From c86fa165793feed23d8efd97f6de28b0ca2bfa5f Mon Sep 17 00:00:00 2001 From: Yew Mun Date: Tue, 21 May 2024 16:26:21 +0100 Subject: [PATCH] Create a Conda environment file for easy environment creation --- environment.yml | 337 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 337 insertions(+) create mode 100644 environment.yml diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..c1ae342 --- /dev/null +++ b/environment.yml @@ -0,0 +1,337 @@ +name: pocketflow +channels: + - pyg + - schrodinger + - pytorch + - nvidia + - defaults + - conda-forge +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - alabaster=0.7.12 + - apbs=1.5 + - asttokens=2.0.5 + - babel=2.11.0 + - backcall=0.2.0 + - backports=1.0 + - backports.functools_lru_cache=2.0.0 + - blas=1.0 + - boost=1.70.0 + - boost-cpp=1.70.0 + - brotli-python=1.0.9 + - brotlipy=0.7.0 + - bzip2=1.0.8 + - c-ares=1.19.0 + - ca-certificates=2024.2.2 + - cairo=1.16.0 + - certifi=2024.2.2 + - cffi=1.15.1 + - charset-normalizer=2.0.4 + - colorama=0.4.6 + - comm=0.1.2 + - cryptography=39.0.1 + - cuda-cudart=11.7.99 + - cuda-cupti=11.7.101 + - cuda-libraries=11.7.1 + - cuda-nvrtc=11.7.99 + - cuda-nvtx=11.7.91 + - cuda-runtime=11.7.1 + - curl=7.88.1 + - dbus=1.13.18 + - debugpy=1.5.1 + - decorator=5.1.1 + - docutils=0.18.1 + - executing=0.8.3 + - expat=2.4.9 + - ffmpeg=4.3 + - fontconfig=2.14.1 + - freemol=1.158 + - freetype=2.12.1 + - giflib=5.2.1 + - glew=2.0.0 + - glib=2.69.1 + - gmp=6.2.1 + - gnutls=3.6.13 + - gst-plugins-base=1.14.1 + - gstreamer=1.14.1 + - h5py=3.7.0 + - hdf4=4.2.13 + - hdf5=1.10.6 + - icu=58.2 + - idna=3.4 + - imagesize=1.4.1 + - importlib_metadata=6.0.0 + - intel-openmp=2023.1.0 + - ipykernel=6.19.2 + - ipython=8.12.0 + - ipywidgets=8.0.7 + - jedi=0.18.1 + - jinja2=3.1.2 + - jpeg=9e + - jupyter_client=8.1.0 + - jupyter_core=5.3.0 + - jupyterlab_widgets=3.0.8 + - krb5=1.20.1 + - lame=3.100 + - lcms2=2.12 + - ld_impl_linux-64=2.38 + - lerc=3.0 + - libblas=3.9.0 + - libcblas=3.9.0 + - libclang=10.0.1 + - libcublas=11.10.3.66 + - libcufft=10.7.2.124 + - libcufile=1.9.1.3 + - libcurand=10.3.5.147 + - libcurl=7.88.1 + - libcusolver=11.4.0.1 + - libcusparse=11.7.4.91 + - libdeflate=1.17 + - libedit=3.1.20221030 + - libev=4.33 + - libevent=2.1.12 + - libffi=3.4.4 + - libgcc-ng=13.2.0 + - libgfortran-ng=7.5.0 + - libgfortran4=7.5.0 + - libglu=9.0.0 + - libgomp=13.2.0 + - libholoplaycore=0.1.0_rc4 + - libiconv=1.17 + - liblapack=3.9.0 + - libllvm10=10.0.1 + - libnetcdf=4.8.1 + - libnghttp2=1.52.0 + - libnpp=11.7.4.75 + - libnvjpeg=11.8.0.2 + - libopenblas=0.3.18 + - libpng=1.6.39 + - libpq=12.15 + - libsodium=1.0.18 + - libssh2=1.10.0 + - libstdcxx-ng=11.2.0 + - libtiff=4.5.0 + - libuuid=1.41.5 + - libwebp=1.2.4 + - libwebp-base=1.2.4 + - libxcb=1.15 + - libxkbcommon=1.0.1 + - libxml2=2.9.14 + - libxslt=1.1.35 + - libzip=1.8.0 + - lz4-c=1.9.4 + - matplotlib-inline=0.1.6 + - mengine=1 + - mkl=2023.1.0 + - mkl-service=2.4.0 + - mkl_fft=1.3.6 + - mkl_random=1.2.2 + - mpeg_encode=1 + - mtz2ccp4_px=1.0 + - ncurses=6.4 + - nest-asyncio=1.5.6 + - nettle=3.6 + - nspr=4.35 + - nss=3.89.1 + - openbabel=3.1.1 + - openh264=2.1.1 + - openssl=3.3.0 + - packaging=23.0 + - pandas=1.4.2 + - parso=0.8.3 + - pcre=8.45 + - pdb2pqr=2.1.2+pymol + - pexpect=4.8.0 + - pickleshare=0.7.5 + - pillow=9.4.0 + - pixman=0.40.0 + - platformdirs=2.5.2 + - ply=3.11 + - pmw=2.0.1+3 + - prompt-toolkit=3.0.36 + - prompt_toolkit=3.0.36 + - ptyprocess=0.7.0 + - pure_eval=0.2.2 + - pycairo=1.21.0 + - pycparser=2.21 + - pygments=2.15.1 + - pymol=2.4.1 + - pyopenssl=23.0.0 + - pyqt=5.15.7 + - pyqt5-sip=12.11.0 + - pysocks=1.7.1 + - python=3.8.12 + - python-dateutil=2.8.2 + - python-lmdb=1.3.0 + - python_abi=3.8 + - pytorch=1.13.0 + - pytorch-cluster=1.6.1 + - pytorch-cuda=11.7 + - pytorch-mutex=1.0 + - pytorch-scatter=2.1.1 + - pytorch-sparse=0.6.17 + - pytorch-spline-conv=1.2.2 + - pytz=2023.3.post1 + - pyzmq=25.1.0 + - qt-main=5.15.2 + - qt-webengine=5.15.9 + - qtwebkit=5.212 + - rdkit=2019.09.3 + - readline=8.2 + - rigimol=1.3 + - setuptools=67.8.0 + - sip=6.6.2 + - six=1.16.0 + - snowballstemmer=2.2.0 + - sphinx=5.0.2 + - sphinx_rtd_theme=1.1.1 + - sphinxcontrib-applehelp=1.0.2 + - sphinxcontrib-devhelp=1.0.2 + - sphinxcontrib-htmlhelp=2.0.0 + - sphinxcontrib-jsmath=1.0.1 + - sphinxcontrib-qthelp=1.0.3 + - sphinxcontrib-serializinghtml=1.1.5 + - sqlite=3.41.2 + - stack_data=0.2.0 + - tbb=2021.8.0 + - tk=8.6.12 + - toml=0.10.2 + - torchaudio=0.13.0 + - torchvision=0.14.0 + - tornado=6.2 + - traitlets=5.7.1 + - typing_extensions=4.6.3 + - urllib3=1.26.16 + - wcwidth=0.2.5 + - wheel=0.38.4 + - widgetsnbextension=4.0.8 + - xorg-kbproto=1.0.7 + - xorg-libx11=1.7.2 + - xorg-libxext=1.3.4 + - xorg-xextproto=7.3.0 + - xorg-xproto=7.0.31 + - xz=5.2.10 + - zeromq=4.3.4 + - zlib=1.2.13 + - zstd=1.5.5 + - pip + - pip: + - absl-py==1.4.0 + - anyio==4.0.0 + - appdirs==1.4.4 + - argon2-cffi==23.1.0 + - argon2-cffi-bindings==21.2.0 + - arrow==1.3.0 + - async-lru==2.0.4 + - attrs==23.1.0 + - beautifulsoup4==4.12.2 + - bleach==6.1.0 + - cachetools==5.3.1 + - click==8.1.7 + - contourpy==1.1.0 + - cycler==0.11.0 + - defusedxml==0.7.1 + - docker-pycreds==0.4.0 + - easydict==1.10 + - et-xmlfile==1.1.0 + - exceptiongroup==1.1.3 + - fastjsonschema==2.18.1 + - fonttools==4.40.0 + - fqdn==1.5.1 + - gitdb==4.0.11 + - gitpython==3.1.40 + - google-auth==2.21.0 + - google-auth-oauthlib==1.0.0 + - grpcio==1.56.0 + - imageio==2.33.1 + - importlib-metadata==6.7.0 + - importlib-resources==5.12.0 + - ipython-genutils==0.2.0 + - isoduration==20.11.0 + - jax==0.4.13 + - jaxlib==0.4.13 + - joblib==1.2.0 + - json5==0.9.14 + - jsonpointer==2.4 + - jsonschema==4.19.2 + - jsonschema-specifications==2023.7.1 + - jupyter==1.0.0 + - jupyter-console==6.6.3 + - jupyter-events==0.8.0 + - jupyter-lsp==2.2.0 + - jupyter-server==2.9.1 + - jupyter-server-terminals==0.4.4 + - jupyterlab==4.0.7 + - jupyterlab-pygments==0.2.2 + - jupyterlab-server==2.25.0 + - kiwisolver==1.4.4 + - markdown==3.4.3 + - markupsafe==2.1.3 + - matplotlib==3.7.1 + - meeko==0.4.0 + - mistune==3.0.2 + - ml-dtypes==0.2.0 + - msgpack==1.0.7 + - nbclient==0.8.0 + - nbconvert==7.10.0 + - nbformat==5.9.2 + - notebook==7.0.6 + - notebook-shim==0.2.3 + - numpy==1.23.0 + - nvidia-cublas-cu11==11.11.3.6 + - nvidia-cufft-cu11==10.9.0.58 + - oauthlib==3.2.2 + - openpyxl==3.1.2 + - opt-einsum==3.3.0 + - overrides==7.4.0 + - pandocfilters==1.5.0 + - pip==23.3.2 + - pkgutil-resolve-name==1.3.10 + - prometheus-client==0.18.0 + - protobuf==4.23.3 + - psutil==5.9.5 + - pyasn1==0.5.0 + - pyasn1-modules==0.3.0 + - https://data.pyg.org/whl/torch-1.13.0%2Bcu117/pyg_lib-0.2.0%2Bpt113cu117-cp38-cp38-linux_x86_64.whl + - pyparsing==3.1.0 + - python-json-logger==2.0.7 + - pyyaml==6.0 + - qtconsole==5.4.4 + - qtpy==2.4.1 + - referencing==0.30.2 + - requests==2.31.0 + - requests-oauthlib==1.3.1 + - rfc3339-validator==0.1.4 + - rfc3986-validator==0.1.1 + - rpds-py==0.10.6 + - rsa==4.9 + - scikit-learn==1.2.2 + - scipy==1.10.1 + - seaborn==0.12.2 + - send2trash==1.8.2 + - sentry-sdk==1.39.1 + - setproctitle==1.3.3 + - smmap==5.0.1 + - sniffio==1.3.0 + - soupsieve==2.5 + - tensorboard==2.13.0 + - tensorboard-data-server==0.7.1 + - terminado==0.17.1 + - threadpoolctl==3.1.0 + - tinycss2==1.2.1 + - tomli==2.0.1 + - torch-geometric==2.3.1 + - torchdiffeq==0.2.3 + - tqdm==4.65.0 + - types-python-dateutil==2.8.19.14 + - uri-template==1.3.0 + - vina==1.2.5 + - wandb==0.16.1 + - webcolors==1.13 + - webencodings==0.5.1 + - websocket-client==1.6.4 + - werkzeug==2.3.6 + - xgboost==1.0.2 + - zipp==3.15.0 + - zuko==1.0.1