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//interface
    --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"
  # Configuration for the architecture-agnostic jobs
  PY_VERSION: "3.11"  # Keep in sync with version in environment.yml


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


  build-internal:
    name: Build CCD and wheel for reusing it in several CI jobs
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          # Make sure to fetch the latest tag,
          # so 'switcher.py' works correctly in 'docs' job
          fetch-depth: 0
          fetch-tags: true
      - uses: actions/setup-python@v5
        with:
          python-version: ${{ env.PY_VERSION }}
      - name: Get current CCD for hashing
        run: wget https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
      - name: Cache CCD
        uses: actions/cache@v4
        id: cache-ccd
        with:
          path: ./src/biotite/structure/info/components.bcif
          key: cache-${{ hashFiles('src/biotite/setup_ccd.py') }}-${{ hashFiles('components.cif.gz') }}
      - name: Remove CCD used for hashing
        run: rm components.cif.gz
      - name: Build internal CCD
        if: steps.cache-ccd.outputs.cache-hit != 'true'
        run: |
          pip install -e .
          python -m biotite.setup_ccd
      - name: Install build backend
        run: pip install build
      - name: Build distribution
        run: python -m build --wheel
      - uses: actions/upload-artifact@v4
        with:
          name: internal-build
          path: ./dist/*.whl
      - uses: actions/upload-artifact@v4
        with:
          name: ccd
          path: ./src/biotite/structure/info/components.bcif


  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
      - build-internal
    strategy:
      matrix:
        include: ${{ fromJson(needs.generate-wheels-matrix.outputs.include) }}
    runs-on: ${{ matrix.os }}
    steps:
      - uses: actions/checkout@v4
      - name: Add internal CCD to Biotite
        uses: actions/download-artifact@v4
        with:
          name: ccd
          path: src/biotite/structure/info

      # 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


  sdist:
    name: Build source distribution
    runs-on: ubuntu-latest
    needs:
      - build-internal
    steps:
    - uses: actions/checkout@v4
    - name: Add internal CCD to Biotite
      uses: actions/download-artifact@v4
      with:
        name: ccd
        path: src/biotite/structure/info
    - 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
    needs:
      - build-internal
    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:
          environment-file: environment.yml
          miniforge-version: latest
      - 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
          tests//interface


  test-muscle5:
    name: Test interface to Muscle 5

    runs-on: ubuntu-latest
    needs:
      - build-internal
    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: ${{ env.PY_VERSION }}
      - 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


  docs:
    name: Build documentation

    runs-on: ubuntu-latest
    needs:
      - build-internal
    defaults:
      run:
        shell: bash -l {0}
    env:
      NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }}

    steps:
    - uses: actions/checkout@v4
    - 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:
      - build-internal
    steps:
      - uses: actions/checkout@v4
      - uses: actions/download-artifact@v4
        with:
          name: internal-build
          path: dist
      - uses: actions/setup-python@v5
        with:
          python-version: ${{ env.PY_VERSION }}
      - 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
      id-token: write
    needs:
    - lint
    - test-and-build
    - sdist
    - test-interfaces
    - test-muscle5
    runs-on: ubuntu-latest
    environment:
      name: publish
      url: https://pypi.org/p/biotite
    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@release/v1
      if: github.event_name == 'release' && github.event.action == 'published'


  upload-ccd:
    name: Upload CCD to GitHub Releases
    permissions:
      contents: write
    needs:
    - build-internal
    runs-on: ubuntu-latest
    steps:
    - uses: actions/download-artifact@v4
      with:
        name: ccd
        path: 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//components.bcif


  upload-docs:
    name: Upload documentation to GitHub Releases and documentation website
    if: github.event_name == 'release' && github.event.action == 'published'
    permissions:
      contents: write
    needs:
    - docs
    runs-on: ubuntu-latest
    steps:
    - uses: actions/setup-python@v5
      with:
        python-version: "3.12"
    - name: Install dependencies for documentation upload
      run: pip install requests
    - uses: actions/checkout@v4
    - uses: actions/download-artifact@v4
      with:
        name: documentation
        path: dist
    - uses: softprops/action-gh-release@v2.0.5
      with:
        files: dist/doc.zip
    - name: Unzip documentation
      run: unzip dist/doc.zip -d build
    - name: Assemble multi-version documentation
      run: >
        python .github/workflows/multiversion_docs.py
        build/doc/_static/switcher.json
        dist/assembled_doc
    - name: Upload documentation to website (skip for patch releases)
      if: endsWith(github.event.release.tag_name, 0)
      uses: easingthemes/ssh-deploy@v5.1.0
      with:
        SSH_PRIVATE_KEY: ${{ secrets.DOC_PRIVATE_KEY }}
        REMOTE_HOST: ${{ secrets.DOC_HOST }}
        REMOTE_USER: ${{ secrets.DOC_USER }}
        SOURCE: "dist/assembled_doc/*"
        TARGET: "biotite"
        SCRIPT_BEFORE: "rm -r biotite/*"