644 --- a/tests/test_apig_wsgi.py +++ b/tests/test_apig_wsgi.py @@ -472,6 +472,29 @@ def test_full_event(simple_app): assert simple_app.environ["apig_wsgi.full_event"] == event +def test_elb_health_check(simple_app): + """ + Check compatibility with health check events as per: + https://docs.aws.amazon.com/elasticloadbalancing/latest/application/lambda-functions.html#enable-health-checks-lambda # noqa: B950 + """ + event = { + "requestContext": {"elb": {"targetGroupArn": "..."}}, + "httpMethod": "GET", + "path": "/", + "queryStringParameters": {}, + "headers": {"user-agent": "ELB-HealthChecker/2.0"}, + "body": "", + "isBase64Encoded": False, + } + + simple_app.handler(event, None) + + environ = simple_app.environ + assert environ["SERVER_NAME"] == "" + assert environ["SERVER_PORT"] == "" + assert environ["wsgi.url_scheme"] == "http" + + def test_context(simple_app): context = ContextStub(aws_request_id="test-request-id")

ELB Health Checks not handled Hello! Thank you for your tool it's great. We have a little issue when using a lambda as an ELB target when we turn on health check because the event looks like this: ``` { "requestContext": { "elb": { "targetGroupArn": "arn:aws:elasticloadbalancing:region:123456789012:targetgroup/my-target-group/6d0ecf831eec9f09" } }, "httpMethod": "GET", "path": "/", "queryStringParameters": {}, "headers": { "user-agent": "ELB-HealthChecker/2.0" }, "body": "", "isBase64Encoded": false } ``` source: https://docs.aws.amazon.com/elasticloadbalancing/latest/application/lambda-functions.html#enable-health-checks-lambda This has almost no headers leading to this error ``` File "/var/task/flask/app.py", line 2306, in wsgi_app ctx = self.request_context(environ) File "/var/task/flask/app.py", line 2223, in request_context return RequestContext(self, environ) File "/var/task/flask/ctx.py", line 284, in __init__ self.url_adapter = app.create_url_adapter(self.request) File "/var/task/flask/app.py", line 2040, in create_url_adapter subdomain=subdomain) File "/var/task/werkzeug/routing.py", line 1502, in bind_to_environ wsgi_server_name = get_host(environ).lower() File "/var/task/werkzeug/wsgi.py", line 168, in get_host rv = environ["SERVER_NAME"] ``` i found with some testing that i can patch the event like this to make it work: ``` def elb_health_check_patcher(handler): @wraps(handler) def wrapper(event, context): user_agent = event.get('headers', {}).get('user-agent') if user_agent == "ELB-HealthChecker/2.0": event['headers']['x-forwarded-proto'] = 'http' event['headers']['host'] = 'elb-health-check' return handler(event, context) return wrapper handler = elb_health_check_patcher(make_lambda_handler(my_app)) ``` I may propose a PR soon if you're open to :)

0.0

d42e72a00409c1ce51011db1d46ecd9a1667984a

[ "tests/test_apig_wsgi.py::test_elb_health_check" ]

[ "tests/test_apig_wsgi.py::test_get", "tests/test_apig_wsgi.py::test_get_missing_content_type", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::test_get_binary_support_binary", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]", "tests/test_apig_wsgi.py::test_get_binary_support_no_content_type", "tests/test_apig_wsgi.py::test_post", "tests/test_apig_wsgi.py::test_post_binary_support", "tests/test_apig_wsgi.py::test_querystring_none", "tests/test_apig_wsgi.py::test_querystring_none_single", "tests/test_apig_wsgi.py::test_querystring_empty", "tests/test_apig_wsgi.py::test_querystring_empty_single", "tests/test_apig_wsgi.py::test_querystring_one", "tests/test_apig_wsgi.py::test_querystring_one_single", "tests/test_apig_wsgi.py::test_querystring_encoding_value", "tests/test_apig_wsgi.py::test_querystring_encoding_key", "tests/test_apig_wsgi.py::test_querystring_multi", "tests/test_apig_wsgi.py::test_plain_header", "tests/test_apig_wsgi.py::test_plain_header_single", "tests/test_apig_wsgi.py::test_plain_header_multi", "tests/test_apig_wsgi.py::test_special_headers", "tests/test_apig_wsgi.py::test_special_content_type", "tests/test_apig_wsgi.py::test_special_host", "tests/test_apig_wsgi.py::test_special_x_forwarded_for", "tests/test_apig_wsgi.py::test_x_forwarded_proto", "tests/test_apig_wsgi.py::test_x_forwarded_port", "tests/test_apig_wsgi.py::test_no_headers", "tests/test_apig_wsgi.py::test_headers_None", "tests/test_apig_wsgi.py::test_exc_info", "tests/test_apig_wsgi.py::test_request_context", "tests/test_apig_wsgi.py::test_full_event", "tests/test_apig_wsgi.py::test_context" ]

{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2020-07-10 18:59:38+00:00

isc

884

adamchainz__apig-wsgi-187

diff --git a/HISTORY.rst b/HISTORY.rst index 724abe9..f4bc806 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -3,6 +3,9 @@ History ======= * Support Python 3.9. +* Fix query string parameter encoding so that symbols are correctly re-encoded + for WSGI, for API Gateway format version 1 + (`Issue #186 <https://github.com/adamchainz/apig-wsgi/pull/186>`__). 2.9.0 (2020-10-12) ------------------ @@ -11,7 +14,8 @@ History * Always send ``isBase64Encoded`` in responses, as per the AWS documentation. * Support `format version 2 <https://docs.aws.amazon.com/apigateway/latest/developerguide/http-api-develop-integrations-lambda.html>`, - which was introduced by API Gateway for “HTTP API's”. + which was introduced by API Gateway for “HTTP API's” + (`Issue #124 <https://github.com/adamchainz/apig-wsgi/pull/124>`__).. * ``binary_support`` now defaults to ``None``, which means that it will automatically enable binary support for format version 2 events. diff --git a/src/apig_wsgi.py b/src/apig_wsgi.py index a261c38..424d008 100644 --- a/src/apig_wsgi.py +++ b/src/apig_wsgi.py @@ -2,6 +2,7 @@ import sys from base64 import b64decode, b64encode from collections import defaultdict from io import BytesIO +from urllib.parse import urlencode __all__ = ("make_lambda_handler",) @@ -87,14 +88,13 @@ def get_environ_v1(event, context, binary_support): # Multi-value query strings need explicit activation on ALB if "multiValueQueryStringParameters" in event: - # may be None when testing on console - multi_params = event["multiValueQueryStringParameters"] or {} + environ["QUERY_STRING"] = urlencode( + # may be None when testing on console + event["multiValueQueryStringParameters"] or (), + doseq=True, + ) else: - single_params = event.get("queryStringParameters") or {} - multi_params = {key: [value] for key, value in single_params.items()} - environ["QUERY_STRING"] = "&".join( - "{}={}".format(key, val) for (key, vals) in multi_params.items() for val in vals - ) + environ["QUERY_STRING"] = urlencode(event.get("queryStringParameters") or ()) # Multi-value headers need explicit activation on ALB if "multiValueHeaders" in event:

adamchainz/apig-wsgi

afaf2e5ae3279b15657431b24dcc01105ec2a5ce

diff --git a/tests/test_apig_wsgi.py b/tests/test_apig_wsgi.py index 6eca17c..2c98ab4 100644 --- a/tests/test_apig_wsgi.py +++ b/tests/test_apig_wsgi.py @@ -328,19 +328,19 @@ class TestV1Events: assert simple_app.environ["QUERY_STRING"] == "foo=bar" - def test_querystring_encoding_value(self, simple_app): - event = make_v1_event(qs_params={"foo": ["a%20bar"]}) + def test_querystring_encoding_plus_value(self, simple_app): + event = make_v1_event(qs_params={"a": ["b+c"]}, qs_params_multi=False) simple_app.handler(event, None) - assert simple_app.environ["QUERY_STRING"] == "foo=a%20bar" + assert simple_app.environ["QUERY_STRING"] == "a=b%2Bc" - def test_querystring_encoding_key(self, simple_app): - event = make_v1_event(qs_params={"a%20foo": ["bar"]}) + def test_querystring_encoding_plus_key(self, simple_app): + event = make_v1_event(qs_params={"a+b": ["c"]}, qs_params_multi=False) simple_app.handler(event, None) - assert simple_app.environ["QUERY_STRING"] == "a%20foo=bar" + assert simple_app.environ["QUERY_STRING"] == "a%2Bb=c" def test_querystring_multi(self, simple_app): event = make_v1_event(qs_params={"foo": ["bar", "baz"]}) @@ -349,6 +349,20 @@ class TestV1Events: assert simple_app.environ["QUERY_STRING"] == "foo=bar&foo=baz" + def test_querystring_multi_encoding_plus_value(self, simple_app): + event = make_v1_event(qs_params={"a": ["b+c", "d"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a=b%2Bc&a=d" + + def test_querystring_multi_encoding_plus_key(self, simple_app): + event = make_v1_event(qs_params={"a+b": ["c"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a%2Bb=c" + def test_plain_header(self, simple_app): event = make_v1_event(headers={"Test-Header": ["foobar"]})

QueryStringParameters encoding issue Hi, I suspect an issue while providing queryParameters. When performing a query to my API using <API_ROOT>/logs?start_time=2020-10-12T14:00:00%2B02:00&end_time=2020-10-12T15:00:00%2B02:00 I get my query string values in Flask endpoint as: start_time = "2020-10-12T14:00:00 02:00" end_time = "2020-10-12T15:00:00 02:00" and it should be : start_time = "2020-10-12T14:00:00+02:00" end_time = "2020-10-12T15:00:00+02:00" Note: The "+" has been removed I think this is because API Gateway is providing queryStringParameters decoded and your are not encoding them back to store them in environ["QUERY_STRING"]. If we look to what other WSGI adapters (like Zappa) are doing: ``` if 'multiValueQueryStringParameters' in event_info: query = event_info['multiValueQueryStringParameters'] query_string = urlencode(query, doseq=True) if query else '' else: query = event_info.get('queryStringParameters', {}) query_string = urlencode(query) if query else '' ``` Hope it helps.

0.0

afaf2e5ae3279b15657431b24dcc01105ec2a5ce

[ "tests/test_apig_wsgi.py::TestV1Events::test_querystring_encoding_plus_value", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_encoding_plus_key", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_multi_encoding_plus_value", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_multi_encoding_plus_key" ]

[ "tests/test_apig_wsgi.py::TestV1Events::test_get", "tests/test_apig_wsgi.py::TestV1Events::test_get_missing_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_get_single_header", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_no_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_post", "tests/test_apig_wsgi.py::TestV1Events::test_post_binary_support", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_none", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_none_single", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_empty", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_empty_single", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_one", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_one_single", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_multi", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header_single", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header_multi", "tests/test_apig_wsgi.py::TestV1Events::test_special_headers", "tests/test_apig_wsgi.py::TestV1Events::test_special_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_special_host", "tests/test_apig_wsgi.py::TestV1Events::test_special_x_forwarded_for", "tests/test_apig_wsgi.py::TestV1Events::test_x_forwarded_proto", "tests/test_apig_wsgi.py::TestV1Events::test_x_forwarded_port", "tests/test_apig_wsgi.py::TestV1Events::test_no_headers", "tests/test_apig_wsgi.py::TestV1Events::test_headers_None", "tests/test_apig_wsgi.py::TestV1Events::test_exc_info", "tests/test_apig_wsgi.py::TestV1Events::test_request_context", "tests/test_apig_wsgi.py::TestV1Events::test_full_event", "tests/test_apig_wsgi.py::TestV1Events::test_elb_health_check", "tests/test_apig_wsgi.py::TestV1Events::test_context", "tests/test_apig_wsgi.py::TestV2Events::test_get", "tests/test_apig_wsgi.py::TestV2Events::test_get_missing_content_type", "tests/test_apig_wsgi.py::TestV2Events::test_cookie", "tests/test_apig_wsgi.py::TestV2Events::test_two_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_mixed_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_set_one_cookie", "tests/test_apig_wsgi.py::TestV2Events::test_set_two_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV2Events::test_special_headers", "tests/test_apig_wsgi.py::TestUnknownVersionEvents::test_errors" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2020-10-12 22:45:22+00:00

mit

885

adamchainz__apig-wsgi-272

diff --git a/HISTORY.rst b/HISTORY.rst index 6b356b4..cd7d803 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,6 +2,8 @@ History ======= +* Fix handling of query string encoding in ALB deployments. + 2.11.0 (2021-05-10) ------------------- diff --git a/example/README.rst b/example/README.rst index b0d17a3..c00ff7b 100644 --- a/example/README.rst +++ b/example/README.rst @@ -47,7 +47,13 @@ other requirements into it, and run the deployment playbook: source venv/bin/activate python -m pip install -U pip wheel python -m pip install -r requirements.txt - ansible-playbook playbook.yml + +To run the playbook, you'll need to specify a VPC ID and two subnet IDs in order +to create an ALB. + +.. code-block:: sh + + ansible-playbook playbook.yml -e "vpc_id=vpc-12345678" -e "subnet_id_1=subnet-12345678" -e "subnet_id_2=subnet-12345678" Ansible should complete with a ``PLAY RECAP`` at the end like: diff --git a/example/deployment/files/cloudformation_site.yml b/example/deployment/files/cloudformation_site.yml index ac2fcfa..72f4716 100644 --- a/example/deployment/files/cloudformation_site.yml +++ b/example/deployment/files/cloudformation_site.yml @@ -16,6 +16,15 @@ Parameters: LambdaIAMRoleArn: Type: String + VpcId: + Type: String + + SubnetId1: + Type: String + + SubnetId2: + Type: String + Resources: # Lambda @@ -33,13 +42,20 @@ Resources: Runtime: python3.8 Timeout: 20 - LambdaPermission: + LambdaPermissionAPIGW: Type: AWS::Lambda::Permission Properties: Action: lambda:InvokeFunction FunctionName: !GetAtt LambdaFunction.Arn Principal: apigateway.amazonaws.com + LambdaPermissionALB: + Type: AWS::Lambda::Permission + Properties: + Action: lambda:InvokeFunction + FunctionName: !GetAtt LambdaFunction.Arn + Principal: elasticloadbalancing.amazonaws.com + # new style HTTP API HttpApi: @@ -110,6 +126,49 @@ Resources: DeploymentId: !Ref Deployment StageName: prod + # ALB + + LoadBalancer: + Type: AWS::ElasticLoadBalancingV2::LoadBalancer + Properties: + Scheme: internet-facing + Subnets: + - !Ref SubnetId1 + - !Ref SubnetId2 + SecurityGroups: [!Ref SecurityGroup] + + TargetGroup: + Type: AWS::ElasticLoadBalancingV2::TargetGroup + DependsOn: LambdaPermissionALB + Properties: + TargetType: lambda + Targets: + - Id: !GetAtt LambdaFunction.Arn + TargetGroupAttributes: + - Key: lambda.multi_value_headers.enabled + Value: True + + HttpListener: + Type: AWS::ElasticLoadBalancingV2::Listener + Properties: + LoadBalancerArn: !Ref LoadBalancer + Port: 80 + Protocol: HTTP + DefaultActions: + - TargetGroupArn: !Ref TargetGroup + Type: forward + + SecurityGroup: + Type: AWS::EC2::SecurityGroup + Properties: + GroupDescription: Allow http on port 80 + VpcId: !Ref VpcId + SecurityGroupIngress: + - IpProtocol: tcp + FromPort: 80 + ToPort: 80 + CidrIp: 0.0.0.0/0 + Outputs: HttpApiUrl: @@ -117,3 +176,6 @@ Outputs: RestApiUrl: Value: !Sub https://${RestApi}.execute-api.${AWS::Region}.amazonaws.com/${StageApi}/ + + AlbUrl: + Value: !GetAtt LoadBalancer.DNSName diff --git a/example/deployment/playbook.yml b/example/deployment/playbook.yml index 1eae34c..728919a 100755 --- a/example/deployment/playbook.yml +++ b/example/deployment/playbook.yml @@ -95,6 +95,9 @@ PackageS3Key: '{{ zip_name }}' PackageS3ObjectVersion: '{{ (s3_result.stdout|from_json).VersionId }}' LambdaIAMRoleArn: '{{ base_stack_result.stack_outputs.LambdaIAMRoleArn }}' + VpcId: '{{ vpc_id }}' + SubnetId1: '{{ subnet_id_1 }}' + SubnetId2: '{{ subnet_id_2 }}' register: site_stack_result - name: debug @@ -102,3 +105,4 @@ msg: | New style "HTTP API" using v2 events at {{ site_stack_result.stack_outputs.HttpApiUrl }} Old style REST API using v1 events at {{ site_stack_result.stack_outputs.RestApiUrl }} + ALB at {{ site_stack_result.stack_outputs.AlbUrl }} diff --git a/src/apig_wsgi.py b/src/apig_wsgi.py index a8f41b5..814cab3 100644 --- a/src/apig_wsgi.py +++ b/src/apig_wsgi.py @@ -13,6 +13,8 @@ DEFAULT_NON_BINARY_CONTENT_TYPE_PREFIXES = ( "application/vnd.api+json", ) +RESERVED_URI_CHARACTERS = r"!#$&'()*+,/:;=?@[]%" + def make_lambda_handler( wsgi_app, binary_support=None, non_binary_content_type_prefixes=None @@ -37,13 +39,19 @@ def make_lambda_handler( non_binary_content_type_prefixes = tuple(non_binary_content_type_prefixes) def handler(event, context): - # Assume version 1 since ALB isn't documented as sending a version. - version = event.get("version", "1.0") - if version == "1.0": + # ALB doesn't send a version, but requestContext will contain a key named 'elb'. + if "requestContext" in event and "elb" in event["requestContext"]: + version = "alb" + else: + version = event.get("version", "1.0") + + if version in ("1.0", "alb"): # Binary support deafults 'off' on version 1 event_binary_support = binary_support or False environ = get_environ_v1( - event, context, binary_support=event_binary_support + event, + context, + encode_query_params=(version == "1.0"), ) response = V1Response( binary_support=event_binary_support, @@ -65,7 +73,7 @@ def make_lambda_handler( return handler -def get_environ_v1(event, context, binary_support): +def get_environ_v1(event, context, encode_query_params): body = get_body(event) environ = { "CONTENT_LENGTH": str(len(body)), @@ -87,15 +95,24 @@ def get_environ_v1(event, context, binary_support): "apig_wsgi.multi_value_headers": False, } + if encode_query_params: + safe_chars = "" + else: + safe_chars = RESERVED_URI_CHARACTERS + # Multi-value query strings need explicit activation on ALB if "multiValueQueryStringParameters" in event: environ["QUERY_STRING"] = urlencode( # may be None when testing on console event["multiValueQueryStringParameters"] or (), doseq=True, + safe=safe_chars, ) else: - environ["QUERY_STRING"] = urlencode(event.get("queryStringParameters") or ()) + environ["QUERY_STRING"] = urlencode( + event.get("queryStringParameters") or (), + safe=safe_chars, + ) # Multi-value headers need explicit activation on ALB if "multiValueHeaders" in event:

adamchainz/apig-wsgi

066f0b7c1e81e81dd4991c388f46ddfc4ddaf94e

diff --git a/tests/test_apig_wsgi.py b/tests/test_apig_wsgi.py index 71c1fbf..e107817 100644 --- a/tests/test_apig_wsgi.py +++ b/tests/test_apig_wsgi.py @@ -106,6 +106,7 @@ def make_v1_event( event["isBase64Encoded"] = True else: event["body"] = body + event["isBase64Encoded"] = False if request_context is not None: event["requestContext"] = request_context @@ -538,6 +539,81 @@ class TestV1Events: assert response["body"] == "Hi there!" +# ALB tests + + +def make_alb_event(*args, request_context=None, **kwargs): + if request_context is None: + request_context = {} + request_context["elb"] = { + "targetGroupArn": "arn:aws:elasticloadbalancing:::targetgroup/etc" + } + + event = make_v1_event(*args, request_context=request_context, **kwargs) + + del event["version"] + if "isBase64Encoded" not in event: + event["isBase64Encoded"] = False + + return event + + +class TestAlbEvents: + # Query string params from ALB are the same as rawQueryStringParameters + # in API GW V2... that is they don't need to be encoded. + def test_querystring_encoding_plus_value(self, simple_app): + event = make_alb_event(qs_params={"a": ["b+c"]}, qs_params_multi=False) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a=b+c" + + def test_querystring_encoding_plus_key(self, simple_app): + event = make_alb_event(qs_params={"a+b": ["c"]}, qs_params_multi=False) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a+b=c" + + def test_querystring_multi(self, simple_app): + event = make_alb_event(qs_params={"foo": ["bar", "baz"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "foo=bar&foo=baz" + + def test_querystring_multi_encoding_plus_value(self, simple_app): + event = make_alb_event(qs_params={"a": ["b+c", "d"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a=b+c&a=d" + + def test_querystring_multi_encoding_plus_key(self, simple_app): + event = make_alb_event(qs_params={"a+b": ["c"]}) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a+b=c" + + def test_querystring_contains_encoded_value(self, simple_app): + event = make_alb_event(qs_params={"a": ["foo%3Dbar"]}, qs_params_multi=False) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a=foo%3Dbar" + + def test_querystring_multi_contains_encoded_value(self, simple_app): + # a = ['foo=bar', '$20', '100%'] + event = make_alb_event( + qs_params={"a": ["foo%3Dbar", "%2420", "100%25"]}, qs_params_multi=True + ) + + simple_app.handler(event, None) + + assert simple_app.environ["QUERY_STRING"] == "a=foo%3Dbar&a=%2420&a=100%25" + + # v2 tests

Query Params - difference between API GW and ALB I noticed if I go to a URL with a query string like this: `?x=foo%3Dbar` The event sent to a lambda from ALB contains: ```json "queryStringParameters": { "x": "foo%3Dbar" } ``` And the event sent from API Gateway contains: ```json "queryStringParameters": { "x": "foo=bar" } ``` For the ALB, the QUERY_STRING in the WSGI environment is set to: ``` x=foo%253Dbar ``` And for API Gateway, it is set to: ``` x=foo%3Dbar ``` So I think the processing of query params for ALB needs to not urlencode the data. I am working on a PR for this and will hopefully submit later today.

0.0

066f0b7c1e81e81dd4991c388f46ddfc4ddaf94e

[ "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_encoding_plus_value", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_encoding_plus_key", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi_encoding_plus_value", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi_encoding_plus_key", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_contains_encoded_value", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi_contains_encoded_value" ]

[ "tests/test_apig_wsgi.py::TestV1Events::test_get", "tests/test_apig_wsgi.py::TestV1Events::test_get_missing_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_get_single_header", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_no_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_post", "tests/test_apig_wsgi.py::TestV1Events::test_post_binary_support", "tests/test_apig_wsgi.py::TestV1Events::test_path_unquoting", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_none", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_none_single", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_empty", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_empty_single", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_one", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_one_single", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_encoding_plus_value", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_encoding_plus_key", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_multi", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_multi_encoding_plus_value", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_multi_encoding_plus_key", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header_single", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header_multi", "tests/test_apig_wsgi.py::TestV1Events::test_special_headers", "tests/test_apig_wsgi.py::TestV1Events::test_special_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_special_host", "tests/test_apig_wsgi.py::TestV1Events::test_special_x_forwarded_for", "tests/test_apig_wsgi.py::TestV1Events::test_x_forwarded_proto", "tests/test_apig_wsgi.py::TestV1Events::test_x_forwarded_port", "tests/test_apig_wsgi.py::TestV1Events::test_no_headers", "tests/test_apig_wsgi.py::TestV1Events::test_headers_None", "tests/test_apig_wsgi.py::TestV1Events::test_exc_info", "tests/test_apig_wsgi.py::TestV1Events::test_request_context", "tests/test_apig_wsgi.py::TestV1Events::test_full_event", "tests/test_apig_wsgi.py::TestV1Events::test_elb_health_check", "tests/test_apig_wsgi.py::TestV1Events::test_context", "tests/test_apig_wsgi.py::TestV1Events::test_empty_and_uncloseable_content", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi", "tests/test_apig_wsgi.py::TestV2Events::test_get", "tests/test_apig_wsgi.py::TestV2Events::test_get_missing_content_type", "tests/test_apig_wsgi.py::TestV2Events::test_cookie", "tests/test_apig_wsgi.py::TestV2Events::test_two_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_mixed_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_set_one_cookie", "tests/test_apig_wsgi.py::TestV2Events::test_set_two_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV2Events::test_plain_header", "tests/test_apig_wsgi.py::TestV2Events::test_special_headers", "tests/test_apig_wsgi.py::TestV2Events::test_path_unquoting", "tests/test_apig_wsgi.py::TestV2Events::test_empty_and_uncloseable_content", "tests/test_apig_wsgi.py::TestUnknownVersionEvents::test_errors" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-08-24 10:00:38+00:00

mit

886

adamchainz__apig-wsgi-290

diff --git a/HISTORY.rst b/HISTORY.rst index b2d240b..c1e65a8 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,6 +2,10 @@ History ======= +* Handle ``requestContext`` being ``None``, as can happen from Lambda invoke. + + Thanks to scottmn for the report in `Issue #289 <https://github.com/adamchainz/apig-wsgi/issues/289>`__. + 2.12.0 (2021-08-24) ------------------- diff --git a/src/apig_wsgi/__init__.py b/src/apig_wsgi/__init__.py index 2d1389d..0217ad6 100644 --- a/src/apig_wsgi/__init__.py +++ b/src/apig_wsgi/__init__.py @@ -58,7 +58,11 @@ def make_lambda_handler( def handler(event: Dict[str, Any], context: Any) -> Dict[str, Any]: # ALB doesn't send a version, but requestContext will contain a key named 'elb'. - if "requestContext" in event and "elb" in event["requestContext"]: + if ( + "requestContext" in event + and isinstance(event["requestContext"], dict) + and "elb" in event["requestContext"] + ): version = "alb" else: version = event.get("version", "1.0")

adamchainz/apig-wsgi

87e53add20433c5a8b8550b1958d4160e95ab49c

diff --git a/tests/test_apig_wsgi.py b/tests/test_apig_wsgi.py index 7697d40..528ae91 100644 --- a/tests/test_apig_wsgi.py +++ b/tests/test_apig_wsgi.py @@ -1,7 +1,17 @@ import sys from base64 import b64encode from io import BytesIO -from typing import Any, Callable, Dict, Generator, Iterable, List, Optional, Tuple +from typing import ( + Any, + Callable, + Dict, + Generator, + Iterable, + List, + Optional, + Tuple, + Union, +) import pytest @@ -82,6 +92,13 @@ class ContextStub: # v1 tests +class Sentinel: + pass + + +SENTINEL = Sentinel() + + def make_v1_event( *, method: str = "GET", @@ -92,7 +109,7 @@ def make_v1_event( headers_multi: bool = True, body: str = "", binary: bool = False, - request_context: Optional[Dict[str, Any]] = None, + request_context: Union[Dict[str, Any], None, Sentinel] = SENTINEL, ) -> Dict[str, Any]: if headers is None: headers = {"Host": ["example.com"]} @@ -125,7 +142,7 @@ def make_v1_event( event["body"] = body event["isBase64Encoded"] = False - if request_context is not None: + if request_context is not SENTINEL: event["requestContext"] = request_context return event @@ -507,6 +524,14 @@ class TestV1Events: assert simple_app.environ["apig_wsgi.request_context"] == context + def test_request_context_none(self, simple_app: App) -> None: + # Invoking lambdas can lead to requestContext being JSON null + event = make_v1_event(request_context=None) + + simple_app.handler(event, None) + + # Simply don't crash + def test_full_event(self, simple_app: App) -> None: event = make_v1_event()

Error when requestContext is None ### Python Version 3.8 ### Package Version 2.12.0 ### Description I have a lambda that is called through API Gateway, but can also be invoked directly via a lambda client. Upgrading to 2.12.0 started causing this error when invoked via client. ``` [ERROR] TypeError: argument of type 'NoneType' is not iterable Traceback (most recent call last): File "/var/task/apig_wsgi/__init__.py", line 61, in handler if "requestContext" in event and "elb" in event["requestContext"]: ``` This is being done from Kotlin code, using `com.amazonaws.services.lambda.AWSLambda` client. When an `AwsProxyRequest` object is constructed, it has `requestContext=null` by default. This results in the error above. I can update my invoke code to set a dummy requestContext, but I do believe it is valid to be None in the direct lambda invocation use case. Does it make sense to add a `not None` check here for requestContext? Thanks.

0.0

87e53add20433c5a8b8550b1958d4160e95ab49c

[ "tests/test_apig_wsgi.py::TestV1Events::test_request_context_none" ]

[ "tests/test_apig_wsgi.py::TestV1Events::test_get", "tests/test_apig_wsgi.py::TestV1Events::test_get_missing_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_get_single_header", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV1Events::test_get_binary_support_no_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_post", "tests/test_apig_wsgi.py::TestV1Events::test_post_binary_support", "tests/test_apig_wsgi.py::TestV1Events::test_path_unquoting", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_none", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_none_single", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_empty", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_empty_single", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_one", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_one_single", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_encoding_plus_value", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_encoding_plus_key", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_multi", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_multi_encoding_plus_value", "tests/test_apig_wsgi.py::TestV1Events::test_querystring_multi_encoding_plus_key", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header_single", "tests/test_apig_wsgi.py::TestV1Events::test_plain_header_multi", "tests/test_apig_wsgi.py::TestV1Events::test_special_headers", "tests/test_apig_wsgi.py::TestV1Events::test_special_content_type", "tests/test_apig_wsgi.py::TestV1Events::test_special_host", "tests/test_apig_wsgi.py::TestV1Events::test_special_x_forwarded_for", "tests/test_apig_wsgi.py::TestV1Events::test_x_forwarded_proto", "tests/test_apig_wsgi.py::TestV1Events::test_x_forwarded_port", "tests/test_apig_wsgi.py::TestV1Events::test_no_headers", "tests/test_apig_wsgi.py::TestV1Events::test_headers_None", "tests/test_apig_wsgi.py::TestV1Events::test_exc_info", "tests/test_apig_wsgi.py::TestV1Events::test_request_context", "tests/test_apig_wsgi.py::TestV1Events::test_full_event", "tests/test_apig_wsgi.py::TestV1Events::test_elb_health_check", "tests/test_apig_wsgi.py::TestV1Events::test_context", "tests/test_apig_wsgi.py::TestV1Events::test_empty_and_uncloseable_content", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_encoding_plus_value", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_encoding_plus_key", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi_encoding_plus_value", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi_encoding_plus_key", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_contains_encoded_value", "tests/test_apig_wsgi.py::TestAlbEvents::test_querystring_multi_contains_encoded_value", "tests/test_apig_wsgi.py::TestV2Events::test_get", "tests/test_apig_wsgi.py::TestV2Events::test_get_missing_content_type", "tests/test_apig_wsgi.py::TestV2Events::test_cookie", "tests/test_apig_wsgi.py::TestV2Events::test_two_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_mixed_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_set_one_cookie", "tests/test_apig_wsgi.py::TestV2Events::test_set_two_cookies", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::TestV2Events::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]", "tests/test_apig_wsgi.py::TestV2Events::test_plain_header", "tests/test_apig_wsgi.py::TestV2Events::test_special_headers", "tests/test_apig_wsgi.py::TestV2Events::test_path_unquoting", "tests/test_apig_wsgi.py::TestV2Events::test_empty_and_uncloseable_content", "tests/test_apig_wsgi.py::TestUnknownVersionEvents::test_errors" ]

{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2021-09-23 20:25:57+00:00

mit

887

adamchainz__apig-wsgi-80

diff --git a/HISTORY.rst b/HISTORY.rst index c6365ca..3669cc5 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -7,6 +7,7 @@ Pending Release .. Insert new release notes below this line * Update Python support to 3.5-3.7, as 3.4 has reached its end of life. +* Return binary content for gzipped responses with text or JSON content types. 2.2.0 (2019-04-15) ------------------ diff --git a/apig_wsgi.py b/apig_wsgi.py index aa36d78..be2930f 100644 --- a/apig_wsgi.py +++ b/apig_wsgi.py @@ -101,14 +101,7 @@ class Response(object): def as_apig_response(self): response = {"statusCode": self.status_code, "headers": dict(self.headers)} - - content_type = self._get_content_type() - should_send_binary = self.binary_support and ( - content_type is None - or not content_type.startswith(("text/", "application/json")) - ) - - if should_send_binary: + if self._should_send_binary(): response["isBase64Encoded"] = True response["body"] = b64encode(self.body.getvalue()).decode("utf-8") else: @@ -116,10 +109,31 @@ class Response(object): return response + def _should_send_binary(self): + """ + Determines if binary response should be sent to API Gateway + """ + if not self.binary_support: + return False + + content_type = self._get_content_type() + non_binary_content_types = ("text/", "application/json") + if not content_type.startswith(non_binary_content_types): + return True + + content_encoding = self._get_content_encoding() + # Content type is non-binary but the content encoding might be. + return "gzip" in content_encoding.lower() + def _get_content_type(self): - content_type_headers = [ - v for k, v in self.headers if k.lower() == "content-type" - ] - if len(content_type_headers): - return content_type_headers[-1] + return self._get_header("content-type") or "" + + def _get_content_encoding(self): + return self._get_header("content-encoding") or "" + + def _get_header(self, header_name): + header_name = header_name.lower() + matching_headers = [v for k, v in self.headers if k.lower() == header_name] + if len(matching_headers): + return matching_headers[-1] return None

adamchainz/apig-wsgi

80868a1a740711fe1fdf3c523d0e400c788a1b14

diff --git a/test_apig_wsgi.py b/test_apig_wsgi.py index 6a921ea..72531fd 100644 --- a/test_apig_wsgi.py +++ b/test_apig_wsgi.py @@ -21,6 +21,11 @@ def simple_app(): yield app +parametrize_text_content_type = pytest.mark.parametrize( + "text_content_type", ["text/plain", "text/html", "application/json"] +) + + def make_event( method="GET", qs_params=None, @@ -69,14 +74,15 @@ def test_get_missing_content_type(simple_app): assert response == {"statusCode": 200, "headers": {}, "body": "Hello World\n"} -def test_get_binary_support_text(simple_app): +@parametrize_text_content_type +def test_get_binary_support_text(simple_app, text_content_type): simple_app.handler = make_lambda_handler(simple_app, binary_support=True) + simple_app.headers = [("Content-Type", text_content_type)] response = simple_app.handler(make_event(), None) - assert response == { "statusCode": 200, - "headers": {"Content-Type": "text/plain"}, + "headers": {"Content-Type": text_content_type}, "body": "Hello World\n", } @@ -96,6 +102,27 @@ def test_get_binary_support_binary(simple_app): } +@parametrize_text_content_type +def test_get_binary_support_binary_text_with_gzip_content_encoding( + simple_app, text_content_type +): + simple_app.handler = make_lambda_handler(simple_app, binary_support=True) + simple_app.headers = [ + ("Content-Type", text_content_type), + ("Content-Encoding", "gzip"), + ] + simple_app.response = b"\x13\x37" + + response = simple_app.handler(make_event(), None) + + assert response == { + "statusCode": 200, + "headers": {"Content-Type": text_content_type, "Content-Encoding": "gzip"}, + "body": b64encode(b"\x13\x37").decode("utf-8"), + "isBase64Encoded": True, + } + + def test_get_binary_support_no_content_type(simple_app): simple_app.handler = make_lambda_handler(simple_app, binary_support=True) simple_app.headers = []

Ability to send binary response with `text/` or `application/json` content type Problem -------- `Response.as_apig_response` is hardcoded to not return binary response when the content-type of the response is either `text/*` or `application/json`. https://github.com/adamchainz/apig-wsgi/blob/b0ce56cbb3ff67586c398f57bc13590bf0961940/apig_wsgi.py#L105-L109 This becomes a problem for use cases like returning a gzip response from the application with the above content types. Possible Solution ----------------- **Check if the `Content-Encoding` header has `gzip` in it or not, and return the binary response based on that.** This fix would keep the hardcoded values, something like this should work: ```python def _should_send_binary(self): """Determines if binary response should be sent to API Gateway """ non_binary_content_types = ("text/", "application/json") content_type = self._get_content_type() or '' content_encoding = self._get_content_encoding() or '' supports_binary = self.binary_support is_binary_content_type = not content_type.startswith(non_binary_content_types) if supports_binary and is_binary_content_type: return True # Content type is non-binary but the content encoding is. elif supports_binary and not is_binary_content_type: return 'gzip' in content_encoding.lower() return False ``` **Allow `Response` class to be extended so that users can handle this logic on their own.** This can be done by introducing the same `Response._should_send_binary` method which defaults to the current behaviour. The `make_lambda_handler` function can then be allowed to have an argument like `response_class` to facilitate this. I can create a PR for either of the fixes which seem more appropriate to you. What do you think about this?

