fix requirements.txt

requirements.txt

@@ -1,29 +1,217 @@
+absl-py==2.1.0
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.3
+aiohttp==3.10.10
+aiosignal==1.3.1
+annotated-types==0.7.0
+anyio==4.6.2.post1
+argon2-cffi==23.1.0
+argon2-cffi-bindings==21.2.0
+arrow==1.3.0
+asttokens==2.4.1
+async-lru==2.0.4
+async-timeout==4.0.3
+attrs==24.2.0
+babel==2.16.0
+beautifulsoup4==4.12.3
+bio==1.7.1
+biopython==1.84
+biothings-client==0.3.1
+biotite==0.41.2
+bleach==6.2.0
+cachetools==5.5.0
+certifi==2024.8.30
+cffi==1.17.1
+charset-normalizer==3.4.0
+click==8.1.7
+comm==0.2.2
+debugpy==1.8.7
+decorator==5.1.1
+defusedxml==0.7.1
+docker-pycreds==0.4.0
+exceptiongroup==1.2.2
+executing==2.1.0
+fastapi==0.115.4
+fastjsonschema==2.20.0
+fastpdb==1.3.1
+ffmpy==0.4.0
 filelock==3.16.1
+fqdn==1.5.1
+frozenlist==1.5.0
 fsspec==2024.10.0
+gcsfs==2024.10.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-api-core==2.22.0
+google-auth==2.35.0
+google-auth-oauthlib==1.2.1
+google-cloud-core==2.4.1
+google-cloud-storage==2.18.2
+google-crc32c==1.6.0
+google-resumable-media==2.7.2
+googleapis-common-protos==1.65.0
+gprofiler-official==1.0.0
+gradio==5.5.0
+gradio_client==1.4.2
+gradio_molecule3d==0.0.6
+grpcio==1.67.1
+h11==0.14.0
+httpcore==1.0.6
+httpx==0.27.2
+huggingface-hub==0.26.2
+idna==3.10
+ipykernel==6.29.5
+ipython==8.29.0
+ipywidgets==8.1.5
+isoduration==20.11.0
+jedi==0.19.1
 Jinja2==3.1.4
-MarkupSafe==3.0.2
+joblib==1.4.2
+json5==0.9.25
+jsonpointer==3.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2024.10.1
+jupyter-events==0.10.0
+jupyter-lsp==2.2.5
+jupyter_client==8.6.3
+jupyter_core==5.7.2
+jupyter_server==2.14.2
+jupyter_server_terminals==0.5.3
+jupyterlab==4.3.0
+jupyterlab_pygments==0.3.0
+jupyterlab_server==2.27.3
+jupyterlab_widgets==3.0.13
+lightning==2.4.0
+lightning-utilities==0.11.8
+Markdown==3.7
+markdown-it-py==3.0.0
+MarkupSafe==2.1.5
+matplotlib-inline==0.1.7
+mdurl==0.1.2
+mistune==3.0.2
 mpmath==1.3.0
+msgpack==1.1.0
+multidict==6.1.0
+mygene==3.2.2
+nbclient==0.10.0
+nbconvert==7.16.4
+nbformat==5.10.4
+nest-asyncio==1.6.0
 networkx==3.4.2
-numpy==2.1.3
-nvidia-cublas-cu12==12.1.3.1
-nvidia-cuda-cupti-cu12==12.1.105
-nvidia-cuda-nvrtc-cu12==12.1.105
-nvidia-cuda-runtime-cu12==12.1.105
+notebook_shim==0.2.4
+numpy==1.26.4
+nvidia-cublas-cu12==12.4.5.8
+nvidia-cuda-cupti-cu12==12.4.127
+nvidia-cuda-nvrtc-cu12==12.4.127
+nvidia-cuda-runtime-cu12==12.4.127
 nvidia-cudnn-cu12==9.1.0.70
-nvidia-cufft-cu12==11.0.2.54
-nvidia-curand-cu12==10.3.2.106
