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Build workflow (#96)
* Improve dependency handling * Propagate test results to make * Start build wheels actions prototype * Add linux before-build script * Add toml cibuild linux section * Add cibw corrections * small correction to wheel build process * small correction to wheel build process * Remove unnecessary data from TOML file * Testing cibw workflow * New attempt to build * New attempt cibuild * Add dummy extension to fix ciwb problems * Correct project toml * Force wheels to be set as not pure * Add support for musllinux * Fix ibw_before_build_linux.sh * Relax hci test to pass with aarch architecture * Exclude musllinux aarch64 as there is not scipy for it * Exclude python 3.13t as there is not scipy for it * Add test to built wheels * Add fix to test to built wheels * Add option to include pyci package data * Fix option to include pyci package data * Fix option to include pyci package data * Try fix on option to include pyci package data * Test pyci wheels * Add actions to publish package
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‎.github/workflows/build_wheels.yml‎

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# Workflow to build and test wheels.
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name: Wheel builder
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on:
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push:
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tags:
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# Trigger on version tags (e.g., v1.0.0)
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- "v[0-9].[0-9].[0-9]*"
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- "[0-9].[0-9].[0-9]*"
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# Trigger on pre-release tags (e.g., v1.0.0-alpha.1)
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- "v[0-9].[0-9].[0-9]*-*"
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- "[0-9].[0-9].[0-9]*-*"
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env:
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# The name of the package to be published to PyPI and TestPyPI.
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PYPI_NAME: qc-PyCI
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permissions:
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contents: read # to fetch code (actions/checkout)
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# ensure that only one wheel builder runs at a time
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concurrency:
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group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
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cancel-in-progress: true
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jobs:
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build_wheels:
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name: Wheel, ${{ matrix.python[0] }}-${{ matrix.buildplat[1] }}
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${{ matrix.buildplat[2] }} ${{ matrix.buildplat[3] }}
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${{ matrix.buildplat[4] }}
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runs-on: ${{ matrix.buildplat[0] }}
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strategy:
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# Ensure that a wheel builder finishes even if another fails
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fail-fast: false
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matrix:
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# If need to exclude several configurations see:
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# https://github.com/github/feedback/discussions/7835#discussioncomment-1769026
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buildplat:
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# Different architectures are in different jobs because the need of different compiler configurations
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- [ubuntu-22.04, manylinux, x86_64, "", ""]
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- [ubuntu-22.04, musllinux, x86_64, "", ""]
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- [ubuntu-24.04-arm, manylinux, aarch64, "", ""]
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# - [ubuntu-24.04-arm, musllinux, aarch64, "", ""]
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# - [macos-13, macosx, x86_64, openblas, "10.13"]
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# - [macos-13, macosx, x86_64, accelerate, "14.0"]
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# - [macos-14, macosx, arm64, openblas, "12.3"]
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# - [macos-14, macosx, arm64, accelerate, "14.0"]
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# - [windows-2019, win, AMD64, "", ""]
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# python[0] is the python version of the wheel and python[1] is the python version of the configuration
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python: [["cp39", "3.9"],["cp310", "3.10"], ["cp311", "3.11"], ["cp312", "3.12"], ["cp313", "3.13"]]
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env:
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# set 32-bit flag accessable in the build script
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IS_32_BIT: ${{ matrix.buildplat[2] == 'x86' }}
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steps:
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- name: Checkout pyci
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: win_amd64 - mingw-w64
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# TODO: finish the windows build actions
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run: |
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# mingw-w64
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if [[ ${{ matrix.buildplat[0] }} == 'windows-2019' && ${{ matrix.buildplat[2] }} == 'AMD64' ]]; then
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choco install -y mingw
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export PATH="/c/Program Files/mingw-w64/x86_64-8.1.0-posix-seh-rt_v6-rev0/mingw64/bin:$PATH"
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echo "PATH=$PATH" >> $GITHUB_ENV
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fi
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- name: windows - set PKG_CONFIG_PATH
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if: ${{ runner.os == 'Windows' }}
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run: |
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$env:CIBW = "${{ github.workspace }}"
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# It seems somewhere in the env passing, `\` is not
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# passed through, so convert it to '/'
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$env:CIBW=$env:CIBW.replace("\","/")
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echo "CIBW_ENVIRONMENT=PKG_CONFIG_PATH=$env:CIBW" >> $env:GITHUB_ENV
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- name: Setup macOS
