Add type hints to openslide package
#317
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| name: Python | |
| on: | |
| push: | |
| branches: [main] | |
| tags: ["*"] | |
| pull_request: | |
| branches: [main] | |
| permissions: | |
| contents: read | |
| env: | |
| PYTHONUNBUFFERED: 1 | |
| jobs: | |
| pre-commit: | |
| name: Rerun pre-commit checks | |
| runs-on: ubuntu-latest | |
| outputs: | |
| dist-base: ${{ steps.paths.outputs.dist }} | |
| docs-base: ${{ steps.paths.outputs.docs }} | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.13' | |
| - name: Run pre-commit hooks | |
| uses: pre-commit/[email protected] | |
| - name: Define artifact paths | |
| id: paths | |
| run: | | |
| suffix="$GITHUB_RUN_NUMBER-$(echo $GITHUB_SHA | cut -c-10)" | |
| echo "dist=openslide-python-dist-$suffix" >> $GITHUB_OUTPUT | |
| echo "docs=openslide-python-docs-$suffix" >> $GITHUB_OUTPUT | |
| tests: | |
| name: Tests | |
| needs: pre-commit | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, ubuntu-24.04-aarch64, macos-latest] | |
| python-version: [3.8, 3.9, "3.10", "3.11", "3.12", "3.13"] | |
| openslide: [system, wheel] | |
| include: | |
| - os: ubuntu-latest | |
| python-version: "3.13" | |
| openslide: system | |
| sdist: sdist | |
| # Python 3.8 is too old to support universal binaries, and | |
| # setup-python's Python 3.9 and 3.10 won't build them. Use the | |
| # last upstream patch releases that ship with installers. | |
| # https://github.com/actions/setup-python/issues/439#issuecomment-1247646682 | |
| - os: macos-latest | |
| python-version: "3.9" | |
| upstream-python: 3.9.13 | |
| - os: macos-latest | |
| python-version: "3.10" | |
| upstream-python: 3.10.11 | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| if: matrix.upstream-python == null | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Set up Python ${{ matrix.python-version }} (macOS fallback) | |
| if: matrix.upstream-python != null | |
| run: | | |
| pkgdir="${{ runner.temp }}/python" | |
| mkdir -p "$pkgdir/bin" | |
| pkg="$pkgdir/python.pkg" | |
| curl -Lfo "$pkg" \ | |
| "https://www.python.org/ftp/python/${{ matrix.upstream-python }}/python-${{ matrix.upstream-python }}-macos11.pkg" | |
| sudo installer -pkg "$pkg" -target / | |
| for bin in python pip; do | |
| ln -s /usr/local/bin/${bin}3 $pkgdir/bin/${bin} | |
| done | |
| export PATH="$pkgdir/bin:$PATH" | |
| echo "PATH=$PATH" >> $GITHUB_ENV | |
| python -V | |
| pip -V | |
| - name: Install Python tools | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install auditwheel build jinja2 pytest | |
| - name: Install OpenSlide (system) | |
| if: matrix.openslide == 'system' | |
| run: | | |
| case "${{ matrix.os }}" in | |
| ubuntu-latest) | |
| echo OS_ARCH_TAG=linux-x86_64 >> $GITHUB_ENV | |
| sudo apt-get install libopenslide0 | |
| ;; | |
| ubuntu-24.04-aarch64) | |
| echo OS_ARCH_TAG=linux-aarch64 >> $GITHUB_ENV | |
| sudo apt-get install libopenslide0 | |
| ;; | |
| macos-latest) | |
| echo OS_ARCH_TAG=macos-arm64-x86_64 >> $GITHUB_ENV | |
| echo DYLD_LIBRARY_PATH=/opt/homebrew/lib >> $GITHUB_ENV | |
| brew install openslide | |
| ;; | |
| esac | |
| - name: Install OpenSlide (wheel) | |
| if: matrix.openslide == 'wheel' | |
| run: pip install openslide-bin | |
| - name: Build dist | |
| run: | | |
| if [ -z "${{ matrix.sdist }}" ]; then | |
| wheel_only=-w | |
| fi | |
| python -m build $wheel_only | |
| case "${{ matrix.os }}" in | |
| ubuntu-*) | |
| mkdir old | |
| mv dist/*.whl old/ | |
| auditwheel repair --only-plat -w dist old/*whl | |
| ;; | |
| macos-*) | |
| if [ "${{ matrix.python-version }}" != 3.8 -a ! -e dist/*universal2* ]; then | |
| echo "Wheel is not universal:" | |
| ls dist | |
| exit 1 | |
| fi | |
| esac | |
| if [ -z "$wheel_only" ]; then | |
| mkdir -p "artifacts/src/${{ needs.pre-commit.outputs.dist-base }}" | |
| mv dist/*.tar.gz "artifacts/src/${{ needs.pre-commit.outputs.dist-base }}" | |
| fi | |
| mkdir -p "artifacts/whl/${{ needs.pre-commit.outputs.dist-base }}" | |
| mv dist/* "artifacts/whl/${{ needs.pre-commit.outputs.dist-base }}" | |
| # from system builds, save version-specific wheels and oldest abi3 wheel | |
| python -c 'import sys | |
| if sys.version_info < (3, 12) and "${{ matrix.openslide }}" == "system": | |
| print("archive_wheel=1")' >> $GITHUB_ENV | |
| - name: Install | |
| run: pip install artifacts/whl/${{ needs.pre-commit.outputs.dist-base }}/*.whl | |
| - name: Run tests | |
| run: pytest -v | |
| - name: Tile slide | |
| run: python examples/deepzoom/deepzoom_tile.py --viewer -o tiled tests/fixtures/small.svs | |
| - name: Archive sdist | |
| if: matrix.sdist | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ needs.pre-commit.outputs.dist-base }}-source | |
