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README.md

@@ -1,14 +1,13 @@
 ---
-title: Esm2Text
-emoji: 👀
-colorFrom: yellow
-colorTo: green
+title: ESM2Text
+emoji: 😻
+colorFrom: indigo
+colorTo: pink
 sdk: gradio
 sdk_version: 5.1.0
 app_file: app.py
 pinned: false
-license: cc-by-nc-4.0
-short_description: Generate a protein's function using its amino acid sequence
+short_description: Chatbot
 ---
 
 Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference

app.py

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+import os
+from threading import Thread
+from typing import Iterator
+
+import gradio as gr
+import spaces
+import torch
+from transformers import AutoModelForCausalLM, AutoTokenizer, TextIteratorStreamer
+
+DESCRIPTION = """\
+# ESM2Text Demo
+"""
+
+MAX_MAX_NEW_TOKENS = 256
+DEFAULT_MAX_NEW_TOKENS = 100
+
+
+device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
+
+
+tokenizer = AutoTokenizer.from_pretrained('habdine/Esm2Text-Base-v1-1', 
+                                            trust_remote_code=True)
+model = AutoModelForCausalLM.from_pretrained('habdine/Esm2Text-Base-v1-1',
+                                             device_map="auto",
+                                            trust_remote_code=True)
+model.eval()
+
+
+@spaces.GPU(duration=90)
+def generate(
+    message: str,
+    max_new_tokens: int = 1024,
+    do_sample: bool = False,
+    temperature: float = 0.6,
+    top_p: float = 0.9,
+    top_k: int = 50,
+    repetition_penalty: float = 1.2,
+) -> Iterator[str]:
+
+
+    streamer = TextIteratorStreamer(tokenizer, timeout=20.0, skip_prompt=True, skip_special_tokens=True)
+    generate_kwargs = dict(
+        protein_sequence=message,
+        tokenizer=tokenizer,
+        device=device,
+        streamer=streamer,
+        max_new_tokens=max_new_tokens,
+        do_sample=do_sample,
+        top_p=top_p,
+        top_k=top_k,
+        temperature=temperature,
+        num_beams=1,
+        repetition_penalty=repetition_penalty,
+    )
+    t = Thread(target=model.generate, kwargs=generate_kwargs)
+    t.start()
+
+    outputs = []
+    for text in streamer:
+        outputs.append(text)
+        yield "".join(outputs)
+
+
+chat_interface = gr.ChatInterface(
+    fn=generate,
+    additional_inputs=[
+        gr.Slider(
+            label="Max new tokens",
+            minimum=1,
+            maximum=MAX_MAX_NEW_TOKENS,
+            step=1,
+            value=DEFAULT_MAX_NEW_TOKENS,
+        ),
+        gr.Checkbox(label="Do Sample"),
+        gr.Slider(
+            label="Temperature",
+            minimum=0.1,
+            maximum=4.0,
+            step=0.1,
+            value=0.6,
+        ),
+        gr.Slider(
+            label="Top-p (nucleus sampling)",
+            minimum=0.05,
+            maximum=1.0,
+            step=0.05,
+            value=0.9,
+        ),
+        gr.Slider(
+            label="Top-k",
+            minimum=1,
+            maximum=1000,
+            step=1,
+            value=50,
+        ),
+        gr.Slider(
+            label="Repetition penalty",
+            minimum=1.0,
+            maximum=2.0,
+            step=0.05,
+            value=1.0,
+        ),
+    ],
+    stop_btn=None,
+    examples=[
+        ['AEQAERYEEMVEFMEKL'],
+        ["MAVVLPAVVEELLSEMAAAVQESARIPDEYLLSLKFLFGSSATQALDLVDRQSITLISSPSGRRVYQVLGSSSKTYTCLASCHYCSCPAFAFSVLRKSDSILCKHLLAVYLSQVMRTCQQLSVSDKQLTDILLMEKKQEA"],
+    ],
+    cache_examples=False,
+    type="messages",
+)
+
+with gr.Blocks(css_paths="style.css", fill_height=True) as demo:
+    gr.Markdown(DESCRIPTION)
+    gr.DuplicateButton(value="Duplicate Space for private use", elem_id="duplicate-button")
+    chat_interface.render()
+
+if __name__ == "__main__":
+    demo.queue(max_size=20).launch()

