Better read merging for long reads. New clustering methods for long r… #178
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| name: Build | |
| on: [push, pull_request, workflow_dispatch] | |
| jobs: | |
| build_wheels: | |
| name: Build wheels on ${{ matrix.os }} | |
| env: | |
| PREFIX: "/usr/local/" | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-20.04, macOS-13] | |
| #os: [ubuntu-latest, macOS-11] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set correct paths for Homebrew on macOS | |
| if: matrix.os == 'macOS-13' | |
| run: | | |
| BREW_PREFIX=$(brew --prefix) | |
| export PATH="$BREW_PREFIX/bin:$PATH" | |
| export LIBRARY_PATH="$BREW_PREFIX/lib:$LIBRARY_PATH" | |
| export PKG_CONFIG_PATH="$BREW_PREFIX/lib/pkgconfig:$PKG_CONFIG_PATH" | |
| - name: Install project dependencies | |
| run: which python; python -m pip install -r requirements.txt | |
| - name: Build wheels | |
| uses: pypa/cibuildwheel@v2.21.3 | |
| env: | |
| CIBW_PROJECT_REQUIRES_PYTHON: ">=3.10,<3.13" # >=3.8 <3.12 | |
| CIBW_SKIP: "*-win32 *-manylinux_i686 pp* *musl* " # cp311-macosx* | |
| CIBW_ARCHS_MACOS: "x86_64 arm64" | |
| CIBW_ARCHS_LINUX: "auto" | |
| CIBW_BEFORE_ALL_MACOS: | | |
| bash ci/osx-deps | |
| CIBW_BEFORE_ALL_LINUX: bash ci/manylinux-deps | |
| CIBW_BEFORE_BUILD_MACOS: | | |
| ln -s /Library/Frameworks/Python.framework/Versions/3.11/include/python3.11/cpython/longintrepr.h /Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 | |
| which python3 | |
| python3 -m pip install -r requirements.txt | |
| CIBW_BEFORE_BUILD_LINUX: pip install -r requirements.txt | |
| CIBW_REPAIR_WHEEL_COMMAND_MACOS: delocate-wheel --require-archs x86_64 -w {dest_dir} -v {wheel} --require-target-macos-version 13.0 | |
| CIBW_TEST_SKIP: "*-macosx_arm64" | |
| CIBW_TEST_REQUIRES: cython click>=8.0 numpy scipy pandas pysam>=0.22.0 networkx>=2.4 scikit-learn>=0.22 sortedcontainers lightgbm | |
| CIBW_TEST_COMMAND: dysgu test --verbose | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: wheelhouse-${{ matrix.os }}-${{ github.run_id }} | |
| path: ./wheelhouse/*.whl |