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if: startsWith( matrix.buildplat[0], 'macos-' )
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run: |
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if [[ ${{ matrix.buildplat[3] }} == 'accelerate' ]]; then
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echo CIBW_CONFIG_SETTINGS=\"setup-args=-Dblas=accelerate\" >> "$GITHUB_ENV"
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# Always use preinstalled gfortran for Accelerate builds
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ln -s $(which gfortran-13) gfortran
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export PATH=$PWD:$PATH
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echo "PATH=$PATH" >> "$GITHUB_ENV"
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LIB_PATH=$(dirname $(gfortran --print-file-name libgfortran.dylib))
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fi
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if [[ ${{ matrix.buildplat[4] }} == '10.13' ]]; then
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# 20241017 macos-13 images span Xcode 14.1-->15.2
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XCODE_VER='14.1'
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else
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XCODE_VER='15.2'
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fi
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CIBW="sudo xcode-select -s /Applications/Xcode_${XCODE_VER}.app"
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echo "CIBW_BEFORE_ALL=$CIBW" >> $GITHUB_ENV
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# setting SDKROOT necessary when using the gfortran compiler
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# installed in cibw_before_build_macos.sh
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sudo xcode-select -s /Applications/Xcode_${XCODE_VER}.app
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CIBW="MACOSX_DEPLOYMENT_TARGET=${{ matrix.buildplat[4] }}\
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SDKROOT=$(xcrun --sdk macosx --show-sdk-path)\
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PKG_CONFIG_PATH=${{ github.workspace }}"
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echo "CIBW_ENVIRONMENT=$CIBW" >> "$GITHUB_ENV"
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echo "REPAIR_PATH=$LIB_PATH" >> "$GITHUB_ENV"
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PREFIX=DYLD_LIBRARY_PATH="\$(dirname \$(gfortran --print-file-name libgfortran.dylib))"
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# remove libgfortran from location used for linking (if any), to
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# check wheel has bundled things correctly and all tests pass without
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# needing installed gfortran
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POSTFIX=" sudo rm -rf /opt/gfortran-darwin-x86_64-native &&\
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sudo rm -rf /usr/local/gfortran/lib"
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CIBW="$PREFIX delocate-listdeps -d {wheel} && echo "-----------" &&\
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$PREFIX delocate-wheel -v $EXCLUDE --require-archs \
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{delocate_archs} -w {dest_dir} {wheel} && echo "-----------" &&\
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delocate-listdeps -d {dest_dir}/*.whl && echo "-----------" &&\
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$POSTFIX"
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# Rename x86 Accelerate wheel to test on macOS 13 runner
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if [[ ${{ matrix.buildplat[0] }} == 'macos-13' && ${{ matrix.buildplat[4] }} == '14.0' ]]; then
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CIBW+=" && mv {dest_dir}/\$(basename {wheel}) \
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{dest_dir}/\$(echo \$(basename {wheel}) | sed 's/14_0/13_0/')"
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fi
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# macos-arm64-openblas wheels that target macos-12 need a
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# MACOS_DEPLOYMENT_TARGET of 12.3 otherwise delocate complains.
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# Unclear of cause, possibly build tool related.
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# This results in wheels that have 12_3 in their name. Since Python
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# has no concept of minor OS versions in packaging land rename the
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# wheel back to 12.
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if [[ ${{ matrix.buildplat[0] }} == 'macos-14' && ${{ matrix.buildplat[4] }} == '12.3' ]]; then
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CIBW+=" && echo \$(ls {dest_dir}) && \
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mv {dest_dir}/*.whl \$(find {dest_dir} -type f -name '*.whl' | sed 's/12_3/12_0/')"
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fi
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echo "CIBW_REPAIR_WHEEL_COMMAND_MACOS=$CIBW" >> "$GITHUB_ENV"
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- name: Build wheels
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uses: pypa/cibuildwheel@7940a4c0e76eb2030e473a5f864f291f63ee879b # v2.21.3
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env:
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CIBW_BUILD: ${{ matrix.python[0] }}-${{ matrix.buildplat[1] }}*
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CIBW_ARCHS: ${{ matrix.buildplat[2] }}
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CIBW_PRERELEASE_PYTHONS: True
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CIBW_FREE_THREADED_SUPPORT: True
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CIBW_OUTPUT_DIR: ./wheelhouse
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CIBW_BUILD_VERBOSITY: 2
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CIBW_ENVIRONMENT: CFLAGS="-I/project/pyci/include" LDFLAGS="-L/project/pyci"
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- name: Rename macOS wheels
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if: startsWith( matrix.buildplat[0], 'macos-' )
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run: |
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# macos-x86_64-accelerate wheels targeting macos-14 were renamed to 13
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# so they could be tested. Shift wheel name back to targeting 14.
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if [[ ${{ matrix.buildplat[0] }} == 'macos-13' && ${{ matrix.buildplat[4] }} == '14.0' ]]; then
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mv ./wheelhouse/*.whl $(find ./wheelhouse -type f -name '*.whl' | sed 's/13_0/14_0/')
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fi
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# - name: Test the build wheels
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# run: |
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# # Install the built wheels