0.0

80868a1a740711fe1fdf3c523d0e400c788a1b14

[ "test_apig_wsgi.py::test_get_binary_support_binary_text_with_gzip_content_encoding[text/plain]", "test_apig_wsgi.py::test_get_binary_support_binary_text_with_gzip_content_encoding[text/html]", "test_apig_wsgi.py::test_get_binary_support_binary_text_with_gzip_content_encoding[application/json]" ]

[ "test_apig_wsgi.py::test_get", "test_apig_wsgi.py::test_get_missing_content_type", "test_apig_wsgi.py::test_get_binary_support_text[text/plain]", "test_apig_wsgi.py::test_get_binary_support_text[text/html]", "test_apig_wsgi.py::test_get_binary_support_text[application/json]", "test_apig_wsgi.py::test_get_binary_support_binary", "test_apig_wsgi.py::test_get_binary_support_no_content_type", "test_apig_wsgi.py::test_post", "test_apig_wsgi.py::test_post_binary_support", "test_apig_wsgi.py::test_querystring_none", "test_apig_wsgi.py::test_querystring_empty", "test_apig_wsgi.py::test_querystring_one", "test_apig_wsgi.py::test_plain_header", "test_apig_wsgi.py::test_special_headers", "test_apig_wsgi.py::test_no_headers", "test_apig_wsgi.py::test_headers_None", "test_apig_wsgi.py::test_exc_info", "test_apig_wsgi.py::test_request_context" ]

{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2019-08-18 23:01:41+00:00

isc

888

adamchainz__apig-wsgi-93

diff --git a/HISTORY.rst b/HISTORY.rst index 4b65c01..1ed117d 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -13,6 +13,9 @@ Pending Release (`docs <https://docs.python.org/3.8/library/importlib.metadata.html#distribution-versions>`__ / `backport <https://pypi.org/project/importlib-metadata/>`__). * Update Python support to 3.5-3.8. +* Add `application/vnd.api+json` to default non-binary content type prefixes. +* Add support for custom non-binary content type prefixes. This lets you control + which content types should be treated as plain text when binary support is enabled. 2.3.0 (2019-08-19) ------------------ diff --git a/README.rst b/README.rst index 8f54234..3404304 100644 --- a/README.rst +++ b/README.rst @@ -39,8 +39,8 @@ Python 3.5-3.8 supported. Usage ===== -``make_lambda_handler(app, binary_support=False)`` --------------------------------------------------- +``make_lambda_handler(app, binary_support=False, non_binary_content_type_prefixes=None)`` +----------------------------------------------------------------------------------------- ``app`` should be a WSGI app, for example from Django's ``wsgi.py`` or Flask's ``Flask()`` object. @@ -53,8 +53,10 @@ using ``'*/*'`` is the best way to do it, since it is used to match the request 'Accept' header as well, which WSGI applications are likely to ignore). Note that binary responses aren't sent if your response has a 'Content-Type' -starting 'text/html' or 'application/json' - this is to support sending larger -text responses. +starting 'text/', 'application/json' or 'application/vnd.api+json' - this +is to support sending larger text responses. To support other content types +than the ones specified above, you can set `non_binary_content_type_prefixes` +to a list of content type prefixes of your choice. If the event from API Gateway contains the ``requestContext`` key, for example from custom request authorizers, this will be available in the WSGI environ diff --git a/src/apig_wsgi.py b/src/apig_wsgi.py index e804a20..f6bd5ee 100644 --- a/src/apig_wsgi.py +++ b/src/apig_wsgi.py @@ -5,16 +5,41 @@ from urllib.parse import urlencode __all__ = ("make_lambda_handler",) +DEFAULT_NON_BINARY_CONTENT_TYPE_PREFIXES = ( + "text/", + "application/json", + "application/vnd.api+json", +) -def make_lambda_handler(wsgi_app, binary_support=False): + +def make_lambda_handler( + wsgi_app, binary_support=False, non_binary_content_type_prefixes=None +): """ Turn a WSGI app callable into a Lambda handler function suitable for running on API Gateway. + + Parameters + ---------- + wsgi_app : function + WSGI Application callable + binary_support : bool + Whether to support returning APIG-compatible binary responses + non_binary_content_type_prefixes : tuple of str + Tuple of content type prefixes which should be considered "Non-Binary" when + `binray_support` is True. This prevents apig_wsgi from unexpectedly encoding + non-binary responses as binary. """ + if non_binary_content_type_prefixes is None: + non_binary_content_type_prefixes = DEFAULT_NON_BINARY_CONTENT_TYPE_PREFIXES + non_binary_content_type_prefixes = tuple(non_binary_content_type_prefixes) def handler(event, context): environ = get_environ(event, binary_support=binary_support) - response = Response(binary_support=binary_support) + response = Response( + binary_support=binary_support, + non_binary_content_type_prefixes=non_binary_content_type_prefixes, + ) result = wsgi_app(environ, response.start_response) response.consume(result) return response.as_apig_response() @@ -73,11 +98,12 @@ def get_environ(event, binary_support): class Response(object): - def __init__(self, binary_support): + def __init__(self, binary_support, non_binary_content_type_prefixes): self.status_code = 500 self.headers = [] self.body = BytesIO() self.binary_support = binary_support + self.non_binary_content_type_prefixes = non_binary_content_type_prefixes def start_response(self, status, response_headers, exc_info=None): if exc_info is not None: @@ -113,8 +139,7 @@ class Response(object): return False content_type = self._get_content_type() - non_binary_content_types = ("text/", "application/json") - if not content_type.startswith(non_binary_content_types): + if not content_type.startswith(self.non_binary_content_type_prefixes): return True content_encoding = self._get_content_encoding()

adamchainz/apig-wsgi

af9d96d0ac950f9b04e6d365acf0b3a4f5e8e690

diff --git a/tests/test_apig_wsgi.py b/tests/test_apig_wsgi.py index 72531fd..f6b77e9 100644 --- a/tests/test_apig_wsgi.py +++ b/tests/test_apig_wsgi.py @@ -6,6 +6,8 @@ import pytest from apig_wsgi import make_lambda_handler +CUSTOM_NON_BINARY_CONTENT_TYPE_PREFIXES = ["test/custom", "application/vnd.custom"] + @pytest.fixture() def simple_app(): @@ -21,8 +23,14 @@ def simple_app(): yield app -parametrize_text_content_type = pytest.mark.parametrize( - "text_content_type", ["text/plain", "text/html", "application/json"] +parametrize_default_text_content_type = pytest.mark.parametrize( + "text_content_type", + ["text/plain", "text/html", "application/json", "application/vnd.api+json"], +) + + +parametrize_custom_text_content_type = pytest.mark.parametrize( + "text_content_type", CUSTOM_NON_BINARY_CONTENT_TYPE_PREFIXES ) @@ -74,8 +82,8 @@ def test_get_missing_content_type(simple_app): assert response == {"statusCode": 200, "headers": {}, "body": "Hello World\n"} -@parametrize_text_content_type -def test_get_binary_support_text(simple_app, text_content_type): +@parametrize_default_text_content_type +def test_get_binary_support_default_text_content_types(simple_app, text_content_type): simple_app.handler = make_lambda_handler(simple_app, binary_support=True) simple_app.headers = [("Content-Type", text_content_type)] @@ -87,6 +95,23 @@ def test_get_binary_support_text(simple_app, text_content_type): } +@parametrize_custom_text_content_type +def test_get_binary_support_custom_text_content_types(simple_app, text_content_type): + simple_app.handler = make_lambda_handler( + simple_app, + binary_support=True, + non_binary_content_type_prefixes=CUSTOM_NON_BINARY_CONTENT_TYPE_PREFIXES, + ) + simple_app.headers = [("Content-Type", text_content_type)] + + response = simple_app.handler(make_event(), None) + assert response == { + "statusCode": 200, + "headers": {"Content-Type": text_content_type}, + "body": "Hello World\n", + } + + def test_get_binary_support_binary(simple_app): simple_app.handler = make_lambda_handler(simple_app, binary_support=True) simple_app.headers = [("Content-Type", "application/octet-stream")] @@ -102,8 +127,8 @@ def test_get_binary_support_binary(simple_app): } -@parametrize_text_content_type -def test_get_binary_support_binary_text_with_gzip_content_encoding( +@parametrize_default_text_content_type +def test_get_binary_support_binary_default_text_with_gzip_content_encoding( simple_app, text_content_type ): simple_app.handler = make_lambda_handler(simple_app, binary_support=True) @@ -123,6 +148,31 @@ def test_get_binary_support_binary_text_with_gzip_content_encoding( } +@parametrize_custom_text_content_type +def test_get_binary_support_binary_custom_text_with_gzip_content_encoding( + simple_app, text_content_type +): + simple_app.handler = make_lambda_handler( + simple_app, + binary_support=True, + non_binary_content_type_prefixes=CUSTOM_NON_BINARY_CONTENT_TYPE_PREFIXES, + ) + simple_app.headers = [ + ("Content-Type", text_content_type), + ("Content-Encoding", "gzip"), + ] + simple_app.response = b"\x13\x37" + + response = simple_app.handler(make_event(), None) + + assert response == { + "statusCode": 200, + "headers": {"Content-Type": text_content_type, "Content-Encoding": "gzip"}, + "body": b64encode(b"\x13\x37").decode("utf-8"), + "isBase64Encoded": True, + } + + def test_get_binary_support_no_content_type(simple_app): simple_app.handler = make_lambda_handler(simple_app, binary_support=True) simple_app.headers = []

Ability to have custom white list for non binary content types ## Problem The `Response` class has a whitelist of "non binary content types" which includes: - `text/*` - `application/json` https://github.com/adamchainz/apig-wsgi/blob/f24dd8df21a4ab693992ababf4cfb9735af27b57/src/apig_wsgi.py#L116 All other response types are assumed to be binary if `binary_support` is True. This becomes a problem if you want to return text content for other content types. For example, [JSON:API](https://jsonapi.org/) APIs have `application/vnd.api+json` content type. ## Possible solution The library should provide ability to either extend the `Response` class or pass the `non_binary_content_types` directly to `make_lambda_handler` call. ```python wsgi_handler = make_lambda_handler(application, binary_support=True, response_class=MyResponse) wsgi_handler = make_lambda_handler(application, binary_support=True, non_binary_content_types=my_content_type_list) ``` I can create PR for either of these approaches. What do you think?

0.0

af9d96d0ac950f9b04e6d365acf0b3a4f5e8e690

[ "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[application/vnd.api+json]", "tests/test_apig_wsgi.py::test_get_binary_support_custom_text_content_types[test/custom]", "tests/test_apig_wsgi.py::test_get_binary_support_custom_text_content_types[application/vnd.custom]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[test/custom]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_custom_text_with_gzip_content_encoding[application/vnd.custom]" ]

[ "tests/test_apig_wsgi.py::test_get", "tests/test_apig_wsgi.py::test_get_missing_content_type", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[text/plain]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[text/html]", "tests/test_apig_wsgi.py::test_get_binary_support_default_text_content_types[application/json]", "tests/test_apig_wsgi.py::test_get_binary_support_binary", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/plain]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[text/html]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/json]", "tests/test_apig_wsgi.py::test_get_binary_support_binary_default_text_with_gzip_content_encoding[application/vnd.api+json]", "tests/test_apig_wsgi.py::test_get_binary_support_no_content_type", "tests/test_apig_wsgi.py::test_post", "tests/test_apig_wsgi.py::test_post_binary_support", "tests/test_apig_wsgi.py::test_querystring_none", "tests/test_apig_wsgi.py::test_querystring_empty", "tests/test_apig_wsgi.py::test_querystring_one", "tests/test_apig_wsgi.py::test_plain_header", "tests/test_apig_wsgi.py::test_special_headers", "tests/test_apig_wsgi.py::test_no_headers", "tests/test_apig_wsgi.py::test_headers_None", "tests/test_apig_wsgi.py::test_exc_info", "tests/test_apig_wsgi.py::test_request_context" ]

{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2019-11-13 19:03:20+00:00

isc

889

adamchainz__ec2-metadata-166

diff --git a/src/ec2_metadata.py b/src/ec2_metadata.py index ec3e695..a03813d 100644 --- a/src/ec2_metadata.py +++ b/src/ec2_metadata.py @@ -1,3 +1,5 @@ +import time + import requests from cached_property import cached_property @@ -10,6 +12,7 @@ SERVICE_URL = "http://169.254.169.254/2016-09-02/" DYNAMIC_URL = SERVICE_URL + "dynamic/" METADATA_URL = SERVICE_URL + "meta-data/" USERDATA_URL = SERVICE_URL + "user-data/" +TOKEN_TTL_SECONDS = 21600 class BaseLazyObject(object): @@ -24,8 +27,26 @@ class EC2Metadata(BaseLazyObject): if session is None: session = requests.Session() self._session = session + self._token_updated_at = 0 + + def _ensure_fresh_token(self): + """ Update the metadata token if needed. + + Tokens are rotated 1 minute before they would expire. + """ + now = time.time() + if now - self._token_updated_at > (TOKEN_TTL_SECONDS - 60): + token = self._session.put( + "http://169.254.169.254/latest/api/token", + headers={ + "X-aws-ec2-metadata-token-ttl-seconds": str(TOKEN_TTL_SECONDS) + }, + ).text + self._session.headers.update({"X-aws-ec2-metadata-token": token}) + self._token_updated_at = now def _get_url(self, url, allow_404=False): + self._ensure_fresh_token() resp = self._session.get(url, timeout=1.0) if resp.status_code != 404 or not allow_404: resp.raise_for_status()

adamchainz/ec2-metadata

2607b63c8ecb07c82b8716d6738814000fc3437d

diff --git a/tests/test_ec2_metadata.py b/tests/test_ec2_metadata.py index 0e4b43d..e71ccf1 100644 --- a/tests/test_ec2_metadata.py +++ b/tests/test_ec2_metadata.py @@ -4,6 +4,7 @@ import requests from ec2_metadata import ( DYNAMIC_URL, METADATA_URL, + TOKEN_TTL_SECONDS, USERDATA_URL, NetworkInterface, ec2_metadata, @@ -16,11 +17,20 @@ def clear_it(): example_mac = "00:11:22:33:44:55" +example_token = "AABBCC" # EC2Metadata tests +def _mock_token_request(requests_mock): + requests_mock.put( + "http://169.254.169.254/latest/api/token", + headers={"X-aws-ec2-metadata-token-ttl-seconds": str(TOKEN_TTL_SECONDS)}, + text=example_token, + ) + + def add_identity_doc_response(requests_mock, overrides=None): identity_doc = { "accountId": "123456789012", @@ -35,6 +45,7 @@ def add_identity_doc_response(requests_mock, overrides=None): } if overrides: identity_doc.update(overrides) + _mock_token_request(requests_mock) requests_mock.get(DYNAMIC_URL + "instance-identity/document", json=identity_doc) return identity_doc @@ -45,17 +56,20 @@ def test_account_id(requests_mock): def test_account_id_error(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(DYNAMIC_URL + "instance-identity/document", status_code=500) with pytest.raises(requests.exceptions.HTTPError): ec2_metadata.account_id def test_ami_id(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "ami-id", text="ami-12345678") assert ec2_metadata.ami_id == "ami-12345678" def test_ami_id_cached(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "ami-id", text="ami-12345678") ec2_metadata.ami_id requests_mock.get(METADATA_URL + "ami-id", status_code=500) @@ -63,6 +77,7 @@ def test_ami_id_cached(requests_mock): def test_ami_id_cached_cleared(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "ami-id", text="ami-12345678") ec2_metadata.ami_id @@ -74,42 +89,50 @@ def test_ami_id_cached_cleared(requests_mock): def test_ami_launch_index(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "ami-launch-index", text="0") assert ec2_metadata.ami_launch_index == 0 def test_ami_manifest_path(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "ami-manifest-path", text="(unknown)") assert ec2_metadata.ami_manifest_path == "(unknown)" def test_availability_zone(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "placement/availability-zone", text="eu-west-1a") assert ec2_metadata.availability_zone == "eu-west-1a" def test_iam_info(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "iam/info", text="{}") assert ec2_metadata.iam_info == {} def test_iam_info_none(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "iam/info", status_code=404) assert ec2_metadata.iam_info is None def test_iam_info_unexpected(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "iam/info", status_code=500) with pytest.raises(requests.exceptions.HTTPError): ec2_metadata.iam_info def test_instance_action(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "instance-action", text="none") assert ec2_metadata.instance_action == "none" def test_instance_id(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "instance-id", text="i-12345678") assert ec2_metadata.instance_id == "i-12345678" @@ -120,6 +143,7 @@ def test_instance_identity(requests_mock): def test_instance_profile_arn(requests_mock): + _mock_token_request(requests_mock) requests_mock.get( METADATA_URL + "iam/info", text='{"InstanceProfileArn": "arn:foobar"}' ) @@ -127,11 +151,13 @@ def test_instance_profile_arn(requests_mock): def test_instance_profile_arn_none(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "iam/info", status_code=404) assert ec2_metadata.instance_profile_arn is None def test_instance_profile_id(requests_mock): + _mock_token_request(requests_mock) requests_mock.get( METADATA_URL + "iam/info", text='{"InstanceProfileId": "some-id"}' ) @@ -139,31 +165,37 @@ def test_instance_profile_id(requests_mock): def test_instance_profile_id_none(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "iam/info", status_code=404) assert ec2_metadata.instance_profile_id is None def test_instance_type(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "instance-type", text="t2.nano") assert ec2_metadata.instance_type == "t2.nano" def test_kernel_id(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "kernel-id", text="aki-dc9ed9af") assert ec2_metadata.kernel_id == "aki-dc9ed9af" def test_kernel_id_none(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "kernel-id", status_code=404) assert ec2_metadata.kernel_id is None def test_mac(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "mac", text=example_mac) assert ec2_metadata.mac == example_mac def test_network_interfaces(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "network/interfaces/macs/", text=example_mac + "/") assert ec2_metadata.network_interfaces == { example_mac: NetworkInterface(example_mac, ec2_metadata) @@ -171,6 +203,7 @@ def test_network_interfaces(requests_mock): def test_private_hostname(requests_mock): + _mock_token_request(requests_mock) requests_mock.get( METADATA_URL + "local-hostname", text="ip-172-30-0-0.eu-west-1.compute.internal" ) @@ -178,11 +211,13 @@ def test_private_hostname(requests_mock): def test_private_ipv4(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "local-ipv4", text="172.30.0.0") assert ec2_metadata.private_ipv4 == "172.30.0.0" def test_public_hostname(requests_mock): + _mock_token_request(requests_mock) requests_mock.get( METADATA_URL + "public-hostname", text="ec2-1-2-3-4.compute-1.amazonaws.com" ) @@ -190,16 +225,19 @@ def test_public_hostname(requests_mock): def test_public_hostname_none(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "public-hostname", status_code=404) assert ec2_metadata.public_hostname is None def test_public_ipv4(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "public-ipv4", text="1.2.3.4") assert ec2_metadata.public_ipv4 == "1.2.3.4" def test_public_ipv4_none(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "public-ipv4", status_code=404) assert ec2_metadata.public_ipv4 is None @@ -210,18 +248,21 @@ def test_region(requests_mock): def test_reservation_id(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "reservation-id", text="r-12345678901234567") assert ec2_metadata.reservation_id == "r-12345678901234567" def test_security_groups_single(requests_mock): # most common case: a single SG + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "security-groups", text="security-group-one") assert ec2_metadata.security_groups == ["security-group-one"] def test_security_groups_two(requests_mock): # another common case: multiple SGs + _mock_token_request(requests_mock) requests_mock.get( METADATA_URL + "security-groups", text="security-group-one\nsecurity-group-2" ) @@ -231,16 +272,19 @@ def test_security_groups_two(requests_mock): def test_security_groups_emptystring(requests_mock): # Check '' too. Can't create an instance without a SG on EC2 but we should # safely handle it, perhaps it's possible in e.g. OpenStack. + _mock_token_request(requests_mock) requests_mock.get(METADATA_URL + "security-groups", text="") assert ec2_metadata.security_groups == [] def test_user_data_none(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(USERDATA_URL, status_code=404) assert ec2_metadata.user_data is None def test_user_data_something(requests_mock): + _mock_token_request(requests_mock) requests_mock.get(USERDATA_URL, content=b"foobar") assert ec2_metadata.user_data == b"foobar" @@ -250,6 +294,7 @@ def test_user_data_something(requests_mock): def add_interface_response(requests_mock, url, text="", **kwargs): full_url = METADATA_URL + "network/interfaces/macs/" + example_mac + url + _mock_token_request(requests_mock) requests_mock.get(full_url, text=text, **kwargs)

Update to version 2.0 https://aws.amazon.com/blogs/security/defense-in-depth-open-firewalls-reverse-proxies-ssrf-vulnerabilities-ec2-instance-metadata-service/ This requires a new "knock" PUT request to get a session token before accessing any bits of data.

0.0

2607b63c8ecb07c82b8716d6738814000fc3437d

[ "tests/test_ec2_metadata.py::test_network_interface_equal", "tests/test_ec2_metadata.py::test_network_interface_not_equal", "tests/test_ec2_metadata.py::test_network_interface_not_equal_class", "tests/test_ec2_metadata.py::test_network_interface_repr" ]

[]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }

2020-03-06 02:57:13+00:00

isc

890

adamchainz__ec2-metadata-350

diff --git a/HISTORY.rst b/HISTORY.rst index 9a6d9e6..23dbfa2 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,6 +2,10 @@ History ======= +* Return ``None`` for ``availability_zone_id`` when the underlying endpoint returns HTTP 404. + + Thanks to Amir Rossert in `PR #350 <https://github.com/adamchainz/ec2-metadata/pull/350>`__. + 2.9.0 (2022-03-25) ------------------ diff --git a/README.rst b/README.rst index 1671b48..f435b1f 100644 --- a/README.rst +++ b/README.rst @@ -133,8 +133,8 @@ See AWS docs page `Retrieve the target lifecycle state through instance metadata The name of the current AZ e.g. ``'eu-west-1a'``. -``availability_zone_id: str`` -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +``availability_zone_id: str | None`` +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The unique, cross-account ID of the current AZ e.g. ``'use1-az6'``. See AWS docs page `AZ IDs for your AWS resources diff --git a/src/ec2_metadata/__init__.py b/src/ec2_metadata/__init__.py index 0db8376..520d9aa 100644 --- a/src/ec2_metadata/__init__.py +++ b/src/ec2_metadata/__init__.py @@ -98,8 +98,13 @@ class EC2Metadata(BaseLazyObject): return self._get_url(f"{self.metadata_url}placement/availability-zone").text @cached_property - def availability_zone_id(self) -> str: - return self._get_url(f"{self.metadata_url}placement/availability-zone-id").text + def availability_zone_id(self) -> str | None: + resp = self._get_url( + f"{self.metadata_url}placement/availability-zone-id", allow_404=True + ) + if resp.status_code == 404: + return None + return resp.text @cached_property def ami_launch_index(self) -> int:

adamchainz/ec2-metadata

d72b0da489514e46519f49bd080860afb9fd3189

diff --git a/tests/test_ec2_metadata.py b/tests/test_ec2_metadata.py index 24f6af1..55f701b 100644 --- a/tests/test_ec2_metadata.py +++ b/tests/test_ec2_metadata.py @@ -161,6 +161,14 @@ def test_availability_zone_id(em_requests_mock): assert ec2_metadata.availability_zone_id == "use1-az6" +def test_availability_zone_id_none(em_requests_mock): + em_requests_mock.get( + "http://169.254.169.254/latest/meta-data/placement/availability-zone-id", + status_code=404, + ) + assert ec2_metadata.availability_zone_id is None + + def test_domain(em_requests_mock): em_requests_mock.get( "http://169.254.169.254/latest/meta-data/services/domain",

availability_zone_id may return 404 ### Python Version 3.8.10 ### Package Version 2.7.0 ### Description In some cases `ec2_metadata.availability_zone_id` returns 404 ``` ----> 1 ec2_metadata.availability_zone_id File functools.py:967, in __get__(self, instance, owner) File ec2_metadata/__init__.py:87, in availability_zone_id(self) File ec2_metadata/__init__.py:65, in _get_url(self, url, allow_404) File requests/models.py:960, in raise_for_status(self) HTTPError: 404 Client Error: Not Found for url: http://169.254.169.254/latest/meta-data/placement/availability-zone-id ``` I assume that all that is needed is to use `allow_404` in `_get_url`

0.0

d72b0da489514e46519f49bd080860afb9fd3189

[ "tests/test_ec2_metadata.py::test_availability_zone_id_none" ]

[ "tests/test_ec2_metadata.py::test_instance_profile_name", "tests/test_ec2_metadata.py::test_network_interface_repr", "tests/test_ec2_metadata.py::test_public_hostname_none", "tests/test_ec2_metadata.py::test_tags_one", "tests/test_ec2_metadata.py::test_kernel_id", "tests/test_ec2_metadata.py::test_network_interface_owner_id", "tests/test_ec2_metadata.py::test_instance_profile_id", "tests/test_ec2_metadata.py::test_instance_type", "tests/test_ec2_metadata.py::test_iam_info_none", "tests/test_ec2_metadata.py::test_network_interface_device_number", "tests/test_ec2_metadata.py::test_instance_profile_arn_none", "tests/test_ec2_metadata.py::test_network_interface_subnet_ipv4_cidr_block", "tests/test_ec2_metadata.py::test_region", "tests/test_ec2_metadata.py::test_network_interface_subnet_id", "tests/test_ec2_metadata.py::test_autoscaling_target_lifecycle_state_none", "tests/test_ec2_metadata.py::test_network_interface_vpc_ipv4_cidr_block", "tests/test_ec2_metadata.py::test_network_interface_ipv6s", "tests/test_ec2_metadata.py::test_tags_multiple", "tests/test_ec2_metadata.py::test_ami_id_cached", "tests/test_ec2_metadata.py::test_spot_instance_action_none", "tests/test_ec2_metadata.py::test_account_id_token_error", "tests/test_ec2_metadata.py::test_security_groups_emptystring", "tests/test_ec2_metadata.py::test_instance_profile_arn", "tests/test_ec2_metadata.py::test_network_interface_vpc_ipv6_cidr_blocks_none", "tests/test_ec2_metadata.py::test_instance_identity", "tests/test_ec2_metadata.py::test_network_interface_private_ipv4s", "tests/test_ec2_metadata.py::test_tags_len", "tests/test_ec2_metadata.py::test_network_interface_public_ipv4s_empty", "tests/test_ec2_metadata.py::test_domain", "tests/test_ec2_metadata.py::test_ami_id_cached_cleared", "tests/test_ec2_metadata.py::test_public_ipv4_none", "tests/test_ec2_metadata.py::test_network_interfaces", "tests/test_ec2_metadata.py::test_tags_empty", "tests/test_ec2_metadata.py::test_ami_manifest_path", "tests/test_ec2_metadata.py::test_network_interface_ipv4_associations", "tests/test_ec2_metadata.py::test_network_interface_vpc_ipv6_cidr_blocks", "tests/test_ec2_metadata.py::test_availability_zone", "tests/test_ec2_metadata.py::test_network_interface_vpc_id", "tests/test_ec2_metadata.py::test_network_interface_not_equal", "tests/test_ec2_metadata.py::test_kernel_id_none", "tests/test_ec2_metadata.py::test_private_hostname", "tests/test_ec2_metadata.py::test_network_interface_public_ipv4s", "tests/test_ec2_metadata.py::test_iam_security_credentials_none", "tests/test_ec2_metadata.py::test_account_id_error", "tests/test_ec2_metadata.py::test_iam_security_credentials", "tests/test_ec2_metadata.py::test_instance_profile_id_none", "tests/test_ec2_metadata.py::test_tags_repeat_access", "tests/test_ec2_metadata.py::test_network_interface_subnet_ipv6_cidr_blocks_none", "tests/test_ec2_metadata.py::test_instance_action", "tests/test_ec2_metadata.py::test_network_interface_vpc_ipv4_cidr_blocks_none", "tests/test_ec2_metadata.py::test_autoscaling_target_lifecycle_state_in_service", "tests/test_ec2_metadata.py::test_account_id", "tests/test_ec2_metadata.py::test_tags_not_enabled", "tests/test_ec2_metadata.py::test_network_interface_public_hostname_none", "tests/test_ec2_metadata.py::test_network_interface_interface_id", "tests/test_ec2_metadata.py::test_availability_zone_id", "tests/test_ec2_metadata.py::test_user_data_none", "tests/test_ec2_metadata.py::test_reservation_id", "tests/test_ec2_metadata.py::test_network_interface_public_hostname", "tests/test_ec2_metadata.py::test_network_interface_not_equal_class", "tests/test_ec2_metadata.py::test_network_interface_ipv6s_none", "tests/test_ec2_metadata.py::test_iam_info_unexpected", "tests/test_ec2_metadata.py::test_security_groups_two", "tests/test_ec2_metadata.py::test_spot_instance_action", "tests/test_ec2_metadata.py::test_network_interface_private_hostname", "tests/test_ec2_metadata.py::test_custom_session", "tests/test_ec2_metadata.py::test_network_interface_equal", "tests/test_ec2_metadata.py::test_user_data_something", "tests/test_ec2_metadata.py::test_network_interface_vpc_ipv4_cidr_blocks", "tests/test_ec2_metadata.py::test_security_groups_single", "tests/test_ec2_metadata.py::test_partition", "tests/test_ec2_metadata.py::test_instance_id", "tests/test_ec2_metadata.py::test_network_interface_subnet_ipv4_cidr_block_none", "tests/test_ec2_metadata.py::test_mac", "tests/test_ec2_metadata.py::test_private_ipv4", "tests/test_ec2_metadata.py::test_ami_launch_index", "tests/test_ec2_metadata.py::test_public_hostname", "tests/test_ec2_metadata.py::test_tags_iter", "tests/test_ec2_metadata.py::test_public_ipv4", "tests/test_ec2_metadata.py::test_network_interface_subnet_ipv6_cidr_blocks", "tests/test_ec2_metadata.py::test_ami_id", "tests/test_ec2_metadata.py::test_network_interface_vpc_ipv4_cidr_block_none", "tests/test_ec2_metadata.py::test_network_interface_security_group_ids", "tests/test_ec2_metadata.py::test_iam_info", "tests/test_ec2_metadata.py::test_network_interface_security_groups" ]

{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2022-03-06 15:47:09+00:00

mit

891

adamchainz__pip-lock-121

diff --git a/HISTORY.rst b/HISTORY.rst index 9f9cc5b..568f9d1 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -12,6 +12,7 @@ History ``importlib.metadata.version("pip-lock")`` (`docs <https://docs.python.org/3.8/library/importlib.metadata.html#distribution-versions>`__ / `backport <https://pypi.org/project/importlib-metadata/>`__). +* Fix parsing of package names featuring extras e.g. ``package[extra1,extra2]``. 2.0.0 (2019-02-28) ------------------ diff --git a/src/pip_lock.py b/src/pip_lock.py index 9d93bfa..3c1e7a0 100644 --- a/src/pip_lock.py +++ b/src/pip_lock.py @@ -40,8 +40,11 @@ def get_package_versions(lines, ignore_external=False): if ignore_external and line.startswith("-e"): continue - name, version_plus = line.split("==", 1) - versions[name.lower()] = version_plus.split(" ", 1)[0] + full_name, version_and_extras = line.split("==", 1) + # Strip extras + name = full_name.split("[", 1)[0].lower() + version = version_and_extras.split(" ", 1)[0] + versions[name] = version return versions

adamchainz/pip-lock

4a0e0106254aeceb13f7ff068ce295424b1d44a2

diff --git a/tests/test_pip_lock.py b/tests/test_pip_lock.py index da3f02a..c4a3881 100644 --- a/tests/test_pip_lock.py +++ b/tests/test_pip_lock.py @@ -17,7 +17,7 @@ def create_file(tmpdir, name, text): return str(t) -class TestReadPip(object): +class TestReadPip: def test_read(self, tmpdir): path = create_file(tmpdir, "requirements.txt", "package1==1.0\npackage2==1.1") assert read_pip(path) == ["package1==1.0", "package2==1.1"] @@ -33,7 +33,7 @@ class TestReadPip(object): assert read_pip(path) == [""] -class TestGetPackageVersion(object): +class TestGetPackageVersion: def test_version(self): assert get_package_versions(["package1==1.0", "package2==1.1"]) == { "package1": "1.0", @@ -53,7 +53,7 @@ class TestGetPackageVersion(object): assert get_package_versions(["https://www.google.com"]) == {} -class TestGetMismatches(object): +class TestGetMismatches: def setUp(self, tmpdir): super(TestGetMismatches, self).setUp() self.requirements_path = create_file( @@ -115,8 +115,17 @@ class TestGetMismatches(object): assert get_mismatches(requirements_path) == {} + @mock.patch("pip_lock.pip_freeze") + def test_package_with_extra(self, pip_freeze, tmpdir): + pip_freeze.return_value = ["package==1.1"] + requirements_path = create_file( + tmpdir, "requirements.txt", "package[anextra]==1.1" + ) + + assert get_mismatches(requirements_path) == {} + -class TestPrintErrors(object): +class TestPrintErrors: def test_errors(self, capsys): print_errors(["error message 1", "error message 2"]) _, err = capsys.readouterr() @@ -131,7 +140,7 @@ class TestPrintErrors(object): assert "post text" in err -class TestCheckRequirements(object): +class TestCheckRequirements: @mock.patch("pip_lock.get_mismatches") def test_no_mismatches(self, get_mismatches): get_mismatches.return_value = {}

pip-lock does detect dependencies with setup extras There are requirement mismatches with requirements.txt * Package django-storages[boto3] is in requirements.txt but not in virtualenv

0.0

4a0e0106254aeceb13f7ff068ce295424b1d44a2

[ "tests/test_pip_lock.py::TestGetMismatches::test_package_with_extra" ]

[ "tests/test_pip_lock.py::TestReadPip::test_read", "tests/test_pip_lock.py::TestReadPip::test_include", "tests/test_pip_lock.py::TestReadPip::test_empty", "tests/test_pip_lock.py::TestGetPackageVersion::test_version", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_empty", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_comments", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_includes", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_urls", "tests/test_pip_lock.py::TestGetMismatches::test_relative_requirements_file", "tests/test_pip_lock.py::TestGetMismatches::test_version_mismatch", "tests/test_pip_lock.py::TestGetMismatches::test_missing", "tests/test_pip_lock.py::TestGetMismatches::test_no_mismatches", "tests/test_pip_lock.py::TestGetMismatches::test_no_mismatches_case_insensitive", "tests/test_pip_lock.py::TestGetMismatches::test_empty", "tests/test_pip_lock.py::TestGetMismatches::test_editable_packages", "tests/test_pip_lock.py::TestPrintErrors::test_errors", "tests/test_pip_lock.py::TestPrintErrors::test_pre_post_text", "tests/test_pip_lock.py::TestCheckRequirements::test_no_mismatches", "tests/test_pip_lock.py::TestCheckRequirements::test_mismatches", "tests/test_pip_lock.py::TestCheckRequirements::test_relative_requirements_file" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2019-12-19 11:50:52+00:00

isc

892

adamchainz__pip-lock-208

diff --git a/HISTORY.rst b/HISTORY.rst index ed86591..e15c981 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,6 +2,9 @@ History ======= +* Fix to ignore lines that represent arguments to pip, such as + ``--find-links``. + 2.2.0 (2020-12-13) ------------------ diff --git a/src/pip_lock.py b/src/pip_lock.py index 38edddf..a050b3f 100644 --- a/src/pip_lock.py +++ b/src/pip_lock.py @@ -27,7 +27,7 @@ def get_package_versions(lines, ignore_external_and_at=False): for line in lines: line = line.strip() - if len(line) == 0 or line.startswith("#") or line.startswith("-r "): + if len(line) == 0 or line.startswith(("#", "-")): continue if line.startswith("https://"):

adamchainz/pip-lock

a70ab3c56a094044a1de38f9c66c29d9f022b274

diff --git a/tests/test_pip_lock.py b/tests/test_pip_lock.py index cca27a5..7dde0c4 100644 --- a/tests/test_pip_lock.py +++ b/tests/test_pip_lock.py @@ -49,6 +49,9 @@ class TestGetPackageVersion: def test_ignore_includes(self): assert get_package_versions(["-r example.txt"]) == {} + def test_ignore_arguments(self): + assert get_package_versions(["--find-links file:./wheels"]) == {} + def test_ignore_urls(self): assert get_package_versions(["https://www.google.com"]) == {}

Crashes on lines providing arguments to pip For example `--find-links`

0.0

a70ab3c56a094044a1de38f9c66c29d9f022b274

[ "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_arguments" ]

[ "tests/test_pip_lock.py::TestReadPip::test_read", "tests/test_pip_lock.py::TestReadPip::test_include", "tests/test_pip_lock.py::TestReadPip::test_empty", "tests/test_pip_lock.py::TestGetPackageVersion::test_version", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_empty", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_comments", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_includes", "tests/test_pip_lock.py::TestGetPackageVersion::test_ignore_urls", "tests/test_pip_lock.py::TestGetMismatches::test_relative_requirements_file", "tests/test_pip_lock.py::TestGetMismatches::test_version_mismatch", "tests/test_pip_lock.py::TestGetMismatches::test_missing", "tests/test_pip_lock.py::TestGetMismatches::test_no_mismatches", "tests/test_pip_lock.py::TestGetMismatches::test_no_mismatches_case_insensitive", "tests/test_pip_lock.py::TestGetMismatches::test_empty", "tests/test_pip_lock.py::TestGetMismatches::test_editable_packages_ignored", "tests/test_pip_lock.py::TestGetMismatches::test_at_packages_ignored", "tests/test_pip_lock.py::TestGetMismatches::test_package_with_extra", "tests/test_pip_lock.py::TestPrintErrors::test_errors", "tests/test_pip_lock.py::TestPrintErrors::test_pre_post_text", "tests/test_pip_lock.py::TestCheckRequirements::test_no_mismatches", "tests/test_pip_lock.py::TestCheckRequirements::test_mismatches", "tests/test_pip_lock.py::TestCheckRequirements::test_relative_requirements_file" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2021-01-22 11:34:16+00:00

mit

893

adamchainz__time-machine-101

diff --git a/HISTORY.rst b/HISTORY.rst index 0178c5f..3548383 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,6 +2,8 @@ History ======= +* Prevent ``ImportError`` on Windows where ``time.tzset()`` is unavailable. + 2.0.0 (2021-01-17) ------------------ diff --git a/src/time_machine.py b/src/time_machine.py index ed2cfb2..9b4de81 100644 --- a/src/time_machine.py +++ b/src/time_machine.py @@ -5,7 +5,6 @@ import os import sys import uuid from time import gmtime as orig_gmtime -from time import tzset from types import GeneratorType from typing import Optional from unittest import TestCase, mock @@ -21,6 +20,12 @@ except ImportError: # Dummy value that won't compare equal to any value CLOCK_REALTIME = float("inf") +try: + from time import tzset +except ImportError: # pragma: no cover + # Windows + tzset = None + try: # Python 3.8+ or have installed backports.zoneinfo from zoneinfo import ZoneInfo @@ -137,13 +142,13 @@ class Coordinates: self._start() def _start(self): - if self._destination_tzname is not None: + if tzset is not None and self._destination_tzname is not None: self._orig_tz = os.environ.get("TZ") os.environ["TZ"] = self._destination_tzname tzset() def _stop(self): - if self._destination_tzname is not None: + if tzset is not None and self._destination_tzname is not None: if self._orig_tz is None: del os.environ["TZ"] else:

adamchainz/time-machine

5b2536a1bfb47dc0619d7d03302cf1edc5a51112

diff --git a/tests/test_time_machine.py b/tests/test_time_machine.py index 8f6aa5f..ce7695b 100644 --- a/tests/test_time_machine.py +++ b/tests/test_time_machine.py @@ -379,6 +379,17 @@ def test_destination_datetime_tzinfo_zoneinfo_nested(): assert time.tzname == orig_tzname [email protected](ZoneInfo is None, reason="Requires ZoneInfo") +def test_destination_datetime_tzinfo_zoneinfo_windows(): + orig_timezone = time.timezone + + pretend_windows_no_tzset = mock.patch.object(time_machine, "tzset", new=None) + + dest = LIBRARY_EPOCH_DATETIME.replace(tzinfo=ZoneInfo("Africa/Addis_Ababa")) + with pretend_windows_no_tzset, time_machine.travel(dest): + assert time.timezone == orig_timezone + + @time_machine.travel(EPOCH_DATETIME.replace(tzinfo=None) + dt.timedelta(seconds=120)) def test_destination_datetime_naive(): assert time.time() == EPOCH + 120.0

[v2] ImportError for tzset on Windows In one of my project, I received an automatic update to update time-machine to the newly published v2 and my CI crashes on Windows (Python 3.7, 3.8 and 3.9) with the following error: ``` ImportError: cannot import name 'tzset' from 'time' (unknown location) ``` I don't own a Windows machine, but one can check the logs here: https://github.com/browniebroke/netlify-builds/pull/27/checks?check_run_id=1716666697#step:6:52 Not really urgent or anything, but I thought I report the problem. Is it a missing dependency or something different with the stdlib?

