test_python.yml

name: test-python-package

on: [push, pull_request]

jobs:
  build-and-test:
    outputs:
      VERSION: ${{ steps.get-version.outputs.VERSION }}
    runs-on: ubuntu-latest
    steps:
    - name: Checkout code
      uses: nschloe/action-cached-lfs-checkout@v1

    - uses: actions/setup-python@v4
      name: Install Python
      with:
          python-version: '3.10'

    - uses: ./.github/actions/setup-rust
      with:
        cache: true

    - name: Install dependencies
      run: |
        sudo pip install --upgrade pip
        pip install --user coverage pytest hypothesis==6.72.4 wheel

    - name: Build wheel files
      run: |
        cd ${GITHUB_WORKSPACE}/snapatac2-python
        mkdir ${GITHUB_WORKSPACE}/wheel_files
        pip wheel . --wheel-dir ${GITHUB_WORKSPACE}/wheel_files

    - name: Test Python package
      run: |
        pip install --user ${GITHUB_WORKSPACE}/wheel_files/*.whl
        coverage run -m pytest ${GITHUB_WORKSPACE}/snapatac2-python/tests

    - name: Get SnapATAC2 version
      id: get-version
      run: |
        VERSION_NUMBER=$(python -c "import snapatac2;print(snapatac2.__version__)")
        echo $VERSION_NUMBER
        echo "VERSION=$VERSION_NUMBER" >> $GITHUB_OUTPUT

    - name: Upload Coverage to Codecov
      uses: codecov/codecov-action@v3

    - name: Upload wheel files as artifacts
      uses: actions/upload-artifact@v4
      with:
        name: wheel-files
        path: ./wheel_files/snapatac2*.whl

  build-wheel:
    needs: build-and-test
    if: ${{ startsWith(github.ref, 'refs/tags/') || contains(github.event.head_commit.message, '[wheel]') }}
    uses: kaizhang/SnapATAC2/.github/workflows/wheels.yml@main

  publish:
    needs: build-wheel
    runs-on: ubuntu-latest
    permissions:
      id-token: write
    if: ${{ startsWith(github.ref, 'refs/tags') }}
    steps:
    - name: Download wheel files
      uses: actions/download-artifact@v4
      with:
        path: dist
        pattern: snapatac2-*
        merge-multiple: true

    - name: Publish to PyPI
      uses: pypa/gh-action-pypi-publish@v1.8.14

#  build-docker:
#    needs: [build-and-test, build-wheel]
#    if: ${{ startsWith(github.ref, 'refs/tags/') || contains(github.event.head_commit.message, '[docker]') }}
#    runs-on: ubuntu-latest
#    steps:
#      - name: Docker
#        uses: ./.github/actions/build-docker-image
#        with:
#          snapatac2-version: ${{ needs.build-and-test.outputs.VERSION }}
#          python-version: 3.11
#          username: ${{ secrets.dockerhub_username }}
#          password: ${{ secrets.dockerhub_token }}