Migrated from GitHub

data/.editorconfig

@@ -0,0 +1,21 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

data/.pre-commit-config.yaml

@@ -0,0 +1,44 @@
+fail_fast: false
+default_language_version:
+    python: python3
+default_stages:
+    - pre-commit
+    - pre-push
+minimum_pre_commit_version: 2.16.0
+repos:
+    - repo: https://github.com/rbubley/mirrors-prettier
+      rev: v3.4.2
+      hooks:
+          - id: prettier
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.8.6
+      hooks:
+          - id: ruff
+            args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
+          - id: ruff-format
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v5.0.0
+      hooks:
+          - id: detect-private-key
+          - id: check-ast
+          - id: end-of-file-fixer
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: trailing-whitespace
+          - id: check-case-conflict
+    - repo: https://github.com/pre-commit/mirrors-mypy
+      rev: v1.14.1
+      hooks:
+          - id: mypy
+            args: [--no-strict-optional, --ignore-missing-imports]
+            additional_dependencies:
+                ["types-setuptools", "types-requests", "types-attrs"]
+    - repo: local
+      hooks:
+          - id: forbid-to-commit
+            name: Don't commit rej files
+            entry: |
+                Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+                Fix the merge conflicts manually and remove the .rej files.
+            language: fail
+            files: '.*\.rej$'

data/.readthedocs.yml

@@ -0,0 +1,18 @@
+version: 2
+build:
+    os: ubuntu-24.04
+    tools:
+        python: "3.12"
+    commands:
+        - asdf plugin add uv
+        - asdf install uv latest
+        - asdf global uv latest
+        - uv venv
+        - uv pip install .[docs]
+        - .venv/bin/python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
+sphinx:
+    configuration: docs/conf.py
+    fail_on_warning: false
+
+submodules:
+    include: all

data/CODE_OF_CONDUCT.md

@@ -0,0 +1,74 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our
+project and our community a harassment-free experience for everyone,
+regardless of age, body size, disability, ethnicity, gender identity and
+expression, level of experience, nationality, personal appearance, race,
+religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+- The use of sexualized language or imagery and unwelcome sexual
+  attention or advances
+- Trolling, insulting/derogatory comments, and personal or political
+  attacks
+- Public or private harassment
+- Publishing others’ private information, such as a physical or
+  electronic address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of
+acceptable behavior and are expected to take appropriate and fair
+corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit,
+or reject comments, commits, code, wiki edits, issues, and other
+contributions that are not aligned to this Code of Conduct, or to ban
+temporarily or permanently any contributor for other behaviors that they
+deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public
+spaces when an individual is representing the project or its community.
+Examples of representing a project or community include using an
+official project e-mail address, posting via an official social media
+account, or acting as an appointed representative at an online or
+offline event. Representation of a project may be further defined and
+clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may
+be reported by opening an issue. The project team
+will review and investigate all complaints, and will respond in a way
+that it deems appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an
+incident. Further details of specific enforcement policies may be posted
+separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in
+good faith may face temporary or permanent repercussions as determined
+by other members of the project’s leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the Contributor Covenant, version 1.4,
+available at <https://www.contributor-covenant.org/version/1/4/code-of-conduct.html>

data/LICENSE

@@ -0,0 +1,201 @@
+Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
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+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
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+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
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+      incidental, or consequential damages of any character arising as a
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+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
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+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
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+   Copyright 2022  Lukas Heumos
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
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+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

data/codecov.yml

@@ -0,0 +1,13 @@
+comment: false
+coverage:
+    status:
+        project:
+            default:
+                target: auto
+        patch:
+            default:
+                enabled: no
+    ignore:
+        - "test/"
+github_checks:
+    annotations: false

data/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = ehrapy
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

data/docs/_ext/edit_on_github.py

@@ -0,0 +1,50 @@
+"""Based on gist.github.com/MantasVaitkunas/7c16de233812adcb7028."""
+
+import os
+import warnings
+from typing import Any, Optional
+
+from sphinx.application import Sphinx
+
+__licence__ = "BSD (3 clause)"
+
+
+def get_github_repo(app: Sphinx, path: str) -> str:
+    if path.endswith(".ipynb"):
+        return str(app.config.github_nb_repo)
+    if "auto_examples" in path:
+        return str(app.config.github_nb_repo)
+    if "auto_tutorials" in path:
+        return str(app.config.github_nb_repo)
+    return str(app.config.github_repo)
+
+
+def _html_page_context(
+    app: Sphinx, _pagename: str, templatename: str, context: dict[str, Any], doctree: Any | None
+) -> None:
+    # doctree is None - otherwise viewcode fails
+    if templatename != "page.html" or doctree is None:
+        return
+
+    if not app.config.github_repo:
+        return
+
+    if not app.config.github_nb_repo:
+        nb_repo = f"{app.config.github_repo}_notebooks"
+        app.config.github_nb_repo = nb_repo
+
+    path = os.path.relpath(doctree.get("source"), app.builder.srcdir)
+    repo = get_github_repo(app, path)
+
+    # For sphinx_rtd_theme.
+    context["display_github"] = True
+    context["github_user"] = "theislab"
+    context["github_version"] = "master"
+    context["github_repo"] = repo
+    context["conf_py_path"] = "/docs/source/"
+
+
+def setup(app: Sphinx) -> None:
+    app.add_config_value("github_nb_repo", "", True)
+    app.add_config_value("github_repo", "", True)
+    app.connect("html-page-context", _html_page_context)

