Github actions + minimal install requirements + removed dependency on hardcoded path

.github/workflows/python-app.yml

@@ -0,0 +1,46 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python application
+
+on:
+  push:
+    branches:
+      - main
+      - '**'
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [ubuntu-latest] #, macos-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        miniconda-version: "latest"
+        channels: bioconda, conda-forge, defaults
+        use-only-tar-bz2: true
+        auto-update-conda: true
+#        auto-activate-base: true
+        activate-environment: test
+        python-version: 3.8
+    - name: Install dependencies
+      shell: bash -el {0}
+      run: |
+        conda install --file=requirements_conda.txt
+        pip install -r ./requirements_pip.txt
+    - name: Test
+      shell: bash -el {0}
+      run: |
+        cd example
+        python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -m ../trained_models/rtmscore_model1.pth
+        python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -ac -m ../trained_models/rtmscore_model1.pth
+        python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -rc -m ../trained_models/rtmscore_model1.pth
+        python  rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -m ../trained_models/rtmscore_model1.pth

example/rtmscore.py

@@ -15,7 +15,8 @@
 torch.multiprocessing.set_sharing_strategy('file_system')
 
 #you need to set the babel libdir first if you need to generate the pocket
-os.environ["BABEL_LIBDIR"] = "/home/shenchao/.conda/envs/my2/lib/openbabel/3.1.0"
+env_path=os.environ['CONDA_PREFIX']
+os.environ["BABEL_LIBDIR"] = os.path.join(env_path,"lib","openbabel","3.1.0")
 
 def Input():
 	p = argparse.ArgumentParser()

