From 5a1192e2c7b9de1761afccecbbae5f41ddb0bfaa Mon Sep 17 00:00:00 2001 From: Stefan+o Date: Wed, 20 Nov 2024 20:25:11 +0100 Subject: [PATCH] Updated requirements.txt --- README.md | 5 +- requirements.txt | 516 +++++++++++++++++++++++++++-------------------- 2 files changed, 305 insertions(+), 216 deletions(-) diff --git a/README.md b/README.md index a5716c4..f09c0a5 100644 --- a/README.md +++ b/README.md @@ -38,8 +38,11 @@ The folder [data/studies](data/studies/) contains the training and test data use To install the package, open your terminal and run the following commands: ```bash -pip install git+https://github.com/ribesstefano/PROTAC-Degradation-Predictor.git +git clone --branch=main --depth=1 https://github.com/ribesstefano/PROTAC-Degradation-Predictor.git +cd PROTAC-Degradation-Predictor +pip install . ``` + The package has been developed on a Linux machine with Python 3.10.8. It is recommended to use a virtual environment to avoid conflicts with other packages. diff --git a/requirements.txt b/requirements.txt index 09e4016..a9b3d46 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,302 +1,388 @@ -absl-py==1.4.0 -accelerate==0.34.2 -aiohttp==3.8.3 -aiosignal==1.2.0 -alabaster==0.7.16 -alembic==1.12.0 -anyio==3.7.1 +_libgcc_mutex=0.1=main +_openmp_mutex=5.1=1_gnu +_py-xgboost-mutex=2.0=cpu_0 +abseil-cpp=20211102.0=h27087fc_1 +absl-py=1.4.0=pyhd8ed1ab_0 +accelerate=0.21.0=pyhd8ed1ab_0 +aiohttp=3.8.3=py310h5eee18b_0 +aiosignal=1.2.0=pyhd8ed1ab_0 +alembic=1.12.0=pyhd8ed1ab_0 +anyio=3.7.1=pyhd8ed1ab_0 +arrow=1.2.3=pyhd8ed1ab_0 +arrow-cpp=11.0.0=py310h7516544_0 +async-timeout=4.0.2=pyhd8ed1ab_0 +aws-c-common=0.4.57=he1b5a44_1 +aws-c-event-stream=0.1.6=h72b8ae1_3 +aws-checksums=0.1.9=h346380f_0 +aws-sdk-cpp=1.8.185=hce553d0_0 +backports=1.0=pyhd8ed1ab_3 +backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0 +beautifulsoup4=4.12.2=pyha770c72_0 +binaryornot=0.4.4=py_1 +blas=1.0=mkl +blessed=1.19.1=pyhe4f9e05_2 +blinker=1.6.2=pyhd8ed1ab_0 +boltons=23.0.0=pyhd8ed1ab_0 +boost-cpp=1.73.0=h7f8727e_12 +bottleneck=1.3.5=py310ha9d4c09_0 +brotlipy=0.7.0=py310h5764c6d_1004 +bzip2=1.0.8=h7f98852_4 +c-ares=1.19.0=h5eee18b_0 +ca-certificates=2023.08.22=h06a4308_0 +cachecontrol=0.12.14=pyhd8ed1ab_0 +certifi=2023.7.22=py310h06a4308_0 +cffi=1.15.1=py310h5eee18b_3 +chardet=5.1.0=py310hff52083_0 +charset-normalizer=2.0.4=pyhd8ed1ab_0 +cleo=2.0.1=pyhd8ed1ab_0 +click=8.0.4=py310hff52083_0 +cmaes=0.10.0=pyhd8ed1ab_0 +colorama=0.4.6=pyhd8ed1ab_0 +colorlog=6.7.0=py310hff52083_1 +conda=23.7.4=py310hff52083_0 +conda-content-trust=0.1.3=pyhd8ed1ab_0 +conda-package-handling=1.9.0=py310h5eee18b_1 +cookiecutter=2.3.0=pyh1a96a4e_0 +crashtest=0.4.1=pyhd8ed1ab_0 +croniter=1.3.15=pyhd8ed1ab_0 +cryptography=38.0.1=py310h9ce1e76_0 +cuda-cudart=11.8.89=0 +cuda-cupti=11.8.87=0 +cuda-libraries=11.8.0=0 +cuda-nvrtc=11.8.89=0 +cuda-nvtx=11.8.86=0 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argon2-cffi-bindings==21.2.0 -arrow==1.2.3 