pypi.yml

name: Publish to PyPI

on: 
  workflow_dispatch:
    inputs: 
      tag:
        description: Git tag to publish (default to current commit)
        default: ''
    inputs:
      use_test:
        description: Deploy target
        required: true
        type: choice
        option:
          - Test PyPI
          - PyPI

jobs:
  build-wheels:
    name: Build wheels on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        # macos-13 is an intel runner, macos-14 is apple silicon
        os: [ubuntu-latest, windows-latest, macos-13, macos-14]

    steps:
      - uses: actions/checkout@v4
        with:
          fetch-tags: true
          ref: ${{ inputs.tag }}
            
      - uses: actions/setup-python@v5
        with:
          python-version: '3.x'
      - run: pip install platformdirs

      # Step credit: https://github.com/Cryptex-github/ril-py/blob/main/.github/workflows/py-binding.yml
      - name: Display cibuildwheel cache dir
        id: cibuildwheel-cache
        run: |
          from platformdirs import user_cache_path
          import os

          with open(os.getenv('GITHUB_OUTPUT'), 'w') as f:
            f.write(f"dir={str(user_cache_path(appname='cibuildwheel', appauthor='pypa'))}")
        shell: python

      - name: Cache cibuildwheel 
        id: cache-cibuildwheel
        uses: actions/cache@v4
        with:
          path: ${{ steps.cibuildwheel-cache.outputs.dir }}
          key: cibuildwheel-cache-${{ matrix.os }}
        
      - name: Cache test files 
        id: cache-test-files
        uses: actions/cache@v4
        with:
          path: ${{ github.workspace }}/bpcells-pytest-data-cache
          key: test-files-cache-${{ matrix.os }}

      - name: Cache dependency libs
        id: cache-libs
        uses: actions/cache@v4
        with:
          path: ${{ github.workspace }}/lib-cache
          key: lib-cache-v2-${{ matrix.os }}
      
      #https://learn.microsoft.com/en-us/vcpkg/consume/binary-caching-github-actions-cache
      - name: Export GitHub Actions cache environment variables
        if: steps.cache-libs.outputs.cache-hit != 'true' && runner.os == 'Windows'
        uses: actions/github-script@v7
        with:
          script: |
            core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || '');
            core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || '');

      - name: Install dependency libs (Windows)
        if: steps.cache-libs.outputs.cache-hit != 'true' && runner.os == 'Windows'
        run: |
          vcpkg install hdf5 eigen3 highway[contrib] zlib
          vcpkg export --raw hdf5 eigen3 highway zlib --output-dir=${{ github.workspace }} --output=vcpkg-export
          XCOPY /I /E ${{ github.workspace }}\vcpkg-export\installed\x64-windows ${{ github.workspace }}\lib-cache
        env: 
          VCPKG_BINARY_SOURCES: "clear;x-gha,readwrite"

      - name: Build wheels
        uses: pypa/cibuildwheel@v2.19.1
        with:
          package-dir: python
        env:
          CIBW_ENVIRONMENT_LINUX: >-
            CXX="ccache g++"
          CIBW_BEFORE_ALL_LINUX: >-
            LIB_CACHE=/host/$LIB_CACHE bash {package}/scripts/install_ccache_linux.sh &&
            ${{ steps.cache-libs.outputs.cache-hit != 'true' && 'python {package}/scripts/install_deps.py /host/$GITHUB_WORKSPACE/lib-cache &&' || '' }}
            cp -r /host/$GITHUB_WORKSPACE/lib-cache/* /usr/local

          # We need to set MACOSX_DEPLOYMENT_TARGET="10.15" on macos-13 because otherwise
          # it tries to target a MacOS verision before std::filesystem is available (10.9 currently)
          CIBW_ENVIRONMENT_MACOS: >-
            CXX="ccache g++"
            CPATH="$GITHUB_WORKSPACE/lib-cache/include"
            LIBRARY_PATH="$GITHUB_WORKSPACE/lib-cache/lib:$GITHUB_WORKSPACE/lib-cache/lib64"
            ${{ matrix.os == 'macos-13' && 'MACOSX_DEPLOYMENT_TARGET="10.15"' || '' }}
          CIBW_BEFORE_ALL_MACOS: >-
            brew install ccache &&
            python {package}/scripts/install_deps.py $GITHUB_WORKSPACE/lib-cache
          
          # VCPKG_BINARY_SOURCES from: https://learn.microsoft.com/en-us/vcpkg/consume/binary-caching-github-actions-cache
          CIBW_ENVIRONMENT_WINDOWS: >- 
            LIBRARY_PATH="$GITHUB_WORKSPACE\\lib-cache\\lib"
            CPATH="$GITHUB_WORKSPACE\\lib-cache\\include"
            BPCELLS_PYTEST_DATA_CACHE="$GITHUB_WORKSPACE\\bpcells-pytest-data-cache"
          # As of 8/26/2024, a delvewheel dependency version bump (pefile) broke delvewheel, so pin these 
          CIBW_BEFORE_ALL_WINDOWS: >-
            pip install delvewheel
          # See https://github.com/adang1345/delvewheel/issues/54 for explanation of `--add-path C:/Windows/System32`
          CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: >-
            delvewheel repair --add-path $GITHUB_WORKSPACE/lib-cache/bin --add-path C:/Windows/System32 --wheel-dir {dest_dir} {wheel} 

          CIBW_TEST_REQUIRES: pytest h5py anndata
          CIBW_TEST_COMMAND: BPCELLS_PYTEST_DATA_CACHE="$GITHUB_WORKSPACE/bpcells-pytest-data-cache" pytest {package}/tests
          # Data cache folder is already set
          CIBW_TEST_COMMAND_WINDOWS: pytest {package}/tests

      - uses: actions/upload-artifact@v4
        with:
          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
          path: ./wheelhouse/*.whl

  build-sdist:
    name: Build sdist
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
      with:
        fetch-tags: true
    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: "3.x"
    - name: Install pypa/build
      run: >-
        python3 -m
        pip install
        build
        --user
    - name: Build a source tarball
      run: python3 -m build --sdist python
      
    - name: Store the distribution packages
      uses: actions/upload-artifact@v4
      with:
        name: sdist
        path: python/dist/

  publish-to-testpypi:
    name: Publish Python package to TestPyPI
    if: ${{ inputs.use_test == 'Test PyPI' }}
    needs:
    - build-wheels
    - build-sdist
    runs-on: ubuntu-latest

    environment:
      name: pypi
      url: https://test.pypi.org/p/bpcells

    permissions:
      id-token: write  # IMPORTANT: mandatory for trusted publishing

    steps:
    - name: Download all the dists
      uses: actions/download-artifact@v4
      with:
        path: dist/
    - name: Publish distribution 📦 to TestPyPI
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        # Our .whl files are nested two-layers deep, so this will do
        # twine upload dist/*/*.whl
        packages-dir: dist/*
        repository-url: https://test.pypi.org/legacy/

  publish-to-pypi:
    name: Publish Python package to PyPI
    if: ${{ inputs.use_test == 'PyPI' }}
    needs:
    - build-wheels
    - build-sdist
    runs-on: ubuntu-latest

    environment:
      name: pypi
      url: https://pypi.org/p/bpcells

    permissions:
      id-token: write  # IMPORTANT: mandatory for trusted publishing

    steps:
    - name: Download all the dists
      uses: actions/download-artifact@v4
      with:
        path: dist/
    - name: Publish distribution 📦 to PyPI
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        # Our .whl files are nested two-layers deep, so this will do
        # twine upload dist/*/*.whl
        packages-dir: dist/*
        repository-url: https://pypi.org/legacy/