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# pip install pytest
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# pip install ./wheelhouse/*.whl
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# # Test the installed wheels
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# pytest project/pyci
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- uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4.4.3
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with:
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path: ./wheelhouse/*.whl
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name: ${{ matrix.python[0] }}-${{ matrix.buildplat[1] }}
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${{ matrix.buildplat[2] }} ${{ matrix.buildplat[3] }}
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${{ matrix.buildplat[4] }}
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# TODO: Test the build wheels
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# - name: Test the build wheels
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# TODO: Upload the build wheels to the release
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publish-to-pypi:
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name: Publish Python distribution to PyPI
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# only publish to PyPI on tag pushes
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if: startsWith(github.ref, 'refs/tags/')
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needs:
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- build_wheels
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runs-on: ubuntu-latest
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environment:
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name: PyPI-Release
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url: https://pypi.org/project/${{ env.PYPI_NAME }}
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permissions:
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id-token: write
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steps:
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- name: Download all the dists
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uses: actions/download-artifact@v4
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with:
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name: python-package-distributions
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path: ./wheelhouse/*.whl
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- name: Publish distribution to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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env:
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TWINE_USERNAME: "__token__"
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TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
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github-release:
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name: Sign the Python distribution with Sigstore and upload them to GitHub Release
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needs:
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- publish-to-pypi
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runs-on: ubuntu-latest
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permissions:
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contents: write
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id-token: write
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steps:
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- name: Download all the dists
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uses: actions/download-artifact@v4
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with:
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name: python-package-distributions
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path: ./wheelhouse
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- name: Sign the dists with Sigstore
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uses: sigstore/[email protected]
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with:
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inputs: >-
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./wheelhouse/*.whl
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- name: Create GitHub Release
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env:
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GITHUB_TOKEN: ${{ github.token }}
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run: >-
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gh release create
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"${{ github.ref_name }}"
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--repo "${{ github.repository }}"
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--notes ""
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- name: Upload artifact signatures to GitHub Release
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env:
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GITHUB_TOKEN: ${{ github.token }}
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run: >-
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gh release upload
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"${{ github.ref_name }}" wheelhouse/**
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--repo "${{ github.repository }}"
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publish-to-testpypi:
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name: Publish Python distribution to TestPyPI
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# if: ${{ github.ref == "refs/heads/master" && github.repository_owner == "theochem" }}
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needs:
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- build_wheels
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runs-on: ubuntu-latest
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environment:
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name: TestPyPI
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url: https://test.pypi.org/project/${{ env.PYPI_NAME }}
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permissions:
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id-token: write
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steps:
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- name: Download all the dists
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uses: actions/download-artifact@v4
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with:
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name: python-package-distributions
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path: wheelhouse/
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- name: Publish distribution to TestPyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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repository-url: https://test.pypi.org/legacy/
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env:
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TWINE_USERNAME: "__token__"
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TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}