gitattributes

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+*.7z filter=lfs diff=lfs merge=lfs -text
+*.arrow filter=lfs diff=lfs merge=lfs -text
+*.bin filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.ckpt filter=lfs diff=lfs merge=lfs -text
+*.ftz filter=lfs diff=lfs merge=lfs -text
+*.gz filter=lfs diff=lfs merge=lfs -text
+*.h5 filter=lfs diff=lfs merge=lfs -text
+*.joblib filter=lfs diff=lfs merge=lfs -text
+*.lfs.* filter=lfs diff=lfs merge=lfs -text
+*.mlmodel filter=lfs diff=lfs merge=lfs -text
+*.model filter=lfs diff=lfs merge=lfs -text
+*.msgpack filter=lfs diff=lfs merge=lfs -text
+*.npy filter=lfs diff=lfs merge=lfs -text
+*.npz filter=lfs diff=lfs merge=lfs -text
+*.onnx filter=lfs diff=lfs merge=lfs -text
+*.ot filter=lfs diff=lfs merge=lfs -text
+*.parquet filter=lfs diff=lfs merge=lfs -text
+*.pb filter=lfs diff=lfs merge=lfs -text
+*.pickle filter=lfs diff=lfs merge=lfs -text
+*.pkl filter=lfs diff=lfs merge=lfs -text
+*.pt filter=lfs diff=lfs merge=lfs -text
+*.pth filter=lfs diff=lfs merge=lfs -text
+*.rar filter=lfs diff=lfs merge=lfs -text
+*.safetensors filter=lfs diff=lfs merge=lfs -text
+saved_model/**/* filter=lfs diff=lfs merge=lfs -text
+*.tar.* filter=lfs diff=lfs merge=lfs -text
+*.tar filter=lfs diff=lfs merge=lfs -text
+*.tflite filter=lfs diff=lfs merge=lfs -text
+*.tgz filter=lfs diff=lfs merge=lfs -text
+*.wasm filter=lfs diff=lfs merge=lfs -text
+*.xz filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.zst filter=lfs diff=lfs merge=lfs -text
+*tfevents* filter=lfs diff=lfs merge=lfs -text

pre-commit-config.yaml

@@ -0,0 +1,60 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-executables-have-shebangs
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-shebang-scripts-are-executable
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: ["--fix=lf"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/myint/docformatter
+    rev: v1.7.5
+    hooks:
+      - id: docformatter
+        args: ["--in-place"]
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.10.1
+    hooks:
+      - id: mypy
+        args: ["--ignore-missing-imports"]
+        additional_dependencies:
+          [
+            "types-python-slugify",
+            "types-requests",
+            "types-PyYAML",
+            "types-pytz",
+          ]
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+        language_version: python3.10
+        args: ["--line-length", "119"]
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
+    hooks:
+      - id: nbstripout
+        args:
+          [
+            "--extra-keys",
+            "metadata.interpreter metadata.kernelspec cell.metadata.pycharm",
+          ]
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.8.5
+    hooks:
+      - id: nbqa-black
+      - id: nbqa-pyupgrade
+        args: ["--py37-plus"]
+      - id: nbqa-isort
+        args: ["--float-to-top"]