0.0

5b2536a1bfb47dc0619d7d03302cf1edc5a51112

[ "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_windows", "tests/test_time_machine.py::test_traveller_object", "tests/test_time_machine.py::test_move_to_datetime_with_tzinfo_zoneinfo", "tests/test_time_machine.py::test_fixture_unused" ]

[ "tests/test_time_machine.py::test_import_without_clock_realtime", "tests/test_time_machine.py::test_datetime_now_no_args", "tests/test_time_machine.py::test_datetime_now_no_args_no_tick", "tests/test_time_machine.py::test_datetime_now_arg", "tests/test_time_machine.py::test_datetime_utcnow", "tests/test_time_machine.py::test_datetime_utcnow_no_tick", "tests/test_time_machine.py::test_date_today", "tests/test_time_machine.py::test_time_clock_gettime_realtime", "tests/test_time_machine.py::test_time_clock_gettime_monotonic_unaffected", "tests/test_time_machine.py::test_time_clock_gettime_ns_realtime", "tests/test_time_machine.py::test_time_clock_gettime_ns_monotonic_unaffected", "tests/test_time_machine.py::test_time_gmtime_no_args", "tests/test_time_machine.py::test_time_gmtime_no_args_no_tick", "tests/test_time_machine.py::test_time_gmtime_arg", "tests/test_time_machine.py::test_time_localtime", "tests/test_time_machine.py::test_time_localtime_no_tick", "tests/test_time_machine.py::test_time_localtime_arg", "tests/test_time_machine.py::test_time_strftime_no_args", "tests/test_time_machine.py::test_time_strftime_no_args_no_tick", "tests/test_time_machine.py::test_time_strftime_arg", "tests/test_time_machine.py::test_time_time", "tests/test_time_machine.py::test_time_time_windows", "tests/test_time_machine.py::test_time_time_no_tick", "tests/test_time_machine.py::test_time_time_ns", "tests/test_time_machine.py::test_time_time_ns_no_tick", "tests/test_time_machine.py::test_nestable", "tests/test_time_machine.py::test_unsupported_type", "tests/test_time_machine.py::test_exceptions_dont_break_it", "tests/test_time_machine.py::test_destination_datetime", "tests/test_time_machine.py::test_destination_datetime_tzinfo_non_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_nested", "tests/test_time_machine.py::test_destination_datetime_naive", "tests/test_time_machine.py::test_destination_date", "tests/test_time_machine.py::test_destination_string", "tests/test_time_machine.py::test_destination_callable_lambda_float", "tests/test_time_machine.py::test_destination_callable_lambda_string", "tests/test_time_machine.py::test_destination_generator", "tests/test_time_machine.py::test_function_decorator", "tests/test_time_machine.py::test_coroutine_decorator", "tests/test_time_machine.py::test_class_decorator_fails_non_testcase", "tests/test_time_machine.py::UnitTestMethodTests::test_method_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_class_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_stacked_method_decorator", "tests/test_time_machine.py::UnitTestClassCustomSetUpClassTests::test_class_decorator", "tests/test_time_machine.py::test_shift_with_timedelta", "tests/test_time_machine.py::test_shift_integer_delta", "tests/test_time_machine.py::test_shift_negative_delta", "tests/test_time_machine.py::test_shift_wrong_delta", "tests/test_time_machine.py::test_shift_when_tick", "tests/test_time_machine.py::test_move_to_datetime", "tests/test_time_machine.py::test_move_to_datetime_no_tick", "tests/test_time_machine.py::test_move_to_past_datetime", "tests/test_time_machine.py::test_uuid1", "tests/test_time_machine.py::test_fixture_used", "tests/test_time_machine.py::test_fixture_used_twice" ]

{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-01-18 10:34:15+00:00

mit

894

adamchainz__time-machine-152

diff --git a/HISTORY.rst b/HISTORY.rst index 3265158..5390cf4 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,6 +2,10 @@ History ======= +* Allow passing ``tick`` to ``Coordinates.move_to()`` and the pytest fixture’s + ``time_machine.move_to()``. This allows freezing or unfreezing of time when + travelling. + 2.2.0 (2021-07-02) ------------------ diff --git a/README.rst b/README.rst index c4dc27b..d95ff70 100644 --- a/README.rst +++ b/README.rst @@ -235,12 +235,14 @@ Here’s a worked example changing the current timezone: The ``start()`` method and entry of the context manager both return a ``Coordinates`` object that corresponds to the given "trip" in time. This has a couple methods that can be used to travel to other times. -``move_to(destination)`` -^^^^^^^^^^^^^^^^^^^^^^^^ +``move_to(destination, tick=None)`` +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ``move_to()`` moves the current time to a new destination. ``destination`` may be any of the types supported by ``travel``. +``tick`` may be set to a boolean, to change the ``tick`` flag of ``travel``. + For example: .. code-block:: python diff --git a/src/time_machine/__init__.py b/src/time_machine/__init__.py index 7f297a9..a8302b8 100644 --- a/src/time_machine/__init__.py +++ b/src/time_machine/__init__.py @@ -163,12 +163,18 @@ class Coordinates: self._destination_timestamp_ns += int(total_seconds * NANOSECONDS_PER_SECOND) - def move_to(self, destination: DestinationType) -> None: + def move_to( + self, + destination: DestinationType, + tick: Optional[bool] = None, + ) -> None: self._stop() timestamp, self._destination_tzname = extract_timestamp_tzname(destination) self._destination_timestamp_ns = int(timestamp * NANOSECONDS_PER_SECOND) self._requested = False self._start() + if tick is not None: + self._tick = tick def _start(self) -> None: if HAVE_TZSET and self._destination_tzname is not None: @@ -421,13 +427,19 @@ if pytest is not None: # pragma: no branch self.traveller = None self.coordinates = None - def move_to(self, destination: DestinationType) -> None: + def move_to( + self, + destination: DestinationType, + tick: Optional[bool] = None, + ) -> None: if self.traveller is None: - self.traveller = travel(destination) + if tick is None: + tick = True + self.traveller = travel(destination, tick=tick) self.coordinates = self.traveller.start() else: assert self.coordinates is not None - self.coordinates.move_to(destination) + self.coordinates.move_to(destination, tick=tick) def stop(self) -> None: if self.traveller is not None:

adamchainz/time-machine

665670beddc1f330ce182984bfd1fddeda0587a1

diff --git a/tests/test_time_machine.py b/tests/test_time_machine.py index ccf3862..175a7d5 100644 --- a/tests/test_time_machine.py +++ b/tests/test_time_machine.py @@ -633,6 +633,20 @@ def test_move_to_datetime_with_tzinfo_zoneinfo(): assert time.daylight == orig_daylight +def test_move_to_datetime_change_tick_on(): + with time_machine.travel(EPOCH, tick=False) as traveller: + traveller.move_to(EPOCH_PLUS_ONE_YEAR_DATETIME, tick=True) + assert time.time() == EPOCH_PLUS_ONE_YEAR + assert time.time() > EPOCH_PLUS_ONE_YEAR + + +def test_move_to_datetime_change_tick_off(): + with time_machine.travel(EPOCH, tick=True) as traveller: + traveller.move_to(EPOCH_PLUS_ONE_YEAR_DATETIME, tick=False) + assert time.time() == EPOCH_PLUS_ONE_YEAR + assert time.time() == EPOCH_PLUS_ONE_YEAR + + # uuid tests @@ -664,6 +678,19 @@ def test_fixture_used(time_machine): assert time.time() == EPOCH +def test_fixture_used_tick_false(time_machine): + time_machine.move_to(EPOCH, tick=False) + assert time.time() == EPOCH + assert time.time() == EPOCH + + +def test_fixture_used_tick_true(time_machine): + time_machine.move_to(EPOCH, tick=True) + original = time.time() + assert original == EPOCH + assert original < time.time() < EPOCH + 10.0 + + def test_fixture_used_twice(time_machine): time_machine.move_to(EPOCH) assert time.time() == EPOCH

Freeze time instead of just shifting it Hi! This library looks very cool, even more with the added support for pytest. I have a question which might be more related with me not understanding the use cases or purpose than the tool itself. I thought I would be able to tell the library: everytime I call now I want you to return this. Instead what I found is that when I call the `move_to` method in the time_machine fixture, time goes back to that time but the starts moving forward accurately. What I wanted to be able to do is to always get the same value when utcnow is called so I can test the value of queries that I am generating on the fly. Is this possible? Thanks!

0.0

665670beddc1f330ce182984bfd1fddeda0587a1

[ "tests/test_time_machine.py::test_move_to_datetime_change_tick_on", "tests/test_time_machine.py::test_move_to_datetime_change_tick_off", "tests/test_time_machine.py::test_fixture_used_tick_false", "tests/test_time_machine.py::test_fixture_used_tick_true" ]

[ "tests/test_time_machine.py::test_import_without_clock_realtime", "tests/test_time_machine.py::test_datetime_now_no_args", "tests/test_time_machine.py::test_datetime_now_no_args_no_tick", "tests/test_time_machine.py::test_datetime_now_arg", "tests/test_time_machine.py::test_datetime_utcnow", "tests/test_time_machine.py::test_datetime_utcnow_no_tick", "tests/test_time_machine.py::test_date_today", "tests/test_time_machine.py::test_time_clock_gettime_realtime", "tests/test_time_machine.py::test_time_clock_gettime_monotonic_unaffected", "tests/test_time_machine.py::test_time_clock_gettime_ns_realtime", "tests/test_time_machine.py::test_time_clock_gettime_ns_monotonic_unaffected", "tests/test_time_machine.py::test_time_gmtime_no_args", "tests/test_time_machine.py::test_time_gmtime_no_args_no_tick", "tests/test_time_machine.py::test_time_gmtime_arg", "tests/test_time_machine.py::test_time_localtime", "tests/test_time_machine.py::test_time_localtime_no_tick", "tests/test_time_machine.py::test_time_localtime_arg", "tests/test_time_machine.py::test_time_strftime_no_args", "tests/test_time_machine.py::test_time_strftime_no_args_no_tick", "tests/test_time_machine.py::test_time_strftime_arg", "tests/test_time_machine.py::test_time_time", "tests/test_time_machine.py::test_time_time_windows", "tests/test_time_machine.py::test_time_time_no_tick", "tests/test_time_machine.py::test_time_time_ns", "tests/test_time_machine.py::test_time_time_ns_no_tick", "tests/test_time_machine.py::test_nestable", "tests/test_time_machine.py::test_unsupported_type", "tests/test_time_machine.py::test_exceptions_dont_break_it", "tests/test_time_machine.py::test_destination_datetime", "tests/test_time_machine.py::test_destination_datetime_tzinfo_non_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_nested", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_windows", "tests/test_time_machine.py::test_destination_int", "tests/test_time_machine.py::test_destination_datetime_naive", "tests/test_time_machine.py::test_destination_date", "tests/test_time_machine.py::test_destination_string", "tests/test_time_machine.py::test_destination_callable_lambda_float", "tests/test_time_machine.py::test_destination_callable_lambda_string", "tests/test_time_machine.py::test_destination_generator", "tests/test_time_machine.py::test_traveller_object", "tests/test_time_machine.py::test_function_decorator", "tests/test_time_machine.py::test_coroutine_decorator", "tests/test_time_machine.py::test_class_decorator_fails_non_testcase", "tests/test_time_machine.py::UnitTestMethodTests::test_method_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_class_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_stacked_method_decorator", "tests/test_time_machine.py::UnitTestClassCustomSetUpClassTests::test_class_decorator", "tests/test_time_machine.py::test_shift_with_timedelta", "tests/test_time_machine.py::test_shift_integer_delta", "tests/test_time_machine.py::test_shift_negative_delta", "tests/test_time_machine.py::test_shift_wrong_delta", "tests/test_time_machine.py::test_shift_when_tick", "tests/test_time_machine.py::test_move_to_datetime", "tests/test_time_machine.py::test_move_to_datetime_no_tick", "tests/test_time_machine.py::test_move_to_past_datetime", "tests/test_time_machine.py::test_move_to_datetime_with_tzinfo_zoneinfo", "tests/test_time_machine.py::test_uuid1", "tests/test_time_machine.py::test_fixture_unused", "tests/test_time_machine.py::test_fixture_used", "tests/test_time_machine.py::test_fixture_used_twice" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-07-05 15:02:34+00:00

mit

895

adamchainz__time-machine-207

diff --git a/HISTORY.rst b/HISTORY.rst index 78e067b..7af039e 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,6 +2,10 @@ History ======= +* Add ``time_machine.escape_hatch``, which provides functions to bypass time-machine. + + Thanks to Matt Pegler for the feature request in `Issue #206 <https://github.com/adamchainz/time-machine/issues/206>`__. + 2.4.1 (2021-11-27) ------------------ diff --git a/README.rst b/README.rst index 4532090..f23ce06 100644 --- a/README.rst +++ b/README.rst @@ -310,6 +310,52 @@ For example: assert dt.date.today().isoformat() == "2015-10-21" +``escape_hatch`` +---------------- + +The ``escape_hatch`` object provides functions to bypass time-machine. +These allow you to call the real datetime functions, without any mocking. +It also provides a way to check if time-machine is currently time travelling. + +These capabilities are useful in rare circumstances. +For example, if you need to authenticate with an external service during time travel, you may need the real value of ``datetime.now()``. + +The functions are: + +* ``escape_hatch.is_travelling() -> bool`` - returns ``True`` if ``time_machine.travel()`` is active, ``False`` otherwise. + +* ``escape_hatch.datetime.datetime.now()`` - wraps the real ``datetime.datetime.now()``. + +* ``escape_hatch.datetime.datetime.utcnow()`` - wraps the real ``datetime.datetime.utcnow()``. + +* ``escape_hatch.time.clock_gettime()`` - wraps the real ``time.clock_gettime()``. + +* ``escape_hatch.time.clock_gettime_ns()`` - wraps the real ``time.clock_gettime_ns()``. + +* ``escape_hatch.time.gmtime()`` - wraps the real ``time.gmtime()``. + +* ``escape_hatch.time.localtime()`` - wraps the real ``time.localtime()``. + +* ``escape_hatch.time.strftime()`` - wraps the real ``time.strftime()``. + +* ``escape_hatch.time.time()`` - wraps the real ``time.time()``. + +* ``escape_hatch.time.time_ns()`` - wraps the real ``time.time_ns()``. + +For example: + +.. code-block:: python + + import time_machine + + + with time_machine.travel(...): + if time_machine.escape_hatch.is_travelling(): + print("We need to go back to the future!") + + real_now = time_machine.escape_hatch.datetime.datetime.now() + external_authenticate(now=real_now) + Caveats ======= diff --git a/src/time_machine/__init__.py b/src/time_machine/__init__.py index 0e67b1b..4c57870 100644 --- a/src/time_machine/__init__.py +++ b/src/time_machine/__init__.py @@ -77,6 +77,9 @@ DestinationType = Union[ TypingGenerator[DestinationBaseType, None, None], ] +# copied from typeshed: +_TimeTuple = Tuple[int, int, int, int, int, int, int, int, int] + def extract_timestamp_tzname( destination: DestinationType, @@ -389,10 +392,6 @@ def localtime(secs: Optional[float] = None) -> struct_time: return _time_machine.original_localtime(coordinates_stack[-1].time()) -# copied from typeshed: -_TimeTuple = Tuple[int, int, int, int, int, int, int, int, int] - - def strftime(format: str, t: Union[_TimeTuple, struct_time, None] = None) -> str: if t is not None: return _time_machine.original_strftime(format, t) @@ -453,3 +452,63 @@ if pytest is not None: # pragma: no branch yield fixture finally: fixture.stop() + + +# escape hatch + + +class _EscapeHatchDatetimeDatetime: + def now(self, tz: Optional[dt.tzinfo] = None) -> dt.datetime: + return _time_machine.original_now(tz) + + def utcnow(self) -> dt.datetime: + return _time_machine.original_utcnow() + + +class _EscapeHatchDatetime: + def __init__(self) -> None: + self.datetime = _EscapeHatchDatetimeDatetime() + + +class _EscapeHatchTime: + def clock_gettime(self, clk_id: int) -> float: + return _time_machine.original_clock_gettime(clk_id) + + if sys.version_info >= (3, 7): + + def clock_gettime_ns(self, clk_id: int) -> int: + return _time_machine.original_clock_gettime_ns(clk_id) + + def gmtime(self, secs: Optional[float] = None) -> struct_time: + return _time_machine.original_gmtime(secs) + + def localtime(self, secs: Optional[float] = None) -> struct_time: + return _time_machine.original_localtime(secs) + + def strftime( + self, format: str, t: Union[_TimeTuple, struct_time, None] = None + ) -> str: + if t is not None: + return _time_machine.original_strftime(format, t) + else: + return _time_machine.original_strftime(format) + + def time(self) -> float: + return _time_machine.original_time() + + if sys.version_info >= (3, 7): + + def time_ns(self) -> int: + return _time_machine.original_time_ns() + + +class _EscapeHatch: + def __init__(self) -> None: + self.datetime = _EscapeHatchDatetime() + self.time = _EscapeHatchTime() + + def is_travelling(self) -> bool: + return bool(coordinates_stack) + + +escape_hatch = _EscapeHatch()

adamchainz/time-machine

29a9f0aa44204c9bf236f350fdc5015fd10e8e2c

diff --git a/tests/test_time_machine.py b/tests/test_time_machine.py index a23a99e..8cb4f63 100644 --- a/tests/test_time_machine.py +++ b/tests/test_time_machine.py @@ -222,18 +222,18 @@ def test_time_localtime_arg(): assert local_time.tm_mday == 1 -def test_time_strftime_no_args(): +def test_time_strftime_format(): with time_machine.travel(EPOCH): assert time.strftime("%Y-%m-%d") == "1970-01-01" assert int(time.strftime("%Y")) >= 2020 -def test_time_strftime_no_args_no_tick(): +def test_time_strftime_format_no_tick(): with time_machine.travel(EPOCH, tick=False): assert time.strftime("%S") == "00" -def test_time_strftime_arg(): +def test_time_strftime_format_t(): with time_machine.travel(EPOCH): assert ( time.strftime("%Y-%m-%d", time.localtime(EPOCH_PLUS_ONE_YEAR)) @@ -718,3 +718,100 @@ def test_fixture_used_twice(time_machine): time_machine.move_to(EPOCH_PLUS_ONE_YEAR) assert time.time() == EPOCH_PLUS_ONE_YEAR + + +# escape hatch tests + + +class TestEscapeHatch: + def test_is_travelling_false(self): + assert time_machine.escape_hatch.is_travelling() is False + + def test_is_travelling_true(self): + with time_machine.travel(EPOCH): + assert time_machine.escape_hatch.is_travelling() is True + + def test_datetime_now(self): + real_now = dt.datetime.now() + + with time_machine.travel(EPOCH): + eh_now = time_machine.escape_hatch.datetime.datetime.now() + assert eh_now >= real_now + + def test_datetime_now_tz(self): + real_now = dt.datetime.now(tz=dt.timezone.utc) + + with time_machine.travel(EPOCH): + eh_now = time_machine.escape_hatch.datetime.datetime.now(tz=dt.timezone.utc) + assert eh_now >= real_now + + def test_datetime_utcnow(self): + real_now = dt.datetime.utcnow() + + with time_machine.travel(EPOCH): + eh_now = time_machine.escape_hatch.datetime.datetime.utcnow() + assert eh_now >= real_now + + @py_have_clock_gettime + def test_time_clock_gettime(self): + now = time.clock_gettime(time.CLOCK_REALTIME) + + with time_machine.travel(EPOCH + 180.0): + eh_now = time_machine.escape_hatch.time.clock_gettime(time.CLOCK_REALTIME) + assert eh_now >= now + + @py_3_7_plus + @py_have_clock_gettime + def test_time_clock_gettime_ns(self): + now = time.clock_gettime_ns(time.CLOCK_REALTIME) + + with time_machine.travel(EPOCH + 190.0): + eh_now = time_machine.escape_hatch.time.clock_gettime_ns( + time.CLOCK_REALTIME + ) + assert eh_now >= now + + def test_time_gmtime(self): + now = time.gmtime() + + with time_machine.travel(EPOCH): + eh_now = time_machine.escape_hatch.time.gmtime() + assert eh_now >= now + + def test_time_localtime(self): + now = time.localtime() + + with time_machine.travel(EPOCH): + eh_now = time_machine.escape_hatch.time.localtime() + assert eh_now >= now + + def test_time_strftime_no_arg(self): + today = dt.date.today() + + with time_machine.travel(EPOCH): + eh_formatted = time_machine.escape_hatch.time.strftime("%Y-%m-%d") + eh_today = dt.datetime.strptime(eh_formatted, "%Y-%m-%d").date() + assert eh_today >= today + + def test_time_strftime_arg(self): + with time_machine.travel(EPOCH): + formatted = time_machine.escape_hatch.time.strftime( + "%Y-%m-%d", + time.localtime(EPOCH_PLUS_ONE_YEAR), + ) + assert formatted == "1971-01-01" + + def test_time_time(self): + now = time.time() + + with time_machine.travel(EPOCH): + eh_now = time_machine.escape_hatch.time.time() + assert eh_now >= now + + @py_3_7_plus + def test_time_time_ns(self): + now = time.time_ns() + + with time_machine.travel(EPOCH): + eh_now = time_machine.escape_hatch.time.time_ns() + assert eh_now >= now

Flag that we're time traveling, with access to true datetime ### Description In some of our integration tests we make API calls to external services. Some of these require a timestamp for use in authentication. I know that excluding some modules from time-machine isn't possible due to the implementation, but having some signal that we're time traveling would suffice, along with access to the unpatched datetime module.

0.0

29a9f0aa44204c9bf236f350fdc5015fd10e8e2c

[ "tests/test_time_machine.py::TestEscapeHatch::test_is_travelling_false", "tests/test_time_machine.py::TestEscapeHatch::test_is_travelling_true", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_now", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_now_tz", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_utcnow", "tests/test_time_machine.py::TestEscapeHatch::test_time_clock_gettime", "tests/test_time_machine.py::TestEscapeHatch::test_time_clock_gettime_ns", "tests/test_time_machine.py::TestEscapeHatch::test_time_gmtime", "tests/test_time_machine.py::TestEscapeHatch::test_time_localtime", "tests/test_time_machine.py::TestEscapeHatch::test_time_strftime_no_arg", "tests/test_time_machine.py::TestEscapeHatch::test_time_strftime_arg", "tests/test_time_machine.py::TestEscapeHatch::test_time_time", "tests/test_time_machine.py::TestEscapeHatch::test_time_time_ns" ]

[ "tests/test_time_machine.py::test_import_without_clock_realtime", "tests/test_time_machine.py::test_datetime_now_no_args", "tests/test_time_machine.py::test_datetime_now_no_args_no_tick", "tests/test_time_machine.py::test_datetime_now_arg", "tests/test_time_machine.py::test_datetime_utcnow", "tests/test_time_machine.py::test_datetime_utcnow_no_tick", "tests/test_time_machine.py::test_date_today", "tests/test_time_machine.py::test_time_clock_gettime_realtime", "tests/test_time_machine.py::test_time_clock_gettime_monotonic_unaffected", "tests/test_time_machine.py::test_time_clock_gettime_ns_realtime", "tests/test_time_machine.py::test_time_clock_gettime_ns_monotonic_unaffected", "tests/test_time_machine.py::test_time_gmtime_no_args", "tests/test_time_machine.py::test_time_gmtime_no_args_no_tick", "tests/test_time_machine.py::test_time_gmtime_arg", "tests/test_time_machine.py::test_time_localtime", "tests/test_time_machine.py::test_time_localtime_no_tick", "tests/test_time_machine.py::test_time_localtime_arg", "tests/test_time_machine.py::test_time_strftime_format", "tests/test_time_machine.py::test_time_strftime_format_no_tick", "tests/test_time_machine.py::test_time_strftime_format_t", "tests/test_time_machine.py::test_time_time", "tests/test_time_machine.py::test_time_time_windows", "tests/test_time_machine.py::test_time_time_no_tick", "tests/test_time_machine.py::test_time_time_ns", "tests/test_time_machine.py::test_time_time_ns_no_tick", "tests/test_time_machine.py::test_nestable", "tests/test_time_machine.py::test_unsupported_type", "tests/test_time_machine.py::test_exceptions_dont_break_it", "tests/test_time_machine.py::test_destination_datetime", "tests/test_time_machine.py::test_destination_datetime_tzinfo_non_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_nested", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_no_orig_tz", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_windows", "tests/test_time_machine.py::test_destination_int", "tests/test_time_machine.py::test_destination_datetime_naive", "tests/test_time_machine.py::test_destination_date", "tests/test_time_machine.py::test_destination_string", "tests/test_time_machine.py::test_destination_callable_lambda_float", "tests/test_time_machine.py::test_destination_callable_lambda_string", "tests/test_time_machine.py::test_destination_generator", "tests/test_time_machine.py::test_traveller_object", "tests/test_time_machine.py::test_function_decorator", "tests/test_time_machine.py::test_coroutine_decorator", "tests/test_time_machine.py::test_class_decorator_fails_non_testcase", "tests/test_time_machine.py::UnitTestMethodTests::test_method_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_class_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_stacked_method_decorator", "tests/test_time_machine.py::UnitTestClassCustomSetUpClassTests::test_class_decorator", "tests/test_time_machine.py::test_shift_with_timedelta", "tests/test_time_machine.py::test_shift_integer_delta", "tests/test_time_machine.py::test_shift_negative_delta", "tests/test_time_machine.py::test_shift_wrong_delta", "tests/test_time_machine.py::test_shift_when_tick", "tests/test_time_machine.py::test_move_to_datetime", "tests/test_time_machine.py::test_move_to_datetime_no_tick", "tests/test_time_machine.py::test_move_to_past_datetime", "tests/test_time_machine.py::test_move_to_datetime_with_tzinfo_zoneinfo", "tests/test_time_machine.py::test_move_to_datetime_change_tick_on", "tests/test_time_machine.py::test_move_to_datetime_change_tick_off", "tests/test_time_machine.py::test_uuid1", "tests/test_time_machine.py::test_fixture_unused", "tests/test_time_machine.py::test_fixture_used", "tests/test_time_machine.py::test_fixture_used_tick_false", "tests/test_time_machine.py::test_fixture_used_tick_true", "tests/test_time_machine.py::test_fixture_used_twice" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-12-14 07:56:53+00:00

mit

896

adamchainz__time-machine-298

diff --git a/CHANGELOG.rst b/CHANGELOG.rst index c524071..71b1598 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -2,6 +2,10 @@ Changelog ========= +* Add support for ``datetime.timedelta`` to ``time_machine.travel()``. + + Thanks to Nate Dudenhoeffer in `PR #298 <https://github.com/adamchainz/time-machine/pull/298>`__. + * Add ``shift()`` method to the ``time_machine`` pytest fixture. Thanks to Stefaan Lippens in `PR #312 <https://github.com/adamchainz/time-machine/pull/312>`__. diff --git a/README.rst b/README.rst index 755325c..88db11f 100644 --- a/README.rst +++ b/README.rst @@ -77,6 +77,9 @@ It may be: If it has ``tzinfo`` set to a |zoneinfo-instance|_, the current timezone will also be mocked. * A ``datetime.date``. This will be converted to a UTC datetime with the time 00:00:00. +* A ``datetime.timedelta``. + This will be interpreted relative to the current time. + If already within a ``travel()`` block, the ``shift()`` method is easier to use (documented below). * A ``float`` or ``int`` specifying a `Unix timestamp <https://en.m.wikipedia.org/wiki/Unix_time>`__ * A string, which will be parsed with `dateutil.parse <https://dateutil.readthedocs.io/en/stable/parser.html>`__ and converted to a timestamp. Again, if the result is naive, it will be assumed to have the UTC time zone. diff --git a/src/time_machine/__init__.py b/src/time_machine/__init__.py index c0d6bda..4fa2142 100644 --- a/src/time_machine/__init__.py +++ b/src/time_machine/__init__.py @@ -84,6 +84,7 @@ DestinationBaseType = Union[ int, float, dt.datetime, + dt.timedelta, dt.date, str, ] @@ -124,6 +125,8 @@ def extract_timestamp_tzname( if dest.tzinfo is None: dest = dest.replace(tzinfo=dt.timezone.utc) timestamp = dest.timestamp() + elif isinstance(dest, dt.timedelta): + timestamp = time() + dest.total_seconds() elif isinstance(dest, dt.date): timestamp = dt.datetime.combine( dest, dt.time(0, 0), tzinfo=dt.timezone.utc

adamchainz/time-machine

ac337ab7dc568675de7f90c8fb387160e3f08496

diff --git a/tests/test_time_machine.py b/tests/test_time_machine.py index 9736be4..0f086bf 100644 --- a/tests/test_time_machine.py +++ b/tests/test_time_machine.py @@ -444,6 +444,24 @@ def test_destination_date(): assert time.time() == EPOCH +def test_destination_timedelta(): + now = time.time() + with time_machine.travel(dt.timedelta(seconds=3600)): + assert now + 3600 <= time.time() <= now + 3601 + + +def test_destination_timedelta_negative(): + now = time.time() + with time_machine.travel(dt.timedelta(seconds=-3600)): + assert now - 3600 <= time.time() <= now - 3599 + + +def test_destination_timedelta_nested(): + with time_machine.travel(EPOCH): + with time_machine.travel(dt.timedelta(seconds=10)): + assert time.time() == EPOCH + 10.0 + + @time_machine.travel("1970-01-01 00:01 +0000") def test_destination_string(): assert time.time() == EPOCH + 60.0

Allow passing dt.timedelta objects to travel() It would offset the current time by the given amount, which would be pretty useful for some tests that check "X is true until N minutes in the future"

0.0

ac337ab7dc568675de7f90c8fb387160e3f08496

[ "tests/test_time_machine.py::test_destination_timedelta", "tests/test_time_machine.py::test_destination_timedelta_negative", "tests/test_time_machine.py::test_destination_timedelta_nested" ]

[ "tests/test_time_machine.py::test_import_without_clock_realtime", "tests/test_time_machine.py::test_datetime_now_no_args", "tests/test_time_machine.py::test_datetime_now_no_args_no_tick", "tests/test_time_machine.py::test_datetime_now_arg", "tests/test_time_machine.py::test_datetime_utcnow", "tests/test_time_machine.py::test_datetime_utcnow_no_tick", "tests/test_time_machine.py::test_date_today", "tests/test_time_machine.py::test_time_clock_gettime_realtime", "tests/test_time_machine.py::test_time_clock_gettime_monotonic_unaffected", "tests/test_time_machine.py::test_time_clock_gettime_ns_realtime", "tests/test_time_machine.py::test_time_clock_gettime_ns_monotonic_unaffected", "tests/test_time_machine.py::test_time_gmtime_no_args", "tests/test_time_machine.py::test_time_gmtime_no_args_no_tick", "tests/test_time_machine.py::test_time_gmtime_arg", "tests/test_time_machine.py::test_time_localtime", "tests/test_time_machine.py::test_time_localtime_no_tick", "tests/test_time_machine.py::test_time_localtime_arg", "tests/test_time_machine.py::test_time_montonic", "tests/test_time_machine.py::test_time_monotonic_ns", "tests/test_time_machine.py::test_time_strftime_format", "tests/test_time_machine.py::test_time_strftime_format_no_tick", "tests/test_time_machine.py::test_time_strftime_format_t", "tests/test_time_machine.py::test_time_time", "tests/test_time_machine.py::test_time_time_windows", "tests/test_time_machine.py::test_time_time_no_tick", "tests/test_time_machine.py::test_time_time_ns", "tests/test_time_machine.py::test_time_time_ns_no_tick", "tests/test_time_machine.py::test_nestable", "tests/test_time_machine.py::test_unsupported_type", "tests/test_time_machine.py::test_exceptions_dont_break_it", "tests/test_time_machine.py::test_destination_datetime", "tests/test_time_machine.py::test_destination_datetime_tzinfo_non_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_nested", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_no_orig_tz", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_windows", "tests/test_time_machine.py::test_destination_int", "tests/test_time_machine.py::test_destination_datetime_naive", "tests/test_time_machine.py::test_destination_date", "tests/test_time_machine.py::test_destination_string", "tests/test_time_machine.py::test_destination_callable_lambda_float", "tests/test_time_machine.py::test_destination_callable_lambda_string", "tests/test_time_machine.py::test_destination_generator", "tests/test_time_machine.py::test_traveller_object", "tests/test_time_machine.py::test_function_decorator", "tests/test_time_machine.py::test_coroutine_decorator", "tests/test_time_machine.py::test_class_decorator_fails_non_testcase", "tests/test_time_machine.py::TestMethodDecorator::test_method_decorator", "tests/test_time_machine.py::UnitTestMethodTests::test_method_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_class_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_stacked_method_decorator", "tests/test_time_machine.py::UnitTestClassCustomSetUpClassTests::test_class_decorator", "tests/test_time_machine.py::test_shift_with_timedelta", "tests/test_time_machine.py::test_shift_integer_delta", "tests/test_time_machine.py::test_shift_negative_delta", "tests/test_time_machine.py::test_shift_wrong_delta", "tests/test_time_machine.py::test_shift_when_tick", "tests/test_time_machine.py::test_move_to_datetime", "tests/test_time_machine.py::test_move_to_datetime_no_tick", "tests/test_time_machine.py::test_move_to_past_datetime", "tests/test_time_machine.py::test_move_to_datetime_with_tzinfo_zoneinfo", "tests/test_time_machine.py::test_move_to_datetime_change_tick_on", "tests/test_time_machine.py::test_move_to_datetime_change_tick_off", "tests/test_time_machine.py::test_uuid1", "tests/test_time_machine.py::test_fixture_unused", "tests/test_time_machine.py::test_fixture_used", "tests/test_time_machine.py::test_fixture_used_tick_false", "tests/test_time_machine.py::test_fixture_used_tick_true", "tests/test_time_machine.py::test_fixture_move_to_twice", "tests/test_time_machine.py::test_fixture_move_to_and_shift", "tests/test_time_machine.py::test_fixture_shift_without_move_to", "tests/test_time_machine.py::TestEscapeHatch::test_is_travelling_false", "tests/test_time_machine.py::TestEscapeHatch::test_is_travelling_true", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_now", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_now_tz", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_utcnow", "tests/test_time_machine.py::TestEscapeHatch::test_time_clock_gettime", "tests/test_time_machine.py::TestEscapeHatch::test_time_clock_gettime_ns", "tests/test_time_machine.py::TestEscapeHatch::test_time_gmtime", "tests/test_time_machine.py::TestEscapeHatch::test_time_localtime", "tests/test_time_machine.py::TestEscapeHatch::test_time_monotonic", "tests/test_time_machine.py::TestEscapeHatch::test_time_monotonic_ns", "tests/test_time_machine.py::TestEscapeHatch::test_time_strftime_no_arg", "tests/test_time_machine.py::TestEscapeHatch::test_time_strftime_arg", "tests/test_time_machine.py::TestEscapeHatch::test_time_time", "tests/test_time_machine.py::TestEscapeHatch::test_time_time_ns" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2022-11-03 01:33:14+00:00

mit

897

adamchainz__time-machine-433

diff --git a/CHANGELOG.rst b/CHANGELOG.rst index d83e48d..5984577 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -2,6 +2,10 @@ Changelog ========= +* Fix segmentation fault when the first ``travel()`` call in a process uses a ``timedelta``. + + Thanks to Marcin Sulikowski for the report in `Issue #431 <https://github.com/adamchainz/time-machine/issues/431>`__. + 2.14.0 (2024-03-03) ------------------- diff --git a/src/time_machine/__init__.py b/src/time_machine/__init__.py index 877b325..2553b3d 100644 --- a/src/time_machine/__init__.py +++ b/src/time_machine/__init__.py @@ -5,6 +5,7 @@ import functools import inspect import os import sys +import time as time_module import uuid from collections.abc import Generator from time import gmtime as orig_gmtime @@ -126,7 +127,7 @@ def extract_timestamp_tzname( dest = dest.replace(tzinfo=dt.timezone.utc) timestamp = dest.timestamp() elif isinstance(dest, dt.timedelta): - timestamp = time() + dest.total_seconds() + timestamp = time_module.time() + dest.total_seconds() elif isinstance(dest, dt.date): timestamp = dt.datetime.combine( dest, dt.time(0, 0), tzinfo=dt.timezone.utc

adamchainz/time-machine

8e28b9e74c3d6a50b7d6ec09a9e50903d4dc8bdd

diff --git a/tests/test_time_machine.py b/tests/test_time_machine.py index 11dc433..5557148 100644 --- a/tests/test_time_machine.py +++ b/tests/test_time_machine.py @@ -3,6 +3,7 @@ from __future__ import annotations import asyncio import datetime as dt import os +import subprocess import sys import time import typing @@ -10,6 +11,7 @@ import uuid from contextlib import contextmanager from importlib.util import module_from_spec from importlib.util import spec_from_file_location +from textwrap import dedent from unittest import SkipTest from unittest import TestCase from unittest import mock @@ -472,6 +474,25 @@ def test_destination_timedelta(): assert now + 3600 <= time.time() <= now + 3601 +def test_destination_timedelta_first_travel_in_process(): + # Would previously segfault + subprocess.run( + [ + sys.executable, + "-c", + dedent( + """ + from datetime import timedelta + import time_machine + with time_machine.travel(timedelta()): + pass + """ + ), + ], + check=True, + ) + + def test_destination_timedelta_negative(): now = time.time() with time_machine.travel(dt.timedelta(seconds=-3600)):

Segmentation fault in `time_machine_travel(timedelta())` ### Python Version 3.12 ### pytest Version _No response_ ### Package Version 2.14.0 ### Description The following Python script: ```py from datetime import timedelta import time_machine with time_machine.travel(timedelta()): pass ``` crashes due to a segmentation fault in the constructor of the `travel` class. The crash happens when the constructor tries to determine the destination timestamp like this: ```py timestamp = time() + dest.total_seconds() ``` where `time()` calls `result = _time_machine.original_time()` which crashes if time_machine's patches are not applied yet and thus the `original_time` function pointer is still `NULL`.