‎Makefile‎

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@@ -74,7 +74,7 @@ all: pyci/_pyci.so.$(PYCI_VERSION) pyci/_pyci.so.$(VERSION_MAJOR) pyci/_pyci.so
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.PHONY: test
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test:
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$(PYTHON) -m pytest -sv ./pyci
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@set -e; $(PYTHON) -m pytest -sv ./pyci
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.PHONY: clean
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clean:
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ln -sf $(notdir $(<)) $(@)
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deps/eigen:
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@git clone https://gitlab.com/libeigen/eigen.git $(@)
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[ -d $@ ] || git clone https://gitlab.com/libeigen/eigen.git $@
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deps/spectra:
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@git clone https://github.com/yixuan/spectra.git $(@)
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[ -d $@ ] || git clone https://github.com/yixuan/spectra.git $@
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deps/parallel-hashmap:
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@git clone https://github.com/greg7mdp/parallel-hashmap.git $(@)
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[ -d $@ ] || git clone https://github.com/greg7mdp/parallel-hashmap.git $@
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deps/pybind11:
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@git clone https://github.com/pybind/pybind11.git $(@)
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[ -d $@ ] || git clone https://github.com/pybind/pybind11.git $@

‎pyci/test/test_routines.py‎

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assert len(wfn) == np.prod([comb(wfn.nbasis, occ, exact=True) for occ in occs])
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else:
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assert len(wfn) == comb(wfn.nbasis, occs[0], exact=True)
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npt.assert_allclose(es[0], energy, rtol=0.0, atol=1.0e-9)
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npt.assert_allclose(es[0], energy, rtol=0.0, atol=2.0e-9)
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@pytest.mark.parametrize(

‎pyproject.toml‎

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[build-system]
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# Required packages for building the project
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requires = [
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# "scikit-build-core >= 0.9.10",
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"setuptools_scm>=8", # For version management
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"setuptools>=61.0.0", # For building the package
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"pytest>=8.0.0", # For running tests
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]
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# build-backend = "scikit_build_core.build"
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build-backend = "setuptools.build_meta"
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[project]
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# Basic project metadata
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"pyci",
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"pyci.fanci",
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"pyci.test",
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"pyci.fanci.test"
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"pyci.fanci.test",
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]
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[tool.setuptools.package-data]
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# Non-Python files to include in the package
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"pyci" = [
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"_pyci.so", # Compiled C++ extension
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"_pyci.so.0.6.1", # Compiled C++ extension
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"include/*.h", # C++ header files
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"src/*.cpp" # C++ source files
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]
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"data/*.npy", # NumPy data files
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"data/*.npz" # Compressed NumPy data files
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]
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# Build configuration
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[tool.scikit-build]
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sdist.exclude = [
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".github",
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"tests/data/*.fchk",
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"examples/*.fchk"
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"pyci.fanci.test" = [
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"data/*.fcidump", # Test input files
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"data/*.npy", # NumPy data files
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"data/*.npz" # Compressed NumPy data files
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]
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metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
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[tool.cibuildwheel]
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# Switch to using build
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build-frontend = "build"
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[tool.cibuildwheel.linux]
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before-build = "bash {project}/tools/wheels/cibw_before_build_linux.sh"
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# Version management configuration
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[tool.setuptools_scm]

‎setup.cfg‎

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[pycodestyle]
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max-line-length=100
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ignore=E127,E201,E203,E231,E241,E402,E741
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[options.package_data]
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pyci = _pyci.so

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