StarDist 0.9.1 #96
Workflow file for this run
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| # adapted from: | |
| # - https://github.com/pypa/cibuildwheel/blob/main/examples/github-deploy.yml | |
| # - https://github.com/scikit-learn/scikit-learn/blob/main/.github/workflows/wheels.yml | |
| # - https://github.com/scikit-image/scikit-image/blob/main/.github/workflows/wheels_recipe.yml | |
| name: Build and upload to PyPI | |
| on: | |
| push: | |
| branches: | |
| - wheels | |
| release: | |
| types: | |
| - published | |
| jobs: | |
| build_wheels_linux_windows: | |
| name: Build ${{ matrix.py }} wheels on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, windows-latest] | |
| py: [cp36, cp37, cp38, cp39, cp310, cp311, cp312] | |
| include: | |
| - cibw_test_requires: 'pytest tensorflow' | |
| - os: ubuntu-latest | |
| py: cp37 | |
| cibw_test_requires: 'pytest tensorflow urllib3<2' # ImportError: urllib3 v2.0 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with 'OpenSSL 1.0.2k-fips 26 Jan 2017'. See: https://github.com/urllib3/urllib3/issues/2168 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.x' | |
| - name: Install cibuildwheel | |
| run: python -m pip install cibuildwheel | |
| - name: Build wheels for CPython (Linux and Windows) | |
| run: python -m cibuildwheel --output-dir dist | |
| env: | |
| # only build for platforms where tensorflow is available | |
| CIBW_BUILD: "${{ matrix.py }}-*{x86_64,win_amd64}" | |
| CIBW_SKIP: "*musllinux*" | |
| # numba is a requirement and only has wheels for manylinux2014 | |
| CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014 | |
| CIBW_BUILD_VERBOSITY: 1 | |
| CIBW_TEST_REQUIRES: "${{ matrix.cibw_test_requires }}" | |
| CIBW_TEST_COMMAND: pytest -v -m "not gpu" {project} | |
| # CIBW_TEST_SKIP: "*musllinux*" | |
| - name: Upload wheels | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: dist | |
| path: ./dist/*.whl | |
| build_wheels_mac: | |
| # build wheels for macOS, using an x86_64-based runner to build both x86_64 and arm64 wheels | |
| # (better would be to build arm64 wheels on an arm64-based runner, but c++ compilation throws errors and haven't debugged why) | |
| # - arm64 wheels can only be build for python 3.7+ | |
| # - arm64 wheels cannot be tested on an x86_64-based runner, so they are tested in a separate job | |
| # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories | |
| name: Build ${{ matrix.py }}-${{ matrix.cibw_arch }} wheels on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macos-13] # runner hardware is x86_64 (intel) | |
| # os: [macos-14] # runner hardware is arm64 (apple silicon) -> compiling c++ throws error | |
| py: [cp36, cp37, cp38, cp39, cp310, cp311, cp312] | |
| cibw_arch: [x86_64, arm64] | |
| include: | |
| - cibw_test_requires: 'pytest tensorflow' | |
| exclude: | |
| - py: cp36 | |
| cibw_arch: arm64 | |
| - py: cp37 | |
| cibw_arch: arm64 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.x' | |
| - name: Install cibuildwheel | |
| run: python -m pip install cibuildwheel | |
| - name: Install conda | |
| shell: bash | |
| run: | | |
| set -ex | |
| MINIFORGE_URL="https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-$(uname -m).sh" | |
| MINIFORGE_PATH="$HOME/miniforge" | |
| curl -L --retry 10 $MINIFORGE_URL -o ./miniforge.sh | |
| bash ./miniforge.sh -b -p $MINIFORGE_PATH | |
| echo "CONDA_HOME=$MINIFORGE_PATH" >> $GITHUB_ENV | |
| - name: Build wheels for CPython (macOS) | |
| run: | | |
| if [[ "$CIBW_ARCHS_MACOS" == "arm64" ]]; then | |
| # SciPy requires 12.0 on arm to prevent kernel panics | |
| # https://github.com/scipy/scipy/issues/14688 | |
| export MACOSX_DEPLOYMENT_TARGET=12.0 | |
| OPENMP_URL="https://anaconda.org/conda-forge/llvm-openmp/11.1.0/download/osx-arm64/llvm-openmp-11.1.0-hf3c4609_1.tar.bz2" | |
| else | |
| export MACOSX_DEPLOYMENT_TARGET=10.9 | |
| OPENMP_URL="https://anaconda.org/conda-forge/llvm-openmp/11.1.0/download/osx-64/llvm-openmp-11.1.0-hda6cdc1_1.tar.bz2" | |
| fi | |
| echo MACOSX_DEPLOYMENT_TARGET=${MACOSX_DEPLOYMENT_TARGET} | |
| # use conda to install llvm-openmp and use it for building | |
| sudo "$CONDA_HOME/bin/conda" create -n build $OPENMP_URL | |
| PREFIX="$CONDA_HOME/envs/build" | |
| export CC=/usr/bin/clang | |
| export CXX=/usr/bin/clang++ | |
| export CFLAGS="$CFLAGS -I$PREFIX/include" | |
| export CXXFLAGS="$CXXFLAGS -I$PREFIX/include" | |
| export LDFLAGS="$LDFLAGS -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lomp" | |
| python -m cibuildwheel --output-dir dist | |
| env: | |
| CIBW_BUILD: "${{ matrix.py }}-*" | |
| CIBW_ARCHS_MACOS: ${{ matrix.cibw_arch }} | |
| CIBW_BUILD_VERBOSITY: 1 | |
| CIBW_TEST_REQUIRES: "${{ matrix.cibw_test_requires }}" | |
| CIBW_TEST_COMMAND: pytest -v -m "not gpu" {project} | |
| - name: Upload wheels | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: dist | |
| path: ./dist/*.whl | |
| test_wheels_mac_arm64: | |
| # test arm64 wheels for macOS using an arm64-based runner | |
| name: Test py${{ matrix.python-version }}-${{ matrix.arch }} wheels on ${{ matrix.os }} | |
| needs: [build_wheels_mac] | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macos-14] # runner hardware is arm64 (apple silicon) | |
| arch: [arm64] | |
| python-version: ['3.8', '3.9', '3.10', '3.11', '3.12'] | |
| steps: | |
| - name: Download wheels | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist | |
| - name: Install Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Upgrade pip | |
| run: python -m pip install --upgrade pip | |
| - name: Install TensorFlow and PyTest | |
| run: pip install pytest tensorflow | |
| - name: Install wheel | |
| run: pip install ./dist/*cp$(echo "${{ matrix.python-version }}" | tr -d .)*${{ matrix.arch }}*.whl | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Run tests | |
| run: pytest -v -m "not gpu" | |
| build_sdist: | |
| name: Build source distribution | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Build sdist | |
| run: pipx run build --sdist | |
| - name: Upload sdist | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist/*.tar.gz | |
| upload_pypi: | |
| name: Upload to PyPI | |
| needs: [build_wheels_linux_windows, test_wheels_mac_arm64, build_sdist] | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'release' && github.event.action == 'published' | |
| steps: | |
| - name: Download wheels and sdist | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist | |
| - name: Check that package version matches git tag ${{ github.ref_name }} | |
| shell: bash | |
| run: | | |
| ls -l dist | |
| test -f "dist/stardist-${{ github.ref_name }}.tar.gz" | |
| - name: Publish to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| verbose: true | |
| # password: ${{ secrets.TESTPYPI_API_TOKEN }} | |
| # repository-url: https://test.pypi.org/legacy/ |