0.0

8e28b9e74c3d6a50b7d6ec09a9e50903d4dc8bdd

[ "tests/test_time_machine.py::test_destination_timedelta_first_travel_in_process" ]

[ "tests/test_time_machine.py::test_import_without_clock_realtime", "tests/test_time_machine.py::test_datetime_now_no_args", "tests/test_time_machine.py::test_datetime_now_no_args_no_tick", "tests/test_time_machine.py::test_datetime_now_arg", "tests/test_time_machine.py::test_datetime_utcnow", "tests/test_time_machine.py::test_datetime_utcnow_no_tick", "tests/test_time_machine.py::test_date_today", "tests/test_time_machine.py::test_time_clock_gettime_realtime", "tests/test_time_machine.py::test_time_clock_gettime_monotonic_unaffected", "tests/test_time_machine.py::test_time_clock_gettime_ns_realtime", "tests/test_time_machine.py::test_time_clock_gettime_ns_monotonic_unaffected", "tests/test_time_machine.py::test_time_gmtime_no_args", "tests/test_time_machine.py::test_time_gmtime_no_args_no_tick", "tests/test_time_machine.py::test_time_gmtime_arg", "tests/test_time_machine.py::test_time_localtime", "tests/test_time_machine.py::test_time_localtime_no_tick", "tests/test_time_machine.py::test_time_localtime_arg", "tests/test_time_machine.py::test_time_montonic", "tests/test_time_machine.py::test_time_monotonic_ns", "tests/test_time_machine.py::test_time_strftime_format", "tests/test_time_machine.py::test_time_strftime_format_no_tick", "tests/test_time_machine.py::test_time_strftime_format_t", "tests/test_time_machine.py::test_time_time", "tests/test_time_machine.py::test_time_time_windows", "tests/test_time_machine.py::test_time_time_no_tick", "tests/test_time_machine.py::test_time_time_ns", "tests/test_time_machine.py::test_time_time_ns_no_tick", "tests/test_time_machine.py::test_nestable", "tests/test_time_machine.py::test_unsupported_type", "tests/test_time_machine.py::test_exceptions_dont_break_it", "tests/test_time_machine.py::test_destination_datetime", "tests/test_time_machine.py::test_destination_datetime_tzinfo_non_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_nested", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_no_orig_tz", "tests/test_time_machine.py::test_destination_datetime_tzinfo_zoneinfo_windows", "tests/test_time_machine.py::test_destination_int", "tests/test_time_machine.py::test_destination_datetime_naive", "tests/test_time_machine.py::test_destination_date", "tests/test_time_machine.py::test_destination_timedelta", "tests/test_time_machine.py::test_destination_timedelta_negative", "tests/test_time_machine.py::test_destination_timedelta_nested", "tests/test_time_machine.py::test_destination_string", "tests/test_time_machine.py::test_destination_string_naive[1970-01-01", "tests/test_time_machine.py::test_destination_string_naive[1970-01-01-UTC-0]", "tests/test_time_machine.py::test_destination_string_naive[1970-01-01-Europe/Amsterdam--3600]", "tests/test_time_machine.py::test_destination_string_naive[1970-01-01-US/Eastern-18000]", "tests/test_time_machine.py::test_destination_callable_lambda_float", "tests/test_time_machine.py::test_destination_callable_lambda_string", "tests/test_time_machine.py::test_destination_generator", "tests/test_time_machine.py::test_traveller_object", "tests/test_time_machine.py::test_function_decorator", "tests/test_time_machine.py::test_coroutine_decorator", "tests/test_time_machine.py::test_class_decorator_fails_non_testcase", "tests/test_time_machine.py::ClassDecoratorInheritanceTests::test_ineheritance_correctly_rebound", "tests/test_time_machine.py::TestMethodDecorator::test_method_decorator", "tests/test_time_machine.py::UnitTestMethodTests::test_method_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_class_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_stacked_method_decorator", "tests/test_time_machine.py::UnitTestClassCustomSetUpClassTests::test_class_decorator", "tests/test_time_machine.py::test_shift_with_timedelta", "tests/test_time_machine.py::test_shift_integer_delta", "tests/test_time_machine.py::test_shift_negative_delta", "tests/test_time_machine.py::test_shift_wrong_delta", "tests/test_time_machine.py::test_shift_when_tick", "tests/test_time_machine.py::test_move_to_datetime", "tests/test_time_machine.py::test_move_to_datetime_no_tick", "tests/test_time_machine.py::test_move_to_past_datetime", "tests/test_time_machine.py::test_move_to_datetime_with_tzinfo_zoneinfo", "tests/test_time_machine.py::test_move_to_datetime_change_tick_on", "tests/test_time_machine.py::test_move_to_datetime_change_tick_off", "tests/test_time_machine.py::test_uuid1", "tests/test_time_machine.py::test_fixture_unused", "tests/test_time_machine.py::test_fixture_used", "tests/test_time_machine.py::test_fixture_used_tick_false", "tests/test_time_machine.py::test_fixture_used_tick_true", "tests/test_time_machine.py::test_fixture_move_to_twice", "tests/test_time_machine.py::test_fixture_move_to_and_shift", "tests/test_time_machine.py::test_fixture_shift_without_move_to", "tests/test_time_machine.py::TestEscapeHatch::test_is_travelling_false", "tests/test_time_machine.py::TestEscapeHatch::test_is_travelling_true", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_now", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_now_tz", "tests/test_time_machine.py::TestEscapeHatch::test_datetime_utcnow", "tests/test_time_machine.py::TestEscapeHatch::test_time_clock_gettime", "tests/test_time_machine.py::TestEscapeHatch::test_time_clock_gettime_ns", "tests/test_time_machine.py::TestEscapeHatch::test_time_gmtime", "tests/test_time_machine.py::TestEscapeHatch::test_time_localtime", "tests/test_time_machine.py::TestEscapeHatch::test_time_monotonic", "tests/test_time_machine.py::TestEscapeHatch::test_time_monotonic_ns", "tests/test_time_machine.py::TestEscapeHatch::test_time_strftime_no_arg", "tests/test_time_machine.py::TestEscapeHatch::test_time_strftime_arg", "tests/test_time_machine.py::TestEscapeHatch::test_time_time", "tests/test_time_machine.py::TestEscapeHatch::test_time_time_ns" ]

{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2024-03-22 23:03:40+00:00

mit

898

adamchainz__time-machine-54

diff --git a/HISTORY.rst b/HISTORY.rst index 485c825..f5a2f8c 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -1,6 +1,12 @@ History ======= +* Correctly return naive datetimes from ``datetime.utcnow()`` whilst time + travelling. + + Thanks to Søren Pilgård and Bart Van Loon for the report in + `Issue #52 <https://github.com/adamchainz/time-machine/issues/52>`__. + 1.2.0 (2020-07-08) ------------------ diff --git a/src/time_machine.py b/src/time_machine.py index 0832f6a..d0ed6ff 100644 --- a/src/time_machine.py +++ b/src/time_machine.py @@ -206,7 +206,7 @@ def utcnow(): if not coordinates_stack: return _time_machine.original_utcnow() else: - return dt.datetime.fromtimestamp(time(), dt.timezone.utc) + return dt.datetime.utcfromtimestamp(time()) # time module

adamchainz/time-machine

48a2a4df24ba188533fdf03f6cfc4b78db33f17a

diff --git a/tests/test_time_machine.py b/tests/test_time_machine.py index bf85da5..4eacde2 100644 --- a/tests/test_time_machine.py +++ b/tests/test_time_machine.py @@ -88,6 +88,7 @@ def test_datetime_utcnow(): assert now.minute == 0 assert now.second == 0 assert now.microsecond == 0 + assert now.tzinfo is None assert dt.datetime.utcnow() >= LIBRARY_EPOCH_DATETIME

datetime.datetime.utcnow() should not have tzinfo Hi, I find this library very neat and have started using it in multiple tests. But there is one issue: ```python In [1]: import datetime In [2]: import time_machine In [3]: @time_machine.travel("2020-07-28 13:15:30.478705") ...: def foo(): ...: return datetime.datetime.utcnow() ...: In [4]: datetime.datetime.utcnow() Out[4]: datetime.datetime(2020, 7, 31, 13, 46, 25, 828701) In [5]: foo() Out[5]: datetime.datetime(2020, 7, 28, 13, 15, 30, 478705, tzinfo=datetime.timezone.utc) ``` time_machine adds a timezone on datetime instances created via `.utcnow()` but this is wrong according to python. It even specifies it directly in the documentation https://docs.python.org/3/library/datetime.html#datetime.datetime.utcnow > Return the current UTC date and time, **with tzinfo None**. This change in the behaviour of the datetime library can cause changes in behaviour of the tested code. Eg. when serialized to a string it adds "+00:00"

0.0

48a2a4df24ba188533fdf03f6cfc4b78db33f17a

[ "tests/test_time_machine.py::test_datetime_utcnow" ]

[ "tests/test_time_machine.py::test_import_without_clock_realtime", "tests/test_time_machine.py::test_datetime_now_no_args", "tests/test_time_machine.py::test_datetime_now_no_args_no_tick", "tests/test_time_machine.py::test_datetime_now_arg", "tests/test_time_machine.py::test_datetime_utcnow_no_tick", "tests/test_time_machine.py::test_date_today", "tests/test_time_machine.py::test_time_clock_gettime_realtime", "tests/test_time_machine.py::test_time_clock_gettime_monotonic_unaffected", "tests/test_time_machine.py::test_time_clock_gettime_ns_realtime", "tests/test_time_machine.py::test_time_clock_gettime_ns_monotonic_unaffected", "tests/test_time_machine.py::test_time_gmtime_no_args", "tests/test_time_machine.py::test_time_gmtime_no_args_no_tick", "tests/test_time_machine.py::test_time_gmtime_arg", "tests/test_time_machine.py::test_time_localtime", "tests/test_time_machine.py::test_time_localtime_no_tick", "tests/test_time_machine.py::test_time_localtime_arg", "tests/test_time_machine.py::test_time_strftime_no_args", "tests/test_time_machine.py::test_time_strftime_no_args_no_tick", "tests/test_time_machine.py::test_time_strftime_arg", "tests/test_time_machine.py::test_time_time", "tests/test_time_machine.py::test_time_time_no_tick", "tests/test_time_machine.py::test_time_time_ns", "tests/test_time_machine.py::test_time_time_ns_no_tick", "tests/test_time_machine.py::test_nestable", "tests/test_time_machine.py::test_unsupported_type", "tests/test_time_machine.py::test_exceptions_dont_break_it", "tests/test_time_machine.py::test_destination_datetime", "tests/test_time_machine.py::test_destination_datetime_timezone", "tests/test_time_machine.py::test_destination_datetime_naive", "tests/test_time_machine.py::test_destination_date", "tests/test_time_machine.py::test_destination_string", "tests/test_time_machine.py::test_destination_callable_lambda_float", "tests/test_time_machine.py::test_destination_callable_lambda_string", "tests/test_time_machine.py::test_destination_generator", "tests/test_time_machine.py::test_traveller_object", "tests/test_time_machine.py::test_function_decorator", "tests/test_time_machine.py::test_coroutine_decorator", "tests/test_time_machine.py::test_class_decorator_fails_non_testcase", "tests/test_time_machine.py::UnitTestMethodTests::test_method_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_class_decorator", "tests/test_time_machine.py::UnitTestClassTests::test_stacked_method_decorator", "tests/test_time_machine.py::UnitTestClassCustomSetUpClassTests::test_class_decorator", "tests/test_time_machine.py::test_tz_offset_float", "tests/test_time_machine.py::test_tz_offset_timedelta", "tests/test_time_machine.py::test_tz_offset_unsupported_type", "tests/test_time_machine.py::test_shift_with_timedelta", "tests/test_time_machine.py::test_shift_integer_delta", "tests/test_time_machine.py::test_shift_negative_delta", "tests/test_time_machine.py::test_shift_wrong_delta", "tests/test_time_machine.py::test_shift_when_tick", "tests/test_time_machine.py::test_move_to_datetime", "tests/test_time_machine.py::test_move_to_datetime_when_tick", "tests/test_time_machine.py::test_move_to_past_datetime", "tests/test_time_machine.py::test_move_to_past_datetime_when_tick", "tests/test_time_machine.py::test_uuid1" ]

{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2020-08-29 21:48:07+00:00

isc

899

adamgilman__furlong-5

diff --git a/.gitignore b/.gitignore index 894a44c..06f9e54 100644 --- a/.gitignore +++ b/.gitignore @@ -5,7 +5,11 @@ __pycache__/ # C extensions *.so - +bin/* +include/* +lib/* +man/* +pip-selfcheck.json # Distribution / packaging .Python build/ diff --git a/README.md b/README.md new file mode 100644 index 0000000..12231f7 --- /dev/null +++ b/README.md @@ -0,0 +1,34 @@ +# Hello Furlong +Furlong aims to make units conversions easy and pythonic with a simple to understand and magical interface. Simply declare the unit and value and convert to anything you can think of. If we don't support a unit conversion, open a pull request to add it for everyone! + +## How it works +Bring Furlong into your project with a simple name, f is recommended but, not required + +`from furlong import Furlong as f` + +Declare the unit and value of the base measurement + +`length_of_wall = f(inches=300)` + +Then convert to any unit you'd like! + +``` +length_of_wall.asCentimeters() +30.48 +``` + +Done! + +## Error handling + +* [TODO] + +## Units supported + +* ### Length + * inches + * centimeters + +* ### Volume + +* ### Weight diff --git a/furlong/__init__.py b/furlong/__init__.py new file mode 100644 index 0000000..10cb1e8 --- /dev/null +++ b/furlong/__init__.py @@ -0,0 +1,1 @@ +from .furlong import Furlong \ No newline at end of file diff --git a/furlong/furlong.py b/furlong/furlong.py new file mode 100644 index 0000000..b23faeb --- /dev/null +++ b/furlong/furlong.py @@ -0,0 +1,19 @@ +class Furlong(object): + conversion_table = { + 'inches' : ('centimeters', 2.54), + } + def __init__(self, **kwargs): + for key, value in kwargs.items(): + self.unit = key + self.value = value + + for base, conv in Furlong.conversion_table.items(): + func_name, conv_value = Furlong.conversion_table[base] + func_name = "as" + func_name.title() + setattr(self, func_name, self._make_convertor( conv_value )) + + def _make_convertor(self, conv_value): + def _convertor(): + return self.value * conv_value + + return _convertor \ No newline at end of file

adamgilman/furlong

42e6917523242f349a9b825bf0a91f1643856645

diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/tests_fobject.py b/tests/tests_fobject.py new file mode 100644 index 0000000..4196907 --- /dev/null +++ b/tests/tests_fobject.py @@ -0,0 +1,17 @@ +import unittest +from furlong import Furlong as f + +class TestSimpleConversionTests(unittest.TestCase): + def test_fixed_conversion_test(self): + self.assertEqual( f(inches=12).asCentimeters(), 30.48 ) + + +class TestDyanmicFunctionNaming(unittest.TestCase): + def test_dyanmic_function_exists(self): + test_conv = { + 'testbase' : ('testconv', -1111), + } + f.conversion_table.update( test_conv ) + self.assertIsInstance( f(testbase=1), f ) + self.assertTrue( callable( f(testbase=1).asTestconv ) ) + self.assertEqual( f(testbase=2).asTestconv(), -2222 ) \ No newline at end of file

Provide a simple interface for unit conversions Declare a unit type ``` length = f(inches=12) length.asCentimeters() 30.48 ``` Simple and extensible

0.0

42e6917523242f349a9b825bf0a91f1643856645

[ "tests/tests_fobject.py::TestSimpleConversionTests::test_fixed_conversion_test", "tests/tests_fobject.py::TestDyanmicFunctionNaming::test_dyanmic_function_exists" ]

[]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_added_files" ], "has_test_patch": true, "is_lite": false }

2018-07-14 09:55:52+00:00

mit

900

adamjstewart__fiscalyear-5

diff --git a/.travis.yml b/.travis.yml index f829e95..416d131 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,13 +1,15 @@ language: python +dist: xenial + python: - - 2.6 - 2.7 - - 3.3 - 3.4 - 3.5 - 3.6 + - 3.7 + - 3.8-dev -script: py.test --cov=fiscalyear +script: pytest --cov=fiscalyear after_success: codecov diff --git a/LICENSE b/LICENSE index 247c0b8..f2c31c2 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2017 Adam J. Stewart +Copyright (c) 2017-2019 Adam J. Stewart Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.rst b/README.rst index b7d0874..30cf856 100644 --- a/README.rst +++ b/README.rst @@ -7,6 +7,12 @@ .. image:: https://readthedocs.org/projects/fiscalyear/badge/?version=latest :target: https://fiscalyear.readthedocs.io +.. image:: https://badge.fury.io/py/fiscalyear.svg + :target: https://pypi.org/project/fiscalyear/ + +.. image:: https://anaconda.org/conda-forge/fiscalyear/badges/version.svg + :target: https://anaconda.org/conda-forge/fiscalyear + Overview ======== diff --git a/docs/installation.rst b/docs/installation.rst index 8355ecf..41a9b4c 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -17,6 +17,16 @@ The recommended way to install ``fiscalyear`` is with ``pip``. The fiscalyear module will now appear with your base Python installation. +Anaconda +-------- + +You can also install ``fiscalyear`` with the ``conda`` package manager. + +.. code-block:: console + + $ conda install -c conda-forge fiscalyear + + Spack ----- diff --git a/fiscalyear.py b/fiscalyear.py index c6f8ddc..f3a7640 100644 --- a/fiscalyear.py +++ b/fiscalyear.py @@ -24,10 +24,41 @@ START_MONTH = 10 START_DAY = 1 +def _validate_fiscal_calendar_params(start_year, start_month, start_day): + """Raise an Exception if the calendar parameters are invalid. + + :param start_year: Relationship between the start of the fiscal year and + the calendar year. Possible values: ``'previous'`` or ``'same'``. + :type start_year: str + :param start_month: The first month of the fiscal year + :type start_month: int or str + :param start_day: The first day of the first month of the fiscal year + :type start_day: int or str + :raises TypeError: If ``start_year`` is not a ``str``. + :raises ValueError: If ``start_year`` is not ``'previous'`` or ``'same'`` + :raises ValueError: If ``start_month`` or ``start_day`` is not an int or + int-like string + :raises ValueError: If ``start_month`` or ``start_day`` is out of range + """ + if not isinstance(start_year, str): + raise TypeError("'start_year' must be a 'str', not: '%s'" % type(str)) + if start_year not in ('previous', 'same'): + msg = "'start_year' must be either 'previous' or 'same', not: '%s'" + raise ValueError(msg % start_year) + _check_day(start_month, start_day) + + +def setup_fiscal_calendar(start_year, start_month, start_day): + """Change the global calendar settings.""" + _validate_fiscal_calendar_params(start_year, start_month, start_day) + global START_YEAR, START_MONTH, START_DAY + START_YEAR = start_year + START_MONTH = start_month + START_DAY = start_day + + @contextlib.contextmanager -def fiscal_calendar(start_year=None, - start_month=None, - start_day=None): +def fiscal_calendar(start_year=None, start_month=None, start_day=None): """A context manager that lets you modify the start of the fiscal calendar inside the scope of a with-statement. @@ -38,43 +69,22 @@ def fiscal_calendar(start_year=None, :type start_month: int or str :param start_day: The first day of the first month of the fiscal year :type start_day: int or str - :raises AssertionError: If ``start_year`` is not ``'previous'`` or ``'same'`` - :raises TypeError: If ``start_month`` or ``start_day`` is not an int or int-like string + :raises ValueError: If ``start_year`` is not ``'previous'`` or ``'same'`` + :raises TypeError: If ``start_month`` or ``start_day`` is not an int or + int-like string :raises ValueError: If ``start_month`` or ``start_day`` is out of range """ - global START_YEAR - global START_MONTH - global START_DAY - - # Use default values if not changed - if start_year is None: - start_year = START_YEAR - if start_month is None: - start_month = START_MONTH - if start_day is None: - start_day = START_DAY - - assert isinstance(start_year, str) - assert start_year == 'previous' or start_year == 'same' - start_month = _check_month(start_month) - start_day = _check_day(start_month, start_day) - - # Backup previous values - old_start_year = START_YEAR - old_start_month = START_MONTH - old_start_day = START_DAY + # If arguments are omitted, use the currently active values. + start_year = START_YEAR if start_year is None else start_year + start_month = START_MONTH if start_month is None else start_month + start_day = START_DAY if start_day is None else start_day # Temporarily change global variables - START_YEAR = start_year - START_MONTH = start_month - START_DAY = start_day - + previous_values = (START_YEAR, START_MONTH, START_DAY) + setup_fiscal_calendar(start_year, start_month, start_day) yield - # Restore previous values - START_YEAR = old_start_year - START_MONTH = old_start_month - START_DAY = old_start_day + setup_fiscal_calendar(*previous_values) def _check_int(value): @@ -225,11 +235,9 @@ class FiscalYear(object): return self == item elif isinstance(item, FiscalQuarter): return self._fiscal_year == item.fiscal_year - elif (isinstance(item, FiscalDateTime) or - isinstance(item, datetime.datetime)): + elif isinstance(item, datetime.datetime): return self.start <= item <= self.end - elif (isinstance(item, FiscalDate) or - isinstance(item, datetime.date)): + elif isinstance(item, datetime.date): return self.start.date() <= item <= self.end.date() else: raise TypeError("can't compare '%s' to '%s'" % ( @@ -405,11 +413,9 @@ class FiscalQuarter(object): """ if isinstance(item, FiscalQuarter): return self == item - elif (isinstance(item, FiscalDateTime) or - isinstance(item, datetime.datetime)): + elif isinstance(item, datetime.datetime): return self.start <= item <= self.end - elif (isinstance(item, FiscalDate) or - isinstance(item, datetime.date)): + elif isinstance(item, datetime.date): return self.start.date() <= item <= self.end.date() else: raise TypeError("can't compare '%s' to '%s'" % ( diff --git a/setup.cfg b/setup.cfg index 4bca33d..d928416 100644 --- a/setup.cfg +++ b/setup.cfg @@ -4,3 +4,6 @@ test=pytest [build_sphinx] source-dir=docs build-dir=docs/_build + +[metadata] +license-file = LICENSE diff --git a/setup.py b/setup.py index 7939d81..05153b5 100755 --- a/setup.py +++ b/setup.py @@ -42,6 +42,8 @@ setuptools.setup( 'Programming Language :: Python :: 3.4', 'Programming Language :: Python :: 3.5', 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', + 'Programming Language :: Python :: 3.8', # Type of package 'Topic :: Office/Business :: Financial :: Accounting',

adamjstewart/fiscalyear

77c5c0c82a62de36e77284e924f744bb1e770a31

diff --git a/test_fiscalyear.py b/test_fiscalyear.py index 690835f..5b2779f 100644 --- a/test_fiscalyear.py +++ b/test_fiscalyear.py @@ -9,8 +9,143 @@ import pytest US_FEDERAL = ('previous', 10, 1) UK_PERSONAL = ('same', 4, 6) -# Default to U.S. -fiscalyear.START_YEAR, fiscalyear.START_MONTH, fiscalyear.START_DAY = US_FEDERAL + +class TestCheckInt(object): + @pytest.mark.parametrize("value, exception", [ + ('asdf', TypeError), + ("-999", TypeError), + # Technically speaking, _check_int should accept negative integers + # but this isn't a public function + datetime doesn't handle them + # anyway. + (float(), TypeError), + (object(), TypeError), + ]) + def test_invalid_input(self, value, exception): + with pytest.raises(exception): + fiscalyear._check_int(value) + + @pytest.mark.parametrize("value", [1, 2, 0, -1, -2, "1", "0", "999"]) + def test_valid_input(self, value): + assert int(value) == fiscalyear._check_int(value) + + +class TestCheckYear(object): + @pytest.mark.parametrize("value, exception", [ + ('asdf', TypeError), + (float(), TypeError), + (object(), TypeError), + ("-1", TypeError), + (-1, ValueError), + (0, ValueError), + ("0", ValueError), + (10000, ValueError), + ("10000", ValueError), + ]) + def test_invalid_input(self, value, exception): + with pytest.raises(exception): + fiscalyear._check_year(value) + + @pytest.mark.parametrize("value", [1, 2, "1", "999"]) + def test_valid_input(self, value): + assert int(value) == fiscalyear._check_year(value) + + +class TestCheckDay(object): + @pytest.mark.parametrize("month, day, exception", [ + (1, 'asdf', TypeError), + (1, "-999", TypeError), + (1, float(), TypeError), + (1, object(), TypeError), + (1, -1, ValueError), + (1, "-1", TypeError), + (1, 0, ValueError), + (1, "0", ValueError), + (1, 32, ValueError), + (1, 32, ValueError), + ]) + def test_invalid_input(self, month, day, exception): + with pytest.raises(exception): + fiscalyear._check_day(month, day) + + @pytest.mark.parametrize("month, day", [(1, 1), (1, 2), (1, "1"), (1, 31), (1, "31")]) + def test_valid_input(self, month, day): + assert int(day) == fiscalyear._check_day(month, day) + + +class TestCheckQuarter(object): + @pytest.mark.parametrize("value, exception", [ + ('asdf', TypeError), + (float(), TypeError), + (object(), TypeError), + ("-1", TypeError), + (-1, ValueError), + (0, ValueError), + ("0", ValueError), + (5, ValueError), + ("5", ValueError), + ]) + def test_invalid_input(self, value, exception): + with pytest.raises(exception): + fiscalyear._check_quarter(value) + + @pytest.mark.parametrize("value", [1, 2, "1", "4"]) + def test_valid_input(self, value): + assert int(value) == fiscalyear._check_quarter(value) + + +class TestCalendarSettingsValidator(object): + @pytest.mark.parametrize("arguments, exception", [ + (dict(start_year='asdf', start_month=12, start_day=1), ValueError), + (dict(start_year=float(1999), start_month=12, start_day=1), TypeError), + (dict(start_year=object(), start_month=12, start_day=1), TypeError), + + (dict(start_year='same', start_month='asdf', start_day=1), TypeError), + (dict(start_year='same', start_month=float(12), start_day=1), TypeError), + (dict(start_year='same', start_month=object(), start_day=1), TypeError), + (dict(start_year='same', start_month=-1, start_day=1), ValueError), + (dict(start_year='same', start_month=0, start_day=1), ValueError), + (dict(start_year='same', start_month=13, start_day=1), ValueError), + + (dict(start_year='same', start_month=12, start_day='asdf'), TypeError), + (dict(start_year='same', start_month=12, start_day=float(1)), TypeError), + (dict(start_year='same', start_month=12, start_day=object()), TypeError), + (dict(start_year='same', start_month=12, start_day=0), ValueError), + (dict(start_year='same', start_month=12, start_day=-1), ValueError), + (dict(start_year='same', start_month=12, start_day=32), ValueError), + ]) + def test_invalid_input(self, arguments, exception): + with pytest.raises(exception): + fiscalyear._validate_fiscal_calendar_params(**arguments) + + @pytest.mark.parametrize("arguments", [ + dict(start_year='same', start_month=1, start_day=1), + dict(start_year='same', start_month=1, start_day=31), + dict(start_year='same', start_month=12, start_day=1), + dict(start_year='previous', start_month=1, start_day=1), + dict(start_year='previous', start_month=1, start_day=31), + dict(start_year='previous', start_month=12, start_day=1), + ]) + def test_valid_input(self, arguments): + fiscalyear._validate_fiscal_calendar_params(**arguments) + + +class TestSetupFiscalCalendar(object): + + def test_setup_fiscal_calendar(self): + # Test defaults + day = fiscalyear.FiscalDate(2017, 12, 1) + assert day.fiscal_year == 2018 + assert day.quarter == 1 + + # Change fiscal year settings + fiscalyear.setup_fiscal_calendar("same", 1, 1) + assert day.fiscal_year == 2017 + assert day.quarter == 4 + + # Restore defaults and re-test + fiscalyear.setup_fiscal_calendar("previous", 10, 1) + assert day.fiscal_year == 2018 + assert day.quarter == 1 class TestFiscalCalendar: @@ -86,6 +221,10 @@ class TestFiscalCalendar: assert fiscalyear.START_DAY == 1 def test_wrong_type(self): + with pytest.raises(TypeError): + with fiscalyear.fiscal_calendar(start_year=6.5): + pass + with pytest.raises(TypeError): with fiscalyear.fiscal_calendar(start_month=6.5): pass

Add a function for easily changing the global "START_*" parameters I think it would make sense to have a function that would make changing the global parameters easier. E.g. ``` python def setup_fiscal_year(start_year, start_month, start_day): global START_YEAR, START_MONTH, START_DAY START_YEAR = start_year START_MONTH = start_month START_DAY = start_day def test_setup_fiscal_year(): # test defaults day = fiscalyear.FiscalDate(2017, 12, 1) assert day.fiscal_year == 2018 assert day.quarter == 1 # change fiscal year settings fiscalyear.setup_fiscal_year("same", 1, 1) assert day.fiscal_year == 2017 assert day.quarter == 4 # restore defaults and re-test fiscalyear.setup_fiscal_year("previous", 10, 1) assert day.fiscal_year == 2018 assert day.quarter == 1 ``` This could also make it possible to change the Fiscal Year settings even if you don't import the whole module. E.g. ``` python In [4]: from fiscalyear import FiscalQuarter, setup_fiscal_year In [5]: quarter = FiscalQuarter(2018, 1) In [6]: quarter.start Out[6]: FiscalDateTime(2017, 10, 1, 0, 0) In [7]: setup_fiscal_year('same', 1, 1) In [8]: quarter.start Out[8]: FiscalDateTime(2018, 1, 1, 0, 0) ```

0.0

77c5c0c82a62de36e77284e924f744bb1e770a31

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"test_fiscalyear.py::TestFiscalCalendar::test_out_of_range", "test_fiscalyear.py::TestFiscalYear::test_basic", "test_fiscalyear.py::TestFiscalYear::test_repr", "test_fiscalyear.py::TestFiscalYear::test_str", "test_fiscalyear.py::TestFiscalYear::test_from_string", "test_fiscalyear.py::TestFiscalYear::test_wrong_type", "test_fiscalyear.py::TestFiscalYear::test_out_of_range", "test_fiscalyear.py::TestFiscalYear::test_prev_fiscal_year", "test_fiscalyear.py::TestFiscalYear::test_next_fiscal_year", "test_fiscalyear.py::TestFiscalYear::test_start", "test_fiscalyear.py::TestFiscalYear::test_end", "test_fiscalyear.py::TestFiscalYear::test_q1", "test_fiscalyear.py::TestFiscalYear::test_q2", "test_fiscalyear.py::TestFiscalYear::test_q3", "test_fiscalyear.py::TestFiscalYear::test_q4", "test_fiscalyear.py::TestFiscalYear::test_contains", "test_fiscalyear.py::TestFiscalYear::test_less_than", "test_fiscalyear.py::TestFiscalYear::test_less_than_equals", "test_fiscalyear.py::TestFiscalYear::test_equals", "test_fiscalyear.py::TestFiscalYear::test_not_equals", "test_fiscalyear.py::TestFiscalYear::test_greater_than", "test_fiscalyear.py::TestFiscalYear::test_greater_than_equals", "test_fiscalyear.py::TestFiscalQuarter::test_basic", "test_fiscalyear.py::TestFiscalQuarter::test_repr", "test_fiscalyear.py::TestFiscalQuarter::test_str", "test_fiscalyear.py::TestFiscalQuarter::test_from_string", "test_fiscalyear.py::TestFiscalQuarter::test_wrong_type", "test_fiscalyear.py::TestFiscalQuarter::test_out_of_range", "test_fiscalyear.py::TestFiscalQuarter::test_prev_quarter", "test_fiscalyear.py::TestFiscalQuarter::test_next_quarter", "test_fiscalyear.py::TestFiscalQuarter::test_start", "test_fiscalyear.py::TestFiscalQuarter::test_end", "test_fiscalyear.py::TestFiscalQuarter::test_bad_start_year", "test_fiscalyear.py::TestFiscalQuarter::test_q1_start", "test_fiscalyear.py::TestFiscalQuarter::test_q1_end", "test_fiscalyear.py::TestFiscalQuarter::test_q2_start", "test_fiscalyear.py::TestFiscalQuarter::test_q2_end", "test_fiscalyear.py::TestFiscalQuarter::test_q3_start", "test_fiscalyear.py::TestFiscalQuarter::test_q3_end", "test_fiscalyear.py::TestFiscalQuarter::test_q4_start", "test_fiscalyear.py::TestFiscalQuarter::test_q4_end", "test_fiscalyear.py::TestFiscalQuarter::test_contains", "test_fiscalyear.py::TestFiscalQuarter::test_less_than", "test_fiscalyear.py::TestFiscalQuarter::test_less_than_equals", "test_fiscalyear.py::TestFiscalQuarter::test_equals", "test_fiscalyear.py::TestFiscalQuarter::test_not_equals", "test_fiscalyear.py::TestFiscalQuarter::test_greater_than", "test_fiscalyear.py::TestFiscalQuarter::test_greater_than_equals", "test_fiscalyear.py::TestFiscalDate::test_basic", "test_fiscalyear.py::TestFiscalDate::test_fiscal_year", "test_fiscalyear.py::TestFiscalDate::test_prev_fiscal_year", "test_fiscalyear.py::TestFiscalDate::test_next_fiscal_year", "test_fiscalyear.py::TestFiscalDate::test_prev_quarter", "test_fiscalyear.py::TestFiscalDate::test_next_quarter", "test_fiscalyear.py::TestFiscalDateTime::test_basic", "test_fiscalyear.py::TestFiscalDateTime::test_fiscal_year", "test_fiscalyear.py::TestFiscalDateTime::test_prev_fiscal_year", "test_fiscalyear.py::TestFiscalDateTime::test_next_fiscal_year", "test_fiscalyear.py::TestFiscalDateTime::test_prev_quarter", "test_fiscalyear.py::TestFiscalDateTime::test_next_quarter" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2018-02-08 16:57:16+00:00

mit

901

adamjstewart__fiscalyear-9

diff --git a/fiscalyear.py b/fiscalyear.py index 661c703..d4a569f 100644 --- a/fiscalyear.py +++ b/fiscalyear.py @@ -530,7 +530,12 @@ class FiscalQuarter(object): if month < START_MONTH: year += 1 - return FiscalDateTime(year, month, START_DAY, 0, 0, 0) + # Find the last day of the month + # If START_DAY is later, choose last day of month instead + max_day = calendar.monthrange(year, month)[1] + day = min(START_DAY, max_day) + + return FiscalDateTime(year, month, day, 0, 0, 0) @property def end(self):

adamjstewart/fiscalyear

a59cde7a881a85c5a65e523623e23668c2cb991c

diff --git a/test_fiscalyear.py b/test_fiscalyear.py index 2395737..f80953c 100644 --- a/test_fiscalyear.py +++ b/test_fiscalyear.py @@ -275,6 +275,35 @@ class TestFiscalCalendar: with fiscalyear.fiscal_calendar(start_month=2, start_day=29): pass + def test_corner_cases(self): + # start_day does not exist in all months + with fiscalyear.fiscal_calendar(start_month=5, start_day=31): + # Non-leap year + assert fiscalyear.FiscalQuarter(2019, 1).start.day == 31 + assert fiscalyear.FiscalQuarter(2019, 1).end.day == 30 + + assert fiscalyear.FiscalQuarter(2019, 2).start.day == 31 + assert fiscalyear.FiscalQuarter(2019, 2).end.day == 29 + + assert fiscalyear.FiscalQuarter(2019, 3).start.day == 30 + assert fiscalyear.FiscalQuarter(2019, 3).end.day == 27 + + assert fiscalyear.FiscalQuarter(2019, 4).start.day == 28 + assert fiscalyear.FiscalQuarter(2019, 4).end.day == 30 + + # Leap year + assert fiscalyear.FiscalQuarter(2020, 1).start.day == 31 + assert fiscalyear.FiscalQuarter(2020, 1).end.day == 30 + + assert fiscalyear.FiscalQuarter(2020, 2).start.day == 31 + assert fiscalyear.FiscalQuarter(2020, 2).end.day == 29 + + assert fiscalyear.FiscalQuarter(2020, 3).start.day == 30 + assert fiscalyear.FiscalQuarter(2020, 3).end.day == 28 + + assert fiscalyear.FiscalQuarter(2020, 4).start.day == 29 + assert fiscalyear.FiscalQuarter(2020, 4).end.day == 30 + class TestFiscalYear:

FiscalCalendar starting on 31st day of the month throws ValueError If the `FiscalCalendar` starts on the 31st of any month with 31 days, then `FiscalDate().quarter` throws a `ValueError`. Example code: ```python from fiscalyear import FiscalDate, FiscalYear, fiscal_calendar with fiscal_calendar(start_month=12, start_day=31): fiscal_date = FiscalDate(2019, 10, 22) fiscal_date.quarter ``` Traceback: ``` Traceback (most recent call last): File "<input>", line 3, in <module> File "/site-packages/fiscalyear.py", line 594, in quarter if self in q: File "/site-packages/fiscalyear.py", line 413, in __contains__ return self.start.date() <= item <= self.end.date() File "/site-packages/fiscalyear.py", line 493, in end next_start = self.next_quarter.start File "/site-packages/fiscalyear.py", line 485, in start return FiscalDateTime(year, month, START_DAY, 0, 0, 0) ValueError: day is out of range for month ``` The quarters generated are: * December 31st * March 31st * June 31st ← Not a valid day, so it breaks.