requirements.txt

@@ -0,0 +1,241 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile pyproject.toml -o requirements.txt
+accelerate==1.0.0
+    # via gemma-2-9b-it (pyproject.toml)
+aiofiles==23.2.1
+    # via gradio
+annotated-types==0.7.0
+    # via pydantic
+anyio==4.6.0
+    # via
+    #   gradio
+    #   httpx
+    #   starlette
+certifi==2024.8.30
+    # via
+    #   httpcore
+    #   httpx
+    #   requests
+charset-normalizer==3.3.2
+    # via requests
+click==8.1.7
+    # via
+    #   typer
+    #   uvicorn
+exceptiongroup==1.2.2
+    # via anyio
+fastapi==0.115.0
+    # via gradio
+ffmpy==0.4.0
+    # via gradio
+filelock==3.16.1
+    # via
+    #   huggingface-hub
+    #   torch
+    #   transformers
+    #   triton
+fsspec==2024.9.0
+    # via
+    #   gradio-client
+    #   huggingface-hub
+    #   torch
+gradio==5.0.1
+    # via
+    #   gemma-2-9b-it (pyproject.toml)
+    #   spaces
+gradio-client==1.4.0
+    # via gradio
+h11==0.14.0
+    # via
+    #   httpcore
+    #   uvicorn
+hf-transfer==0.1.8
+    # via gemma-2-9b-it (pyproject.toml)
+httpcore==1.0.5
+    # via httpx
+httpx==0.27.2
+    # via
+    #   gradio
+    #   gradio-client
+    #   spaces
+huggingface-hub==0.25.1
+    # via
+    #   accelerate
+    #   gradio
+    #   gradio-client
+    #   tokenizers
+    #   transformers
+idna==3.10
+    # via
+    #   anyio
+    #   httpx
+    #   requests
+jinja2==3.1.4
+    # via
+    #   gradio
+    #   torch
+markdown-it-py==3.0.0
+    # via rich
+markupsafe==2.1.5
+    # via
+    #   gradio
+    #   jinja2
+mdurl==0.1.2
+    # via markdown-it-py
+mpmath==1.3.0
+    # via sympy
+networkx==3.3
+    # via torch
+numpy==2.1.1
+    # via
+    #   accelerate
+    #   gradio
+    #   pandas
+    #   transformers
+nvidia-cublas-cu12==12.1.3.1
+    # via
+    #   nvidia-cudnn-cu12
+    #   nvidia-cusolver-cu12
+    #   torch
+nvidia-cuda-cupti-cu12==12.1.105
+    # via torch
+nvidia-cuda-nvrtc-cu12==12.1.105
+    # via torch
+nvidia-cuda-runtime-cu12==12.1.105
+    # via torch
+nvidia-cudnn-cu12==9.1.0.70
+    # via torch
+nvidia-cufft-cu12==11.0.2.54
+    # via torch
+nvidia-curand-cu12==10.3.2.106
+    # via torch
+nvidia-cusolver-cu12==11.4.5.107
+    # via torch
+nvidia-cusparse-cu12==12.1.0.106
+    # via
+    #   nvidia-cusolver-cu12
+    #   torch
+nvidia-nccl-cu12==2.20.5
+    # via torch
+nvidia-nvjitlink-cu12==12.6.68
+    # via
+    #   nvidia-cusolver-cu12
+    #   nvidia-cusparse-cu12
+nvidia-nvtx-cu12==12.1.105
+    # via torch
+orjson==3.10.7
+    # via gradio
+packaging==24.1
+    # via
+    #   accelerate
+    #   gradio
+    #   gradio-client
+    #   huggingface-hub
+    #   spaces
+    #   transformers
+pandas==2.2.3
+    # via gradio
+pillow==10.4.0
+    # via gradio
+psutil==5.9.8
+    # via
+    #   accelerate
+    #   spaces
+pydantic==2.9.2
+    # via
+    #   fastapi
+    #   gradio
+    #   spaces
+pydantic-core==2.23.4
+    # via pydantic
+pydub==0.25.1
+    # via gradio
+pygments==2.18.0
+    # via rich
+python-dateutil==2.9.0.post0
+    # via pandas
+python-multipart==0.0.12
+    # via gradio
+pytz==2024.2
+    # via pandas
+pyyaml==6.0.2
+    # via
+    #   accelerate
+    #   gradio
+    #   huggingface-hub
+    #   transformers
+regex==2024.9.11
+    # via transformers
+requests==2.32.3
+    # via
+    #   huggingface-hub
+    #   spaces
+    #   transformers
+rich==13.8.1
+    # via typer
+ruff==0.6.8
+    # via gradio
+safetensors==0.4.5
+    # via
+    #   accelerate
+    #   transformers
+semantic-version==2.10.0
+    # via gradio
+shellingham==1.5.4
+    # via typer
+six==1.16.0
+    # via python-dateutil
+sniffio==1.3.1
+    # via
+    #   anyio
+    #   httpx
+spaces==0.30.3
+    # via gemma-2-9b-it (pyproject.toml)
+starlette==0.38.6
+    # via fastapi
+sympy==1.13.3
+    # via torch
+tokenizers==0.20.0
+    # via transformers
+tomlkit==0.12.0
+    # via gradio
+torch==2.4.0
+    # via
+    #   gemma-2-9b-it (pyproject.toml)
+    #   accelerate
+tqdm==4.66.5
+    # via
+    #   huggingface-hub
+    #   transformers
+transformers==4.45.2
+    # via gemma-2-9b-it (pyproject.toml)
+triton==3.0.0
+    # via torch
+typer==0.12.5
+    # via gradio
+typing-extensions==4.12.2
+    # via
+    #   anyio
+    #   fastapi
+    #   gradio
+    #   gradio-client
+    #   huggingface-hub
+    #   pydantic
+    #   pydantic-core
+    #   spaces
+    #   torch
+    #   typer
+    #   uvicorn
+tzdata==2024.2
+    # via pandas
+urllib3==2.2.3
+    # via requests
+uvicorn==0.31.0
+    # via gradio
+websockets==12.0
+    # via gradio-client
+torch_geometric
+torch_scatter
+torch_sparse
+torch_cluster
+torch_spline_conv

style.css

@@ -0,0 +1,11 @@
+h1 {
+  text-align: center;
+  display: block;
+}
+
+#duplicate-button {
+  margin: auto;
+  color: #fff;
+  background: #1565c0;
+  border-radius: 100vh;
+}