test_and_deploy.yml

# Based on the workflow from https://github.com/biotite-dev/biotite/
# contributed by Daniel Farrell (danpf) and published under the same license

name: "CI & CD"

on:
  workflow_dispatch:
  pull_request:
  release:
    types:
    - published

env:
  CIBW_BUILD: cp310-* cp311-* cp312-*
  CIBW_ARCHS_LINUX: "x86_64"
  CIBW_ARCHS_MACOS: "x86_64 arm64"
  CIBW_ARCHS_WINDOWS: "x86 AMD64"
  # Skip musllinux because it takes too long to compile on GHA
  # since it is emulated. (6+ hours)
  # *note* most of the build time is actually numpy for musllinux
  CIBW_SKIP: "*musllinux* *-manylinux_i686 *-musllinux_i686 *-win32 pp*"
  CIBW_TEST_EXTRAS: test
  CIBW_TEST_COMMAND: pytest {project} --durations=50
  CIBW_DEPENDENCY_VERSIONS: "pinned"
  # Runtime too long due to architecture emulation
  CIBW_TEST_SKIP: "*-macosx_arm64"


jobs:
  lint:
    name: Check code style
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - uses: actions/setup-python@v5
      with:
        python-version: "3.12"
    - name: Install ruff
      run: pip install ruff==0.5.2
    - name: Check code formatting
      run: ruff format --diff
    - name: Lint code base
      run: ruff check

  test-and-build:
    name: "Build & Test"
    strategy:
      matrix:
        os: [ubuntu-latest, windows-latest, macos-latest]

    runs-on: ${{ matrix.os }}
    steps:
      - uses: actions/checkout@v4

      - name: Set up QEMU
        if: runner.os == 'Linux'
        uses: docker/setup-qemu-action@v2
        with:
          platforms: all

      - name: Build & (optionally) test wheels
        uses: pypa/cibuildwheel@v2.19.1

      - uses: actions/upload-artifact@v3
        with:
          name: dist
          path: ./wheelhouse/*.whl
          if-no-files-found: error


  make-sdist:
    name: Build source distribution
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0
        submodules: true
    - name: Build source distribution
      run: pipx run build --sdist
    - uses: actions/upload-artifact@v3
      with:
        name: dist
        path: dist/*.tar.gz
        if-no-files-found: error


  make-doc:
    name: Build documentation

    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}

    steps:
      - uses: actions/checkout@v4
      - uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: hydride
          auto-update-conda: true
          python-version: '3.11'
      - name: Installing dependencies
        run: conda install -c conda-forge sphinx cython numpy numpydoc biotite
      - name: Building documentation
        run: sphinx-build ./doc ./build/doc
      - name: Zipping documentation
        run: cd .//build; zip -r doc.zip doc; cd ..
      - uses: actions/upload-artifact@v3
        with:
          name: doc
          path: build//doc.zip
          if-no-files-found: error


  upload:
    name: Upload to GitHub Releases & PyPI
    permissions:
      contents: write
    needs:
      - lint
      - test-and-build
      - make-sdist
      - make-doc
    runs-on: ubuntu-latest
    steps:
    - uses: actions/download-artifact@v3
    - name: List distributions to be uploaded
      run: ls dist
    - name: Upload to GitHub Releases
      uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844
      if: github.event_name == 'release' && github.event.action == 'published'
      with:
        files: |
          dist//*
          doc//*
    - name: Upload to PyPI
      uses: pypa/gh-action-pypi-publish@c7f29f7adef1a245bd91520e94867e5c6eedddcc
      if: github.event_name == 'release' && github.event.action == 'published'
      with:
        password: ${{ secrets.PYPI_TOKEN }}