requirements_conda.txt

@@ -1,316 +1,15 @@
-# This file may be used to create an environment using:
-# $ conda create --name <env> --file <this file>
-# platform: linux-64
-_libgcc_mutex=0.1=conda_forge
-_openmp_mutex=4.5=1_llvm
-_py-xgboost-mutex=2.0=cpu_0
-_tflow_select=2.1.0=gpu
-abseil-cpp=20210324.0=h9c3ff4c_0
-absl-py=0.13.0=pyhd8ed1ab_0
-aiohttp=3.7.4.post0=py38h497a2fe_0
-alabaster=0.7.12=py_0
-alembic=1.6.5=pyhd8ed1ab_0
-appdirs=1.4.4=pyh9f0ad1d_0
-astor=0.8.1=pyh9f0ad1d_0
-astunparse=1.6.3=pyhd8ed1ab_0
-async-timeout=3.0.1=py_1000
-attrs=21.2.0=pyhd8ed1ab_0
-babel=2.9.1=pyh44b312d_0
-backcall=0.2.0=pypi_0
-backports=1.0=py_2
-backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
-biopandas=0.2.7=pyh9f0ad1d_1
-biopython=1.79=py38h497a2fe_0
-blas=1.0=mkl
-blinker=1.4=py_1
-blosc=1.21.0=h9c3ff4c_0
-bokeh=2.4.0=py38h578d9bd_0
-boost=1.74.0=py38hc10631b_3
-boost-cpp=1.74.0=hc6e9bd1_3
-brotlipy=0.7.0=py38h497a2fe_1001
-bzip2=1.0.8=h7f98852_4
-c-ares=1.17.2=h7f98852_0
-ca-certificates=2021.5.30=ha878542_0
-cached-property=1.5.2=hd8ed1ab_1
-cached_property=1.5.2=pyha770c72_1
-cachetools=4.2.2=pyhd8ed1ab_0
-cairo=1.16.0=h6cf1ce9_1008
-catboost=0.26.1=py38h578d9bd_0
-certifi=2021.5.30=py38h578d9bd_0
-cffi=1.14.6=py38ha65f79e_0
-cftime=1.5.0=py38hb5d20a5_0
-chardet=4.0.0=py38h578d9bd_1
-charset-normalizer=2.0.0=pyhd8ed1ab_0
-chemprop=1.3.1=pyhd8ed1ab_0
-click=8.0.1=py38h578d9bd_0
-cliff=3.8.0=pyhd8ed1ab_0
-cloudpickle=1.6.0=py_0
-cmaes=0.8.2=pyh44b312d_0
-cmd2=2.1.2=py38h578d9bd_0
-colorama=0.4.4=pyh9f0ad1d_0
-colorlog=6.4.1=py38h578d9bd_0
-conda-pack=0+unknown=pypi_0
-configargparse=1.5.2=pypi_0
-cryptography=3.4.7=py38ha5dfef3_0
-cudatoolkit=11.1.1=h6406543_8
-curl=7.78.0=hea6ffbf_0
-cycler=0.10.0=py_2
-cytoolz=0.11.0=py38h497a2fe_3
-dask=2021.8.1=pyhd8ed1ab_0
-dask-core=2021.8.1=pyhd8ed1ab_0
-dataclasses=0.8=pyhc8e2a94_3
-decorator=4.4.2=py_0
-dgl-cuda11.1=0.7.0=py38_0
-dgllife=0.2.8=pypi_0
-distributed=2021.8.1=py38h06a4308_0
-docutils=0.17.1=py38h578d9bd_0
-enum34=1.1.10=py38h32f6830_2
-ffmpeg=4.3=hf484d3e_0
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-filelock=3.0.12=pypi_0
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-future=0.18.2=py38h578d9bd_3
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-gsd=2.4.2=py38hb5d20a5_0
-h5py=2.10.0=nompi_py38h9915d05_106
-hdf4=4.2.13=h3ca952b_2
-hdf5=1.10.6=nompi_h7c3c948_1111
-heapdict=1.0.1=py_0
-hyperopt=0.2.5=pyh9f0ad1d_0
-icu=68.1=h58526e2_0
-idna=3.1=pyhd3deb0d_0
-imagecodecs-lite=2019.12.3=py38h5c078b8_3
-imageio=2.9.0=py_0
-imagesize=1.2.0=py_0
-importlib-metadata=4.6.4=py38h578d9bd_0
-intel-openmp=2021.3.0=h06a4308_3350
-ipython=7.28.0=pypi_0
-isodate=0.6.1=pypi_0
-itsdangerous=2.0.1=pyhd8ed1ab_0
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-jpeg=9d=h36c2ea0_0
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-kiwisolver=1.3.1=py38h1fd1430_1
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-ld_impl_linux-64=2.35.1=h7274673_9
-libcurl=7.78.0=h2574ce0_0
-libedit=3.1.20191231=he28a2e2_2
-libev=4.33=h516909a_1
-libffi=3.3=he6710b0_2
-libgcc-ng=11.1.0=hc902ee8_8
-libgfortran-ng=7.5.0=h14aa051_19
-libgfortran4=7.5.0=h14aa051_19
-libglib=2.68.4=h3e27bee_0
-libiconv=1.16=h516909a_0
-libnetcdf=4.6.1=h2053bdc_4
-libnghttp2=1.43.0=h812cca2_0
-libpng=1.6.37=h21135ba_2
-libprotobuf=3.15.8=h780b84a_0
-libssh2=1.9.0=ha56f1ee_6
-libstdcxx-ng=11.1.0=h56837e0_8
-libtiff=4.1.0=h2733197_1
-libuuid=2.32.1=h7f98852_1000
-libuv=1.42.0=h7f98852_0
-libxcb=1.13=h7f98852_1003
-libxgboost=1.4.0=h9c3ff4c_0
-libxml2=2.9.12=h72842e0_0
-lightgbm=3.2.1=py38h709712a_0
-llvm-openmp=12.0.1=h4bd325d_1
-locket=0.2.0=py_2
-lz4-c=1.9.3=h9c3ff4c_1
-lzo=2.10=h516909a_1000
-mako=1.1.5=pyhd8ed1ab_0
-markdown=3.3.4=pyhd8ed1ab_0
-markupsafe=2.0.1=py38h497a2fe_0
-matplotlib-base=3.4.3=py38hf4fb855_0
-matplotlib-inline=0.1.3=pypi_0
-mdanalysis=2.0.0=py38h709712a_1
-mdtraj=1.9.6=py38hf01b267_1
-meeko=0.1.dev3=pypi_0
-mkl=2021.3.0=h06a4308_520
