github_actions.yml

name: AlphaPulldown-CI-CD

on:
  pull_request:
  push:
    branches:
      - main
  release:
    types: [published]
  workflow_dispatch: 

jobs:
  build-and-test:
    runs-on: ubuntu-20.04
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.11"]
        install-type: ['user', 'developer']

    steps:
      - uses: webfactory/ssh-agent@v0.9.0
        with:
          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
      - uses: actions/checkout@v4
        with:
          submodules: recursive
      - uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
          cache: "pip"
      - run: python -c "import sys; print(sys.version)"
      - run: |
          echo $CONDA/bin >> $GITHUB_PATH
          echo "$GITHUB_WORKSPACE/alphapulldown" >> $GITHUB_PATH
      - if: matrix.install-type == 'user'
        run: |
          conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 hmmer hhsuite modelcif
          eval "$(conda shell.bash hook)"
          conda activate AlphaPulldown
          pip install alphapulldown==2.0.0b6
          pip install -U "jax[cuda12]"
      - if: matrix.install-type == 'developer'
        run: |
          conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 bioconda hmmer hhsuite modelcif
          eval "$(conda shell.bash hook)"
          conda activate AlphaPulldown
          pip install -e .
          pip install -e ColabFold --no-deps
          pip install -e alphafold --no-deps
          pip install -U "jax[cuda12]"
          # export PYTHONPATH=$PWD/AlphaLink2:$PYTHONPATH
          # install dependencies for AlphaLink backend
          # pip install torch==1.13.0+cu117 --extra-index-url https://download.pytorch.org/whl/cu117
          # pip install setuptools==69.5.1 # Downgrade setuptools to avoid crashes when installing unicore
          # git clone https://github.com/dptech-corp/Uni-Core.git
          # cd Uni-Core
          # python setup.py install --disable-cuda-ext
          # cd ..
      - run: |
          eval "$(conda shell.bash hook)"
          conda activate AlphaPulldown
          python test/test_python_imports.py
          pytest -s test/test_custom_db.py
          pytest -s test/test_remove_clashes_low_plddt.py
          pytest -s test/test_modelcif.py
          pytest -s test/test_features_with_templates.py
          pytest -s test/test_post_prediction.py
          export PYTHONPATH=$PWD/alphapulldown/analysis_pipeline:$PYTHONPATH
          # Test analysis pipeline
          conda install -c bioconda biopandas 
          pip install pyrosetta-installer 
          python -c 'import pyrosetta_installer; pyrosetta_installer.install_pyrosetta()'
          pytest -s test/test_pdb_analyser.py
          pytest -s test/test_get_good_inter_pae.py

  build-fold-container:
    runs-on: ubuntu-latest
    steps:
      - uses: webfactory/ssh-agent@v0.9.0
        with:
          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
      - name: Checkout
        uses: actions/checkout@v4

      - name: Free disk space
        run: |
          rm -rf /opt/hostedtoolcache

      - name: Login to Docker Hub
        uses: docker/login-action@v3
        with:
          username: ${{ secrets.DOCKER_USERNAME }}
          password: ${{ secrets.DOCKER_PASSWORD }}

      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v3

      - name: Build and push fold container
        if: github.event_name == 'push'
        uses: docker/build-push-action@v5
        with:
          context: .
          file: ./docker/pulldown.dockerfile
          push: true
          tags: ${{ secrets.DOCKER_USERNAME }}/fold:latest
          ssh: default

      - name: Build and push fold container with version
        if: github.event_name == 'release' && github.event.action == 'published'
        uses: docker/build-push-action@v5
        with:
          context: .
          file: ./docker/pulldown.dockerfile
          push: true
          tags: ${{ secrets.DOCKER_USERNAME }}/fold:${{ github.event.release.tag_name }}
          ssh: default

  build-analysis-container:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Free disk space
        run: |
          rm -rf /opt/hostedtoolcache

      - name: Login to Docker Hub
        uses: docker/login-action@v3
        with:
          username: ${{ secrets.DOCKER_USERNAME }}
          password: ${{ secrets.DOCKER_PASSWORD }}

      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v3

      - name: Build and push analysis container
        if: github.event_name == 'push'
        uses: docker/build-push-action@v5
        with:
          context: .
          file: ./docker/analysis.dockerfile
          push: true
          tags: ${{ secrets.DOCKER_USERNAME }}/fold_analysis:latest

      - name: Build and push analysis container with version
        if: github.event_name == 'release' && github.event.action == 'published'
        uses: docker/build-push-action@v5
        with:
          context: .
          file: ./docker/analysis.dockerfile
          push: true
          tags: ${{ secrets.DOCKER_USERNAME }}/fold_analysis:${{ github.event.release.tag_name }}