github_actions.yml

name: AlphaPulldown-github-CI

on: [pull_request,push]

jobs:
  build:
    runs-on: ubuntu-20.04
    strategy:
      matrix:
        python-version: ["3.10.12", "3.11"]
    steps:
      - uses: actions/checkout@v4
        with:
            submodules: recursive
      - name: Debug List Directory
        run: ls -la -R
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
          cache: "pip"
      - name: Display Python version
        run: python -c "import sys; print(sys.version)"
      - name: Add Conda to System Path
        run: |
          pwd
          echo $CONDA/bin >> $GITHUB_PATH
          echo "$GITHUB_WORKSPACE/alphapulldown" >> $GITHUB_PATH
      - name: Install AlphaPulldown without dependencies
        run: |
          conda create --name AlphaPulldown python=${{ matrix.python-version }}        
          eval "$(conda shell.bash hook)"
          conda activate AlphaPulldown
          conda install -c anaconda conda-build
          conda develop alphapulldown
          conda develop alphapulldown/ColabFold
          conda develop alphafold
          python -c "import alphafold; import os; print('Alphafold module is located at:', alphafold.__file__); alphafold_dir = os.path.dirname(alphafold.__file__); print('Contents of the Alphafold directory:', os.listdir(alphafold_dir))"
      - name: Install dependencies in unifold setup.py
        run: |
          eval "$(conda shell.bash hook)"
          export WORKDIRPATH=$PWD
          conda activate AlphaPulldown
          cd $WORKDIRPATH/unifold && python3 setup.py install
      - name: Install dependencies in AlphaFold setup.py 
        run: |
          eval "$(conda shell.bash hook)"
          export WORKDIRPATH=$PWD
          conda activate AlphaPulldown
          pip install protobuf==4.23.0
          cd $WORKDIRPATH/alphafold && python3 setup.py install
          python -c "import tree"
      - name: Install Dependencies
        run: |
          eval "$(conda shell.bash hook)"
          conda activate AlphaPulldown
          conda install -c omnia -c bioconda -c conda-forge openmm==8.0 pdbfixer==1.9 kalign2 cctbx-base importlib_metadata
          #conda install -c bioconda hmmer hhsuite #this causes conda conflicts
          pip install jax==0.3.25 jaxlib==0.3.25+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
          pip install "absl-py>=0.13.0" dm-haiku "dm-tree>=0.1.6" "h5py>=3.1.0" "ml-collections>=0.1.0" "pandas>=1.3.4" tensorflow "importlib-resources==5.8.0" "nbformat==5.4.0" "py3Dmol==2.0.1" ipython appdirs jupyterlab ipywidgets pytest
      # - name: Check imports of submodules
      #   run : |
      #     eval "$(conda shell.bash hook)"
      #     conda activate AlphaPulldown
      #     # install PyTorch 
      #     pip install torch --pre -f https://download.pytorch.org/whl/nightly/cu121/torch_nightly.html 
      #     # setup unicore
      #     git clone https://github.com/dptech-corp/Uni-Core.git
      #     cd Uni-Core
      #     python3 setup.py install --disable-cuda-ext
      #     python -c "from unifold.alphalink_inference import alphalink_prediction"
      #     python -c "from unifold.dataset import process_ap"
      #     python -c "from unifold.config import model_config"
      #     python -c "from colabfold.batch import get_queries, unserialize_msa, get_msa_and_templates, msa_to_str, build_monomer_feature, parse_fasta"
      - name: Run Tests
        run: |
          eval "$(conda shell.bash hook)"
          conda activate AlphaPulldown
          pytest -s test/test_custom_db.py
          pytest -s test/test_remove_clashes_low_plddt.py
          # python3 -m unittest test/test_crosslink_input.py