publish.yaml

# To create a release, create a tag and push it to GitHub:
#git tag -a "v0.0.1-beta" -m "beta version testing"
#git push --tags
name: Publish BioPandas to PyPI / GitHub

on:
  pull_request:
    branches: [ main ]

jobs:
  test-style:
    name: Run style tests
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3

    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: '3.x'
        cache: 'pip'

    - name: Install package dependencies for testing
      run: pip install .[test]

    - name: Run all the pytest tests
      run: flake8 ./biopandas

  test-pytest:
    name: Run pytest tests
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3

    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: '3.x'
        cache: 'pip'

    - name: Install package dependencies for testing
      run: pip install .[test]

    - name: Run all the pytest tests
      run: pytest ./biopandas -sv

  build-n-publish:
    needs: [test-pytest] # only runs if tests are passing
    if: startsWith(github.ref, 'refs/tags/v')  # Check if the tag starts with 'v'
    name: Build and publish to PyPI
    runs-on: ubuntu-latest

    steps:
      - name: Checkout source
        uses: actions/checkout@v3

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.x"

      - name: Build source and wheel distributions
        run: |
          python -m pip install --upgrade build twine
          python -m build
          twine check --strict dist/*
      - name: Publish distribution to PyPI
        uses: pypa/gh-action-pypi-publish@master
        with:
          user: __token__
          password: ${{ secrets.PYPI_API_TOKEN }}

      - name: Create GitHub Release
        id: create_release
        uses: actions/create-release@v1
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
        with:
          tag_name: ${{ github.ref }}
          release_name: ${{ github.ref }}
          draft: false
          prerelease: true

      - name: Get Asset name
        run: |
          export PKG=$(ls dist/ | grep tar)
          set -- $PKG
          echo "name=$1" >> $GITHUB_ENV
      - name: Upload Release Asset (sdist) to GitHub
        id: upload-release-asset
        uses: actions/upload-release-asset@v1
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        with:
          upload_url: ${{ steps.create_release.outputs.upload_url }}
          asset_path: dist/${{ env.name }}
          asset_name: ${{ env.name }}
          asset_content_type: application/zip