test_and_deploy.yml

---
name: "CI & CD"

on:
  workflow_dispatch:
  push:
    branches:
      - "main"
  pull_request:
  release:
    types:
    - published

concurrency:
  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
  cancel-in-progress: true

env:
  CIBW_BUILD: cp310-* cp311-* cp312-* cp313-*
  CIBW_TEST_EXTRAS: test
  CIBW_TEST_COMMAND: >
    pytest {project}
    --durations=50
    --ignore={project}//tests//sequence//align//test_statistics.py
    --ignore={project}//tests//application
    --ignore={project}//tests//database
    --ignore={project}//tests//test_doctest.py
    --ignore={project}//tests//test_modname.py
  CIBW_DEPENDENCY_VERSIONS: "pinned"
  # Once GHA and cibuildwheel are updated this can be removed
  # mussllinux takes 6+ hrs to build and test so ignore it
  CIBW_TEST_SKIP: "*musllinux* *-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
      # Keep in sync with the ruff version in pyproject.toml
      run: pip install ruff==0.6.9
    - name: Check code formatting
      run: ruff format --diff
    - name: Lint code base
      run: ruff check


  generate-wheels-matrix:
    name: "Generate wheels matrix"
    runs-on: "ubuntu-latest"
    outputs:
      include: ${{ steps.set-matrix.outputs.include }}
    steps:
      - uses: actions/checkout@v4
      - name: Install cibuildwheel
        # MAKE SURE THIS STAYS IN SYNC WITH THE LOWER GHA cibuildwheel
        run: pipx install cibuildwheel==2.20.0
      - id: set-matrix
        run: |
          MATRIX=$(
            {
              cibuildwheel --print-build-identifiers --platform linux \
              | jq -nRc '{"dist": inputs, "os": "ubuntu-latest"}' \
              && cibuildwheel --print-build-identifiers --platform macos \
              | jq -nRc '{"dist": inputs, "os": "macos-latest"}' \
              && cibuildwheel --print-build-identifiers --platform windows \
              | jq -nRc '{"dist": inputs, "os": "windows-latest"}'
            } | jq -sc
          )
          echo "include=$MATRIX" | tee -a $GITHUB_OUTPUT
        env:
          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*"


  test-and-build:
    name: "Build & Test"
    needs: "generate-wheels-matrix"
    strategy:
      matrix:
        include: ${{ fromJson(needs.generate-wheels-matrix.outputs.include) }}
    runs-on: ${{ matrix.os }}
    steps:
      - uses: actions/checkout@v4

      # QEMU enables building/testing for non-native architectures (ie arm64)
      # at the cost of speed
      - name: Set up QEMU
        if: runner.os == 'Linux'
        uses: docker/setup-qemu-action@v3
        with:
          platforms: all

      - name: Build & (optionally) test wheels
        # MAKE SURE THIS STAYS IN SYNC WITH THE UPPER pipx call to cibuildwheel
        uses: pypa/cibuildwheel@v2.20.0
        with:
          only: ${{ matrix.dist }}

      - uses: actions/upload-artifact@v4
        with:
          name: release-${{ matrix.dist }}
          path: ./wheelhouse/*.whl


  make-sdist:
    name: Build source distribution
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: Build source distribution
      run: pipx run build --sdist
    - uses: actions/upload-artifact@v4
      with:
        name: release-sdist
        path: dist//*.tar.gz


  test-interfaces:
    name: Test interfaces to databases and applications

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

    steps:
      - uses: actions/checkout@v4
      - uses: conda-incubator/setup-miniconda@v3
        with:
          environment-file: environment.yml
          miniforge-version: latest
      - name: Build distribution
        run: pip wheel --no-deps -w dist .
      - name: Install distribution
        run: pip install .//dist//*.whl
      - name: "TEMP: Skip DSSP tests"
        # TEMP: Omit DSSP tests for now until conda-forge DSSP is functional
        # (https://github.com/conda-forge/dssp-feedstock/pull/4)
        run: mamba uninstall dssp
      - name: Run tests
        # Running NCBI BLAST and SRA takes too long
        # The tests on the NCBI Entrez database are not reliable enough
        run: >
          pytest
          --durations=50
          --ignore="tests//application//test_blast.py"
          --ignore="tests//application//test_sra.py"
          --ignore="tests//database//test_entrez.py"
          tests//test_doctest.py
          tests//test_modname.py
          tests//database
          tests//application
      # Use the built distribution for other downstream jobs to reduce build time
      - uses: actions/upload-artifact@v4
        with:
          name: internal-build
          path: ./dist/*.whl