0.0

a59cde7a881a85c5a65e523623e23668c2cb991c

[ "test_fiscalyear.py::TestFiscalCalendar::test_corner_cases", "test_fiscalyear.py::TestFiscalQuarter::test_current", "test_fiscalyear.py::TestFiscalQuarter::test_start", "test_fiscalyear.py::TestFiscalQuarter::test_end", "test_fiscalyear.py::TestFiscalQuarter::test_contains", "test_fiscalyear.py::TestFiscalDate::test_basic", "test_fiscalyear.py::TestFiscalDate::test_prev_fiscal_year", "test_fiscalyear.py::TestFiscalDate::test_next_fiscal_year", "test_fiscalyear.py::TestFiscalDate::test_prev_quarter", "test_fiscalyear.py::TestFiscalDate::test_next_quarter", "test_fiscalyear.py::TestFiscalDateTime::test_basic", "test_fiscalyear.py::TestFiscalDateTime::test_prev_fiscal_year", "test_fiscalyear.py::TestFiscalDateTime::test_next_fiscal_year", "test_fiscalyear.py::TestFiscalDateTime::test_prev_quarter", "test_fiscalyear.py::TestFiscalDateTime::test_next_quarter" ]

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"test_fiscalyear.py::TestCheckYear::test_invalid_input[-1-TypeError]", "test_fiscalyear.py::TestCheckYear::test_invalid_input[-1-ValueError]", "test_fiscalyear.py::TestCheckYear::test_invalid_input[0-ValueError0]", "test_fiscalyear.py::TestCheckYear::test_invalid_input[0-ValueError1]", "test_fiscalyear.py::TestCheckYear::test_invalid_input[10000-ValueError0]", "test_fiscalyear.py::TestCheckYear::test_invalid_input[10000-ValueError1]", "test_fiscalyear.py::TestCheckYear::test_valid_input[1_0]", "test_fiscalyear.py::TestCheckYear::test_valid_input[2]", "test_fiscalyear.py::TestCheckYear::test_valid_input[1_1]", "test_fiscalyear.py::TestCheckYear::test_valid_input[999]", "test_fiscalyear.py::TestCheckDay::test_invalid_input[1-asdf-TypeError]", "test_fiscalyear.py::TestCheckDay::test_invalid_input[1--999-TypeError]", "test_fiscalyear.py::TestCheckDay::test_invalid_input[1-0.0-TypeError]", "test_fiscalyear.py::TestCheckDay::test_invalid_input[1-day3-TypeError]", "test_fiscalyear.py::TestCheckDay::test_invalid_input[1--1-ValueError]", "test_fiscalyear.py::TestCheckDay::test_invalid_input[1--1-TypeError]", "test_fiscalyear.py::TestCheckDay::test_invalid_input[1-0-ValueError0]", "test_fiscalyear.py::TestCheckDay::test_invalid_input[1-0-ValueError1]", "test_fiscalyear.py::TestCheckDay::test_invalid_input[1-32-ValueError0]", "test_fiscalyear.py::TestCheckDay::test_invalid_input[1-32-ValueError1]", "test_fiscalyear.py::TestCheckDay::test_valid_input[1-1_0]", "test_fiscalyear.py::TestCheckDay::test_valid_input[1-2]", "test_fiscalyear.py::TestCheckDay::test_valid_input[1-1_1]", "test_fiscalyear.py::TestCheckDay::test_valid_input[1-31_0]", "test_fiscalyear.py::TestCheckDay::test_valid_input[1-31_1]", "test_fiscalyear.py::TestCheckQuarter::test_invalid_input[asdf-TypeError]", "test_fiscalyear.py::TestCheckQuarter::test_invalid_input[0.0-TypeError]", "test_fiscalyear.py::TestCheckQuarter::test_invalid_input[value2-TypeError]", "test_fiscalyear.py::TestCheckQuarter::test_invalid_input[-1-TypeError]", "test_fiscalyear.py::TestCheckQuarter::test_invalid_input[-1-ValueError]", "test_fiscalyear.py::TestCheckQuarter::test_invalid_input[0-ValueError0]", "test_fiscalyear.py::TestCheckQuarter::test_invalid_input[0-ValueError1]", "test_fiscalyear.py::TestCheckQuarter::test_invalid_input[5-ValueError0]", "test_fiscalyear.py::TestCheckQuarter::test_invalid_input[5-ValueError1]", "test_fiscalyear.py::TestCheckQuarter::test_valid_input[1_0]", "test_fiscalyear.py::TestCheckQuarter::test_valid_input[2]", "test_fiscalyear.py::TestCheckQuarter::test_valid_input[1_1]", "test_fiscalyear.py::TestCheckQuarter::test_valid_input[4]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_invalid_input[arguments0-ValueError]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_invalid_input[arguments1-TypeError]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_invalid_input[arguments2-TypeError]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_invalid_input[arguments3-TypeError]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_invalid_input[arguments4-TypeError]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_invalid_input[arguments5-TypeError]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_invalid_input[arguments6-ValueError]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_invalid_input[arguments7-ValueError]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_invalid_input[arguments8-ValueError]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_invalid_input[arguments9-TypeError]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_invalid_input[arguments10-TypeError]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_invalid_input[arguments11-TypeError]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_invalid_input[arguments12-ValueError]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_invalid_input[arguments13-ValueError]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_invalid_input[arguments14-ValueError]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_valid_input[arguments0]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_valid_input[arguments1]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_valid_input[arguments2]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_valid_input[arguments3]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_valid_input[arguments4]", "test_fiscalyear.py::TestValidateFiscalCalendarParams::test_valid_input[arguments5]", "test_fiscalyear.py::TestSetupFiscalCalendar::test_start_year", "test_fiscalyear.py::TestSetupFiscalCalendar::test_start_month", "test_fiscalyear.py::TestSetupFiscalCalendar::test_start_day", "test_fiscalyear.py::TestSetupFiscalCalendar::test_complex", "test_fiscalyear.py::TestFiscalCalendar::test_start_year", "test_fiscalyear.py::TestFiscalCalendar::test_start_month", "test_fiscalyear.py::TestFiscalCalendar::test_start_day", "test_fiscalyear.py::TestFiscalCalendar::test_complex", "test_fiscalyear.py::TestFiscalCalendar::test_nested", "test_fiscalyear.py::TestFiscalCalendar::test_wrong_type", "test_fiscalyear.py::TestFiscalCalendar::test_out_of_range", "test_fiscalyear.py::TestFiscalYear::test_basic", "test_fiscalyear.py::TestFiscalYear::test_current", "test_fiscalyear.py::TestFiscalYear::test_repr", "test_fiscalyear.py::TestFiscalYear::test_str", "test_fiscalyear.py::TestFiscalYear::test_from_string", "test_fiscalyear.py::TestFiscalYear::test_wrong_type", "test_fiscalyear.py::TestFiscalYear::test_out_of_range", "test_fiscalyear.py::TestFiscalYear::test_prev_fiscal_year", "test_fiscalyear.py::TestFiscalYear::test_next_fiscal_year", "test_fiscalyear.py::TestFiscalYear::test_start", "test_fiscalyear.py::TestFiscalYear::test_end", "test_fiscalyear.py::TestFiscalYear::test_q1", "test_fiscalyear.py::TestFiscalYear::test_q2", "test_fiscalyear.py::TestFiscalYear::test_q3", "test_fiscalyear.py::TestFiscalYear::test_q4", "test_fiscalyear.py::TestFiscalYear::test_contains", "test_fiscalyear.py::TestFiscalYear::test_less_than", "test_fiscalyear.py::TestFiscalYear::test_less_than_equals", "test_fiscalyear.py::TestFiscalYear::test_equals", "test_fiscalyear.py::TestFiscalYear::test_not_equals", "test_fiscalyear.py::TestFiscalYear::test_greater_than", "test_fiscalyear.py::TestFiscalYear::test_greater_than_equals", "test_fiscalyear.py::TestFiscalQuarter::test_basic", "test_fiscalyear.py::TestFiscalQuarter::test_repr", "test_fiscalyear.py::TestFiscalQuarter::test_str", "test_fiscalyear.py::TestFiscalQuarter::test_from_string", "test_fiscalyear.py::TestFiscalQuarter::test_wrong_type", "test_fiscalyear.py::TestFiscalQuarter::test_out_of_range", "test_fiscalyear.py::TestFiscalQuarter::test_prev_quarter", "test_fiscalyear.py::TestFiscalQuarter::test_next_quarter", "test_fiscalyear.py::TestFiscalQuarter::test_bad_start_year", "test_fiscalyear.py::TestFiscalQuarter::test_q1_start", "test_fiscalyear.py::TestFiscalQuarter::test_q1_end", "test_fiscalyear.py::TestFiscalQuarter::test_q2_start", "test_fiscalyear.py::TestFiscalQuarter::test_q2_end", "test_fiscalyear.py::TestFiscalQuarter::test_q3_start", "test_fiscalyear.py::TestFiscalQuarter::test_q3_end", "test_fiscalyear.py::TestFiscalQuarter::test_q4_start", "test_fiscalyear.py::TestFiscalQuarter::test_q4_end", "test_fiscalyear.py::TestFiscalQuarter::test_less_than", "test_fiscalyear.py::TestFiscalQuarter::test_less_than_equals", "test_fiscalyear.py::TestFiscalQuarter::test_equals", "test_fiscalyear.py::TestFiscalQuarter::test_not_equals", "test_fiscalyear.py::TestFiscalQuarter::test_greater_than", "test_fiscalyear.py::TestFiscalQuarter::test_greater_than_equals", "test_fiscalyear.py::TestFiscalDate::test_fiscal_year", "test_fiscalyear.py::TestFiscalDateTime::test_fiscal_year" ]

{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }

2019-10-23 01:02:35+00:00

mit

902

adamlwgriffiths__Pyrr-88

diff --git a/CHANGELOG.md b/CHANGELOG.md index 9215a38..624dd4e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](http://keepachangelog.com/) and this project adheres to [Semantic Versioning](http://semver.org/). +## [0.10.3] - 2019-04-19 + +- Fix some of the plane.create_(xz,xy,yz) not inverting correctly. +- Fix incorrect distance in point_height_above_plane. + ## [0.10.2] - 2019-03-13 - Add MANIFEST.in and add /tests and /docs to source dist (#90) diff --git a/pyrr/plane.py b/pyrr/plane.py index 97e5b98..12d06e0 100755 --- a/pyrr/plane.py +++ b/pyrr/plane.py @@ -5,7 +5,8 @@ Planes are represented using a numpy.array of shape (4,). The values represent the plane equation using the values A,B,C,D. The first three values are the normal vector. -The fourth value is the distance of the plane from the origin, down the normal. +The fourth value is the distance of the origin from the plane, down the normal. +A negative value indicates the origin is behind the plane, relative to the normal. .. seealso: http://en.wikipedia.org/wiki/Plane_(geometry) .. seealso: http://mathworld.wolfram.com/Plane.html @@ -17,12 +18,15 @@ from .utils import all_parameters_as_numpy_arrays, parameters_as_numpy_arrays def create(normal=None, distance=0.0, dtype=None): - """Creates a plane that runs along the X,Y plane. + """Creates a plane oriented toward the normal, at distance below the origin. + If no normal is provided, the plane will by created at the origin with a normal + of [0, 0, 1]. - It crosses the origin with a normal of 0,0,1 (+Z). + Negative distance indicates the plane is facing toward the origin. :rtype: numpy.array - :return: A plane that runs along the X,Y plane. + :return: A plane with the specified normal at a distance from the origin of + -distance. """ if normal is None: normal = [0.0, 0.0, 1.0] @@ -75,37 +79,43 @@ def create_from_position(position, normal, dtype=None): normal. """ dtype = dtype or position.dtype - # -d = a * px + b * py + c * pz + # -d = a * x + b * y + c * z n = vector.normalize(normal) d = -np.sum(n * position) - return create(n, d, dtype) + return create(n, -d, dtype) def create_xy(invert=False, distance=0., dtype=None): """Create a plane on the XY plane, starting at the origin with +Z being the up vector. - The distance is the distance along the normal (-Z if inverted, otherwise +Z). + The plane is distance units along the Z axis. -Z if inverted. """ - invert = -1. if invert else 1. - return np.array([0., 0., 1. * invert, distance]) + pl = np.array([0., 0., 1., distance]) + if invert: + pl = invert_normal(pl) + return pl def create_xz(invert=False, distance=0., dtype=None): """Create a plane on the XZ plane, starting at the origin with +Y being the up vector. - The distance is the distance along the normal (-Y if inverted, otherwise +Y). + The plane is distance units along the Y axis. -Y if inverted. """ - invert = -1. if invert else 1. - return np.array([0., 1. * invert, 0., distance]) + pl = np.array([0., 1., 0., distance]) + if invert: + pl = invert_normal(pl) + return pl def create_yz(invert=False, distance=0., dtype=None): """Create a plane on the YZ plane, starting at the origin with +X being the up vector. - The distance is the distance along the normal (-X if inverted, otherwise +X). + The plane is distance units along the X axis. -X if inverted. """ - invert = -1. if invert else 1. - return np.array([1. * invert, 0., 0., distance]) + pl = np.array([1., 0., 0., distance]) + if invert: + pl = invert_normal(pl) + return pl def invert_normal(plane): """Flips the normal of the plane. @@ -127,7 +137,7 @@ def position(plane): :rtype: numpy.array :return: A valid position that lies on the plane. """ - return plane[:3] * plane[3] + return normal(plane) * distance(plane) def normal(plane): """Extracts the normal vector from a plane. @@ -137,3 +147,10 @@ def normal(plane): :return: The normal vector of the plane. """ return plane[:3].copy() + +def distance(plane): + """Distance the plane is from the origin along its the normal. + + Negative value indicates the plane is facing the origin. + """ + return plane[3] diff --git a/pyrr/version.py b/pyrr/version.py index cb94a70..a76b028 100755 --- a/pyrr/version.py +++ b/pyrr/version.py @@ -1,4 +1,5 @@ # -*- coding: utf-8 -*- # the version of software # this is used by the setup.py script -__version__ = '0.10.2' +__version__ = '0.10.3' +

adamlwgriffiths/Pyrr

530820191954abcb9c7c54602fe13ba16912ba48

diff --git a/pyrr/geometric_tests.py b/pyrr/geometric_tests.py index 2f60c2e..601e8f6 100755 --- a/pyrr/geometric_tests.py +++ b/pyrr/geometric_tests.py @@ -5,7 +5,7 @@ various forms data types. from __future__ import absolute_import, division, print_function import math import numpy as np -from . import rectangle, vector, vector3 +from . import rectangle, vector, vector3, plane from .utils import all_parameters_as_numpy_arrays, parameters_as_numpy_arrays, solve_quadratic_equation """ @@ -75,12 +75,12 @@ def point_intersect_rectangle(point, rect): return None return point -@parameters_as_numpy_arrays('ray', 'plane') -def ray_intersect_plane(ray, plane, front_only=False): +@parameters_as_numpy_arrays('ray', 'pl') +def ray_intersect_plane(ray, pl, front_only=False): """Calculates the intersection point of a ray and a plane. :param numpy.array ray: The ray to test for intersection. - :param numpy.array plane: The ray to test for intersection. + :param numpy.array pl: The plane to test for intersection. :param boolean front_only: Specifies if the ray should only hit the front of the plane. Collisions from the rear of the plane will be @@ -103,8 +103,8 @@ def ray_intersect_plane(ray, plane, front_only=False): if rd.n == 0, the ray is parallel to the plane. """ - p = plane[:3] * plane[3] - n = plane[:3] + p = plane.position(pl) + n = plane.normal(pl) rd_n = vector.dot(ray[1], n) if rd_n == 0.0: @@ -306,7 +306,7 @@ def ray_intersect_aabb(ray, aabb): return point @all_parameters_as_numpy_arrays -def point_height_above_plane(point, plane): +def point_height_above_plane(point, pl): """Calculates how high a point is above a plane. :param numpy.array point: The point to check. @@ -316,17 +316,17 @@ def point_height_above_plane(point, plane): negative if the point is behind the plane. """ """ - http://www.vitutor.com/geometry/distance/point_plane.html - d(P) = (AX + BY + CZ + D) / sqrt(A^2 + B^2 + C^2) - - Normal is unit length, so it's length is 1.0. - Therefore, we can ignore the division all together. - Just perform Pn . [XYZ1] + Because we store normalised normal, we can simply + use: n . (p - p0) + where: + n is the plane normal + p is the plane position + p0 is the point """ - return np.dot(plane, [point[0], point[1], point[2], 1.0]) + return vector.dot(plane.normal(pl), point - plane.position(pl)) @all_parameters_as_numpy_arrays -def point_closest_point_on_plane(point, plane): +def point_closest_point_on_plane(point, pl): """Calculates the point on a plane that is closest to a point. :param numpy.array point: The point to check with. @@ -343,8 +343,8 @@ def point_closest_point_on_plane(point, plane): d is the value of normal dot position n is the plane normal """ - n = plane[:3] - p = n * plane[3] + n = plane.normal(pl) + p = n * plane.distance(pl) d = np.dot(p, n) qn = np.dot(point, n) return point + (n * (d - qn)) diff --git a/tests/test_geometric_tests.py b/tests/test_geometric_tests.py index c982b12..0d52e3e 100644 --- a/tests/test_geometric_tests.py +++ b/tests/test_geometric_tests.py @@ -204,6 +204,15 @@ class test_geometric_tests(unittest.TestCase): self.assertEqual(result, None) def test_point_height_above_plane(self): + pl = plane.create([0., 1., 0.], 1.) + p = np.array([0., 1., 0.]) + result = gt.point_height_above_plane(p, pl) + self.assertEqual(result, 0.) + + p = np.array([0., 0., 0.]) + result = gt.point_height_above_plane(p, pl) + self.assertEqual(result, -1.) + v1 = np.array([ 0.0, 0.0, 1.0]) v2 = np.array([ 1.0, 0.0, 1.0]) v3 = np.array([ 0.0, 1.0, 1.0]) @@ -215,6 +224,11 @@ class test_geometric_tests(unittest.TestCase): result = gt.point_height_above_plane(p, pl) self.assertEqual(result, 19.) + pl = plane.create_xz(distance=5.) + p = np.array([0., 5., 0.]) + h = gt.point_height_above_plane(p, pl) + self.assertEqual(h, 0.) + def test_point_closest_point_on_plane(self): pl = np.array([ 0.0, 1.0, 0.0, 0.0]) p = np.array([ 5.0, 20.0, 5.0]) @@ -300,4 +314,3 @@ class test_geometric_tests(unittest.TestCase): if __name__ == '__main__': unittest.main() - diff --git a/tests/test_plane.py b/tests/test_plane.py index 79fa8b8..0cb7ba6 100644 --- a/tests/test_plane.py +++ b/tests/test_plane.py @@ -3,7 +3,7 @@ try: except: import unittest import numpy as np -from pyrr import plane +from pyrr import plane, vector class test_plane(unittest.TestCase): def test_import(self): @@ -15,18 +15,26 @@ class test_plane(unittest.TestCase): result = plane.create() self.assertTrue(np.allclose(result, [0,0,1,0])) - def test_create_2(self): result = plane.create([1.,0.,0.], 5.) self.assertTrue(np.allclose(result, [1.,0.,0.,5.])) def test_create_from_points(self): - vecs = np.array([ - [ 1.0, 0.0, 0.0 ], - [ 0.0, 1.0, 0.0 ], - [ 1.0, 1.0, 0.0 ] - ]) - result = plane.create_from_points(*vecs) + result = plane.create_from_points( + [1., 0., 0.], + [0., 1., 0.], + [1., 1., 0.], + ) self.assertTrue(np.allclose(result, [0.,0.,1.,0.])) + self.assertTrue(np.allclose(plane.position(result), [0., 0., 0.])) + + result = plane.create_from_points( + [1., 1., 0.], + [1., 1., 1.], + [0., 1., 1.], + ) + expected = plane.create([0.,1.,0.], 1.) + self.assertTrue(np.allclose(result, expected)) + self.assertTrue(np.allclose(plane.position(result), [0., 1., 0.])) def test_create_from_position(self): position = np.array([1.0, 0.0, 0.0]) @@ -34,29 +42,42 @@ class test_plane(unittest.TestCase): result = plane.create_from_position(position, normal) self.assertTrue(np.allclose(result, [0., 1., 0., 0.])) + p0 = position + [1., 0., 0.] + p = position + n = vector.normalise(normal) + coplanar = p - p0 + self.assertEqual(np.sum(n * coplanar), 0.) + def test_create_xy(self): result = plane.create_xy() self.assertTrue(np.allclose(result, [0., 0., 1., 0.])) - def test_create_xy_invert_distance(self): + result = plane.create_xy(distance=2.) + self.assertTrue(np.allclose(result, [0., 0., 1., 2.])) + result = plane.create_xy(invert=True, distance=2.) - self.assertTrue(np.allclose(result, [0., 0., -1., 2.])) + self.assertTrue(np.allclose(result, [0., 0., -1., -2.])) def test_create_xz(self): result = plane.create_xz() self.assertTrue(np.allclose(result, [0., 1., 0., 0.])) - def test_create_xz_invert_distance(self): + result = plane.create_xz(distance=2.) + self.assertTrue(np.allclose(result, [0., 1., 0., 2.])) + result = plane.create_xz(invert=True, distance=2.) - self.assertTrue(np.allclose(result, [0., -1., 0., 2.])) + self.assertTrue(np.allclose(result, [0., -1., 0., -2.])) def test_create_yz(self): result = plane.create_yz() self.assertTrue(np.allclose(result, [1., 0., 0., 0.])) - def test_create_yz_invert_distance(self): + result = plane.create_yz(distance=2.) + self.assertTrue(np.allclose(result, [1., 0., 0., 2.])) + result = plane.create_yz(invert=True, distance=2.) - self.assertTrue(np.allclose(result, [-1., 0., 0., 2.])) + print(result) + self.assertTrue(np.allclose(result, [-1., 0., 0., -2.])) def test_invert_normal(self): p = np.array([1.0, 0.0, 0.0, 1.0]) @@ -64,9 +85,12 @@ class test_plane(unittest.TestCase): self.assertTrue(np.allclose(result, [-1.0, 0.0, 0.0, -1.0])) def test_position(self): - p = plane.create_xz(distance=5.) + p = plane.create_xz(distance=-5.) result = plane.position(p) - self.assertTrue(np.allclose(result, [0.,5.,0.])) + self.assertTrue(np.allclose(result, [0.,-5.,0.])) + + p = plane.create_from_position(position=[0., 0., 1.], normal=[0., 0., 1.]) + self.assertTrue(np.allclose(plane.position(p), [0., 0., 1.])) def test_normal(self): p = plane.create_xz(distance=5.) @@ -75,4 +99,3 @@ class test_plane(unittest.TestCase): if __name__ == '__main__': unittest.main() -

Inconsitent Position / Distance to plane Thank you for this useful Library. There is some unexpected behavior for planes concerning the sign of the distance: Take for example the following Plane: ``` plane = pyrr.plane.create_from_position(position=[0, 0, 1], normal=[0, 0, 1]) ``` which returns the expected plane: `array([ 0, 0, 1, -1])`. However `pyrr.plane.position(plane)` returns `array([ 0, 0, -1])`, instead of `[0, 0, 1]` A related issue can be observed when calculating the distance of a point calculated to lie on the plane, which should therefore be 0: ```pyrr.geometric_tests.point_height_above_plane(pyrr.geometric_tests.point_closest_point_on_plane([0, 0, 1], plane), plane)``` but returns -2

0.0

530820191954abcb9c7c54602fe13ba16912ba48

[ "tests/test_geometric_tests.py::test_geometric_tests::test_point_closest_point_on_plane", "tests/test_geometric_tests.py::test_geometric_tests::test_point_height_above_plane", "tests/test_plane.py::test_plane::test_create_from_points", "tests/test_plane.py::test_plane::test_create_xy", "tests/test_plane.py::test_plane::test_create_xz", "tests/test_plane.py::test_plane::test_create_yz", "tests/test_plane.py::test_plane::test_position" ]

[ "tests/test_geometric_tests.py::test_geometric_tests::test_import", "tests/test_geometric_tests.py::test_geometric_tests::test_point_closest_point_on_line", "tests/test_geometric_tests.py::test_geometric_tests::test_point_closest_point_on_line_2", "tests/test_geometric_tests.py::test_geometric_tests::test_point_closest_point_on_line_segment", "tests/test_geometric_tests.py::test_geometric_tests::test_point_closest_point_on_ray", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_line", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_line_invalid", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_line_segment", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_line_segment_invalid", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_rectangle_invalid_intersections_1", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_rectangle_invalid_intersections_2", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_rectangle_invalid_intersections_3", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_rectangle_valid_intersections_1", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_rectangle_valid_intersections_2", "tests/test_geometric_tests.py::test_geometric_tests::test_point_intersect_rectangle_valid_intersections_3", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_coincident_ray", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_coincident_ray_2", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_coincident_ray_3", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_aabb_invalid_1", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_aabb_valid_1", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_aabb_valid_2", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_aabb_valid_3", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_plane", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_plane_front_only", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_plane_invalid", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_sphere_no_solution_1", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_intersect_sphere_no_solution_2", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_parallel_ray", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_parallel_ray_2", "tests/test_geometric_tests.py::test_geometric_tests::test_ray_parallel_ray_3", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_does_intersect_sphere_1", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_does_intersect_sphere_2", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_does_intersect_sphere_3", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_does_intersect_sphere_4", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_penetration_sphere_1", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_penetration_sphere_2", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_penetration_sphere_3", "tests/test_geometric_tests.py::test_geometric_tests::test_sphere_penetration_sphere_4", "tests/test_geometric_tests.py::test_geometric_tests::test_vector_parallel_vector", "tests/test_geometric_tests.py::test_geometric_tests::test_vector_parallel_vector_invalid", "tests/test_plane.py::test_plane::test_create", "tests/test_plane.py::test_plane::test_create_from_position", "tests/test_plane.py::test_plane::test_import", "tests/test_plane.py::test_plane::test_invert_normal", "tests/test_plane.py::test_plane::test_normal" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2019-02-06 12:26:02+00:00

bsd-3-clause

903

adbar__simplemma-114

diff --git a/simplemma/language_detector.py b/simplemma/language_detector.py index 52369a6..f6fab14 100644 --- a/simplemma/language_detector.py +++ b/simplemma/language_detector.py @@ -198,14 +198,18 @@ class LanguageDetector: Returns: float: The proportion of text in the target language(s). """ - return sum( - percentage - for ( - lang_code, - percentage, - ) in self.proportion_in_each_language(text).items() - if lang_code != "unk" - ) + tokens = self._token_sampler.sample_text(text) + if len(tokens) == 0: + return 0 + + in_target = 0 + for token in tokens: + for lang_code in self._lang: + candidate = self._lemmatization_strategy.get_lemma(token, lang_code) + if candidate is not None: + in_target += 1 + break + return in_target / len(tokens) def main_language( self,

adbar/simplemma

fa1d96469ca601b5249b8d5cbb42c1474cfd83bb

diff --git a/tests/test_language_detector.py b/tests/test_language_detector.py index 4affdd1..ad68f0c 100644 --- a/tests/test_language_detector.py +++ b/tests/test_language_detector.py @@ -108,6 +108,15 @@ def test_in_target_language() -> None: == 1.0 ) + langs = ("en", "de") + text = "It was a true gift" + assert ( + LanguageDetector(lang=langs).proportion_in_target_languages(text) + == in_target_language(text, lang=langs) + == 1.0 + ) + in_target_language("It was a true gift", lang=("en", "de")) + def test_main_language(): text = "Dieser Satz ist auf Deutsch."

in_target_language can count words twice and return ratios above 1.0 I noticed that in current `main` version, the `in_target_language` function can return ratios above 1.0 when given more than one language and the words in the input are matching several languages. Example: >>> in_target_language('It was a true gift', lang='en') 1.0 >>> in_target_language('It was a true gift', lang='de') 0.6666666666666666 >>> in_target_language('It was a true gift', lang=('en','de')) 1.6666666666666665 Simplemma 0.9.1 doesn't have this problem: >>> in_target_language('It was a true gift', lang='en') 1.0 >>> in_target_language('It was a true gift', lang='de') 0.6666666666666666 >>> in_target_language('It was a true gift', lang=('en','de')) 1.0 It's not just a question of capping the scores at 1.0. The problem is that a single word can count more than once if it happens to match multiple languages. Below is an example that demonstrates the problem. I added nonsense words that don't match any language, but their presence is compensated by words that are counted twice. Current `main` version: >>> in_target_language('It was a true gift xxx yyy', lang=('en','de')) 1.0 Simplemma 0.9.1: >>> in_target_language('It was a true gift xxx yyy', lang=('en','de')) 0.6

0.0

fa1d96469ca601b5249b8d5cbb42c1474cfd83bb

[ "tests/test_language_detector.py::test_in_target_language" ]

[ "tests/test_language_detector.py::test_proportion_in_each_language", "tests/test_language_detector.py::test_main_language" ]

{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }

2023-09-12 17:03:16+00:00

mit

904

adbar__simplemma-85

diff --git a/simplemma/__init__.py b/simplemma/__init__.py index 74510e6..6a553e8 100644 --- a/simplemma/__init__.py +++ b/simplemma/__init__.py @@ -7,6 +7,7 @@ __license__ = "MIT" __version__ = "0.9.1" +from .dictionary_factory import DictionaryFactory, DefaultDictionaryFactory from .language_detector import LanguageDetector, in_target_language, langdetect from .lemmatizer import Lemmatizer, lemmatize, lemma_iterator, text_lemmatizer, is_known from .tokenizer import Tokenizer, RegexTokenizer, simple_tokenizer @@ -16,5 +17,3 @@ from .token_sampler import ( MostCommonTokenSampler, RelaxedMostCommonTokenSampler, ) -from .dictionary_factory import DictionaryFactory, DefaultDictionaryFactory -from .dictionary_pickler import * diff --git a/simplemma/dictionary_pickler.py b/training/dictionary_pickler.py similarity index 90% rename from simplemma/dictionary_pickler.py rename to training/dictionary_pickler.py index 5f400ee..f0b92e0 100644 --- a/simplemma/dictionary_pickler.py +++ b/training/dictionary_pickler.py @@ -7,15 +7,11 @@ from operator import itemgetter from pathlib import Path from typing import Dict, List, Optional -try: - from .dictionary_factory import SUPPORTED_LANGUAGES - from .strategies.defaultrules import DEFAULT_RULES - from .utils import levenshtein_dist -# local error, also ModuleNotFoundError for Python >= 3.6 -except ImportError: # pragma: no cover - from dictionary_factory import SUPPORTED_LANGUAGES # type: ignore - from strategies.defaultrules import DEFAULT_RULES # type: ignore - from utils import levenshtein_dist # type: ignore +import simplemma +from simplemma.dictionary_factory import SUPPORTED_LANGUAGES +from simplemma.strategies.defaultrules import DEFAULT_RULES +from simplemma.utils import levenshtein_dist + LOGGER = logging.getLogger(__name__) @@ -138,7 +134,7 @@ def _pickle_dict( mydict = dict(sorted(mydict.items(), key=itemgetter(1))) if filepath is None: filename = f"data/{langcode}.plzma" - filepath = str(Path(__file__).parent / filename) + filepath = str(Path(simplemma.__file__).parent / filename) with lzma.open(filepath, "wb") as filehandle: # , filters=my_filters, preset=9 pickle.dump(mydict, filehandle, protocol=4) LOGGER.debug("%s %s", langcode, len(mydict)) diff --git a/eval/eval-requirements.txt b/training/eval/eval-requirements.txt similarity index 100% rename from eval/eval-requirements.txt rename to training/eval/eval-requirements.txt diff --git a/eval/udscore.py b/training/eval/udscore.py similarity index 84% rename from eval/udscore.py rename to training/eval/udscore.py index 34e3a9c..e6bd507 100644 --- a/eval/udscore.py +++ b/training/eval/udscore.py @@ -5,7 +5,8 @@ from collections import Counter from os import makedirs, path from conllu import parse_incr # type: ignore -from simplemma import lemmatize +from simplemma import Lemmatizer, DefaultDictionaryFactory +from simplemma.strategies.default import DefaultStrategy if not path.exists("csv"): makedirs("csv") @@ -66,6 +67,16 @@ for filedata in data_files: with open(filename, "r", encoding="utf-8") as myfile: data_file = myfile.read() start = time.time() + dictionary_factory = DefaultDictionaryFactory() + strategies = DefaultStrategy(greedy=False) + lemmatizer = Lemmatizer( + dictionary_factory=dictionary_factory, + lemmatization_strategy=DefaultStrategy(greedy=False), + ) + greedy_lemmatizer = Lemmatizer( + dictionary_factory=dictionary_factory, + lemmatization_strategy=DefaultStrategy(greedy=True), + ) print("==", filedata, "==") for tokenlist in parse_incr(data_file): for token in tokenlist: @@ -75,13 +86,10 @@ for filedata in data_files: continue initial = bool(token["id"] == 1) + token_form = token["form"].lower() if initial else token["form"] - greedy_candidate = lemmatize( - token["form"], lang=language, greedy=True, initial=initial - ) - candidate = lemmatize( - token["form"], lang=language, greedy=False, initial=initial - ) + candidate = lemmatizer.lemmatize(token_form, lang=language) + greedy_candidate = greedy_lemmatizer.lemmatize(token_form, lang=language) if token["upos"] in ("ADJ", "NOUN"): focus_total += 1

adbar/simplemma

b575330e558851c728af74bb62208af445d6a283

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 4ebd08b..c73b552 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -86,11 +86,11 @@ jobs: flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - name: Code format with black - run: black --check --diff simplemma tests + run: black --check --diff simplemma training tests - name: Type checking with mypy if: matrix.python-version != '3.6' - run: mypy -p simplemma -p tests + run: mypy -p simplemma -p training -p tests - name: Test with pytest run: pytest --cov=./ --cov-report=xml diff --git a/tests/test_dictionary_pickler.py b/tests/test_dictionary_pickler.py index 1dad1fa..95dd1bb 100644 --- a/tests/test_dictionary_pickler.py +++ b/tests/test_dictionary_pickler.py @@ -1,7 +1,7 @@ import os import tempfile -from simplemma import dictionary_pickler +from training import dictionary_pickler TEST_DIR = os.path.abspath(os.path.dirname(__file__))

Separate scripts used to create the dictionaries from actual src & tests `tests/udscore.py` and `src/dictionary_pickler.py` seem to be scripts used to create the dictionaries and validate their quality. I suggest that they are moved to a separate folder `training` or whatever you want

0.0

b575330e558851c728af74bb62208af445d6a283

[ "tests/test_dictionary_pickler.py::test_logic" ]

[]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2023-05-10 17:08:31+00:00

mit

905

aequitas__python-rflink-39

diff --git a/.travis.yml b/.travis.yml index 30fa75f..e52730d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,11 +7,13 @@ python: - 3.8 - 2.7 - pypy3 -install: pip install tox-travis python-coveralls codeclimate-test-reporter +# python-coveralls 5.0 no longer supports python34 +install: pip install tox-travis codeclimate-test-reporter script: tox matrix: allow_failures: - python: 2.7 + - python: 3.4 - python: pypy3 include: - python: 3.7 diff --git a/rflink/parser.py b/rflink/parser.py index 05e7ea0..8a74a52 100644 --- a/rflink/parser.py +++ b/rflink/parser.py @@ -305,7 +305,7 @@ def decode_packet(packet: str) -> PacketType: # convert key=value pairs where needed for attr in filter(None, attrs.strip(DELIM).split(DELIM)): - key, value = attr.lower().split("=") + key, value = attr.lower().split("=", 1) if key in VALUE_TRANSLATION: value = VALUE_TRANSLATION[key](value) name = PACKET_FIELDS.get(key, key) diff --git a/rflink/protocol.py b/rflink/protocol.py index a3c54da..9922910 100644 --- a/rflink/protocol.py +++ b/rflink/protocol.py @@ -151,7 +151,7 @@ class PacketHandling(ProtocolBase): try: packet = decode_packet(raw_packet) except BaseException: - log.exception("failed to parse packet: %s", packet) + log.exception("failed to parse packet data: %s", raw_packet) log.debug("decoded packet: %s", packet)

aequitas/python-rflink

1b2ea3d82e4138fb5b35c763df94aa0a63d24acf

diff --git a/tests/test_parse.py b/tests/test_parse.py index 3f55831..274e0ae 100644 --- a/tests/test_parse.py +++ b/tests/test_parse.py @@ -80,6 +80,10 @@ PROTOCOL_SAMPLES = os.path.join(os.path.dirname(__file__), "protocol_samples.txt "20;00;Internal Pullup on RF-in disabled;", {"message": "Internal Pullup on RF-in disabled"}, ], + [ + "20;9A;FA500;ID=0000db9e;SWITCH=01;CMD=SET_LEVEL=2;", + {"command": "set_level=2"}, + ], ], ) def test_packet_parsing(packet, expect):

decode_packet: too many values to unpack (expected 2) I use rflink integration in my HA setup and often get this in HA log: > 2020-01-22 07:49:56 ERROR (MainThread) [rflink.protocol] failed to parse packet: None > Traceback (most recent call last): > File "/usr/local/lib/python3.7/site-packages/rflink/protocol.py", line 152, in handle_raw_packet > packet = decode_packet(raw_packet) > File "/usr/local/lib/python3.7/site-packages/rflink/parser.py", line 308, in decode_packet > key, value = attr.lower().split("=") > ValueError: too many values to unpack (expected 2) Obvoiusly there is no impact on the functionality, but the messages flood the log. I hope it's possible to rewrite the code so it account for situations like this.