| path: artifacts/src | |
| compression-level: 0 | |
| - name: Archive wheel | |
| if: env.archive_wheel | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ needs.pre-commit.outputs.dist-base }}-${{ env.OS_ARCH_TAG }}-${{ matrix.python-version }} | |
| path: artifacts/whl | |
| compression-level: 0 | |
| windows: | |
| name: Windows | |
| needs: pre-commit | |
| runs-on: windows-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| strategy: | |
| matrix: | |
| python-version: [3.8, 3.9, "3.10", "3.11", "3.12", "3.13"] | |
| openslide: [zip, wheel] | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python tools | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install build flask pytest | |
| - name: Install OpenSlide (zip) | |
| if: matrix.openslide == 'zip' | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| run: | | |
| mkdir -p c:\\openslide | |
| cd c:\\openslide | |
| release=$(gh release list -R openslide/openslide-bin -L 1 \ | |
| --json tagName --exclude-drafts --exclude-pre-releases | \ | |
| jq -r .[0].tagName | \ | |
| tr -d v) | |
| zipname="openslide-bin-${release}-windows-x64" | |
| gh release download -R openslide/openslide-bin "v${release}" \ | |
| --pattern "${zipname}.zip" | |
| 7z x ${zipname}.zip | |
| echo "OPENSLIDE_PATH=c:\\openslide\\${zipname}\\bin" >> $GITHUB_ENV | |
| - name: Install OpenSlide (wheel) | |
| if: matrix.openslide == 'wheel' | |
| run: pip install openslide-bin | |
| - name: Build wheel | |
| run: | | |
| python -m build -w | |
| mkdir -p "artifacts/whl/${{ needs.pre-commit.outputs.dist-base }}" | |
| mv dist/*.whl "artifacts/whl/${{ needs.pre-commit.outputs.dist-base }}" | |
| # from zip builds, save version-specific wheels and oldest abi3 wheel | |
| python -c 'import sys | |
| if sys.version_info < (3, 12) and "${{ matrix.openslide }}" == "zip": | |
| print("archive_wheel=1")' >> $GITHUB_ENV | |
| - name: Install | |
| run: pip install artifacts/whl/${{ needs.pre-commit.outputs.dist-base }}/*.whl | |
| - name: Run tests | |
| # Reads OPENSLIDE_PATH | |
| run: pytest -v | |
| - name: Test library loading in examples | |
| # Reads OPENSLIDE_PATH | |
| run: | | |
| python examples/deepzoom/deepzoom_multiserver.py -h >/dev/null | |
| python examples/deepzoom/deepzoom_server.py -h >/dev/null | |
| python examples/deepzoom/deepzoom_tile.py -h >/dev/null | |
| - name: Tile slide | |
| # Reads OPENSLIDE_PATH | |
| run: python examples/deepzoom/deepzoom_tile.py --viewer -o tiled tests/fixtures/small.svs | |
| - name: Archive wheel | |
| if: env.archive_wheel | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ needs.pre-commit.outputs.dist-base }}-windows-x64-${{ matrix.python-version }} | |
| path: artifacts/whl | |
| compression-level: 0 | |
| docs: | |
| name: Docs | |
| needs: pre-commit | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.13' | |
| - name: Install Python tools | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install sphinx | |
| - name: Build | |
| run: sphinx-build -d doctrees doc artifact/${{ needs.pre-commit.outputs.docs-base }} | |
| - name: Archive | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ needs.pre-commit.outputs.docs-base }} | |
| path: artifact | |
| release: | |
| name: Release | |
| if: github.ref_type == 'tag' | |
| environment: | |
| name: pypi | |
| url: https://pypi.org/p/openslide-python | |
| needs: [pre-commit, tests, windows] | |
| runs-on: ubuntu-latest | |
| concurrency: release-${{ github.ref }} | |
| permissions: | |
| contents: write | |
| id-token: write | |
| steps: | |
| - name: Download artifacts | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: "${{ needs.pre-commit.outputs.dist-base }}-*" | |
| merge-multiple: true | |
| - name: Release to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| packages-dir: ${{ needs.pre-commit.outputs.dist-base }} | |
| repository-url: ${{ vars.PYPI_URL }} | |
| - name: Release to GitHub | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: | | |
| version=$(echo "${{ github.ref_name }}" | sed "s/^v//") | |
| # recompress tarball with xz | |
| gunzip -k "${{ needs.pre-commit.outputs.dist-base }}/openslide-python-${version}.tar.gz" | |
| tar xf "${{ needs.pre-commit.outputs.dist-base }}/openslide-python-${version}.tar" | |
| xz -9 "${{ needs.pre-commit.outputs.dist-base }}/openslide-python-${version}.tar" | |
| # extract changelog | |
| awk -e '/^## / && ok {exit}' \ | |
| -e '/^## / {ok=1; next}' \ | |
| -e 'ok {print}' \ | |
| "openslide-python-$version/CHANGELOG.md" > changes | |
| gh release create --latest --verify-tag \ | |
| --repo "${{ github.repository }}" \ | |
| --title "OpenSlide Python $version" \ | |
| --notes-file changes \ | |
| "${{ github.ref_name }}" \ | |
| "${{ needs.pre-commit.outputs.dist-base }}/"* |