Having trouble with requirements.txt about pocketflow HOT 3 CLOSED

name: PocketFlow
channels:

• conda-forge
• schrodinger
• defaults
  dependencies:
• _libgcc_mutex=0.1
• _openmp_mutex=5.1
• alabaster=0.7.12
• apbs=1.5
• asttokens=2.0.5
• babel=2.11.0
• backcall=0.2.0
• blas=1.0
• boost=1.70.0
• boost-cpp=1.70.0
• brotlipy=0.7.0
• bzip2=1.0.8
• c-ares=1.19.0
• ca-certificates=2023.7.22
• cairo=1.16.0
• certifi=2023.7.22
• cffi=1.15.1
• charset-normalizer=2.0.4
• colorama=0.4.6
• comm=0.1.2
• cryptography=39.0.1
• 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
• fontconfig=2.14.1
• freemol=1.158
• freetype=2.12.1
• giflib=5.2.1
• glew=2.0.0
• glib=2.69.1
• 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
• lcms2=2.12
• ld_impl_linux-64=2.38
• lerc=3.0
• libclang=10.0.1
• libcurl=7.88.1
• libdeflate=1.17
• libedit=3.1.20221030
• libev=4.33
• libevent=2.1.12
• libffi=3.4.4
• libgcc-ng=11.2.0
• libgfortran-ng=7.5.0
• libgfortran4=7.5.0
• libglu=9.0.0
• libgomp=11.2.0
• libholoplaycore=0.1.0_rc4
• libllvm10=10.0.1
• libnetcdf=4.8.1
• libnghttp2=1.52.0
• 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
• nspr=4.35
• nss=3.89.1
• openbabel=3.1.1
• openssl=3.0.10
• 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
• 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
• pytz=2023.3
• 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
• 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
• xz=5.2.10
• zeromq=4.3.4
• zlib=1.2.13
• zstd=1.5.5
• 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
  • pyg-lib==0.2.0+pt113cu117
  • 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==1.13.0+cu117
  • torch-cluster==1.6.1+pt113cu117
  • torch-geometric==2.3.1
  • torch-scatter==2.1.1+pt113cu117
  • torch-sparse==0.6.17+pt113cu117
  • torch-spline-conv==1.2.2+pt113cu117
  • torchaudio==0.13.0+cu117
  • torchdiffeq==0.2.3
  • torchvision==0.14.0+cu117
  • 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

from pocketflow.

Hi, thanks for your attention. The code runs on cuda11.3 or 11.7.

from pocketflow.

Hi, I have managed to get the repository to work. In addition, I have submitted a pull request to replace requirements.txt with environment.yml instead. I have also updated the README.md to provide instructions on how to create the conda environment. 😁

Cheers!
Yew Mun

from pocketflow.