0.0

1b2ea3d82e4138fb5b35c763df94aa0a63d24acf

[ "tests/test_parse.py::test_packet_parsing[20;9A;FA500;ID=0000db9e;SWITCH=01;CMD=SET_LEVEL=2;-expect15]" ]

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{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2020-01-25 20:01:16+00:00

mit

906

aesara-devs__aesara-465

diff --git a/aesara/tensor/math_opt.py b/aesara/tensor/math_opt.py index e90d6b425..ad0eeb92b 100644 --- a/aesara/tensor/math_opt.py +++ b/aesara/tensor/math_opt.py @@ -11,7 +11,6 @@ from functools import reduce import numpy as np import aesara.scalar.basic as aes -from aesara import compile from aesara.assert_op import assert_op from aesara.configdefaults import config from aesara.graph.basic import Constant, Variable @@ -74,6 +73,7 @@ from aesara.tensor.math import ( expm1, ge, int_div, + isinf, log, log1p, makeKeepDims, @@ -2286,34 +2286,33 @@ def local_log1p(fgraph, node): @register_stabilize @register_specialize @local_optimizer([log]) -def local_log_add(fgraph, node): - # log(exp(x)+exp(y)) - # - # Suppose x >= y - # log(exp(x) + exp(y)) - # log(exp(x) * (1 + exp(y)/exp(x))) - # x + log(1 + exp(y)/exp(x)) - # x + log1p(exp(y)/exp(x)) - # x + log1p(exp(y-x)) +def local_log_add_exp(fgraph, node): + # log(exp(x)+exp(y)+exp(z)) = max + log(x-max, y-max, z-max) + if node.op == log: z = node.inputs[0] if z.owner and z.owner.op == add: zi = z.owner.inputs - if len(zi) != 2: - # -- upgrading Maximum to handle multiple inputs wasn't trivial - # TODO - # raise NotImplementedError() - return pre_exp = [x.owner.inputs[0] for x in zi if x.owner and x.owner.op == exp] + # all arguments to add are exp(<something>) if len(pre_exp) == len(zi): - # all arguments to add are exp(<something>) - max_pre = maximum(*pre_exp) - - ret = max_pre + log1p(exp(add(*[p - max_pre for p in pre_exp]))) - ret.tag.values_eq_approx = values_eq_approx_remove_inf + # Do not offset when max_pre = -np.inf, to avoid nan in the output + # Switch statement is placed directly inside add to break the self-symmetry + # of the returned output (otherwise the optimization would not stabilize) + max_pre = reduce(maximum, pre_exp) + ret = max_pre + log( + add( + *[ + switch(isinf(max_pre), exp(max_pre), exp(p - max_pre)) + for p in pre_exp + ] + ) + ) return [ret] +@register_stabilize +@register_specialize @local_optimizer([log]) def local_log_sum_exp(fgraph, node): # log(sum_i(exp(x_i))) = x_max + log(sum_i(exp(x_i - x_max))) @@ -2342,7 +2341,19 @@ def local_log_sum_exp(fgraph, node): max_pre_exp = aet_max(pre_exp, axis=axis) max_pre_exp_keepdims = makeKeepDims(pre_exp, max_pre_exp, axis) - ret = max_pre_exp + log(aet_sum(exp(pre_exp - max_pre_exp_keepdims), axis=axis)) + # Do not offset when max_pre = -np.inf, to avoid nan in the output + # Switch statement is placed directly inside sum to break the self-symmetry + # of the returned output (otherwise the optimization would not stabilize) + ret = max_pre_exp + log( + aet_sum( + switch( + isinf(max_pre_exp_keepdims), + exp(max_pre_exp_keepdims), + exp(pre_exp - max_pre_exp_keepdims), + ), + axis=axis, + ), + ) # Restore the dimshuffle op, if any. if dimshuffle_op: @@ -2351,14 +2362,6 @@ def local_log_sum_exp(fgraph, node): return [ret] -compile.optdb.register( - "local_log_sum_exp", - in2out(local_log_sum_exp, ignore_newtrees=True), - 1.6, - "fast_run", -) - - def add_calculate(num, denum, aslist=False, out_type=None): # TODO: make sure that this function and mul_calculate are similar if out_type is None:

aesara-devs/aesara

b84ac43a8dd23c888131e9b3f5654f81402da76c

diff --git a/tests/tensor/test_math_opt.py b/tests/tensor/test_math_opt.py index 98a1d8a80..55dfbae0b 100644 --- a/tests/tensor/test_math_opt.py +++ b/tests/tensor/test_math_opt.py @@ -1840,10 +1840,7 @@ def test_log1p(): assert [node.op for node in f.maker.fgraph.toposort()] == [log1p] [email protected]( - reason="log(add(exp)) is not stabilized when adding more than 2 elements, see #623" -) -def test_log_add(): +def test_local_log_add_exp(): m = config.mode if m == "FAST_COMPILE": m = "FAST_RUN" @@ -1858,26 +1855,28 @@ def test_log_add(): y = dvector() f = function([x, y], log(exp(x) + exp(y)), mode=m) - f([10000], [10000]) # causes overflow if handled incorrectly - assert np.isfinite(f([10000], [10000])) + # test that it gives the correct result when it doesn't overflow + f([10], [10]) # doesn't causes overflow + utt.assert_allclose(f([10], [10]), 10 + np.log1p(1)) + + assert np.isfinite(f([10000], [10000])) # causes overflow if handled incorrectly utt.assert_allclose(f([10000], [10000]), 10000 + np.log1p(1)) - # test that it give the same result when it don't overflow - f([10], [10]) # don't causes overflow - utt.assert_allclose(f([10], [10]), 10 + np.log1p(1)) + # test that when max = +-inf, optimized output still works correctly + assert f([-np.inf], [-np.inf]) == -np.inf + assert f([np.inf], [np.inf]) == np.inf + assert f([np.inf], [-np.inf]) == np.inf - # test that it also works with more than two args, (this currently fails) + # test that it also works with more than two args x = dvector() y = dvector() f = function([x, y], log(exp(x) + exp(y) + exp(x - y) + exp(x + y)), mode=m) - f([10000], [10000]) # causes overflow if handled incorrectly + assert np.isfinite(f([10000], [10000])) # causes overflow if handled incorrectly utt.assert_allclose(f([10000], [10000]), 20000) # TODO: test that the optimization works in the presence of broadcasting. - # TODO: (write and) test that the optimization works with Sum in addition to working with Add. - def test_local_subtensor_of_dot(): m1 = matrix() @@ -4001,6 +4000,16 @@ def test_local_log_sum_exp3(): assert np.allclose(optimised_ret, 100.0) +def test_local_log_sum_exp_inf(): + # Test that when max = +-inf, optimized output still works correctly + x = vector("x") + f = compile_graph_log_sum_exp(x, axis=0) + + assert f([-np.inf, -np.inf]) == -np.inf + assert f([np.inf, np.inf]) == np.inf + assert f([-np.inf, np.inf]) == np.inf + + def test_local_reciprocal_1_plus_exp(): x = vector("x") y = aet.reciprocal(1 + exp(x))

LogSumExp of `-inf` returns `nan` instead of `-inf` ```python x = at.vector('x') res1 = at.log(at.sum(at.exp(x))) # nan with sum res2 = at.log(at.prod(at.exp(x))) # but not with prod fun = aesara.function([x], [res1, res2]) print(fun(np.array([-np.inf, -np.inf]))) # [array(nan), array(-inf)] ``` for reference in numpy we get `-inf`, together with a divide by zero encountered in log ```python print(np.log(np.sum(np.exp([-np.inf, -np.inf])))) # -inf ``` This showed up in the pymc3 `logsumexp` function which returns `nan` with this input: ```python from pymc3.math import logsumexp x = at.vector('x') res = logsumexp(x) fun = aesara.function([x], res) print(fun(np.array([-np.inf, -np.inf]))) # [nan] ``` Whereas the scipy reference works fine ```python print(scipy.special.logsumexp([-np.inf, -np.inf])) # -inf ``` Weirdly it happens with addition, but not subtraction or multiplication, so maybe the problem is not the sum but the addition? ```python x = at.vector('x') res1 = at.log(at.exp(x[0]) + at.exp(x[1])) res2 = at.log(at.exp(x[0]) - at.exp(x[1])) fun = aesara.function([x], [res1, res2]) print(fun(np.array([-np.inf, -np.inf]))) # [array(nan), array(-inf)]

0.0

b84ac43a8dd23c888131e9b3f5654f81402da76c

[ "tests/tensor/test_math_opt.py::test_local_log_add_exp" ]

[ "tests/tensor/test_math_opt.py::TestGreedyDistribute::test_main", "tests/tensor/test_math_opt.py::TestAlgebraicCanonize::test_muldiv", "tests/tensor/test_math_opt.py::TestAlgebraicCanonize::test_abs_mul_div", "tests/tensor/test_math_opt.py::test_mixeddiv", "tests/tensor/test_math_opt.py::TestFusion::test_add_mul_fusion_inplace", "tests/tensor/test_math_opt.py::TestLocalUselessElemwiseComparison::test_inequality_with_self", "tests/tensor/test_math_opt.py::TestLocalUselessElemwiseComparison::test_shape_add_inequality", "tests/tensor/test_math_opt.py::TestLocalUselessElemwiseComparison::test_and", "tests/tensor/test_math_opt.py::TestLocalUselessElemwiseComparison::test_and_int", "tests/tensor/test_math_opt.py::TestLocalUselessElemwiseComparison::test_or", "tests/tensor/test_math_opt.py::TestLocalUselessElemwiseComparison::test_or_int", "tests/tensor/test_math_opt.py::TestLocalUselessElemwiseComparison::test_xor", "tests/tensor/test_math_opt.py::TestExpLog::test_log_exp", "tests/tensor/test_math_opt.py::TestLocalMergeSwitchSameCond::test_elemwise", "tests/tensor/test_math_opt.py::TestLocalSumProd::test_local_sum_prod_all_to_none", "tests/tensor/test_math_opt.py::TestLocalSumProd::test_local_sum_sum_prod_prod", "tests/tensor/test_math_opt.py::TestLocalSumProd::test_local_sum_sum_int8", "tests/tensor/test_math_opt.py::TestLocalSumProd::test_local_sum_sum_dtype", "tests/tensor/test_math_opt.py::test_local_add_specialize", "tests/tensor/test_math_opt.py::TestIntDivByOne::test1", "tests/tensor/test_math_opt.py::TestIntDivByOne::test3", "tests/tensor/test_math_opt.py::test_local_sumsqr2dot", "tests/tensor/test_math_opt.py::TestSigmoidOpts::test_1msigmoid", "tests/tensor/test_math_opt.py::TestSigmoidOpts::test_perform_sigm_times_exp", "tests/tensor/test_math_opt.py::TestSoftplusOpts::test_logsigm_to_softplus", "tests/tensor/test_math_opt.py::TestSigmoidUtils::test_compute_mul", "tests/tensor/test_math_opt.py::TestSigmoidUtils::test_parse_mul_tree", "tests/tensor/test_math_opt.py::TestSigmoidUtils::test_is_1pexp" ]

{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-06-06 13:15:11+00:00

bsd-3-clause

907

aesara-devs__aesara-779

diff --git a/aesara/tensor/__init__.py b/aesara/tensor/__init__.py index af894fa98..787bd4871 100644 --- a/aesara/tensor/__init__.py +++ b/aesara/tensor/__init__.py @@ -134,6 +134,9 @@ from aesara.tensor.extra_ops import ( # noqa squeeze, unique, unravel_index, + linspace, + logspace, + geomspace, ) from aesara.tensor.shape import ( # noqa reshape, diff --git a/aesara/tensor/extra_ops.py b/aesara/tensor/extra_ops.py index 9db12b045..d054f5d46 100644 --- a/aesara/tensor/extra_ops.py +++ b/aesara/tensor/extra_ops.py @@ -1636,6 +1636,29 @@ class BroadcastTo(Op): broadcast_to_ = BroadcastTo() +def geomspace(start, end, steps, base=10.0): + from aesara.tensor.math import log + + start = at.as_tensor_variable(start) + end = at.as_tensor_variable(end) + return base ** linspace(log(start) / log(base), log(end) / log(base), steps) + + +def logspace(start, end, steps, base=10.0): + start = at.as_tensor_variable(start) + end = at.as_tensor_variable(end) + return base ** linspace(start, end, steps) + + +def linspace(start, end, steps): + start = at.as_tensor_variable(start) + end = at.as_tensor_variable(end) + arr = at.arange(steps) + arr = at.shape_padright(arr, max(start.ndim, end.ndim)) + multiplier = (end - start) / (steps - 1) + return start + arr * multiplier + + def broadcast_to( x: TensorVariable, shape: Union[TensorVariable, Tuple[Variable]] ) -> TensorVariable:

aesara-devs/aesara

980c4c2c72b9c8b51d8627cc75fb655a9fd600ed

diff --git a/tests/tensor/test_extra_ops.py b/tests/tensor/test_extra_ops.py index a6aa85cb0..ce57ae6ae 100644 --- a/tests/tensor/test_extra_ops.py +++ b/tests/tensor/test_extra_ops.py @@ -36,6 +36,9 @@ from aesara.tensor.extra_ops import ( diff, fill_diagonal, fill_diagonal_offset, + geomspace, + linspace, + logspace, ravel_multi_index, repeat, searchsorted, @@ -65,6 +68,11 @@ from aesara.utils import LOCAL_BITWIDTH, PYTHON_INT_BITWIDTH from tests import unittest_tools as utt +def set_test_value(x, v): + x.tag.test_value = v + return x + + def test_cpu_contiguous(): a = fmatrix("a") i = iscalar("i") @@ -1222,3 +1230,28 @@ def test_broadcast_arrays(): assert np.array_equal(x_bcast_val, x_bcast_exp) assert np.array_equal(y_bcast_val, y_bcast_exp) + + [email protected]( + "start, stop, num_samples", + [ + (1, 10, 50), + (np.array([5, 6]), np.array([[10, 10], [10, 10]]), 25), + (1, np.array([5, 6]), 30), + ], +) +def test_space_ops(start, stop, num_samples): + z = linspace(start, stop, num_samples) + aesara_res = function(inputs=[], outputs=z)() + numpy_res = np.linspace(start, stop, num=num_samples) + assert np.allclose(aesara_res, numpy_res) + + z = logspace(start, stop, num_samples) + aesara_res = function(inputs=[], outputs=z)() + numpy_res = np.logspace(start, stop, num=num_samples) + assert np.allclose(aesara_res, numpy_res) + + z = geomspace(start, stop, num_samples) + aesara_res = function(inputs=[], outputs=z)() + numpy_res = np.geomspace(start, stop, num=num_samples) + assert np.allclose(aesara_res, numpy_res)

Implement Op for `linspace` and similar numpy functions The following numpy functions don't have to counterpart in Aesara: * [linspace](https://numpy.org/doc/stable/reference/generated/numpy.linspace.html) * [logspace](https://numpy.org/doc/stable/reference/generated/numpy.logspace.html) * [geomspace](https://numpy.org/doc/stable/reference/generated/numpy.geomspace.html) I am not familiar with all of them, so some might not make sense, or they might be low priority. `linspace` would definitely be nice to have.

0.0

980c4c2c72b9c8b51d8627cc75fb655a9fd600ed

[ "tests/tensor/test_extra_ops.py::test_cpu_contiguous", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_searchsortedOp_on_sorted_input", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_searchsortedOp_wrong_side_kwd", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_searchsortedOp_on_no_1d_inp", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_searchsortedOp_on_float_sorter", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_searchsortedOp_on_int_sorter", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_searchsortedOp_on_right_side", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_infer_shape", "tests/tensor/test_extra_ops.py::TestSearchsortedOp::test_grad", "tests/tensor/test_extra_ops.py::TestDiffOp::test_diffOp", "tests/tensor/test_extra_ops.py::TestDiffOp::test_output_type[x_type0]", "tests/tensor/test_extra_ops.py::TestDiffOp::test_output_type[x_type1]", "tests/tensor/test_extra_ops.py::TestDiffOp::test_output_type[x_type2]", "tests/tensor/test_extra_ops.py::TestDiffOp::test_output_type[x_type3]", "tests/tensor/test_extra_ops.py::TestDiffOp::test_infer_shape", "tests/tensor/test_extra_ops.py::TestDiffOp::test_grad", "tests/tensor/test_extra_ops.py::TestDiffOp::test_grad_not_implemented", "tests/tensor/test_extra_ops.py::TestSqueeze::test_op", "tests/tensor/test_extra_ops.py::TestSqueeze::test_infer_shape", "tests/tensor/test_extra_ops.py::TestSqueeze::test_grad", "tests/tensor/test_extra_ops.py::TestSqueeze::test_var_interface", "tests/tensor/test_extra_ops.py::TestSqueeze::test_axis", "tests/tensor/test_extra_ops.py::TestCompress::test_op", "tests/tensor/test_extra_ops.py::TestRepeat::test_basic", "tests/tensor/test_extra_ops.py::TestRepeat::test_grad", "tests/tensor/test_extra_ops.py::TestRepeat::test_broadcastable", "tests/tensor/test_extra_ops.py::TestBartlett::test_perform", "tests/tensor/test_extra_ops.py::TestBartlett::test_infer_shape", "tests/tensor/test_extra_ops.py::TestFillDiagonal::test_infer_shape", "tests/tensor/test_extra_ops.py::TestFillDiagonalOffset::test_gradient", "tests/tensor/test_extra_ops.py::TestFillDiagonalOffset::test_infer_shape", "tests/tensor/test_extra_ops.py::test_to_one_hot", "tests/tensor/test_extra_ops.py::TestUnique::test_basic_vector[x0-inp0-None]", "tests/tensor/test_extra_ops.py::TestUnique::test_basic_vector[x1-inp1-None]", "tests/tensor/test_extra_ops.py::TestUnique::test_basic_vector[x2-inp2-0]", "tests/tensor/test_extra_ops.py::TestUnique::test_basic_vector[x3-inp3-0]", "tests/tensor/test_extra_ops.py::TestUnique::test_basic_vector[x4-inp4--1]", "tests/tensor/test_extra_ops.py::TestUnique::test_basic_vector[x5-inp5--1]", "tests/tensor/test_extra_ops.py::TestUnique::test_infer_shape[x0-inp0-None]", "tests/tensor/test_extra_ops.py::TestUnique::test_infer_shape[x2-inp2-0]", "tests/tensor/test_extra_ops.py::TestUnique::test_infer_shape[x3-inp3-0]", "tests/tensor/test_extra_ops.py::TestUnique::test_infer_shape[x4-inp4--1]", "tests/tensor/test_extra_ops.py::TestUnique::test_infer_shape[x5-inp5--1]", "tests/tensor/test_extra_ops.py::test_broadcast_shape_symbolic[s1_vals0-s2_vals0-exp_res0]", "tests/tensor/test_extra_ops.py::test_broadcast_shape_symbolic[s1_vals1-s2_vals1-exp_res1]", "tests/tensor/test_extra_ops.py::test_broadcast_shape_symbolic[s1_vals2-s2_vals2-exp_res2]", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_avoid_useless_scalars", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_avoid_useless_subtensors", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_perform", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_gradient[<lambda>-input_dims0]", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_gradient[<lambda>-input_dims1]", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_gradient[<lambda>-input_dims2]", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_gradient[<lambda>-input_dims3]", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_infer_shape", "tests/tensor/test_extra_ops.py::TestBroadcastTo::test_inplace", "tests/tensor/test_extra_ops.py::test_broadcast_arrays", "tests/tensor/test_extra_ops.py::test_space_ops[1-10-50]", "tests/tensor/test_extra_ops.py::test_space_ops[start1-stop1-25]", "tests/tensor/test_extra_ops.py::test_space_ops[1-stop2-30]" ]

[]

{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }

2022-01-22 11:36:31+00:00

bsd-3-clause

908

aesara-devs__aesara-854

diff --git a/aesara/tensor/c_code/dimshuffle.c b/aesara/tensor/c_code/dimshuffle.c index d97df5254..6c67bd1bf 100644 --- a/aesara/tensor/c_code/dimshuffle.c +++ b/aesara/tensor/c_code/dimshuffle.c @@ -31,6 +31,8 @@ int APPLY_SPECIFIC(cpu_dimshuffle)(PyArrayObject *input, PyArrayObject **res, PyArrayObject *transposed_input = (PyArrayObject *)PyArray_Transpose(_input, &permute); + Py_DECREF(_input); + PyDimMem_FREE(permute.ptr); npy_intp *res_shape = PyArray_DIMS(transposed_input); @@ -68,7 +70,7 @@ int APPLY_SPECIFIC(cpu_dimshuffle)(PyArrayObject *input, PyArrayObject **res, *res = (PyArrayObject *)PyArray_Newshape(transposed_input, &reshape_shape, NPY_CORDER); - /* Py_XDECREF(transposed_input); */ + Py_DECREF(transposed_input); PyDimMem_FREE(reshape_shape.ptr);

aesara-devs/aesara

3d8553f7b56caed8686e3db9bfbe5ffea110b70a

diff --git a/tests/tensor/test_elemwise.py b/tests/tensor/test_elemwise.py index 0ad4a76a6..1ad8ca9b2 100644 --- a/tests/tensor/test_elemwise.py +++ b/tests/tensor/test_elemwise.py @@ -1,4 +1,5 @@ import math +import tracemalloc from copy import copy import numpy as np @@ -141,6 +142,41 @@ class TestDimShuffle(unittest_tools.InferShapeTester): # Confirm the broadcasted value in the output assert np.array_equiv(outputs[0].storage[0], 2039) + @pytest.mark.parametrize("inplace", [True, False]) + def test_memory_leak(self, inplace): + import gc + + n = 100_000 + + x = aesara.shared(np.ones(n, dtype=np.float64)) + + y = x.dimshuffle([0, "x"]) + y.owner.op.inplace = inplace + + f = aesara.function([], y, mode=Mode(optimizer=None)) + + assert len(f.maker.fgraph.apply_nodes) == 2 + assert isinstance(f.maker.fgraph.toposort()[0].op, DimShuffle) + + assert f.maker.fgraph.toposort()[0].op.inplace is inplace + + tracemalloc.start() + + blocks_last = None + block_diffs = [] + for i in range(50): + x.set_value(np.ones(n)) + _ = f() + _ = gc.collect() + blocks_i, _ = tracemalloc.get_traced_memory() + if blocks_last is not None: + blocks_diff = (blocks_i - blocks_last) // 10 ** 3 + block_diffs.append(blocks_diff) + blocks_last = blocks_i + + tracemalloc.stop() + assert np.allclose(np.mean(block_diffs), 0) + class TestBroadcast: # this is to allow other types to reuse this class to test their ops

Memory leak in `DimShuffle` ## Description of your problem or feature request **Please provide a minimal, self-contained, and reproducible example.** ```python import os import psutil import aesara from aesara import tensor as at process = psutil.Process(os.getpid()) old_rss = None n = 100_000 x = at.sharedvar.TensorSharedVariable( "test", at.type.dvector, np.ones(n), strict=True ) y = x.dimshuffle([0, "x"]) f = aesara.function([], y) for i in range(100): x.set_value(np.ones(n)) f() if i % 10 == 0: new_rss = process.memory_info().rss if old_rss is not None: print(f"Python process increased RSS by {round((new_rss - old_rss) / 1024**2, 2)} MB") old_rss = new_rss ``` **Please provide the full traceback of any errors.** ```python Python process increased RSS by 6.62 MB Python process increased RSS by 7.74 MB Python process increased RSS by 7.64 MB Python process increased RSS by 7.68 MB Python process increased RSS by 7.64 MB Python process increased RSS by 7.68 MB Python process increased RSS by 7.41 MB Python process increased RSS by 7.63 MB Python process increased RSS by 7.85 MB ``` **Please provide any additional information below.** This happens when the reshape operation is compiled to C. When I run the same code setting `aesara.config.cxx = ""`, the Python process does not increase RSS. ## Versions and main components * Aesara version: 2.4.0 * Aesara config (`python -c "import aesara; print(aesara.config)"`) * Python version: 3.9 * Operating system: Ubuntu 18.04 * How did you install Aesara: (conda/pip) pip

0.0

3d8553f7b56caed8686e3db9bfbe5ffea110b70a

[ "tests/tensor/test_elemwise.py::TestDimShuffle::test_memory_leak[True]", "tests/tensor/test_elemwise.py::TestDimShuffle::test_memory_leak[False]" ]

[ "tests/tensor/test_elemwise.py::TestDimShuffle::test_perform", "tests/tensor/test_elemwise.py::TestDimShuffle::test_c_or_py", "tests/tensor/test_elemwise.py::TestDimShuffle::test_infer_shape", "tests/tensor/test_elemwise.py::TestDimShuffle::test_c_views", "tests/tensor/test_elemwise.py::TestBroadcast::test_perform", "tests/tensor/test_elemwise.py::TestBroadcast::test_c", "tests/tensor/test_elemwise.py::TestBroadcast::test_perform_inplace", "tests/tensor/test_elemwise.py::TestBroadcast::test_c_inplace", "tests/tensor/test_elemwise.py::TestBroadcast::test_fill", "tests/tensor/test_elemwise.py::TestBroadcast::test_fill_var", "tests/tensor/test_elemwise.py::TestBroadcast::test_fill_grad", "tests/tensor/test_elemwise.py::TestBroadcast::test_weird_strides", "tests/tensor/test_elemwise.py::TestBroadcast::test_same_inputs", "tests/tensor/test_elemwise.py::TestCAReduce::test_perform_noopt", "tests/tensor/test_elemwise.py::TestCAReduce::test_perform_nan", "tests/tensor/test_elemwise.py::TestCAReduce::test_c_noopt", "tests/tensor/test_elemwise.py::TestCAReduce::test_infer_shape", "tests/tensor/test_elemwise.py::TestBitOpReduceGrad::test_all_grad", "tests/tensor/test_elemwise.py::TestBitOpReduceGrad::test_any_grad", "tests/tensor/test_elemwise.py::TestElemwise::test_elemwise_grad_bool", "tests/tensor/test_elemwise.py::TestElemwise::test_infer_shape", "tests/tensor/test_elemwise.py::TestElemwise::test_input_dimensions_overflow", "tests/tensor/test_elemwise.py::TestElemwise::test_input_dimensions_match_python", "tests/tensor/test_elemwise.py::test_not_implemented_elemwise_grad" ]

{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }

2022-03-11 02:00:34+00:00

bsd-3-clause

909

aesara-devs__aesara-902

diff --git a/aesara/compile/builders.py b/aesara/compile/builders.py index b714138eb..4328e95e7 100644 --- a/aesara/compile/builders.py +++ b/aesara/compile/builders.py @@ -375,6 +375,11 @@ class OpFromGraph(Op, HasInnerGraph): self.kwargs = kwargs self.input_types = [inp.type for inp in inputs] self.output_types = [out.type for out in outputs] + + self.lop_overrides = lop_overrides + self.grad_overrides = grad_overrides + self.rop_overrides = rop_overrides + if lop_overrides != "default": if grad_overrides != "default": raise ValueError( @@ -732,19 +737,71 @@ class OpFromGraph(Op, HasInnerGraph): ] return ret_l + def __call__(self, *inputs, **kwargs): + # The user interface doesn't expect the shared variable inputs of the + # inner-graph, but, since `Op.make_node` does (and `Op.__call__` + # dispatches to `Op.make_node`), we need to compensate here + num_expected_inps = len(self.inner_inputs) - len(self.shared_inputs) + + if len(inputs) == num_expected_inps: + actual_inputs = inputs + tuple(self.shared_inputs) + return super().__call__(*actual_inputs, **kwargs) + elif len(inputs) == len(self.inner_inputs): + return super().__call__(*inputs, **kwargs) + else: + raise ValueError(f"Expected at least {num_expected_inps} input(s)") + def make_node(self, *inputs): + # The `inputs` received here should correspond to the inputs in the + # `Apply` nodes we produce below + if len(inputs) != len(self.inner_inputs): + raise ValueError(f"Expected {len(self.inner_inputs)} input(s)") + num_expected_inps = len(self.inner_inputs) - len(self.shared_inputs) - if len(inputs) != num_expected_inps: - raise ValueError( - f"Expected {int(num_expected_inps)} inputs, got {len(inputs)}" - ) - inputs = [ - inp_t.filter_variable(inp) for inp, inp_t in zip(inputs, self.input_types) + non_shared_inputs = inputs[:num_expected_inps] + + non_shared_inputs = [ + inp_t.filter_variable(inp) + for inp, inp_t in zip(non_shared_inputs, self.input_types) ] + + shared_inputs = inputs[num_expected_inps:] + local_shared_inputs = self.inner_inputs[num_expected_inps:] + + inner_and_input_shareds = list(zip(local_shared_inputs, shared_inputs)) + + if not all(inp_s == inn_s for inn_s, inp_s in inner_and_input_shareds): + # The shared variables are not equal to the original shared + # variables, so we construct a new `Op` that uses the new shared + # variables instead + replace = { + old_inp: new_inp for old_inp, new_inp in zip(self.inner_inputs, inputs) + } + replace.update(inner_and_input_shareds) + + # If the new shared variables are inconsistent with the inner-graph, + # such errors should arise in this step + new_outputs = clone_replace( + self.inner_outputs, replace=replace, share_inputs=True + ) + + new_op = type(self)( + inputs=non_shared_inputs, + outputs=new_outputs, + inline=self.is_inline, + lop_overrides=self.lop_overrides, + grad_overrides=self.grad_overrides, + rop_overrides=self.rop_overrides, + connection_pattern=self._connection_pattern, + name=self.name, + ) + else: + new_op = self + apply_node = Apply( - self, - list(inputs) + self.shared_inputs, - [type() for type in self.output_types], + new_op, + list(non_shared_inputs) + new_op.shared_inputs, + [type() for type in new_op.output_types], ) return apply_node

aesara-devs/aesara

6ef1452a83681e2ccd582ba12aaa7be778e1ff15

diff --git a/tests/compile/test_builders.py b/tests/compile/test_builders.py index a552c7a09..9d894aae7 100644 --- a/tests/compile/test_builders.py +++ b/tests/compile/test_builders.py @@ -3,6 +3,7 @@ from functools import partial import numpy as np import pytest +import aesara.tensor as at from aesara.compile import shared from aesara.compile.builders import OpFromGraph from aesara.compile.function import function @@ -29,6 +30,12 @@ class TestOpFromGraph(unittest_tools.InferShapeTester): def test_valid_input(self): x, y, z = matrices("xyz") + with pytest.raises(ValueError, match="Expected at least.*"): + OpFromGraph([x], [x])() + + with pytest.raises(ValueError, match=r"Expected 1 input$s$"): + OpFromGraph([x], [x]).make_node() + with pytest.raises(TypeError): OpFromGraph((x,), (x,)) @@ -451,6 +458,39 @@ class TestOpFromGraph(unittest_tools.InferShapeTester): grad_f = grad(f, y) assert grad_f.tag.test_value is not None + def test_make_node_shared(self): + """Make sure we can provide `OpFromGraph.make_node` new shared inputs and get a valid `OpFromGraph`.""" + + x = at.scalar("x") + y = shared(1.0, name="y") + + test_ofg = OpFromGraph([x], [x + y]) + assert test_ofg.inputs == [x] + assert test_ofg.shared_inputs == [y] + + out = test_ofg(x) + + y_clone = y.clone() + assert y_clone != y + y_clone.name = "y_clone" + + out_new = test_ofg.make_node(*(out.owner.inputs[:1] + [y_clone])).outputs[0] + + assert out_new.owner.op.inputs == [x] + assert out_new.owner.op.shared_inputs == [y_clone] + + out_fn = function([x], out_new) + + assert np.array_equal(out_fn(1.0), 2.0) + + y_clone.set_value(2.0) + + assert np.array_equal(out_fn(1.0), 3.0) + + # This should also work, because the containers are the same: + # y.set_value(1.0) + # assert np.array_equal(out_fn(1.0), 2.0) + def test_debugprint(): x, y, z = matrices("xyz") diff --git a/tests/scan/test_opt.py b/tests/scan/test_opt.py index 06eb27372..af14b7930 100644 --- a/tests/scan/test_opt.py +++ b/tests/scan/test_opt.py @@ -4,6 +4,7 @@ import pytest import aesara import aesara.tensor.basic as at from aesara import function, scan, shared +from aesara.compile.builders import OpFromGraph from aesara.compile.io import In from aesara.compile.mode import get_default_mode from aesara.configdefaults import config @@ -550,6 +551,28 @@ class TestPushOutNonSeqScan: utt.assert_allclose(output_opt[0], output_no_opt[0]) utt.assert_allclose(output_opt[1], output_no_opt[1]) + def test_OpFromGraph_shared(self): + """Make sure that a simple `OpFromGraph` with a shared variable can be pushed out.""" + + y = shared(1.0, name="y") + + test_ofg = OpFromGraph([], [1 + y]) + + def inner_func(): + return test_ofg() + + out, out_updates = aesara.scan(inner_func, n_steps=10) + + out_fn = function([], out, updates=out_updates) + + res = out_fn() + assert np.array_equal(res, np.repeat(2.0, 10)) + + y.set_value(2.0) + + res = out_fn() + assert np.array_equal(res, np.repeat(3.0, 10)) + class TestPushOutAddScan: """

`OpFromGraph.make_node`'s expected inputs and actual inputs are inconsistent `OpFromGraph.make_node` expects inputs corresponding to each of its inner-graph inputs, except for the shared variables; however, `OpFromGraph.make_node` also constructs `Apply` nodes such that `Apply.inputs` _contains_ the shared variable inputs of the inner-graph. This leads to an inherent inconsistency that prevents rewrites from reconstructing nodes via `Op.make_node(*Apply.inputs)`. Here's an example in which this issue results in an optimization failure: ```python import aesara import aesara.tensor as at from aesara.compile.builders import OpFromGraph y = aesara.shared(1.0, name="y") test_ofg = OpFromGraph([], [1 + y]) test_ofg.inputs # [] test_ofg.shared_inputs # [y] def inner_func(): return test_ofg() out, out_updates = aesara.scan(inner_func, n_steps=10) with aesara.config.change_flags(on_opt_error="raise"): out_fn = aesara.function([], out) # ERROR (aesara.graph.opt): Optimization failure due to: push_out_non_seq_scan # ERROR (aesara.graph.opt): node: for{cpu,scan_fn}(TensorConstant{10}, TensorConstant{10}, y) # ERROR (aesara.graph.opt): TRACEBACK: # ERROR (aesara.graph.opt): Traceback (most recent call last): # File ".../Aesara/aesara/graph/opt.py", line 1850, in process_node # replacements = lopt.transform(fgraph, node) # File ".../Aesara/aesara/graph/opt.py", line 1055, in transform # return self.fn(fgraph, node) # File ".../Aesara/aesara/scan/opt.py", line 282, in push_out_non_seq_scan # nw_outer_node = nd.op.make_node(*outside_ins) # File ".../Aesara/aesara/compile/builders.py", line 738, in make_node # raise ValueError( # ValueError: Expected 1 inputs, got 2 ```

0.0

6ef1452a83681e2ccd582ba12aaa7be778e1ff15

[ "tests/compile/test_builders.py::TestOpFromGraph::test_valid_input", "tests/compile/test_builders.py::TestOpFromGraph::test_make_node_shared", "tests/scan/test_opt.py::TestPushOutNonSeqScan::test_OpFromGraph_shared" ]

[ "tests/compile/test_builders.py::TestOpFromGraph::test_straightforward[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_straightforward[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_size_changes[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_size_changes[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_grad[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_grad[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_grad_grad[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_grad_grad[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_shared[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_shared[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_shared_grad[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_shared_grad[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_grad_override[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_grad_override[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_lop_override[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_lop_override[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_rop[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_rop[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_rop_override[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_rop_override[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_connection_pattern_override[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_connection_pattern_override[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_nested[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_nested[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_connection_pattern[OpFromGraph]", "tests/compile/test_builders.py::TestOpFromGraph::test_connection_pattern[cls_ofg1]", "tests/compile/test_builders.py::TestOpFromGraph::test_infer_shape", "tests/compile/test_builders.py::TestOpFromGraph::test_compute_test_value", "tests/compile/test_builders.py::test_debugprint", "tests/scan/test_opt.py::TestPushOutDot::test_pushout_all", "tests/scan/test_opt.py::TestScanMerge::test_belongs_to_set", "tests/scan/test_opt.py::TestSaveMem::test_save_mem_reduced_number_of_steps", "tests/scan/test_opt.py::TestSaveMem::test_save_mem_store_steps", "tests/scan/test_opt.py::test_opt_order" ]

{ "failed_lite_validators": [ "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }

2022-04-13 21:10:22+00:00

bsd-3-clause

910

aesara-devs__aesara-928

diff --git a/aesara/scalar/basic.py b/aesara/scalar/basic.py index 0bf12a70a..36a05c387 100644 --- a/aesara/scalar/basic.py +++ b/aesara/scalar/basic.py @@ -2307,6 +2307,8 @@ class Pow(BinaryScalarOp): if ( node.inputs[0].type == node.outputs[0].type and node.inputs[1].type == node.outputs[0].type + and None not in node.inputs[0].type.shape + and None not in node.inputs[1].type.shape and # amdlibm 3.0 do not have a float64 version of this SIMD function node.inputs[0].dtype == "float32" diff --git a/aesara/tensor/elemwise.py b/aesara/tensor/elemwise.py index b678ad16b..ce7d67b5f 100644 --- a/aesara/tensor/elemwise.py +++ b/aesara/tensor/elemwise.py @@ -913,7 +913,7 @@ second dimension checks = cgen.make_checks(orders, idtypes, sub) # Check if all inputs (except broadcasted scalar) are fortran. - # In that case, create an fortran output ndarray. + # In that case, create a fortran output ndarray. z = list(zip(inames, inputs)) alloc_fortran = " && ".join( [ @@ -1071,7 +1071,7 @@ second dimension # If all inputs and outputs are contiguous # and the scalar op define optimized code for that case - # use it! The scalar_op need to check the broadcast flag himself. + # use it! The scalar_op needs to check the type-level shapes itself. if ( all(o.ndim >= 1 for o in node.outputs) and @@ -1088,11 +1088,19 @@ second dimension # compiler to vectorize the code as their won't be as # many ptr and the stride will be hard coded. if all( - [ - io.broadcastable == node.outputs[0].broadcastable - or all(io.broadcastable) - for io in node.inputs + node.outputs - ] + # io.type.shape == node.outputs[1].type.shape + # Elemwise does not specify non-broadcastable static/type-levelshape + # information for its outputs yet + node.outputs[0].type.is_super(io.type) + for io in node.inputs + node.outputs + ) and ( + len(node.inputs) <= 1 + # If either one of the inputs has a `None` shape, we cannot + # assume they will have the same size + or all( + len(set(inp_shape)) == 1 and None not in inp_shape + for inp_shape in zip(*(inp.type.shape for inp in node.inputs)) + ) ): z = onames[0] contig = f""" @@ -1188,7 +1196,7 @@ second dimension return support_code def c_code_cache_version_apply(self, node): - version = [13] # the version corresponding to the c code in this Op + version = [14] # the version corresponding to the c code in this Op # now we insert versions for the ops on which we depend... scalar_node = Apply( diff --git a/aesara/tensor/elemwise_cgen.py b/aesara/tensor/elemwise_cgen.py index cfc5abde8..9e50369fb 100644 --- a/aesara/tensor/elemwise_cgen.py +++ b/aesara/tensor/elemwise_cgen.py @@ -66,10 +66,12 @@ def make_checks(loop_orders, dtypes, sub): if index != "x": # Initialize the variables associated to the jth loop # jump = stride - adjust + # If the variable has size 1 in that dim, we set the stride to zero to + # emulate broadcasting jump = f"({var}_stride{index}) - ({adjust})" init += f""" {var}_n{index} = PyArray_DIMS({var})[{index}]; - {var}_stride{index} = PyArray_STRIDES({var})[{index}] / sizeof({dtype}); + {var}_stride{index} = ({var}_n{index} == 1)? 0 : PyArray_STRIDES({var})[{index}] / sizeof({dtype}); {var}_jump{index}_{j} = {jump}; """ adjust = f"{var}_n{index}*{var}_stride{index}" @@ -90,26 +92,85 @@ def make_checks(loop_orders, dtypes, sub): # elements of to_compare are pairs ( input_variable_idx, input_variable_dim_idx ) if len(to_compare) < 2: continue - j0, x0 = to_compare[0] - for (j, x) in to_compare[1:]: - check += f""" - if (%(lv{j0})s_n{x0} != %(lv{j})s_n{x}) + + # Find first dimension size that is != 1 + jl, xl = to_compare[-1] + non1size_dim_check = f""" + npy_intp non1size_dim{xl}; + non1size_dim{xl} = """ + for (j, x) in to_compare[:-1]: + non1size_dim_check += f"(%(lv{j})s_n{x} != 1) ? %(lv{j})s_n{x} : " + non1size_dim_check += f"%(lv{jl})s_n{xl};" + check += non1size_dim_check + + # Check the nonsize1 dims match + # TODO: This is a bit inefficient because we are comparing one dimension against itself + check += f""" + if (non1size_dim{xl} != 1) {{ - PyErr_Format(PyExc_ValueError, "Input dimension mismatch. (input[%%i].shape[%%i] = %%lld, input[%%i].shape[%%i] = %%lld)", - {j0}, - {x0}, - (long long int) %(lv{j0})s_n{x0}, - {j}, - {x}, - (long long int) %(lv{j})s_n{x} - ); - %(fail)s - }} + """ + for (j, x) in to_compare: + check += f""" + if ((%(lv{j})s_n{x} != non1size_dim{x}) && (%(lv{j})s_n{x} != 1)) + {{ + PyErr_Format(PyExc_ValueError, "Input dimension mismatch. One other input has shape[%%i] = %%lld, but input[%%i].shape[%%i] = %%lld.", + {x}, + (long long int) non1size_dim{x}, + {j}, + {x}, + (long long int) %(lv{j})s_n{x} + ); + %(fail)s + }} """ + check += """ + } + """ return init % sub + check % sub +def compute_broadcast_dimensions(array_name: str, loop_orders, sub) -> str: + """Create c_code to compute broadcasted dimensions of multiple arrays, arising from + Elemwise operations. + + The code returned by this function populates the array `array_name`, but does not + initialize it. + + TODO: We can decide to either specialize C code even further given the input types + or make it general, regardless of whether static broadcastable information is given + """ + dims_c_code = "" + for i, candidates in enumerate(zip(*loop_orders)): + # TODO: Are candidates always either "x" or "i"? If that's the case we can + # simplify some logic here (e.g., we don't need to track the `idx`). + nonx_candidates = tuple( + (idx, c) for idx, c in enumerate(candidates) if c != "x" + ) + + # All inputs are known to be broadcastable + if not nonx_candidates: + dims_c_code += f"{array_name}[{i}] = 1;\n" + continue + + # There is only one informative source of size + if len(nonx_candidates) == 1: + idx, candidate = nonx_candidates[0] + var = sub[f"lv{int(idx)}"] + dims_c_code += f"{array_name}[{i}] = {var}_n{candidate};\n" + continue + + # In this case any non-size 1 variable will define the right size + dims_c_code += f"{array_name}[{i}] = " + for (idx, candidate) in nonx_candidates[:-1]: + var = sub[f"lv{int(idx)}"] + dims_c_code += f"({var}_n{candidate} != 1)? {var}_n{candidate}: " + idx, candidate = nonx_candidates[-1] + var = sub[f"lv{idx}"] + dims_c_code += f"{var}_n{candidate};\n" + return dims_c_code + + def make_alloc(loop_orders, dtype, sub, fortran="0"): """Generate C code to allocate outputs. @@ -125,20 +186,7 @@ def make_alloc(loop_orders, dtype, sub, fortran="0"): if type.startswith("AESARA_COMPLEX"): type = type.replace("AESARA_COMPLEX", "NPY_COMPLEX") nd = len(loop_orders[0]) - init_dims = "" - # For each dimension, the tensors are either all broadcasted, in - # which case the output will also be broadcastable (dimension = - # 1), or one or more are not broadcasted, in which case the number - # of elements of the output in that dimension will be equal to the - # number of elements of any of them. - for i, candidates in enumerate(zip(*loop_orders)): - for j, candidate in enumerate(candidates): - if candidate != "x": - var = sub[f"lv{int(j)}"] - init_dims += f"dims[{i}] = {var}_n{candidate};\n" - break - else: - init_dims += f"dims[{i}] = 1;\n" + init_dims = compute_broadcast_dimensions("dims", loop_orders, sub) # TODO: it would be interesting to allocate the output in such a # way that its contiguous dimensions match one of the input's @@ -310,26 +358,8 @@ def make_reordered_loop( """ # Get the (sorted) total number of iterations of each loop - # Get totals in the initial order - # For each dimension, the tensors are either all broadcasted, in - # which case there is only one iteration of the loop, or one or - # more are not broadcasted, in which case the number of elements - # of any of them will be equal to the number of iterations we have - # to do. - totals = [] - for i, candidates in enumerate(zip(*init_loop_orders)): - for j, candidate in enumerate(candidates): - if candidate != "x": - var = sub[f"lv{int(j)}"] - total = f"{var}_n{candidate}" - break - else: - total = "1" - totals.append(total) - - declare_totals = f""" - int init_totals[{nnested}] = {{{", ".join(totals)}}}; - """ + declare_totals = f"int init_totals[{nnested}];\n" + declare_totals += compute_broadcast_dimensions("init_totals", init_loop_orders, sub) # Sort totals to match the new order that was computed by sorting # the loop vector. One integer variable per loop is declared.

aesara-devs/aesara

b60cf7240a6d17ed80db2bd9b43c6faf377d64fe

diff --git a/tests/tensor/test_elemwise.py b/tests/tensor/test_elemwise.py index c2b2d230b..1b298a92a 100644 --- a/tests/tensor/test_elemwise.py +++ b/tests/tensor/test_elemwise.py @@ -206,77 +206,117 @@ class TestBroadcast: return np.asarray(np.random.random(shp), dtype=aesara.config.floatX) def with_linker(self, linker, op, type, rand_val): - for xsh, ysh in [ - ((3, 5), (3, 5)), - ((3, 5), (1, 5)), - ((3, 5), (3, 1)), - ((1, 5), (5, 1)), - ((1, 1), (1, 1)), - ((self.openmp_minsize,), (self.openmp_minsize,)), - ( - (self.openmp_minsize_sqrt, self.openmp_minsize_sqrt), - (self.openmp_minsize_sqrt, self.openmp_minsize_sqrt), - ), - ((2, 3, 4, 5), (2, 3, 4, 5)), - ((2, 3, 4, 5), (1, 3, 1, 5)), - ((2, 3, 4, 5), (1, 1, 1, 1)), - ((), ()), - ]: - x = type(aesara.config.floatX, [(entry == 1) for entry in xsh])("x") - y = type(aesara.config.floatX, [(entry == 1) for entry in ysh])("y") - e = op(aes.add)(x, y) - f = make_function(copy(linker).accept(FunctionGraph([x, y], [e]))) - xv = rand_val(xsh) - yv = rand_val(ysh) - zv = xv + yv - - unittest_tools.assert_allclose(f(xv, yv), zv) + for shape_info in ("complete", "only_broadcastable", "none"): + for xsh, ysh in [ + ((3, 5), (3, 5)), + ((3, 5), (1, 5)), + ((3, 5), (3, 1)), + ((1, 5), (5, 1)), + ((1, 1), (1, 1)), + ((self.openmp_minsize,), (self.openmp_minsize,)), + ( + (self.openmp_minsize_sqrt, self.openmp_minsize_sqrt), + (self.openmp_minsize_sqrt, self.openmp_minsize_sqrt), + ), + ((2, 3, 4, 5), (2, 3, 4, 5)), + ((2, 3, 4, 5), (1, 3, 1, 5)), + ((2, 3, 4, 5), (1, 1, 1, 1)), + ((), ()), + ]: + if shape_info == "complete": + x_type = type(aesara.config.floatX, shape=xsh) + y_type = type(aesara.config.floatX, shape=ysh) + elif shape_info == "only_broadcastable": + # This condition is here for backwards compatibility, when the only + # type shape provided by Aesara was broadcastable/non-broadcastable + x_type = type( + aesara.config.floatX, + broadcastable=[(entry == 1) for entry in xsh], + ) + y_type = type( + aesara.config.floatX, + broadcastable=[(entry == 1) for entry in ysh], + ) + else: + x_type = type(aesara.config.floatX, shape=[None for _ in xsh]) + y_type = type(aesara.config.floatX, shape=[None for _ in ysh]) - # test Elemwise.infer_shape - # the Shape op don't implement c_code! - if isinstance(linker, PerformLinker): - x = type(aesara.config.floatX, [(entry == 1) for entry in xsh])("x") - y = type(aesara.config.floatX, [(entry == 1) for entry in ysh])("y") + x = x_type("x") + y = y_type("y") e = op(aes.add)(x, y) - f = make_function(copy(linker).accept(FunctionGraph([x, y], [e.shape]))) - assert tuple(f(xv, yv)) == tuple(zv.shape) + f = make_function(copy(linker).accept(FunctionGraph([x, y], [e]))) + xv = rand_val(xsh) + yv = rand_val(ysh) + zv = xv + yv - def with_linker_inplace(self, linker, op, type, rand_val): - for xsh, ysh in [ - ((5, 5), (5, 5)), - ((5, 5), (1, 5)), - ((5, 5), (5, 1)), - ((1, 1), (1, 1)), - ((2, 3, 4, 5), (2, 3, 4, 5)), - ((2, 3, 4, 5), (1, 3, 1, 5)), - ((2, 3, 4, 5), (1, 1, 1, 1)), - ((), ()), - ]: - x = type(aesara.config.floatX, [(entry == 1) for entry in xsh])("x") - y = type(aesara.config.floatX, [(entry == 1) for entry in ysh])("y") - e = op(aes.Add(aes.transfer_type(0)), {0: 0})(x, y) - f = make_function(copy(linker).accept(FunctionGraph([x, y], [e]))) - xv = rand_val(xsh) - yv = rand_val(ysh) - zv = xv + yv + unittest_tools.assert_allclose(f(xv, yv), zv) - f(xv, yv) + # test Elemwise.infer_shape + # the Shape op don't implement c_code! + if isinstance(linker, PerformLinker): + x = x_type("x") + y = y_type("y") + e = op(aes.add)(x, y) + f = make_function( + copy(linker).accept(FunctionGraph([x, y], [e.shape])) + ) + assert tuple(f(xv, yv)) == tuple(zv.shape) - assert (xv == zv).all() - # test Elemwise.infer_shape - # the Shape op don't implement c_code! - if isinstance(linker, PerformLinker): - x = type(aesara.config.floatX, [(entry == 1) for entry in xsh])("x") - y = type(aesara.config.floatX, [(entry == 1) for entry in ysh])("y") + def with_linker_inplace(self, linker, op, type, rand_val): + for shape_info in ("complete", "only_broadcastable", "none"): + for xsh, ysh in [ + ((5, 5), (5, 5)), + ((5, 5), (1, 5)), + ((5, 5), (5, 1)), + ((1, 1), (1, 1)), + ((2, 3, 4, 5), (2, 3, 4, 5)), + ((2, 3, 4, 5), (1, 3, 1, 5)), + ((2, 3, 4, 5), (1, 1, 1, 1)), + ((), ()), + ]: + if shape_info == "complete": + x_type = type(aesara.config.floatX, shape=xsh) + y_type = type(aesara.config.floatX, shape=ysh) + elif shape_info == "only_broadcastable": + # This condition is here for backwards compatibility, when the only + # type shape provided by Aesara was broadcastable/non-broadcastable + x_type = type( + aesara.config.floatX, + broadcastable=[(entry == 1) for entry in xsh], + ) + y_type = type( + aesara.config.floatX, + broadcastable=[(entry == 1) for entry in ysh], + ) + else: + x_type = type(aesara.config.floatX, shape=[None for _ in xsh]) + y_type = type(aesara.config.floatX, shape=[None for _ in ysh]) + + x = x_type("x") + y = y_type("y") e = op(aes.Add(aes.transfer_type(0)), {0: 0})(x, y) - f = make_function(copy(linker).accept(FunctionGraph([x, y], [e.shape]))) + f = make_function(copy(linker).accept(FunctionGraph([x, y], [e]))) xv = rand_val(xsh) yv = rand_val(ysh) zv = xv + yv f(xv, yv) - assert xv.shape == zv.shape + assert (xv == zv).all() + # test Elemwise.infer_shape + # the Shape op don't implement c_code! + if isinstance(linker, PerformLinker): + x = x_type("x") + y = y_type("y") + e = op(aes.Add(aes.transfer_type(0)), {0: 0})(x, y) + f = make_function( + copy(linker).accept(FunctionGraph([x, y], [e.shape])) + ) + xv = rand_val(xsh) + yv = rand_val(ysh) + zv = xv + yv + assert xv.shape == zv.shape + assert tuple(f(xv, yv)) == zv.shape def test_perform(self): self.with_linker(PerformLinker(), self.op, self.type, self.rand_val) @@ -746,10 +786,6 @@ class TestElemwise(unittest_tools.InferShapeTester): def test_input_dimensions_match_python(self): self.check_input_dimensions_match(Mode(linker="py")) - @pytest.mark.xfail( - reason="Elemwise C implementation does not broadcast parameters", - exception=ValueError, - ) @pytest.mark.skipif( not aesara.config.cxx, reason="G++ not available, so we need to skip this test." )

C Elemwise implementation doesn't broadcast variables I'm seeing a very weird error in `Elemwise`: First, here's a basic broadcasting operations in NumPy: ```python import numpy as np x = np.array([[-1.32720483], [ 0.23442016]]) m = np.array([0., 0.]) z = x - m ``` ```python >>> z array([[-1.32720483, -1.32720483], [ 0.23442016, 0.23442016]]) ``` In Aesara, here's the equivalent operation using `TensorConstant`s: ```python import aesara import aesara.tensor as at x_at = at.as_tensor(x) m_at = at.as_tensor(m) z_at = x_at - m_at ``` ```python >>> aesara.dprint(z_at) Elemwise{sub,no_inplace} [id A] '' |TensorConstant{[[-1.32720..23442016]]} [id B] |InplaceDimShuffle{x,0} [id C] '' |TensorConstant{(2,) of 0.0} [id D] ``` The resulting graph is a simple `Elemwise` for the subtraction `Op`–as expected. There's also an `InplaceDimShuffle` that adds a broadcastable dimension to the second argument, so that both inputs have the same number of dimensions. This `InplaceDimShuffle` is equivalent to `np.expand_dims(m, 0)`, which–when subtracted from `x`–yields the same value as `z`. So far, everything is good, because ```python >>> np.array_equal(aesara.function([], z_at)(), z) True ``` Now, when we replace the `TensorConstant`s with generic `TensorVariable`s, we get a strange error: ```python x_v = at.matrix("x") m_v = at.vector("m") z_v = x_v - m_v ``` ```python >>> aesara.function([x_v, m_v], z_v)(x, m) <ipython-input-23-66cc28afa70f> in <module> ----> 1 aesara.function([x_v, m_v], z_v)(x, m) ~/projects/code/python/Aesara/aesara/compile/function/types.py in __call__(self, *args, **kwargs) 989 node=self.fn.nodes[self.fn.position_of_error], 990 thunk=thunk, --> 991 storage_map=getattr(self.fn, "storage_map", None), 992 ) 993 else: ~/projects/code/python/Aesara/aesara/link/utils.py in raise_with_op(fgraph, node, thunk, exc_info, storage_map) 506 # Some exception need extra parameter in inputs. So forget the 507 # extra long error message in that case. --> 508 raise exc_value.with_traceback(exc_trace) 509 510 ~/projects/code/python/Aesara/aesara/compile/function/types.py in __call__(self, *args, **kwargs) 973 outputs = ( 974 self.fn() --> 975 if output_subset is None 976 else self.fn(output_subset=output_subset) 977 ) ValueError: Input dimension mis-match. (input[0].shape[1] = 1, input[1].shape[1] = 2) Apply node that caused the error: Elemwise{sub,no_inplace}(x, InplaceDimShuffle{x,0}.0) Toposort index: 1 Inputs types: [TensorType(float64, matrix), TensorType(float64, row)] Inputs shapes: [(2, 1), (1, 2)] Inputs strides: [(8, 8), (16, 8)] Inputs values: [array([[-1.32720483], [ 0.23442016]]), array([[0., 0.]])] Outputs clients: [['output']] ``` We can emulate this issue using the Python implementation of `Elemwise`, as well: ```python >>> aesara.function([x_v, m_v], z_v, mode="FAST_COMPILE")(x, m) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) ~/projects/code/python/Aesara/aesara/link/vm.py in __call__(self) 312 ): --> 313 thunk() 314 for old_s in old_storage: ~/projects/code/python/Aesara/aesara/graph/op.py in rval(p, i, o, n) 472 def rval(p=p, i=node_input_storage, o=node_output_storage, n=node): --> 473 r = p(n, [x[0] for x in i], o) 474 for o in node.outputs: ~/projects/code/python/Aesara/aesara/tensor/elemwise.py in perform(self, node, inputs, output_storage) 760 base_exc_str = f"Dimension mismatch; shapes are {', '.join(msg)}" --> 761 raise ValueError(base_exc_str) 762 ValueError: Dimension mismatch; shapes are (2, 1), (*, 2) ``` From this output, we can see that this erroneous error is apparently the result of some bad input validation code in `Elemwise`. The same is true for the C implementation, although that's a little less apparent from the output. In this case, the C code for this validation step is [here](https://github.com/pymc-devs/aesara/blob/master/aesara/tensor/elemwise_cgen.py#L98).

0.0

b60cf7240a6d17ed80db2bd9b43c6faf377d64fe

[ "tests/tensor/test_elemwise.py::TestBroadcast::test_c", "tests/tensor/test_elemwise.py::TestBroadcast::test_c_inplace", "tests/tensor/test_elemwise.py::TestElemwise::test_input_dimensions_match_c" ]

[ "tests/tensor/test_elemwise.py::TestDimShuffle::test_perform", "tests/tensor/test_elemwise.py::TestDimShuffle::test_c_or_py", "tests/tensor/test_elemwise.py::TestDimShuffle::test_infer_shape", "tests/tensor/test_elemwise.py::TestDimShuffle::test_c_views", "tests/tensor/test_elemwise.py::TestDimShuffle::test_memory_leak[True]", "tests/tensor/test_elemwise.py::TestDimShuffle::test_memory_leak[False]", "tests/tensor/test_elemwise.py::TestDimShuffle::test_static_shape", "tests/tensor/test_elemwise.py::TestBroadcast::test_perform", "tests/tensor/test_elemwise.py::TestBroadcast::test_perform_inplace", "tests/tensor/test_elemwise.py::TestBroadcast::test_fill", "tests/tensor/test_elemwise.py::TestBroadcast::test_fill_var", "tests/tensor/test_elemwise.py::TestBroadcast::test_fill_grad", "tests/tensor/test_elemwise.py::TestBroadcast::test_weird_strides", "tests/tensor/test_elemwise.py::TestBroadcast::test_same_inputs", "tests/tensor/test_elemwise.py::TestCAReduce::test_perform_noopt", "tests/tensor/test_elemwise.py::TestCAReduce::test_perform_nan", "tests/tensor/test_elemwise.py::TestCAReduce::test_c_noopt", "tests/tensor/test_elemwise.py::TestCAReduce::test_infer_shape", "tests/tensor/test_elemwise.py::TestCAReduce::test_str", "tests/tensor/test_elemwise.py::TestBitOpReduceGrad::test_all_grad", "tests/tensor/test_elemwise.py::TestBitOpReduceGrad::test_any_grad", "tests/tensor/test_elemwise.py::TestElemwise::test_elemwise_grad_bool", "tests/tensor/test_elemwise.py::TestElemwise::test_infer_shape", "tests/tensor/test_elemwise.py::TestElemwise::test_input_dimensions_overflow", "tests/tensor/test_elemwise.py::TestElemwise::test_input_dimensions_match_python", "tests/tensor/test_elemwise.py::TestElemwise::test_str", "tests/tensor/test_elemwise.py::test_not_implemented_elemwise_grad" ]

{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2022-04-25 12:50:52+00:00

bsd-3-clause

911

aesara-devs__aesara-968

diff --git a/aesara/compile/function/types.py b/aesara/compile/function/types.py index 8aa1e3ee8..d1f9eae2f 100644 --- a/aesara/compile/function/types.py +++ b/aesara/compile/function/types.py @@ -785,6 +785,8 @@ class Function: f_cpy.finder[swap[in_ori.variable]] = container in_cpy.variable = swap[in_ori.variable] + f_cpy.trust_input = self.trust_input + f_cpy.unpack_single = self.unpack_single f_cpy.name = name f_cpy.maker.fgraph.name = name return f_cpy

aesara-devs/aesara

104dc0379c3585a0bc8ebb87f61f2ae38d101b83

diff --git a/tests/compile/function/test_types.py b/tests/compile/function/test_types.py index 61322a2e7..ea8b81986 100644 --- a/tests/compile/function/test_types.py +++ b/tests/compile/function/test_types.py @@ -299,7 +299,7 @@ class TestFunction: t() def test_copy(self): - a = scalar() # the a is for 'anonymous' (un-named). + a = scalar() x, s = scalars("xs") f = function( @@ -312,26 +312,34 @@ class TestFunction: ) g = copy.copy(f) - # if they both return, assume that they return equivalent things. + + assert f.unpack_single == g.unpack_single + assert f.trust_input == g.trust_input assert g.container[x].storage is not f.container[x].storage assert g.container[a].storage is not f.container[a].storage assert g.container[s].storage is not f.container[s].storage - assert g.value[a] is f.value[a] # should not have been copied - assert ( - g.value[s] is not f.value[s] - ) # should have been copied because it is mutable. - assert not (g.value[s] != f.value[s]).any() # its contents should be identical + # Should not have been copied + assert g.value[a] is f.value[a] - assert f(2, 1) == g( - 2 - ) # they should be in sync, default value should be copied. - assert f(2, 1) == g( - 2 - ) # they should be in sync, default value should be copied. - f(1, 2) # put them out of sync - assert f(1, 2) != g(1, 2) # they should not be equal anymore. + # Should have been copied because it is mutable + assert g.value[s] is not f.value[s] + + # Their contents should be equal, though + assert np.array_equal(g.value[s], f.value[s]) + + # They should be in sync, default value should be copied + assert np.array_equal(f(2, 1), g(2)) + + # They should be in sync, default value should be copied + assert np.array_equal(f(2, 1), g(2)) + + # Put them out of sync + f(1, 2) + + # They should not be equal anymore + assert not np.array_equal(f(1, 2), g(1, 2)) def test_copy_share_memory(self): x = fscalar("x") @@ -478,9 +486,9 @@ class TestFunction: ori = function([x], out, mode=mode, updates={z: z * 2}) cpy = ori.copy(delete_updates=True) - assert cpy(1)[0] == 4 - assert cpy(1)[0] == 4 - assert cpy(1)[0] == 4 + assert cpy(1) == 4 + assert cpy(1) == 4 + assert cpy(1) == 4 # Test if unused implicit and explicit inputs from delete_updates # are ignored as intended.

Copied function does not respect original single output format ```python import aesara import aesara.tensor as at f1 = aesara.function([], at.constant(1.0)) f2 = f1.copy() print(f1(), f2()) # 1.0 [array(1., dtype=float32)] ```

0.0

104dc0379c3585a0bc8ebb87f61f2ae38d101b83

[ "tests/compile/function/test_types.py::TestFunction::test_copy", "tests/compile/function/test_types.py::TestFunction::test_copy_delete_updates" ]

[ "tests/compile/function/test_types.py::TestFunction::test_empty", "tests/compile/function/test_types.py::TestFunction::test_extra_inputs", "tests/compile/function/test_types.py::TestFunction::test_missing_inputs", "tests/compile/function/test_types.py::TestFunction::test_input_anon_singleton", "tests/compile/function/test_types.py::TestFunction::test_input_anon_unpack", "tests/compile/function/test_types.py::TestFunction::test_naming_rule0", "tests/compile/function/test_types.py::TestFunction::test_naming_rule1", "tests/compile/function/test_types.py::TestFunction::test_naming_rule2", "tests/compile/function/test_types.py::TestFunction::test_naming_rule3", "tests/compile/function/test_types.py::TestFunction::test_naming_rule4", "tests/compile/function/test_types.py::TestFunction::test_state_access[mode0]", "tests/compile/function/test_types.py::TestFunction::test_state_access[mode2]", "tests/compile/function/test_types.py::TestFunction::test_state_access[mode3]", "tests/compile/function/test_types.py::TestFunction::test_same_names", "tests/compile/function/test_types.py::TestFunction::test_weird_names", "tests/compile/function/test_types.py::TestFunction::test_copy_share_memory", "tests/compile/function/test_types.py::TestFunction::test_swap_SharedVariable", "tests/compile/function/test_types.py::TestFunction::test_swap_SharedVariable_with_given", "tests/compile/function/test_types.py::TestFunction::test_shared_state0", "tests/compile/function/test_types.py::TestFunction::test_shared_state1", "tests/compile/function/test_types.py::TestFunction::test_shared_state2", "tests/compile/function/test_types.py::TestFunction::test_shared_state_not_implicit", "tests/compile/function/test_types.py::TestFunction::test_constant_output", "tests/compile/function/test_types.py::TestFunction::test_borrow_input", "tests/compile/function/test_types.py::TestFunction::test_borrow_output", "tests/compile/function/test_types.py::TestFunction::test_disconnected_input", "tests/compile/function/test_types.py::TestFunction::test_masked_input", "tests/compile/function/test_types.py::TestFunction::test_givens_input_var", "tests/compile/function/test_types.py::TestFunction::test_free", "tests/compile/function/test_types.py::TestFunction::test_default_values", "tests/compile/function/test_types.py::TestFunction::test_check_for_aliased_inputs", "tests/compile/function/test_types.py::TestPicklefunction::test_deepcopy", "tests/compile/function/test_types.py::TestPicklefunction::test_deepcopy_trust_input", "tests/compile/function/test_types.py::TestPicklefunction::test_output_keys", "tests/compile/function/test_types.py::TestPicklefunction::test_deepcopy_shared_container", "tests/compile/function/test_types.py::TestPicklefunction::test_pickle", "tests/compile/function/test_types.py::TestPicklefunction::test_multiple_functions", "tests/compile/function/test_types.py::TestPicklefunction::test_pickle_class_with_functions", "tests/compile/function/test_types.py::test_empty_givens_updates" ]

{ "failed_lite_validators": [ "has_short_problem_statement" ], "has_test_patch": true, "is_lite": false }

2022-05-20 03:14:15+00:00

bsd-3-clause

912

aesara-devs__aesara-995

diff --git a/aesara/graph/type.py b/aesara/graph/type.py index f26d72664..f35a6d969 100644 --- a/aesara/graph/type.py +++ b/aesara/graph/type.py @@ -180,10 +180,10 @@ class Type(MetaObject): return None - def is_valid_value(self, data: D) -> bool: + def is_valid_value(self, data: D, strict: bool = True) -> bool: """Return ``True`` for any python object that would be a legal value for a `Variable` of this `Type`.""" try: - self.filter(data, strict=True) + self.filter(data, strict=strict) return True except (TypeError, ValueError): return False diff --git a/aesara/tensor/random/type.py b/aesara/tensor/random/type.py index ff00669c4..68373b08c 100644 --- a/aesara/tensor/random/type.py +++ b/aesara/tensor/random/type.py @@ -1,9 +1,14 @@ +from typing import Generic, TypeVar + import numpy as np import aesara from aesara.graph.type import Type +T = TypeVar("T", np.random.RandomState, np.random.Generator) + + gen_states_keys = { "MT19937": (["state"], ["key", "pos"]), "PCG64": (["state", "has_uint32", "uinteger"], ["state", "inc"]), @@ -18,22 +23,15 @@ gen_states_keys = { numpy_bit_gens = {0: "MT19937", 1: "PCG64", 2: "Philox", 3: "SFC64"} -class RandomType(Type): +class RandomType(Type, Generic[T]): r"""A Type wrapper for `numpy.random.Generator` and `numpy.random.RandomState`.""" - @classmethod - def filter(cls, data, strict=False, allow_downcast=None): - if cls.is_valid_value(data, strict): - return data - else: - raise TypeError() - @staticmethod - def may_share_memory(a, b): + def may_share_memory(a: T, b: T): return a._bit_generator is b._bit_generator -class RandomStateType(RandomType): +class RandomStateType(RandomType[np.random.RandomState]): r"""A Type wrapper for `numpy.random.RandomState`. The reason this exists (and `Generic` doesn't suffice) is that @@ -49,28 +47,38 @@ class RandomStateType(RandomType): def __repr__(self): return "RandomStateType" - @staticmethod - def is_valid_value(a, strict): - if isinstance(a, np.random.RandomState): - return True + def filter(self, data, strict: bool = False, allow_downcast=None): + """ + XXX: This doesn't convert `data` to the same type of underlying RNG type + as `self`. It really only checks that `data` is of the appropriate type + to be a valid `RandomStateType`. + + In other words, it serves as a `Type.is_valid_value` implementation, + but, because the default `Type.is_valid_value` depends on + `Type.filter`, we need to have it here to avoid surprising circular + dependencies in sub-classes. + """ + if isinstance(data, np.random.RandomState): + return data - if not strict and isinstance(a, dict): + if not strict and isinstance(data, dict): gen_keys = ["bit_generator", "gauss", "has_gauss", "state"] state_keys = ["key", "pos"] for key in gen_keys: - if key not in a: - return False + if key not in data: + raise TypeError() for key in state_keys: - if key not in a["state"]: - return False + if key not in data["state"]: + raise TypeError() - state_key = a["state"]["key"] + state_key = data["state"]["key"] if state_key.shape == (624,) and state_key.dtype == np.uint32: - return True + # TODO: Add an option to convert to a `RandomState` instance? + return data - return False + raise TypeError() @staticmethod def values_eq(a, b): @@ -114,7 +122,7 @@ aesara.compile.register_view_op_c_code( random_state_type = RandomStateType() -class RandomGeneratorType(RandomType): +class RandomGeneratorType(RandomType[np.random.Generator]): r"""A Type wrapper for `numpy.random.Generator`. The reason this exists (and `Generic` doesn't suffice) is that @@ -130,16 +138,25 @@ class RandomGeneratorType(RandomType): def __repr__(self): return "RandomGeneratorType" - @staticmethod - def is_valid_value(a, strict): - if isinstance(a, np.random.Generator): - return True + def filter(self, data, strict=False, allow_downcast=None): + """ + XXX: This doesn't convert `data` to the same type of underlying RNG type + as `self`. It really only checks that `data` is of the appropriate type + to be a valid `RandomGeneratorType`. + + In other words, it serves as a `Type.is_valid_value` implementation, + but, because the default `Type.is_valid_value` depends on + `Type.filter`, we need to have it here to avoid surprising circular + dependencies in sub-classes. + """ + if isinstance(data, np.random.Generator): + return data - if not strict and isinstance(a, dict): - if "bit_generator" not in a: - return False + if not strict and isinstance(data, dict): + if "bit_generator" not in data: + raise TypeError() else: - bit_gen_key = a["bit_generator"] + bit_gen_key = data["bit_generator"] if hasattr(bit_gen_key, "_value"): bit_gen_key = int(bit_gen_key._value) @@ -148,16 +165,16 @@ class RandomGeneratorType(RandomType): gen_keys, state_keys = gen_states_keys[bit_gen_key] for key in gen_keys: - if key not in a: - return False + if key not in data: + raise TypeError() for key in state_keys: - if key not in a["state"]: - return False + if key not in data["state"]: + raise TypeError() - return True + return data - return False + raise TypeError() @staticmethod def values_eq(a, b):

aesara-devs/aesara

174117f9b0a2c1ddb13e6244bbb31d6c75c12245

diff --git a/tests/tensor/random/test_type.py b/tests/tensor/random/test_type.py index 5f45af2fe..a34d4cbad 100644 --- a/tests/tensor/random/test_type.py +++ b/tests/tensor/random/test_type.py @@ -56,15 +56,17 @@ class TestRandomStateType: with pytest.raises(TypeError): rng_type.filter(1) - rng = rng.get_state(legacy=False) - assert rng_type.is_valid_value(rng, strict=False) + rng_dict = rng.get_state(legacy=False) - rng["state"] = {} + assert rng_type.is_valid_value(rng_dict) is False + assert rng_type.is_valid_value(rng_dict, strict=False) - assert rng_type.is_valid_value(rng, strict=False) is False + rng_dict["state"] = {} - rng = {} - assert rng_type.is_valid_value(rng, strict=False) is False + assert rng_type.is_valid_value(rng_dict, strict=False) is False + + rng_dict = {} + assert rng_type.is_valid_value(rng_dict, strict=False) is False def test_values_eq(self): @@ -147,15 +149,17 @@ class TestRandomGeneratorType: with pytest.raises(TypeError): rng_type.filter(1) - rng = rng.__getstate__() - assert rng_type.is_valid_value(rng, strict=False) + rng_dict = rng.__getstate__() + + assert rng_type.is_valid_value(rng_dict) is False + assert rng_type.is_valid_value(rng_dict, strict=False) - rng["state"] = {} + rng_dict["state"] = {} - assert rng_type.is_valid_value(rng, strict=False) is False + assert rng_type.is_valid_value(rng_dict, strict=False) is False - rng = {} - assert rng_type.is_valid_value(rng, strict=False) is False + rng_dict = {} + assert rng_type.is_valid_value(rng_dict, strict=False) is False def test_values_eq(self):

