fix flow correction in tiled inference, simplify intensity interpolation #42
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| # adapted from: | |
| # - https://github.com/matplotlib/matplotlib/blob/master/.github/workflows/cibuildwheel.yml | |
| # - https://github.com/scikit-image/scikit-image/blob/master/.github/workflows/cibuildwheel.yml | |
| # - https://github.com/pypa/cibuildwheel/blob/main/examples/github-deploy.yml | |
| # - https://github.com/stardist/stardist/blob/master/.github/workflows/cibuildwheel.yml | |
| name: tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - wheels | |
| release: | |
| types: | |
| - published | |
| pull_request: | |
| branches: [ "main" ] | |
| jobs: | |
| test: | |
| name: Test on ${{ matrix.os }} with Python ${{ matrix.py }} | |
| runs-on: ${{ matrix.os }} | |
| if: github.event_name == 'push' && contains(github.ref, 'main') | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-20.04] | |
| py: [cp311, cp312] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| name: Checkout repository | |
| - uses: actions/setup-python@v4 | |
| name: Install Python | |
| with: | |
| python-version: '3.x' | |
| - name: Install cibuildwheel | |
| run: python -m pip install cibuildwheel | |
| - name: Build wheels for CPython (Linux) | |
| run: | | |
| python -m cibuildwheel --output-dir dist | |
| env: | |
| # only build for specific platforms | |
| CIBW_BUILD: "${{ matrix.py }}-*{x86_64,win_amd64}" | |
| CIBW_SKIP: "*musllinux*" | |
| CIBW_BUILD_VERBOSITY: 1 | |
| CIBW_TEST_REQUIRES: pytest pytest-cov | |
| CIBW_TEST_COMMAND: pytest -v --cov=spotiflow {project} | |
| build_wheels: | |
| name: Build ${{ matrix.py }} wheels on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| if: (github.event_name == 'release' && github.event.action == 'published') || (github.event_name == 'push' && contains(github.ref, 'wheels')) || github.event_name == 'pull_request' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-20.04, windows-2019, macos-13] | |
| py: [cp39, cp310, cp311, cp312] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| name: Checkout repository | |
| - uses: actions/setup-python@v4 | |
| name: Install Python | |
| with: | |
| python-version: '3.x' | |
| - name: Install cibuildwheel | |
| run: python -m pip install cibuildwheel | |
| # https://scikit-learn.org/stable/developers/advanced_installation.html#macos | |
| - name: Setup OpenMP (macOS) | |
| if: startsWith(matrix.os, 'macos') | |
| shell: bash | |
| run: | | |
| brew config | |
| brew install libomp | |
| eval `brew shellenv` | |
| tee -a $GITHUB_ENV << END | |
| CC=/usr/bin/clang | |
| CXX=/usr/bin/clang++ | |
| CFLAGS=${CFLAGS} -I${HOMEBREW_PREFIX}/opt/libomp/include | |
| CXXFLAGS=${CXXFLAGS} -I${HOMEBREW_PREFIX}/opt/libomp/include | |
| LDFLAGS=${LDFLAGS} -Wl,-rpath,${HOMEBREW_PREFIX}/opt/libomp/lib -L${HOMEBREW_PREFIX}/opt/libomp/lib -lomp | |
| END | |
| - name: Build wheels for CPython (macOS) | |
| if: startsWith(matrix.os, 'macos') | |
| run: | | |
| python -m cibuildwheel --output-dir dist | |
| env: | |
| CIBW_BUILD: "${{ matrix.py }}-*" | |
| CIBW_ARCHS_MACOS: arm64 | |
| CIBW_BUILD_VERBOSITY: 1 | |
| CIBW_TEST_REQUIRES: pytest pytest-cov | |
| CIBW_TEST_COMMAND: pytest -v --cov=spotiflow {project} | |
| - name: Build wheels for CPython (Linux and Windows) | |
| if: startsWith(matrix.os, 'macos') == false | |
| run: | | |
| python -m cibuildwheel --output-dir dist | |
| env: | |
| # only build for specific platforms | |
| CIBW_BUILD: "${{ matrix.py }}-*{x86_64,win_amd64}" | |
| CIBW_SKIP: "*musllinux*" | |
| CIBW_BUILD_VERBOSITY: 1 | |
| CIBW_TEST_REQUIRES: pytest pytest-cov | |
| CIBW_TEST_COMMAND: pytest -v --cov=spotiflow {project} | |
| - uses: actions/upload-artifact@v3 | |
| name: Upload wheels | |
| with: | |
| name: dist | |
| path: ./dist/*.whl | |
| build_sdist: | |
| name: Build source distribution | |
| runs-on: ubuntu-latest | |
| if: (github.event_name == 'release' && github.event.action == 'published') || (github.event_name == 'push' && contains(github.ref, 'wheels')) | |
| steps: | |
| - uses: actions/checkout@v4 | |
| name: Checkout repository | |
| - name: Build sdist | |
| run: pipx run build --sdist | |
| - uses: actions/upload-artifact@v3 | |
| name: Upload sdist | |
| with: | |
| name: dist | |
| path: dist/*.tar.gz | |
| upload_pypi: | |
| name: Upload to PyPI | |
| needs: [build_wheels, build_sdist] | |
| runs-on: ubuntu-latest | |
| if: (github.event_name == 'release' && github.event.action == 'published') || (github.event_name == 'push' && contains(github.ref, 'wheels')) | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| name: Download wheels and sdist | |
| with: | |
| name: dist | |
| path: dist | |
| - uses: pypa/gh-action-pypi-publish@release/v1 | |
| name: Publish to PyPI | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| verbose: true |