asttokens==2.4.1 async-lru==2.0.4 -async-timeout==4.0.2 attrs==23.2.0 -Babel==2.14.0 -backcall==0.2.0 -backports.functools-lru-cache==1.6.5 -beautifulsoup4==4.12.2 -binaryornot==0.4.4 +babel==2.14.0 bleach==6.1.0 -blessed==1.19.1 -blinker==1.6.2 -boltons==23.0.0 -Bottleneck==1.3.5 -brotlipy==0.7.0 -build==0.10.0 -CacheControl==0.12.14 cachetools==4.2.4 -certifi==2024.8.30 -cffi==1.15.1 -chardet==5.1.0 -charset-normalizer==2.0.4 -cleo==2.0.1 -click==8.0.4 -cmaes==0.10.0 -colorama==0.4.6 -colorlog==6.7.0 comm==0.2.2 contourpy==1.2.1 -cookiecutter==2.3.0 -crashtest==0.4.1 -croniter==1.3.15 -cryptography==38.0.1 cycler==0.12.1 -dataclasses==0.8 -datasets==3.0.0 -dateutils==0.6.12 debugpy==1.8.1 decorator==5.1.1 -deepdiff==6.2.2 defusedxml==0.7.1 -dill==0.3.6 -distlib==0.3.7 docker-pycreds==0.4.0 -docopt==0.6.2 docstring-parser==0.15 -docutils==0.20.1 -dulwich==0.21.3 -evaluate==0.2.2 -exceptiongroup==1.1.3 executing==2.0.1 -fastapi==0.103.1 fastjsonschema==2.19.1 -filelock==3.9.0 fonttools==4.51.0 fqdn==1.5.1 -frozenlist==1.3.3 -fsspec==2024.6.1 gitdb==4.0.11 -GitPython==3.1.42 -gmpy2==2.1.2 +gitpython==3.1.42 google-auth==1.35.0 -google-auth-oauthlib==0.4.1 -greenlet==1.1.2 -grpcio==1.42.0 -h11==0.14.0 h5py==3.10.0 -html5lib==1.1 httpcore==1.0.5 httpx==0.27.0 -huggingface==0.0.1 -huggingface-hub==0.24.7 -idna==3.4 -imagesize==1.4.1 imbalanced-learn==0.12.0 -importlib-metadata==6.8.0 -importlib-resources==6.0.1 iniconfig==2.0.0 -inquirer==3.1.3 -installer==0.7.0 ipykernel==6.29.4 -ipython==8.12.3 +ipython==8.23.0 ipywidgets==8.1.2 isoduration==20.11.0 -itsdangerous==2.1.2 -jaraco.classes==3.3.0 jedi==0.19.1 -jeepney==0.8.0 -Jinja2==3.1.2 -joblib==1.2.0 json5==0.9.25 jsonargparse==4.23.1 -jsonpatch==1.32 -jsonpointer==2.1 jsonschema==4.21.1 jsonschema-specifications==2023.12.1 jupyter==1.0.0 -jupyter_client==8.6.1 +jupyter-client==8.6.1 jupyter-console==6.6.3 -jupyter_core==5.7.2 +jupyter-core==5.7.2 jupyter-events==0.10.0 jupyter-lsp==2.2.5 -jupyter_server==2.14.0 -jupyter_server_terminals==0.5.3 +jupyter-server==2.14.0 +jupyter-server-terminals==0.5.3 jupyterlab==4.1.6 -jupyterlab_pygments==0.3.0 -jupyterlab_server==2.26.0 -jupyterlab_widgets==3.0.10 -keyring==23.13.1 +jupyterlab-pygments==0.3.0 +jupyterlab-server==2.26.0 +jupyterlab-widgets==3.0.10 kiwisolver==1.4.5 -lightgbm==4.5.0 -lightning==2.0.4 -lightning-cloud==0.5.38 -lightning-utilities==0.9.0 llvmlite==0.42.0 -lockfile==0.12.2 -Mako==1.2.4 -MAPIE==0.8.6 -Markdown==3.4.4 -markdown-it-py==3.0.0 -MarkupSafe==2.1.1 matplotlib==3.8.4 matplotlib-inline==0.1.7 -mdurl==0.1.0 mistune==3.0.2 -mkl-fft==1.3.6 -mkl-random==1.2.2 -mkl-service==2.4.0 -more-itertools==10.1.0 -mpmath==1.3.0 -msgpack==1.0.3 -multidict==6.0.2 -multiprocess==0.70.14 nbclient==0.10.0 nbconvert==7.16.3 nbformat==5.10.4 nest-asyncio==1.6.0 -networkx==3.1 nltk==3.8.1 notebook==7.1.3 -notebook_shim==0.2.4 +notebook-shim==0.2.4 numba==0.59.1 -numexpr==2.8.4 -numpy==1.25.2 -oauthlib==3.2.2 -optuna==3.3.0 -ordered-set==4.1.0 overrides==7.7.0 -packaging==23.0 -pandas==1.5.3 pandocfilters==1.5.1 parso==0.8.4 -pexpect==4.8.0 -pickleshare==0.7.5 -Pillow==9.4.0 -pip==22.3.1 -pipreqs==0.5.0 -pkginfo==1.9.6 -pkgutil_resolve_name==1.3.10 -platformdirs==2.6.2 pluggy==1.5.0 -poetry==1.4.2 -poetry-core==1.5.2 -poetry-plugin-export==1.3.1 -prometheus_client==0.20.0 +prometheus-client==0.20.0 prompt-toolkit==3.0.43 -protobuf==3.20.3 -psutil==5.9.0 -ptyprocess==0.7.0 pure-eval==0.2.2 -pyarrow==17.0.0 -pyasn1==0.4.8 -pyasn1-modules==0.2.7 -pycosat==0.6.4 -pycparser==2.21 -pydantic==1.9.1 -Pygments==2.18.0 -PyJWT==2.8.0 pynndescent==0.5.12 pynvml==11.5.0 -pyOpenSSL==22.0.0 -pyparsing==3.0.9 -pyproject_hooks==1.0.0 -pyrsistent==0.18.1 -PySocks==1.7.1 pytest==8.1.1 -python-dateutil==2.8.2 -python-editor==1.0.4 python-json-logger==2.0.7 -python-multipart==0.0.6 -python-slugify==8.0.1 -pytorch-lightning==2.0.9 -pytz==2022.7.1 -pyu2f==0.1.5 -PyYAML==6.0 pyzmq==26.0.1 qtconsole==5.5.1 -QtPy==2.4.1 -rapidfuzz==2.13.7 +qtpy==2.4.1 rdkit==2023.9.5 rdkit-pypi==2022.9.5 -readchar==4.0.5.dev0 referencing==0.34.0 -regex==2022.7.9 -requests==2.32.3 -requests-oauthlib==1.3.1 -requests-toolbelt==0.10.1 -responses==0.18.0 +requests==2.31.0 rfc3339-validator==0.1.4 rfc3986-validator==0.1.1 -rich==13.5.1 rouge-score==0.1.2 rpds-py==0.18.0 -rsa==4.9 -ruamel.yaml==0.17.21 -ruamel.yaml.clib==0.2.6 -sacremoses==0.0.43 -safetensors==0.4.5 -scikit-learn==1.2.0 -scipy==1.9.3 seaborn==0.13.2 -SecretStorage==3.3.3 -Send2Trash==1.8.3 +send2trash==1.8.3 sentry-sdk==1.41.0 setproctitle==1.3.3 -setuptools==65.5.0 -shellingham==1.5.3 -six==1.16.0 smmap==5.0.1 -sniffio==1.3.0 -snowballstemmer==2.2.0 -soupsieve==2.5 -Sphinx==7.4.7 -sphinx-rtd-theme==2.0.0 -sphinxcontrib-applehelp==2.0.0 -sphinxcontrib-devhelp==2.0.0 -sphinxcontrib-htmlhelp==2.1.0 -sphinxcontrib-jquery==4.1 -sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==2.0.0 -sphinxcontrib-serializinghtml==2.0.0 -SQLAlchemy==1.4.36 stack-data==0.6.3 -starlette==0.27.0 -starsessions==1.3.0 -sympy==1.11.1 -tabulate==0.9.0 -tensorboard==2.6.0 tensorboard-data-server==0.6.1 -tensorboard-plugin-wit==1.8.1 terminado==0.18.1 -text-unidecode==1.3 -threadpoolctl==2.2.0 tinycss2==1.2.1 -tokenizers==0.19.1 -tomli==2.0.1 -tomlkit==0.12.1 -toolz==0.12.0 -torch==2.0.1 -torch-geometric==2.3.1 -torchaudio==2.0.2 -torchmetrics==1.1.2 -torchvision==0.15.2 tornado==6.4 -tqdm==4.66.5 traitlets==5.14.3 -transformers==4.44.2 -triton==2.0.0 -trove-classifiers==2023.8.7 typeshed-client==2.3.0 -typing_extensions==4.7.1 umap-learn==0.5.6 -Unidecode==1.3.6 uri-template==1.3.0 -urllib3==1.26.13 -uvicorn==0.23.2 -virtualenv==20.21.1 wandb==0.16.4 -wcwidth==0.2.6 webcolors==1.13 -webencodings==0.5.1 websocket-client==1.7.0 -websockets==10.3 -Werkzeug==2.3.6 -wheel==0.37.1 -widgetsnbextension==4.0.10 -xgboost==1.5.1 -xxhash==2.0.2 -yarg==0.1.9 -yarl==1.8.1 -zipp==3.16.2 +widgetsnbextension==4.0.10 \ No newline at end of file