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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,18 @@ | ||
| name: Publish to PyPI | ||
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| on: workflow_dispatch | ||
| on: | ||
| workflow_dispatch: | ||
| inputs: | ||
| tag: | ||
| description: Git tag to publish (default to current commit) | ||
| default: '' | ||
| use_test: | ||
| description: Deploy target | ||
| required: true | ||
| type: choice | ||
| options: | ||
| - Test PyPI | ||
| - PyPI | ||
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| jobs: | ||
| build-wheels: | ||
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|
@@ -9,48 +21,193 @@ jobs: | |
| strategy: | ||
| matrix: | ||
| # macos-13 is an intel runner, macos-14 is apple silicon | ||
| # os: [ubuntu-latest, windows-latest, macos-13, macos-14] | ||
| os: [ubuntu-latest] | ||
| os: [ubuntu-latest, windows-latest, macos-13, macos-14] | ||
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| 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 }} | ||
|
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||
| #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 ${{ github.workspace }}\lib-cache | ||
| env: | ||
| VCPKG_BINARY_SOURCES: "clear;x-gha,readwrite" | ||
|
|
||
| - name: Build wheels | ||
| uses: pypa/[email protected] | ||
| with: | ||
| package-dir: python | ||
| # env: | ||
| # CIBW_SOME_OPTION: value | ||
| # ... | ||
| # with: | ||
| # package-dir: . | ||
| # output-dir: wheelhouse | ||
| # config-file: "{package}/pyproject.toml" | ||
| env: | ||
| CIBW_ENVIRONMENT_LINUX: >- | ||
| CXX="ccache g++" | ||
| BPCELLS_NUM_BUILD_JOBS=4 | ||
| CIBW_BEFORE_ALL_LINUX: >- | ||
| LIB_CACHE=/host/$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"' || '' }} | ||
| BPCELLS_NUM_BUILD_JOBS=4 | ||
| 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" | ||
| BPCELLS_NUM_BUILD_JOBS=4 | ||
| # As of 8/26/2024, a delvewheel dependency version bump (pefile) broke delvewheel, so pin these | ||
| CIBW_BEFORE_ALL_WINDOWS: >- | ||
| pip install delvewheel && | ||
| echo $GITHUB_WORKSPACE && | ||
| echo %GITHUB_WORKSPACE% && | ||
| ls %GITHUB_WORKSPACE%/lib-cache/bin | ||
| # See https://github.com/adang1345/delvewheel/issues/54 for explanation of `--add-path C:/Windows/System32` | ||
| CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: >- | ||
| delvewheel repair --add-path %GITHUB_WORKSPACE%/lib-cache/bin --add-path C:/Windows/System32 --wheel-dir {dest_dir} {wheel} | ||
| CIBW_TEST_REQUIRES: pytest h5py anndata | ||
| CIBW_TEST_COMMAND: BPCELLS_PYTEST_DATA_CACHE="$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 | ||
|
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| publish-to-pypi: | ||
| name: >- | ||
| Publish Python 🐍 distribution 📦 to PyPI | ||
| # if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes | ||
|
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| build-sdist: | ||
| name: Build sdist | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| fetch-tags: true | ||
| ref: ${{ inputs.tag }} | ||
| - 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/ | ||
|
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| 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 | ||
|
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||
| permissions: | ||
| id-token: write # IMPORTANT: mandatory for trusted publishing | ||
|
|
||
| steps: | ||
| - name: Download all the dists | ||
| uses: actions/download-artifact@v4.1.7 | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: python-package-distributions | ||
| path: wheelhouse/ | ||
| - name: Publish distribution 📦 to PyPI | ||
| path: dist/ | ||
| merge-multiple: true | ||
| - name: Publish distribution 📦 to TestPyPI | ||
| uses: pypa/gh-action-pypi-publish@release/v1 | ||
| with: | ||
| 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/ | ||
| merge-multiple: true | ||
| - name: Publish distribution 📦 to PyPI | ||
| uses: pypa/gh-action-pypi-publish@release/v1 | ||
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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