[py] Fix for updated pypi controls #39
Workflow file for this run
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| 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/ |