ENH: Allow user-defined slicing over time or channel axes (#43) #71
Workflow file for this run
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| name: Build, test, package | |
| on: [push,pull_request] | |
| env: | |
| itk-git-tag: "v5.4rc01" | |
| itk-wheel-tag: "v5.4rc01" | |
| ITKPythonPackage-git-tag: "5ad02309321621cdc7269b9b68a35013c912271c" | |
| jobs: | |
| build-test-cxx: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| max-parallel: 3 | |
| matrix: | |
| os: [ubuntu-22.04, windows-2022, macos-12] | |
| include: | |
| - os: ubuntu-22.04 | |
| c-compiler: "gcc" | |
| cxx-compiler: "g++" | |
| cmake-build-type: "MinSizeRel" | |
| - os: windows-2022 | |
| c-compiler: "cl.exe" | |
| cxx-compiler: "cl.exe" | |
| cmake-build-type: "Release" | |
| - os: macos-12 | |
| c-compiler: "clang" | |
| cxx-compiler: "clang++" | |
| cmake-build-type: "MinSizeRel" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: 'Specific XCode version' | |
| if: matrix.os == 'macos-12' | |
| run: | | |
| sudo xcode-select -s "/Applications/Xcode_13.2.1.app" | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| - uses: shogo82148/actions-setup-perl@v1 | |
| - uses: ilammy/setup-nasm@v1 | |
| - name: Get specific version of CMake, Ninja | |
| uses: lukka/[email protected] | |
| - name: Download ITK | |
| run: | | |
| cd .. | |
| git clone https://github.com/InsightSoftwareConsortium/ITK.git | |
| cd ITK | |
| git checkout ${{ env.itk-git-tag }} | |
| - name: Build ITK | |
| if: matrix.os != 'windows-2022' | |
| run: | | |
| cd .. | |
| mkdir ITK-build | |
| cd ITK-build | |
| cmake -DCMAKE_C_COMPILER:FILEPATH="${{ matrix.c-compiler }}" -DBUILD_SHARED_LIBS:BOOL=ON -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE:STRING=${{ matrix.cmake-build-type }} -DBUILD_TESTING:BOOL=OFF -GNinja ../ITK | |
| ninja | |
| - name: Build ITK | |
| if: matrix.os == 'windows-2022' | |
| run: | | |
| cd .. | |
| mkdir ITK-build | |
| cd ITK-build | |
| call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat" | |
| cmake -DCMAKE_C_COMPILER:FILEPATH="${{ matrix.c-compiler }}" -DBUILD_SHARED_LIBS:BOOL=ON -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE:STRING=${{ matrix.cmake-build-type }} -DBUILD_TESTING:BOOL=OFF -GNinja ../ITK | |
| ninja | |
| shell: cmd | |
| - name: Fetch CTest driver script | |
| run: | | |
| curl -L https://raw.githubusercontent.com/InsightSoftwareConsortium/ITK/dashboard/itk_common.cmake -O | |
| - name: Configure CTest script | |
| shell: bash | |
| run: | | |
| operating_system="${{ matrix.os }}" | |
| cat > dashboard.cmake << EOF | |
| set(CTEST_SITE "GitHubActions") | |
| file(TO_CMAKE_PATH "\$ENV{GITHUB_WORKSPACE}/.." CTEST_DASHBOARD_ROOT) | |
| file(TO_CMAKE_PATH "\$ENV{GITHUB_WORKSPACE}/" CTEST_SOURCE_DIRECTORY) | |
| file(TO_CMAKE_PATH "\$ENV{GITHUB_WORKSPACE}/../build" CTEST_BINARY_DIRECTORY) | |
| set(dashboard_source_name "${GITHUB_REPOSITORY}") | |
| if(ENV{GITHUB_REF} MATCHES "master") | |
| set(branch "-master") | |
| set(dashboard_model "Continuous") | |
| else() | |
| set(branch "-${GITHUB_REF}") | |
| set(dashboard_model "Experimental") | |
| endif() | |
| set(CTEST_BUILD_NAME "${GITHUB_REPOSITORY}-${operating_system}-\${branch}") | |
| set(CTEST_UPDATE_VERSION_ONLY 1) | |
| set(CTEST_TEST_ARGS \${CTEST_TEST_ARGS} PARALLEL_LEVEL \${PARALLEL_LEVEL}) | |
| set(CTEST_BUILD_CONFIGURATION "Release") | |
| set(CTEST_CMAKE_GENERATOR "Ninja") | |
| set(CTEST_CUSTOM_WARNING_EXCEPTION | |
| \${CTEST_CUSTOM_WARNING_EXCEPTION} | |
| # macOS Azure VM Warning | |
| "ld: warning: text-based stub file" | |
| "Wunused-result" | |
| "file: .+ has no symbols" | |
| "Wpointer-bool-conversion" | |
| "note: prefix with the address-of operator to silence this warning" | |
| "warning C4722: 'riegeli::internal::UnreachableStream::~UnreachableStream': destructor never returns, potential memory leak" | |
| "warning C4722: 'riegeli::internal::CheckFailed::~CheckFailed': destructor never returns, potential memory leak" | |
| "_deps[/\\\\].+-src[/\\\\]" # disable all warnings from external projects | |
| # the following warnings escape the above filter | |