Error w/ deepcopy of pymc v4 model ## Generating a deep copy of pymc v4 model results in aesara error **Please provide a minimal, self-contained, and reproducible example.** ```python from copy import deepcopy import numpy as np import pymc as pm RANDOM_SEED = 8927 rng = np.random.default_rng(RANDOM_SEED) # True parameter values alpha, sigma = 1, 1 beta = [1, 2.5] # Size of dataset size = 100 # Predictor variable X1 = np.random.randn(size) X2 = np.random.randn(size) * 0.2 # Simulate outcome variable Y = alpha + beta[0] * X1 + beta[1] * X2 + rng.normal(size=size) * sigma basic_model = pm.Model() with basic_model: # Priors for unknown model parameters alpha = pm.Normal("alpha", mu=0, sigma=10) beta = pm.Normal("beta", mu=0, sigma=10, shape=2) sigma = pm.HalfNormal("sigma", sigma=1) # Expected value of outcome mu = alpha + beta[0] * X1 + beta[1] * X2 # Likelihood (sampling distribution) of observations Y_obs = pm.Normal("Y_obs", mu=mu, sigma=sigma, observed=Y) model_copy = deepcopy(basic_model) ``` **Please provide the full traceback of any errors.** ```python --------------------------------------------------------------------------- TypeError Traceback (most recent call last) Input In [9], in <cell line: 41>() 38 # Likelihood (sampling distribution) of observations 39 Y_obs = pm.Normal("Y_obs", mu=mu, sigma=sigma, observed=Y) ---> 41 model_copy = deepcopy(basic_model) File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:172, in deepcopy(x, memo, _nil) 170 y = x 171 else: --> 172 y = _reconstruct(x, memo, *rv) 174 # If is its own copy, don't memoize. 175 if y is not x: File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:270, in _reconstruct(x, memo, func, args, state, listiter, dictiter, deepcopy) 268 if state is not None: 269 if deep: --> 270 state = deepcopy(state, memo) 271 if hasattr(y, '__setstate__'): 272 y.__setstate__(state) File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:146, in deepcopy(x, memo, _nil) 144 copier = _deepcopy_dispatch.get(cls) 145 if copier is not None: --> 146 y = copier(x, memo) 147 else: 148 if issubclass(cls, type): File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:230, in _deepcopy_dict(x, memo, deepcopy) 228 memo[id(x)] = y 229 for key, value in x.items(): --> 230 y[deepcopy(key, memo)] = deepcopy(value, memo) 231 return y File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:146, in deepcopy(x, memo, _nil) 144 copier = _deepcopy_dispatch.get(cls) 145 if copier is not None: --> 146 y = copier(x, memo) 147 else: 148 if issubclass(cls, type): File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:230, in _deepcopy_dict(x, memo, deepcopy) 228 memo[id(x)] = y 229 for key, value in x.items(): --> 230 y[deepcopy(key, memo)] = deepcopy(value, memo) 231 return y File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:172, in deepcopy(x, memo, _nil) 170 y = x 171 else: --> 172 y = _reconstruct(x, memo, *rv) 174 # If is its own copy, don't memoize. 175 if y is not x: File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:270, in _reconstruct(x, memo, func, args, state, listiter, dictiter, deepcopy) 268 if state is not None: 269 if deep: --> 270 state = deepcopy(state, memo) 271 if hasattr(y, '__setstate__'): 272 y.__setstate__(state) [... skipping similar frames: _deepcopy_dict at line 230 (1 times), deepcopy at line 146 (1 times)] File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:172, in deepcopy(x, memo, _nil) 170 y = x 171 else: --> 172 y = _reconstruct(x, memo, *rv) 174 # If is its own copy, don't memoize. 175 if y is not x: File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:270, in _reconstruct(x, memo, func, args, state, listiter, dictiter, deepcopy) 268 if state is not None: 269 if deep: --> 270 state = deepcopy(state, memo) 271 if hasattr(y, '__setstate__'): 272 y.__setstate__(state) [... skipping similar frames: deepcopy at line 146 (1 times)] File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:230, in _deepcopy_dict(x, memo, deepcopy) 228 memo[id(x)] = y 229 for key, value in x.items(): --> 230 y[deepcopy(key, memo)] = deepcopy(value, memo) 231 return y File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:146, in deepcopy(x, memo, _nil) 144 copier = _deepcopy_dispatch.get(cls) 145 if copier is not None: --> 146 y = copier(x, memo) 147 else: 148 if issubclass(cls, type): File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:205, in _deepcopy_list(x, memo, deepcopy) 203 append = y.append 204 for a in x: --> 205 append(deepcopy(a, memo)) 206 return y File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:172, in deepcopy(x, memo, _nil) 170 y = x 171 else: --> 172 y = _reconstruct(x, memo, *rv) 174 # If is its own copy, don't memoize. 175 if y is not x: File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:270, in _reconstruct(x, memo, func, args, state, listiter, dictiter, deepcopy) 268 if state is not None: 269 if deep: --> 270 state = deepcopy(state, memo) 271 if hasattr(y, '__setstate__'): 272 y.__setstate__(state) File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:146, in deepcopy(x, memo, _nil) 144 copier = _deepcopy_dispatch.get(cls) 145 if copier is not None: --> 146 y = copier(x, memo) 147 else: 148 if issubclass(cls, type): File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:230, in _deepcopy_dict(x, memo, deepcopy) 228 memo[id(x)] = y 229 for key, value in x.items(): --> 230 y[deepcopy(key, memo)] = deepcopy(value, memo) 231 return y File ~\AppData\Local\Programs\Python\Python39\lib\copy.py:153, in deepcopy(x, memo, _nil) 151 copier = getattr(x, "__deepcopy__", None) 152 if copier is not None: --> 153 y = copier(memo) 154 else: 155 reductor = dispatch_table.get(cls) File ~\.virtualenvs\pymc4-venv\lib\site-packages\aesara\link\basic.py:142, in Container.__deepcopy__(self, memo) 132 r = type(self)( 133 deepcopy(self.type, memo=memo), 134 deepcopy(self.storage, memo=memo), (...) 138 name=deepcopy(self.name, memo=memo), 139 ) 140 # Work around NumPy deepcopy of ndarray with 0 dimension that 141 # don't return an ndarray. --> 142 if r.storage[0] is not None and not self.type.is_valid_value(r.storage[0]): 143 assert not data_was_in_memo 144 assert self.type.is_valid_value(self.storage[0]) TypeError: is_valid_value() missing 1 required positional argument: 'strict' ``` This used to work on pymc3 and theano-pymc ## Versions and main components * Aesara version: 2.66 * Aesara config (`python -c "import aesara; print(aesara.config)"`) * Python version: 3.9 * Operating system: Windows * How did you install Aesara: pip * Pymc version: 4.0

0.0

174117f9b0a2c1ddb13e6244bbb31d6c75c12245

[ "tests/tensor/random/test_type.py::TestRandomStateType::test_filter" ]

[ "tests/tensor/random/test_type.py::test_view_op_c_code", "tests/tensor/random/test_type.py::TestRandomStateType::test_pickle", "tests/tensor/random/test_type.py::TestRandomStateType::test_repr", "tests/tensor/random/test_type.py::TestRandomStateType::test_values_eq", "tests/tensor/random/test_type.py::TestRandomStateType::test_may_share_memory", "tests/tensor/random/test_type.py::TestRandomGeneratorType::test_pickle", "tests/tensor/random/test_type.py::TestRandomGeneratorType::test_repr", "tests/tensor/random/test_type.py::TestRandomGeneratorType::test_may_share_memory" ]

{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2022-06-14 17:50:52+00:00

bsd-3-clause

913

agrc__sweeper-51

diff --git a/.gitignore b/.gitignore index 9fbddef..1fe895c 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,4 @@ __pycache__ dist/ build/ +.env/ diff --git a/.vscode/settings.json b/.vscode/settings.json index 1d21cf6..40c0fd3 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -12,6 +12,7 @@ "pformat", "posix", "pypi", + "pytest", "sdist", "usaddress", "xxhash" diff --git a/readme.md b/readme.md index b9dcff1..d9d1c5f 100644 --- a/readme.md +++ b/readme.md @@ -80,7 +80,7 @@ A normalized string representing the entire address that was passed into the con 1. install required dependencies to work on sweeper - `pip install -e ".[develop]"` 1. install required dependencies to run sweeper tests - - `pip install -e ".[test]"` + - `pip install -e ".[tests]"` 1. run tests: `pytest` ### Uploading to pypi.org diff --git a/src/sweeper/address_parser.py b/src/sweeper/address_parser.py index 5e61825..5cccd1d 100644 --- a/src/sweeper/address_parser.py +++ b/src/sweeper/address_parser.py @@ -7,19 +7,20 @@ A module that parses street addresses into their various parts. import json import pprint from os.path import dirname, join, realpath +from re import compile import usaddress TAG_MAPPING = { 'AddressNumber': 'address_number', - # 'AddressNumberPrefix': 'address1', + 'AddressNumberPrefix': 'address_number', 'AddressNumberSuffix': 'address_number_suffix', 'StreetNamePreDirectional': 'prefix_direction', 'StreetName': 'street_name', - # 'StreetNamePreModifier': 'address1', - # 'StreetNamePreType': 'address1', + # 'StreetNamePreModifier': 'street_name', #: handled in class below + # 'StreetNamePreType': 'street_name', #: handled in class below 'StreetNamePostDirectional': 'street_direction', - # 'StreetNamePostModifier': 'address1', + 'StreetNamePostModifier': 'street_type', 'StreetNamePostType': 'street_type', # 'CornerOf': 'address1', # 'IntersectionSeparator': 'address1', @@ -28,7 +29,7 @@ TAG_MAPPING = { # 'USPSBoxGroupType': 'address1', # 'USPSBoxID': 'address1', # 'USPSBoxType': 'address1', - # 'BuildingName': 'address2', + 'BuildingName': 'unit_id', 'OccupancyType': 'unit_type', 'OccupancyIdentifier': 'unit_id', # 'SubaddressIdentifier': 'address2', @@ -41,6 +42,7 @@ TAG_MAPPING = { TWO_CHAR_DIRECTIONS = ['NO', 'SO', 'EA', 'WE'] with open(join(dirname(realpath(__file__)), 'street_types.json'), 'r') as file: STREET_TYPES = json.loads(file.read()) +HWY_REGEX = compile('(SR|STATE ROUTE|HIGHWAY)') class Address(): @@ -77,6 +79,19 @@ class Address(): if self.po_box is not None: return + try: + #: e.g. US HWY + self.street_name = f'{normalize_street_name_pre_type(self.StreetNamePreType)} {self.street_name}' + del self.StreetNamePreType + except AttributeError: + pass + + try: + self.street_name = f'{self.StreetNamePreModifier} {self.street_name}' + del self.StreetNamePreModifier + except AttributeError: + pass + #: look for two-character prefix directions which usaddress does not handle if self.street_name: street_name_parts = self.street_name.split(' ') @@ -135,6 +150,7 @@ def normalize_direction(direction_text): return direction_text[0].upper() + def normalize_street_type(type_text): ''' returns the standard abbreviation for the input street type @@ -148,6 +164,14 @@ def normalize_street_type(type_text): raise InvalidStreetTypeError(type_text) +def normalize_street_name_pre_type(text): + '''normalizes highways by doing things like replaces SR with HWY and removes US + + No need to worried about casing or "."s because usaddress has already taken care of them by this point. + ''' + return HWY_REGEX.sub('HWY', text).replace('US ', '') + + class InvalidStreetTypeError(Exception): ''' exception for when the street type does not have a corresponding value in street_types.json

agrc/sweeper

75254926a9de985e82bb2fa116948302d4fb8abe

diff --git a/src/sweeper/tests/test_address_parser.py b/src/sweeper/tests/test_address_parser.py index c4f2caf..ae08739 100644 --- a/src/sweeper/tests/test_address_parser.py +++ b/src/sweeper/tests/test_address_parser.py @@ -386,3 +386,89 @@ class TestBadAddresses(): assert address.street_name is None assert address.address_number == '100' assert address.prefix_direction == 'S' + + +class TestHighways(): + '''tests to make sure that state routes and us highways are parsed correctly + ''' + + def test_state_routes(self): + address = Address('910 S SR 22') + + assert address.address_number == '910' + assert address.prefix_direction == 'S' + assert address.street_name == 'HWY 22' + assert address.normalized == '910 S HWY 22' + + def test_state_route_expanded(self): + address = Address('910 S State Route 22') + + assert address.address_number == '910' + assert address.prefix_direction == 'S' + assert address.street_name == 'HWY 22' + assert address.normalized == '910 S HWY 22' + + def test_state_route_with_punctuation(self): + address = Address('910 S S.R. 22') + + assert address.address_number == '910' + assert address.prefix_direction == 'S' + assert address.street_name == 'HWY 22' + assert address.normalized == '910 S HWY 22' + + def test_state_route_casing(self): + address = Address('910 S sr 22') + + assert address.address_number == '910' + assert address.prefix_direction == 'S' + assert address.street_name == 'HWY 22' + assert address.normalized == '910 S HWY 22' + + + def test_highways(self): + address = Address('1910 N US HWY 89') + + assert address.address_number == '1910' + assert address.prefix_direction == 'N' + assert address.street_name == 'HWY 89' + assert address.normalized == '1910 N HWY 89' + + address = Address('1106 S OLD HWY 89') + + assert address.address_number == '1106' + assert address.prefix_direction == 'S' + assert address.street_name == 'OLD HWY 89' + assert address.normalized == '1106 S OLD HWY 89' + + def test_highway_expanded(self): + address = Address('1910 N US highway 89') + + assert address.address_number == '1910' + assert address.prefix_direction == 'N' + assert address.street_name == 'HWY 89' + assert address.normalized == '1910 N HWY 89' + + def test_highway_with_punctuation(self): + address = Address('1910 N U.S. highway 89') + + assert address.address_number == '1910' + assert address.prefix_direction == 'N' + assert address.street_name == 'HWY 89' + assert address.normalized == '1910 N HWY 89' + + def test_highway_casing(self): + address = Address('1910 N u.s. highway 89') + + assert address.address_number == '1910' + assert address.prefix_direction == 'N' + assert address.street_name == 'HWY 89' + assert address.normalized == '1910 N HWY 89' + + def test_street_name_with_sr(self): + address = Address('1910 s woodsrow dr') + + assert address.address_number == '1910' + assert address.prefix_direction == 'S' + assert address.street_name == 'WOODSROW' + assert address.street_type == 'DR' + assert address.normalized == '1910 S WOODSROW DR'

State Routes SR Addresses like 910 S SR 22 or 1910 N US HWY 89 will return 22 and 89 for the street_name

0.0

75254926a9de985e82bb2fa116948302d4fb8abe

[ "src/sweeper/tests/test_address_parser.py::TestHighways::test_state_routes", "src/sweeper/tests/test_address_parser.py::TestHighways::test_state_route_expanded", "src/sweeper/tests/test_address_parser.py::TestHighways::test_state_route_with_punctuation", "src/sweeper/tests/test_address_parser.py::TestHighways::test_state_route_casing", "src/sweeper/tests/test_address_parser.py::TestHighways::test_highways", "src/sweeper/tests/test_address_parser.py::TestHighways::test_highway_expanded", "src/sweeper/tests/test_address_parser.py::TestHighways::test_highway_with_punctuation", "src/sweeper/tests/test_address_parser.py::TestHighways::test_highway_casing" ]

[ "src/sweeper/tests/test_address_parser.py::TestAddressNumber::test_parses_address_number", "src/sweeper/tests/test_address_parser.py::TestAddressNumberSuffix::test_parses_number_suffix", "src/sweeper/tests/test_address_parser.py::TestPrefixDirection::test_parses_prefix_direction", "src/sweeper/tests/test_address_parser.py::TestPrefixDirection::test_no_prefix_direction", "src/sweeper/tests/test_address_parser.py::TestStreetName::test_parses_street_name", "src/sweeper/tests/test_address_parser.py::TestStreetName::test_multi_word_street_name", "src/sweeper/tests/test_address_parser.py::TestStreetName::test_no_prefix_direction_street", "src/sweeper/tests/test_address_parser.py::TestStreetDirection::test_street_direction", "src/sweeper/tests/test_address_parser.py::TestNormalizeDirection::test_normalize_direction", "src/sweeper/tests/test_address_parser.py::TestNormalizeDirection::test_two_characters", "src/sweeper/tests/test_address_parser.py::TestWhiteSpace::test_white_space", "src/sweeper/tests/test_address_parser.py::TestWhiteSpace::test_double_spaces", "src/sweeper/tests/test_address_parser.py::TestNormalizeStreetType::test_normalize_street_type", "src/sweeper/tests/test_address_parser.py::TestNormalizeStreetType::test_raises_exceptions", "src/sweeper/tests/test_address_parser.py::TestNormalizeStreetType::test_street_names_with_types", "src/sweeper/tests/test_address_parser.py::TestUnitParts::test_add_hash_if_no_type", "src/sweeper/tests/test_address_parser.py::TestUnitParts::test_strip_hash_if_type", "src/sweeper/tests/test_address_parser.py::TestPOBox::test_parses_po_boxes", "src/sweeper/tests/test_address_parser.py::test_normalized_address_string", "src/sweeper/tests/test_address_parser.py::test_strip_periods", "src/sweeper/tests/test_address_parser.py::test_steve", "src/sweeper/tests/test_address_parser.py::TestBadAddresses::test_missing_street_names", "src/sweeper/tests/test_address_parser.py::TestHighways::test_street_name_with_sr" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2020-03-26 22:39:19+00:00

mit

914

agronholm__anyio-137

diff --git a/src/anyio/__init__.py b/src/anyio/__init__.py index 2b2cfec..cb1fd4b 100644 --- a/src/anyio/__init__.py +++ b/src/anyio/__init__.py @@ -14,6 +14,7 @@ from typing import TypeVar, Callable, Union, Optional, Awaitable, Coroutine, Any import sniffio +from ._utils import convert_ipv6_sockaddr from .abc import ( Lock, Condition, Event, Semaphore, CapacityLimiter, CancelScope, TaskGroup, IPAddressType, SocketStream, UDPSocket, ConnectedUDPSocket, IPSockAddrType, Listener, SocketListener) @@ -32,8 +33,7 @@ IPPROTO_IPV6 = getattr(socket, 'IPPROTO_IPV6', 41) # https://bugs.python.org/is T_Retval = TypeVar('T_Retval', covariant=True) T_Agen = TypeVar('T_Agen') T_Item = TypeVar('T_Item') -GetAddrInfoReturnType = List[Tuple[AddressFamily, SocketKind, int, str, - Union[Tuple[str, int], Tuple[str, int, int, int]]]] +GetAddrInfoReturnType = List[Tuple[AddressFamily, SocketKind, int, str, Tuple[str, int]]] AnyIPAddressFamily = Literal[AddressFamily.AF_UNSPEC, AddressFamily.AF_INET, AddressFamily.AF_INET6] IPAddressFamily = Literal[AddressFamily.AF_INET, AddressFamily.AF_INET6] @@ -607,15 +607,18 @@ async def create_connected_udp_socket( reuse_port) -def getaddrinfo(host: Union[bytearray, bytes, str], port: Union[str, int, None], *, - family: Union[int, AddressFamily] = 0, type: Union[int, SocketKind] = 0, - proto: int = 0, flags: int = 0) -> Awaitable[GetAddrInfoReturnType]: +async def getaddrinfo(host: Union[bytearray, bytes, str], port: Union[str, int, None], *, + family: Union[int, AddressFamily] = 0, type: Union[int, SocketKind] = 0, + proto: int = 0, flags: int = 0) -> GetAddrInfoReturnType: """ Look up a numeric IP address given a host name. Internationalized domain names are translated according to the (non-transitional) IDNA 2008 standard. + .. note:: 4-tuple IPv6 socket addresses are automatically converted to 2-tuples of + (host, port), unlike what :func:`socket.getaddrinfo` does. + :param host: host name :param port: port number :param family: socket family (`'AF_INET``, ...) @@ -637,8 +640,10 @@ def getaddrinfo(host: Union[bytearray, bytes, str], port: Union[str, int, None], else: encoded_host = host - return _get_asynclib().getaddrinfo(encoded_host, port, family=family, type=type, proto=proto, - flags=flags) + gai_res = await _get_asynclib().getaddrinfo(encoded_host, port, family=family, type=type, + proto=proto, flags=flags) + return [(family, type, proto, canonname, convert_ipv6_sockaddr(sockaddr)) + for family, type, proto, canonname, sockaddr in gai_res] def getnameinfo(sockaddr: IPSockAddrType, flags: int = 0) -> Awaitable[Tuple[str, str]]: diff --git a/src/anyio/_backends/_asyncio.py b/src/anyio/_backends/_asyncio.py index 03d3093..d85e45d 100644 --- a/src/anyio/_backends/_asyncio.py +++ b/src/anyio/_backends/_asyncio.py @@ -854,23 +854,12 @@ class ConnectedUDPSocket(abc.ConnectedUDPSocket): self._transport.sendto(item) -def _convert_ipv6_sockaddr(sockaddr: Optional[IPSockAddrType]) -> Optional[Tuple[str, int]]: - # This is more complicated than it should be because of MyPy - if sockaddr is None: - return None - elif len(sockaddr) == 4 and sockaddr[-1]: - # Add scopeid to the address - return sockaddr[0] + '%' + str(sockaddr[-1]), sockaddr[1] - else: - return sockaddr[:2] - - async def connect_tcp(host: str, port: int, - local_addr: Optional[IPSockAddrType] = None) -> SocketStream: + local_addr: Optional[Tuple[str, int]] = None) -> SocketStream: transport, protocol = cast( Tuple[asyncio.Transport, StreamProtocol], await get_running_loop().create_connection(StreamProtocol, host, port, - local_addr=_convert_ipv6_sockaddr(local_addr)) + local_addr=local_addr) ) transport.pause_reading() return SocketStream(transport, protocol) @@ -892,8 +881,8 @@ async def create_udp_socket( reuse_port: bool ) -> Union[UDPSocket, ConnectedUDPSocket]: result = await get_running_loop().create_datagram_endpoint( - DatagramProtocol, local_addr=_convert_ipv6_sockaddr(local_address), - remote_addr=_convert_ipv6_sockaddr(remote_address), family=family, reuse_port=reuse_port) + DatagramProtocol, local_addr=local_address, remote_addr=remote_address, family=family, + reuse_port=reuse_port) transport = cast(asyncio.DatagramTransport, result[0]) protocol = cast(DatagramProtocol, result[1]) if protocol.exception: diff --git a/src/anyio/_utils.py b/src/anyio/_utils.py index ff68d2c..0f7bdac 100644 --- a/src/anyio/_utils.py +++ b/src/anyio/_utils.py @@ -16,3 +16,26 @@ class ResourceGuard: def __exit__(self, exc_type, exc_val, exc_tb): self._guarded = False + + +def convert_ipv6_sockaddr(sockaddr): + """ + Convert a 4-tuple IPv6 socket address to a 2-tuple (address, port) format. + + If the scope ID is nonzero, it is added to the address, separated with ``%``. + Otherwise the flow id and scope id are simply cut off from the tuple. + Any other kinds of socket addresses are returned as-is. + + :param sockaddr: the result of :meth:`~socket.socket.getsockname` + :return: the converted socket address + + """ + # This is more complicated than it should be because of MyPy + if isinstance(sockaddr, tuple) and len(sockaddr) == 4: + if sockaddr[3]: + # Add scopeid to the address + return sockaddr[0] + '%' + str(sockaddr[3]), sockaddr[1] + else: + return sockaddr[:2] + else: + return sockaddr diff --git a/src/anyio/abc/sockets.py b/src/anyio/abc/sockets.py index f02d1c8..50d8a4d 100644 --- a/src/anyio/abc/sockets.py +++ b/src/anyio/abc/sockets.py @@ -6,7 +6,7 @@ from typing import TypeVar, Tuple, Union, Generic from .streams import UnreliableObjectStream, ByteStream, Listener IPAddressType = Union[str, IPv4Address, IPv6Address] -IPSockAddrType = Union[Tuple[str, int], Tuple[str, int, int, int]] +IPSockAddrType = Tuple[str, int] SockAddrType = Union[IPSockAddrType, str] UDPPacketType = Tuple[bytes, IPSockAddrType] T_Retval = TypeVar('T_Retval') @@ -41,8 +41,7 @@ class _SocketMixin(Generic[T_SockAddr]): """ The bound address of the underlying local socket. - For IPv4 TCP streams, this is a tuple of (IP address, port). - For IPv6 TCP streams, this is a tuple of (IP address, port, flowinfo, scopeid). + For TCP streams, this is a tuple of (IP address, port). For UNIX socket streams, this is the path to the socket. """ @@ -56,8 +55,7 @@ class SocketStream(Generic[T_SockAddr], ByteStream, _SocketMixin[T_SockAddr]): """ The address this socket is connected to. - For IPv4 TCP streams, this is a tuple of (IP address, port). - For IPv6 TCP streams, this is a tuple of (IP address, port, flowinfo, scopeid). + For TCP streams, this is a tuple of (IP address, port). For UNIX socket streams, this is the path to the socket. """ @@ -80,9 +78,4 @@ class ConnectedUDPSocket(UnreliableObjectStream[bytes], _SocketMixin[IPSockAddrT @property @abstractmethod def remote_address(self) -> IPSockAddrType: - """ - The address this socket is connected to. - - For IPv4 sockets, this is a tuple of (IP address, port). - For IPv6 sockets, this is a tuple of (IP address, port, flowinfo, scopeid). - """ + """The address this socket is connected to."""

agronholm/anyio

cfba438b71237aeb93bfb955a8e70edd8f101ac9

diff --git a/tests/test_sockets.py b/tests/test_sockets.py index 24fb5de..7f47bb6 100644 --- a/tests/test_sockets.py +++ b/tests/test_sockets.py @@ -747,8 +747,7 @@ async def test_getaddrinfo_ipv6addr(sock_type): # IDNA trips up over raw IPv6 addresses proto = 0 if platform.system() == 'Windows' else 6 assert await getaddrinfo('::1', 0, type=sock_type) == [ - (socket.AddressFamily.AF_INET6, socket.SocketKind.SOCK_STREAM, proto, '', - ('::1', 0, 0, 0)) + (socket.AddressFamily.AF_INET6, socket.SocketKind.SOCK_STREAM, proto, '', ('::1', 0)) ]

Should we expose the user to 4-tuple IPv6 socket addresses? The result of `sock.getsockname()` for IPv6 sockets is a 4-tuple (address, port, flowinfo, scopeid). The last two fields are specific to IPv6. The flowinfo field is useless/deprecated and the scopeid is only meaningful for link-local addresses. The important part here is that the address field can carry a scope ID by appending it to the address with a `%` separator, like `fe80::dead:beef%1`. Most people are not used to dealing with 4-tuple socket addresses, so maybe it would make sense to make it part of the address always. On the other hand, others might *expect* the usual behavior and get confused when they get 2-tuples instead!

0.0

cfba438b71237aeb93bfb955a8e70edd8f101ac9

[ "tests/test_sockets.py::test_getaddrinfo_ipv6addr[asyncio-SocketKind.SOCK_STREAM0]", "tests/test_sockets.py::test_getaddrinfo_ipv6addr[asyncio-SocketKind.SOCK_STREAM1]", "tests/test_sockets.py::test_getaddrinfo_ipv6addr[asyncio+uvloop-SocketKind.SOCK_STREAM0]", "tests/test_sockets.py::test_getaddrinfo_ipv6addr[asyncio+uvloop-SocketKind.SOCK_STREAM1]" ]

[ "tests/test_sockets.py::TestTCPStream::test_send_receive[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_send_receive[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_send_receive[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_send_receive[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_send_large_buffer[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_send_large_buffer[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_send_large_buffer[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_send_large_buffer[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_send_eof[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_send_eof[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_send_eof[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_send_eof[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_iterate[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_iterate[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_iterate[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_iterate[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_socket_options[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_socket_options[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_socket_options[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_socket_options[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_happy_eyeballs[asyncio-dualstack]", "tests/test_sockets.py::TestTCPStream::test_happy_eyeballs[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_happy_eyeballs[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_happy_eyeballs[asyncio+uvloop-dualstack]", "tests/test_sockets.py::TestTCPStream::test_happy_eyeballs[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_happy_eyeballs[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_connection_refused[asyncio-multi]", "tests/test_sockets.py::TestTCPStream::test_connection_refused[asyncio-single]", "tests/test_sockets.py::TestTCPStream::test_connection_refused[asyncio+uvloop-multi]", "tests/test_sockets.py::TestTCPStream::test_connection_refused[asyncio+uvloop-single]", "tests/test_sockets.py::TestTCPStream::test_receive_timeout[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_receive_timeout[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_receive_timeout[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_receive_timeout[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_concurrent_send[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_concurrent_send[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_concurrent_send[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_concurrent_send[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_concurrent_receive[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_concurrent_receive[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_concurrent_receive[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_concurrent_receive[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_close_during_receive[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_close_during_receive[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_close_during_receive[asyncio+uvloop-ipv4]", "tests/test_sockets.py::TestTCPStream::test_close_during_receive[asyncio+uvloop-ipv6]", "tests/test_sockets.py::TestTCPStream::test_receive_after_close[asyncio-ipv4]", "tests/test_sockets.py::TestTCPStream::test_receive_after_close[asyncio-ipv6]", "tests/test_sockets.py::TestTCPStream::test_receive_after_close[asyncio+uvloop-ipv4]", 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{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2020-07-31 12:55:49+00:00

mit

915

agronholm__anyio-227

diff --git a/docs/versionhistory.rst b/docs/versionhistory.rst index b9fa806..466bc78 100644 --- a/docs/versionhistory.rst +++ b/docs/versionhistory.rst @@ -54,6 +54,7 @@ This library adheres to `Semantic Versioning 2.0 <http://semver.org/>`_. - Added the ``run_sync_from_thread()`` function - Added ``UNIXSocketStream`` as a ``SocketStream`` subclass, capable of sending and receiving file descriptors +- Added thread pooling for asyncio - Added the ``FileReadStream`` and ``FileWriteStream`` classes - Added the ``TaskGroup.start()`` method and a corresponding ``BlockingPortal.start_task()`` method - Added the ``name`` argument to ``BlockingPortal.spawn_task()`` @@ -81,6 +82,8 @@ This library adheres to `Semantic Versioning 2.0 <http://semver.org/>`_. - Changed the asyncio ``TaskGroup.spawn()`` method to avoid the use of a coroutine wrapper on Python 3.8+ and added a hint for hiding the wrapper in tracebacks on earlier Pythons (supported by Pytest, Sentry etc.) +- Changed the default thread limiter on asyncio to be scoped to an event loop so that multiple + running event loops don't conflict with each other **2.2.0** diff --git a/src/anyio/_backends/_asyncio.py b/src/anyio/_backends/_asyncio.py index ac67930..2ba1e8d 100644 --- a/src/anyio/_backends/_asyncio.py +++ b/src/anyio/_backends/_asyncio.py @@ -4,6 +4,7 @@ import concurrent.futures import math import socket import sys +from asyncio.base_events import _run_until_complete_cb # type: ignore from collections import OrderedDict, deque from concurrent.futures import Future from dataclasses import dataclass @@ -11,8 +12,9 @@ from functools import partial, wraps from inspect import ( CORO_RUNNING, CORO_SUSPENDED, GEN_RUNNING, GEN_SUSPENDED, getcoroutinestate, getgeneratorstate) from io import IOBase +from queue import Empty, Queue from socket import AddressFamily, SocketKind, SocketType -from threading import Thread +from threading import Thread, current_thread from types import TracebackType from typing import ( Any, Awaitable, Callable, Collection, Coroutine, Deque, Dict, Generator, List, Optional, @@ -40,6 +42,15 @@ else: if sys.version_info >= (3, 7): from asyncio import all_tasks, create_task, current_task, get_running_loop from asyncio import run as native_run + + def find_root_task() -> asyncio.Task: + for task in all_tasks(): + if task._callbacks: + for cb, context in task._callbacks: # type: ignore + if cb is _run_until_complete_cb or cb.__module__ == 'uvloop.loop': + return task + + raise RuntimeError('Cannot find root task for setting cleanup callback') else: _T = TypeVar('_T') @@ -115,6 +126,14 @@ else: return asyncio.Task.current_task(loop) + def find_root_task() -> asyncio.Task: + for task in all_tasks(): + for cb in task._callbacks: + if cb is _run_until_complete_cb or cb.__module__ == 'uvloop.loop': + return task + + raise RuntimeError('Cannot find root task for setting cleanup callback') + T_Retval = TypeVar('T_Retval') # Check whether there is native support for task names in asyncio (3.8+) @@ -619,47 +638,87 @@ class TaskGroup(abc.TaskGroup): _Retval_Queue_Type = Tuple[Optional[T_Retval], Optional[BaseException]] -async def run_sync_in_worker_thread( - func: Callable[..., T_Retval], *args, cancellable: bool = False, - limiter: Optional['CapacityLimiter'] = None) -> T_Retval: - def thread_worker(): +def _thread_pool_worker(work_queue: Queue, workers: Set[Thread], + idle_workers: Set[Thread]) -> None: + func: Callable + args: tuple + future: asyncio.Future + limiter: CapacityLimiter + thread = current_thread() + while True: try: + func, args, future = work_queue.get(timeout=10) + except Empty: + workers.remove(thread) + return + finally: + idle_workers.discard(thread) + + if func is None: + # Shutdown command received + workers.remove(thread) + return + + if not future.cancelled(): with claim_worker_thread('asyncio'): - threadlocals.loop = loop - result = func(*args) - except BaseException as exc: - if not loop.is_closed(): - loop.call_soon_threadsafe(limiter.release_on_behalf_of, task) - if not cancelled: - loop.call_soon_threadsafe(queue.put_nowait, (None, exc)) + loop = threadlocals.loop = future._loop + try: + result = func(*args) + except BaseException as exc: + idle_workers.add(thread) + if not loop.is_closed() and not future.cancelled(): + loop.call_soon_threadsafe(future.set_exception, exc) + else: + idle_workers.add(thread) + if not loop.is_closed() and not future.cancelled(): + loop.call_soon_threadsafe(future.set_result, result) else: - if not loop.is_closed(): - loop.call_soon_threadsafe(limiter.release_on_behalf_of, task) - if not cancelled: - loop.call_soon_threadsafe(queue.put_nowait, (result, None)) + idle_workers.add(thread) + + work_queue.task_done() + +_threadpool_work_queue: RunVar[Queue] = RunVar('_threadpool_work_queue') +_threadpool_idle_workers: RunVar[Set[Thread]] = RunVar('_threadpool_idle_workers') +_threadpool_workers: RunVar[Set[Thread]] = RunVar('_threadpool_workers') + + +def _loop_shutdown_callback(f: asyncio.Future) -> None: + """This is called when the root task has finished.""" + for _ in range(len(_threadpool_workers.get())): + _threadpool_work_queue.get().put_nowait((None, None, None)) + + +async def run_sync_in_worker_thread( + func: Callable[..., T_Retval], *args, cancellable: bool = False, + limiter: Optional['CapacityLimiter'] = None) -> T_Retval: await checkpoint() - loop = get_running_loop() - task = current_task() - queue: asyncio.Queue[_Retval_Queue_Type] = asyncio.Queue(1) - cancelled = False - limiter = limiter or _default_thread_limiter - await limiter.acquire_on_behalf_of(task) - thread = Thread(target=thread_worker, daemon=True) - thread.start() - exception: Optional[BaseException] = None - with CancelScope(shield=not cancellable): - try: - retval, exception = await queue.get() - except BaseException as exc: - exception = exc - finally: - cancelled = True - if exception is not None: - raise exception - else: - return cast(T_Retval, retval) + # If this is the first run in this event loop thread, set up the necessary variables + try: + work_queue = _threadpool_work_queue.get() + idle_workers = _threadpool_idle_workers.get() + workers = _threadpool_workers.get() + except LookupError: + work_queue = Queue() + idle_workers = set() + workers = set() + _threadpool_work_queue.set(work_queue) + _threadpool_idle_workers.set(idle_workers) + _threadpool_workers.set(workers) + find_root_task().add_done_callback(_loop_shutdown_callback) + + async with (limiter or current_default_thread_limiter()): + with CancelScope(shield=not cancellable): + future: asyncio.Future = asyncio.Future() + work_queue.put_nowait((func, args, future)) + if not idle_workers: + args = (work_queue, workers, idle_workers) + thread = Thread(target=_thread_pool_worker, args=args, name='AnyIO worker thread') + workers.add(thread) + thread.start() + + return await future def run_sync_from_thread(func: Callable[..., T_Retval], *args, @@ -1536,11 +1595,16 @@ class CapacityLimiter(abc.CapacityLimiter): tuple(self._borrowers), len(self._wait_queue)) -def current_default_thread_limiter(): - return _default_thread_limiter +_default_thread_limiter: RunVar[CapacityLimiter] = RunVar('_default_thread_limiter') -_default_thread_limiter = CapacityLimiter(40) +def current_default_thread_limiter(): + try: + return _default_thread_limiter.get() + except LookupError: + limiter = CapacityLimiter(40) + _default_thread_limiter.set(limiter) + return limiter #

agronholm/anyio

8c136ffff989fb12c738bf87183046285b738a63

diff --git a/tests/test_threads.py b/tests/test_threads.py index 9d07ed7..56eb5b8 100644 --- a/tests/test_threads.py +++ b/tests/test_threads.py @@ -9,7 +9,7 @@ import pytest from anyio import ( create_blocking_portal, create_capacity_limiter, create_event, create_task_group, - get_cancelled_exc_class, get_current_task, run_async_from_thread, run_sync_from_thread, + get_cancelled_exc_class, get_current_task, run, run_async_from_thread, run_sync_from_thread, run_sync_in_worker_thread, sleep, start_blocking_portal, wait_all_tasks_blocked) if sys.version_info < (3, 7): @@ -48,6 +48,23 @@ async def test_run_sync_from_thread(): assert result == 3 +def test_run_sync_from_thread_pooling(): + async def main(): + thread_ids = set() + for _ in range(5): + thread_ids.add(await run_sync_in_worker_thread(threading.get_ident)) + + # Expects that all the work has been done in the same worker thread + assert len(thread_ids) == 1 + assert thread_ids.pop() != threading.get_ident() + assert threading.active_count() == initial_count + 1 + + # The thread should not exist after the event loop has been closed + initial_count = threading.active_count() + run(main, backend='asyncio') + assert threading.active_count() == initial_count + + async def test_run_async_from_thread_exception(): async def add(a, b): assert threading.get_ident() == event_loop_thread_id

Use thread pools in run_sync_in_worker_thread() Right now, the asyncio implementation of this starts a new thread every time this function is called. We should be using thread pools instead, like trio does.

0.0

8c136ffff989fb12c738bf87183046285b738a63

[ "tests/test_threads.py::test_run_sync_from_thread_pooling" ]

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"tests/test_threads.py::TestBlockingPortal::test_async_context_manager_error_ignore[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_start_no_value[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_start_no_value[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_start_with_value[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_start_with_value[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_start_crash_before_started_call[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_start_crash_before_started_call[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_start_crash_after_started_call[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_start_crash_after_started_call[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_start_no_started_call[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_start_no_started_call[asyncio+uvloop]", "tests/test_threads.py::TestBlockingPortal::test_start_with_name[asyncio]", "tests/test_threads.py::TestBlockingPortal::test_start_with_name[asyncio+uvloop]" ]

{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }

2021-03-03 21:08:05+00:00

mit

916