data/docs/_ext/typed_returns.py

@@ -0,0 +1,27 @@
+import re
+from collections.abc import Iterable, Iterator
+
+from sphinx.application import Sphinx
+from sphinx.ext.napoleon import NumpyDocstring
+
+
+def _process_return(lines: Iterable[str]) -> Iterator[str]:
+    for line in lines:
+        m = re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line)
+        if m:
+            # Once this is in scanpydoc, we can use the fancy hover stuff
+            yield f'**{m["param"]}** : :class:`~{m["type"]}`'
+        else:
+            yield line
+
+
+def _parse_returns_section(self: NumpyDocstring, section: str) -> list[str]:
+    lines_raw = list(_process_return(self._dedent(self._consume_to_next_section())))
+    lines: list[str] = self._format_block(":returns: ", lines_raw)
+    if lines and lines[-1]:
+        lines.append("")
+    return lines
+
+
+def setup(app: Sphinx) -> None:
+    NumpyDocstring._parse_returns_section = _parse_returns_section

data/docs/_static/SCVI_LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2020 Romain Lopez, Adam Gayoso, Galen Xing, Yosef Lab
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

data/docs/_static/css/overwrite.css

@@ -0,0 +1,74 @@
+/*
+  Furo CSS variables
+  https://github.com/pradyunsg/furo/blob/main/src/furo/assets/styles/variables/_index.scss
+  https://github.com/pradyunsg/furo/blob/main/src/furo/theme/partials/_head_css_variables.html
+https://github.com/streamlink/streamlink/blob/17a4088c38709123c0bcab4a150549bd16d19e07/docs/_static/styles/custom.css
+*/
+
+/* for the sphinx design cards */
+body {
+    --sd-color-shadow: dimgrey;
+}
+
+dt:target,
+span.highlighted {
+    background-color: #f0f0f0;
+}
+
+dl.citation > dt {
+    float: left;
+    margin-right: 15px;
+    font-weight: bold;
+}
+
+/* Parameters normalize size and captialized, */
+dl .field-list dt {
+    font-size: var(--font-size--normal) !important;
+    text-transform: none !important;
+}
+
+/* examples and headings in classes */
+p.rubric {
+    font-size: var(--font-size--normal);
+    text-transform: none;
+    font-weight: 500;
+}
+
+/* adapted from https://github.com/dask/dask-sphinx-theme/blob/main/dask_sphinx_theme/static/css/nbsphinx.css */
+
+.nbinput .prompt,
+.nboutput .prompt {
+    display: none;
+}
+.nboutput .stderr {
+    display: none;
+}
+
+div.nblast.container {
+    padding-bottom: 10px !important;
+    padding-right: 0px;
+    padding-left: 0px;
+}
+
+div.nbinput.container {
+    padding-top: 10px !important;
+    padding-right: 0px;
+    padding-left: 0px;
+}
+
+div.nbinput.container div.input_area div[class*="highlight"] > pre {
+    padding: 10px !important;
+    margin: 0;
+}
+
+p.topic-title {
+    margin-top: 0;
+}
+
+/* so that api methods are small in sidebar */
+li.toctree-l3 {
+    font-size: 81.25% !important;
+}
+li.toctree-l4 {
+    font-size: 75% !important;
+}

data/docs/_static/css/sphinx_gallery.css

@@ -0,0 +1,27 @@
+.sphx-glr-thumbcontainer {
+    background: inherit !important;
+    min-height: 250px !important;
+    margin: 10px !important;
+}
+
+.sphx-glr-thumbcontainer .headerlink {
+    display: none !important;
+}
+
+div.sphx-glr-thumbcontainer span {
+    font-style: normal !important;
+}
+
+.sphx-glr-thumbcontainer a.internal {
+    padding: 140px 10px 0 !important;
+}
+
+.sphx-glr-thumbcontainer .figure {
+    width: 200px !important;
+}
+
+.sphx-glr-thumbcontainer .figure.align-center {
+    text-align: center;
+    margin-left: 0%;
+    transform: translate(0%);
+}