  test-muscle5:
    name: Test interface to Muscle 5

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

    steps:
      - uses: actions/checkout@v4
      - uses: actions/download-artifact@v4
        with:
          name: internal-build
          path: dist
      - uses: conda-incubator/setup-miniconda@v3
        with:
          activate-environment: biotite-dev
          miniforge-version: latest
          python-version: "3.12"
      - name: Install Muscle 5
        run: conda install -c bioconda "muscle=5"
      - name: Install distribution and pytest
        run: pip install .//dist//*.whl pytest
      - name: Test Muscle 5 interface
        run: pytest --durations=50 tests//application//test_msa.py


  make-ccd:
    name: Compile the CCD subset for structure.info from the wwPDB CCD

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

    steps:
    - uses: actions/checkout@v4
    - uses: actions/download-artifact@v4
      with:
        name: internal-build
        path: dist
    - uses: actions/setup-python@v3
      with:
        python-version: "3.12"
    - name: Install distribution
      run: pip install dist//*.whl
    - name: Compile CCD subset
      run: python setup_ccd.py
    - name: Zip CCD
      run: |
          cd src/biotite/structure/info
          zip -r ${{ github.workspace }}//dist//ccd.zip ccd
          cd ${{ github.workspace }}
    - uses: actions/upload-artifact@v4
      with:
        name: ccd
        path: dist//ccd.zip


  make-docs:
    name: Build documentation

    runs-on: ubuntu-20.04
    needs:
      - test-interfaces
    defaults:
      run:
        shell: bash -l {0}
    env:
      NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }}

    steps:
    - uses: actions/checkout@v4
      with:
        # Make sure to fetch the latest tag, so 'switcher.py' works correctly
        fetch-depth: 0
        fetch-tags: true
    - uses: actions/download-artifact@v4
      with:
        name: internal-build
        path: dist
    - uses: conda-incubator/setup-miniconda@v3
      with:
        environment-file: environment.yml
        miniforge-version: latest
    - name: Install distribution
      run: pip install dist//*.whl
    - name: Build base documentation
      run: sphinx-build -a -D plot_gallery=0 doc build//doc
    - name: Build tutorial and gallery
      if: >
        (
          github.event_name == 'release' &&
          github.event.action == 'published'
        )
        || github.event_name == 'workflow_dispatch'
      run: sphinx-build -a doc build//doc
    - name: Zip documentation
      run: |
          cd build
          zip -r ..//dist//doc.zip doc
          cd ..
    - uses: actions/upload-artifact@v4
      with:
        name: documentation
        path: dist//doc.zip


  benchmark:
    name: Run benchmarks
    runs-on: ubuntu-latest
    if: github.event_name != 'release'
    needs:
      - test-interfaces
    steps:
      - uses: actions/checkout@v4
      - uses: actions/download-artifact@v4
        with:
          name: internal-build
          path: dist
      - uses: actions/setup-python@v3
        with:
          python-version: "3.12"
      - name: Install dependencies
        run: pip install dist//*.whl pytest pytest-codspeed
      - name: Run benchmarks
        uses: CodSpeedHQ/action@v3
        with:
          run: pytest --codspeed benchmarks


  upload-package:
    name: Upload package to GitHub Releases & PyPI
    permissions:
      contents: write
    needs:
    - lint
    - test-and-build
    - make-sdist
    - test-interfaces
    - test-muscle5
    runs-on: ubuntu-latest
    steps:
    - uses: actions/download-artifact@v4
      with:
        pattern: release-*
        merge-multiple: true
        path: dist
    - name: List distributions to be uploaded
      run: ls dist
    - name: Upload to GitHub Releases
      uses: softprops/action-gh-release@v2.0.5
      if: github.event_name == 'release' && github.event.action == 'published'
      with:
        files: dist//*
    - name: Upload to PyPI
      uses: pypa/gh-action-pypi-publish@v1.9.0
      if: github.event_name == 'release' && github.event.action == 'published'
      with:
        password: ${{ secrets.PYPI_TOKEN }}


  upload-docs:
    name: Upload documentation to GitHub Releases
    permissions:
      contents: write
    needs:
    - make-docs
    runs-on: ubuntu-latest
    steps:
    - uses: actions/download-artifact@v4
      with:
        name: documentation
        path: dist
    - uses: softprops/action-gh-release@v2.0.5
      if: github.event_name == 'release' && github.event.action == 'published'
      with:
        files: dist//doc.zip