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
          #conda info
          #conda list
          #python -c "import sys; print(sys.path)"
          #echo "Python path: $PYTHONPATH"
          python -c "import alphafold; import os; print('Alphafold module is located at:', alphafold.__file__); alphafold_dir = os.path.dirname(alphafold.__file__); print('Contents of the Alphafold directory:', os.listdir(alphafold_dir))"
      - name: Install Dependencies
        run: |
          eval "$(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: Run Tests
        run: |
          eval "$(conda shell.bash hook)"
          conda activate AlphaPulldown
          pytest test/
      - name: Build and Push to Docker Hub
        uses: mr-smithers-excellent/docker-build-push@v5
        with:
          image: dmolodenskiy/AlphaPulldown
          registry: docker.io
          dockerfile: docker/Dockerfile
          username: ${{ secrets.DOCKER_USERNAME }}
          password: ${{ secrets.DOCKER_PASSWORD }}
          tags: latest