-nvidia-cusolver-cu12==11.4.5.107
-nvidia-cusparse-cu12==12.1.0.106
-nvidia-nccl-cu12==2.20.5
-nvidia-nvjitlink-cu12==12.6.77
-nvidia-nvtx-cu12==12.1.105
-pyg-lib==0.4.0
+nvidia-cufft-cu12==11.2.1.3
+nvidia-curand-cu12==10.3.5.147
+nvidia-cusolver-cu12==11.6.1.9
+nvidia-cusparse-cu12==12.3.1.170
+nvidia-nccl-cu12==2.21.5
+nvidia-nvjitlink-cu12==12.4.127
+nvidia-nvtx-cu12==12.4.127
+oauthlib==3.2.2
+orjson==3.10.11
+overrides==7.7.0
+packaging==24.1
+pandas==2.2.3
+pandocfilters==1.5.1
+parso==0.8.4
+pexpect==4.9.0
+pillow==11.0.0
+pinder==0.4.1
+platformdirs==4.3.6
+plotly==5.24.1
+pooch==1.8.2
+prometheus_client==0.21.0
+prompt_toolkit==3.0.48
+propcache==0.2.0
+proto-plus==1.25.0
+protobuf==5.28.3
+psutil==6.1.0
+ptyprocess==0.7.0
+pure_eval==0.2.3
+pyarrow==18.0.0
+pyasn1==0.6.1
+pyasn1_modules==0.4.1
+pycparser==2.22
+pydantic==2.9.2
+pydantic_core==2.23.4
+pydub==0.25.1
+pyg-lib==0.4.0+pt24cpu
+Pygments==2.18.0
+pyparsing==3.2.0
+python-dateutil==2.9.0.post0
+python-dotenv==1.0.1
+python-json-logger==2.0.7
+python-multipart==0.0.12
+pytorch-lightning==2.4.0
+pytz==2024.2
+PyYAML==6.0.2
+pyzmq==26.2.0
+referencing==0.35.1
+requests==2.32.3
+requests-oauthlib==2.0.0
+rfc3339-validator==0.1.4
+rfc3986-validator==0.1.1
+rich==13.9.4
+rootutils==1.0.7
+rpds-py==0.20.1
+rsa==4.9
+ruff==0.7.2
+safehttpx==0.1.1
+scikit-learn==1.5.2
 scipy==1.14.1
-sympy==1.13.3
-torch==2.4.0
-torch_cluster==1.6.3
-torch_scatter==2.1.2
-torch_sparse==0.6.18
-torch_spline_conv==1.2.2
-triton==3.0.0
+semantic-version==2.10.0
+Send2Trash==1.8.3
+sentry-sdk==2.18.0
+setproctitle==1.3.3
+shellingham==1.5.4
+six==1.16.0
+smmap==5.0.1
+sniffio==1.3.1
+soupsieve==2.6
+stack-data==0.6.3
+starlette==0.41.2
+sympy==1.13.1
+tabulate==0.9.0
+tenacity==9.0.0
+tensorboard==2.18.0
+tensorboard-data-server==0.7.2
+tensorboardX==2.6.2.2
+terminado==0.18.1
+threadpoolctl==3.5.0
+tinycss2==1.4.0
+tomli==2.0.2
+tomlkit==0.12.0
+torch==2.5.1
+torch-geometric==2.6.1
+torch_cluster==1.6.3+pt24cpu
+torch_scatter==2.1.2+pt24cpu
+torch_sparse==0.6.18+pt24cpu
+torch_spline_conv==1.2.2+pt24cpu
+torchmetrics==1.5.1
+torchtyping==0.1.5
+tornado==6.4.1
+tqdm==4.66.6
+traitlets==5.14.3
+triton==3.1.0
+typeguard==2.13.3
+typer==0.13.0
+types-python-dateutil==2.9.0.20241003
 typing_extensions==4.12.2
+tzdata==2024.2
+uri-template==1.3.0
+urllib3==2.2.3
+uvicorn==0.32.0
+wandb==0.18.5
+wcwidth==0.2.13
+webcolors==24.8.0
+webencodings==0.5.1
+websocket-client==1.8.0
+websockets==12.0
+Werkzeug==3.1.2
+widgetsnbextension==4.0.13
+yarl==1.17.1