-mkl-service=2.4.0=py38h497a2fe_0
-mkl_fft=1.3.0=py38h42c9631_2
-mkl_random=1.2.2=py38h1abd341_0
-mmtf-python=1.1.2=py_0
-mock=4.0.3=py38h578d9bd_1
-msgpack-python=1.0.2=py38h1fd1430_1
-multidict=5.1.0=py38h497a2fe_1
-mypy_extensions=0.4.3=py38h578d9bd_3
-ncurses=6.2=he6710b0_1
-netcdf4=1.5.7=py38h0a24e14_0
-nettle=3.6=he412f7d_0
-networkx=2.5.1=pyhd8ed1ab_0
-ninja=1.10.2=h4bd325d_0
-numexpr=2.7.3=py38h51da96c_0
-numpy=1.20.3=py38hf144106_0
-numpy-base=1.20.3=py38h74d4b33_0
-oauthlib=3.1.1=pyhd8ed1ab_0
-ocl-icd=2.3.1=h7f98852_0
-ocl-icd-system=1.0.0=1
-oddt=0.7=pyh500f238_0
-olefile=0.46=pyh9f0ad1d_1
-openbabel=3.1.1=py38hd2c4bc0_1
-openh264=2.1.1=h780b84a_0
-openjpeg=2.4.0=hf7af979_0
-openmm=0.2=pypi_0
-openssl=1.1.1l=h7f98852_0
-opt_einsum=3.3.0=pyhd8ed1ab_1
-optuna=2.9.1=pyhd8ed1ab_0
-packaging=21.0=pyhd8ed1ab_0
-pandas=1.0.3=pypi_0
-pandas-flavor=0.2.0=py_0
-parso=0.8.2=pypi_0
-partd=1.2.0=pyhd8ed1ab_0
-pathlib=1.0.1=py38h578d9bd_4
-patsy=0.5.1=py_0
-pbr=5.6.0=pyhd8ed1ab_0
-pcre=8.45=h9c3ff4c_0
-pdbfixer=1.7=pypi_0
-pexpect=4.8.0=pypi_0
-pickleshare=0.7.5=pypi_0
-pillow=8.3.1=py38h2c7a002_0
-pip=21.0.1=py38h06a4308_0
-pixman=0.40.0=h36c2ea0_0
-pooch=1.5.1=pyhd8ed1ab_0
-prettytable=2.1.0=pyhd8ed1ab_0
-prody=2.1.0=pypi_0
-prompt-toolkit=3.0.20=pypi_0
-protobuf=3.15.8=py38h709712a_0
-psutil=5.8.0=py38h497a2fe_1
-pthread-stubs=0.4=h36c2ea0_1001
-ptyprocess=0.7.0=pypi_0
-pubchempy=1.0.4=pypi_0
-py-xgboost=1.4.0=py38h578d9bd_0
-pyasn1=0.4.8=py_0
-pyasn1-modules=0.2.7=py_0
-pycairo=1.20.1=py38hf61ee4a_0
-pycparser=2.20=pyh9f0ad1d_2
-pydeprecate=0.3.1=pypi_0
-pygments=2.10.0=pyhd8ed1ab_0
-pyjwt=2.1.0=pyhd8ed1ab_0
-pymongo=3.12.0=py38h709712a_0
-pyopenssl=20.0.1=pyhd8ed1ab_0
-pyparsing=2.4.7=pyh9f0ad1d_0
-pyperclip=1.8.2=pyhd8ed1ab_2
-pyscreener=0+unknown=pypi_0
-pysocks=1.7.1=py38h578d9bd_3
-pytables=3.6.1=py38hc386592_3
-python=3.8.11=h12debd9_0_cpython
-python-dateutil=2.8.2=pyhd8ed1ab_0
-python-editor=1.0.4=py_0
-python-flatbuffers=1.12=pyhd8ed1ab_1
-python_abi=3.8=2_cp38
-pytorch=1.9.0=py3.8_cuda11.1_cudnn8.0.5_0
-pytorch-lightning=1.4.4=pypi_0
-pytz=2021.1=pyhd8ed1ab_0
-pyu2f=0.1.5=pyhd8ed1ab_0
-pywavelets=1.1.1=py38h5c078b8_3
-pyyaml=5.4.1=py38h497a2fe_1
-ray=1.6.0=pypi_0
-rdflib=6.1.1=pypi_0
-rdkit=2021.03.5=py38h8c3fb5a_0
-re2=2021.04.01=h9c3ff4c_0
-readline=8.1=h27cfd23_0
-redis=3.5.3=pypi_0
-reportlab=3.5.68=py38hadf75a6_0
-requests=2.26.0=pyhd8ed1ab_0
-requests-oauthlib=1.3.0=pyh9f0ad1d_0
-rsa=4.7.2=pyh44b312d_0
-scikit-image=0.18.3=py38h43a58ef_0
-scikit-learn=0.24.2=py38ha9443f7_0
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-scopy=1.2.5=pypi_0
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-six=1.16.0=pyh6c4a22f_0
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-tensorflow=2.4.1=py38h578d9bd_0
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-termcolor=1.1.0=py_2
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-tifffile=2019.7.26.2=py38_0
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-toolz=0.11.1=py_0
-torch-cluster=1.5.9=pypi_0
-torch-geometric=2.0.3=pypi_0
-torch-scatter=2.0.9=pypi_0
-torch-sparse=0.6.12=pypi_0
-torch-spline-conv=1.2.1=pypi_0
-torchmetrics=0.5.0=pypi_0
-torchvision=0.2.2=py_3
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-vina=1.2.2=pypi_0
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-wheel=0.37.0=pyhd3eb1b0_0
-wrapt=1.12.1=py38h497a2fe_3
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-xgboost=1.4.0=py38h578d9bd_0
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-xorg-libice=1.0.10=h7f98852_0
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-yaml=0.2.5=h516909a_0
-yarl=1.6.3=py38h497a2fe_2
-zict=2.0.0=py_0
-zipp=3.5.0=pyhd8ed1ab_0
-zlib=1.2.11=h7b6447c_3
-zstd=1.4.9=ha95c52a_0
+python=3.8
+torch-scatter=2.0.9
+cudatoolkit-dev=11.1.1
+cudatoolkit=11.1.1
+openbabel
+pillow=9.2.0
+pytorch=1.9.0
+gsd=2.5.3
+mdanalysis=2.0.0
+prody=2.1.0
+rdkit=2022.03.03
+scipy=1.6.2
+seaborn=0.11.2
+matplotlib=3.4.3
+joblib=1.0.1