anndata-rs/.github/workflows/ci.yml at da9dba1b4b81592b73acb91c17c9595a91a79720 · scverse/anndata-rs · GitHub

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name: Continuous integration

on: [push, pull_request]

jobs:
  test_rust_code:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v3

    - uses: actions-rs/toolchain@v1
      with:
        profile: minimal
        toolchain: stable
        override: true

    - name: Cache rust build
      uses: Swatinem/rust-cache@v2

    - name: Test Rust package
      run: cargo test --no-fail-fast

    #- name: benchmark
    #  run: |
    #    cd ${GITHUB_WORKSPACE}/anndata-test-utils && cargo bench
    #    cd ${GITHUB_WORKSPACE}

    #- uses: actions/upload-artifact@v4
    #  with:
    #    name: benchmark
    #    path: target/criterion

  test_python_code:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        anndata_version: ['0.9.*', '0.10.*', '0.11.*', '0.12.*']
    steps:
    - uses: actions/checkout@v3

    - uses: actions-rs/toolchain@v1
      with:
        profile: minimal
        toolchain: stable
        override: true

    - name: Cache rust build
      uses: Swatinem/rust-cache@v2

    - name: Build and test package
      run: |
        pip install --user --upgrade pip
        cd ${GITHUB_WORKSPACE}/python
        pip install --user .[test] anndata==${{ matrix.anndata_version }}
        pytest -v --durations=0 ${GITHUB_WORKSPACE}/python/tests

  build_doc:
    runs-on: ubuntu-latest
    needs: [test_python_code]
    steps:
    - uses: actions/checkout@v3

    - uses: actions-rs/toolchain@v1
      with:
        profile: minimal
        toolchain: stable
        override: true

    - name: Cache rust build
      uses: Swatinem/rust-cache@v2

    - name: Install dependency
      run: |
        pip install --user --upgrade pip
        pip install --user Pygments sphinx==8.* pandoc nbsphinx \
          sphinx-autodoc-typehints sphinx_rtd_theme \
          markupsafe

    - name: Build package
      run: cd ${GITHUB_WORKSPACE}/python && pip install --user .

    - name: Build doc
      run: |
        cd ${GITHUB_WORKSPACE}
        sphinx-build ${GITHUB_WORKSPACE}/python/docs _build/html

    - name: Upload doc
      uses: actions/upload-artifact@v4
      with:
        name: documentation
        path: ./_build/html

  upload_gh-page:
    name: Publish
    runs-on: ubuntu-latest
    needs: [build_doc]
    steps:
    - name: Download
      uses: actions/download-artifact@v4

    - name: Upload doc
      uses: peaceiris/actions-gh-pages@v4
      if: ${{ github.ref == 'refs/heads/main' }}
      with:
        github_token: ${{ secrets.GITHUB_TOKEN }}
        publish_dir: ./documentation
        publish_branch: gh-pages
        force_orphan: true