| "warning: Import validate/validate.proto is unused" | |
| "warning:.+__builtin___memcpy_chk" | |
| "warning:.+__builtin_memchr" | |
| "note: source object allocated here" | |
| ) | |
| set(dashboard_no_clean 1) | |
| set(ENV{CC} ${{ matrix.c-compiler }}) | |
| set(ENV{CXX} ${{ matrix.cxx-compiler }}) | |
| if(WIN32) | |
| set(ENV{PATH} "\${CTEST_DASHBOARD_ROOT}/ITK-build/bin;\$ENV{PATH}") | |
| endif() | |
| set(dashboard_cache " | |
| ITK_DIR:PATH=\${CTEST_DASHBOARD_ROOT}/ITK-build | |
| BUILD_TESTING:BOOL=ON | |
| ") | |
| string(TIMESTAMP build_date "%Y-%m-%d") | |
| message("CDash Build Identifier: \${build_date} \${CTEST_BUILD_NAME}") | |
| message("CTEST_SITE = \${CTEST_SITE}") | |
| include(\${CTEST_SCRIPT_DIRECTORY}/itk_common.cmake) | |
| EOF | |
| cat dashboard.cmake | |
| - name: Build and test | |
| if: matrix.os != 'windows-2022' | |
| run: | | |
| ctest --output-on-failure -j 2 -V -S dashboard.cmake | |
| - name: Build and test | |
| if: matrix.os == 'windows-2022' | |
| run: | | |
| call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat" | |
| ctest --output-on-failure -j 2 -V -S dashboard.cmake | |
| shell: cmd | |
| build-linux-py: | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| max-parallel: 2 | |
| matrix: | |
| python-version: ["38", "39", "310", "311"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: 'Fetch build script' | |
| run: | | |
| curl -L https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKPythonPackage/${{ env.ITKPythonPackage-git-tag }}/scripts/dockcross-manylinux-download-cache-and-build-module-wheels.sh -O | |
| chmod u+x dockcross-manylinux-download-cache-and-build-module-wheels.sh | |
| - name: 'Build 🐍 Python 📦 package' | |
| run: | | |
| export ITK_PACKAGE_VERSION=${{ env.itk-wheel-tag }} | |
| export ITKPYTHONPACKAGE_TAG=${{ env.ITKPythonPackage-git-tag }} | |
| export MANYLINUX_VERSION="_2_28" | |
| echo "Building for manylinux specialization ${MANYLINUX_VERSION}" | |
| pwd | |
| ./dockcross-manylinux-download-cache-and-build-module-wheels.sh cp${{ matrix.python-version }} | |
| - name: Publish Python package as GitHub Artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: LinuxWheel${{ matrix.python-version }} | |
| path: dist/*.whl | |
| build-macos-py: | |
| runs-on: macos-12 | |
| strategy: | |
| max-parallel: 2 | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: 'Specific XCode version' | |
| run: | | |
| sudo xcode-select -s "/Applications/Xcode_13.2.1.app" | |
| - name: Get specific version of CMake, Ninja | |
| uses: lukka/[email protected] | |
| - uses: shogo82148/actions-setup-perl@v1 | |
| - uses: ilammy/setup-nasm@v1 | |
| - name: 'Fetch build script' | |
| run: | | |
| curl -L https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKPythonPackage/${{ env.ITKPythonPackage-git-tag }}/scripts/macpython-download-cache-and-build-module-wheels.sh -O | |
| chmod u+x macpython-download-cache-and-build-module-wheels.sh | |
| - name: 'Build 🐍 Python 📦 package' | |
| run: | | |
| export ITK_PACKAGE_VERSION=${{ env.itk-wheel-tag }} | |
| export ITKPYTHONPACKAGE_TAG=${{ env.ITKPythonPackage-git-tag }} | |
| export MACOSX_DEPLOYMENT_TARGET=10.15 | |
| pwd | |
| ./macpython-download-cache-and-build-module-wheels.sh "${{ matrix.python-version }}" | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Validate build output | |
| shell: bash | |
| run: | | |
| python -m pip install twine | |
| ls dist/ | |
| WHEEL_PATTERN="dist/itk_*macosx*.whl" | |
| EXPECTED_WHEEL_COUNT=1 | |
| WHEEL_COUNT=`(ls ${WHEEL_PATTERN} | wc -l)` | |
| if (( ${WHEEL_COUNT} != ${EXPECTED_WHEEL_COUNT} )); then | |
| echo "Expected ${EXPECTED_WHEEL_COUNT} wheels but found ${WHEEL_COUNT}" | |
| exit 1 | |
| fi | |
| python -m twine check ${WHEEL_PATTERN} | |
| - name: Publish Python package as GitHub Artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: MacOSWheels | |
| path: dist/*.whl | |
| build-windows-py: | |
| runs-on: windows-2022 | |
| strategy: | |
| max-parallel: 2 | |
| matrix: | |
| python-version-minor: ["8", "9", "10", "11"] | |
| steps: | |
| - name: Get specific version of CMake, Ninja | |
| uses: lukka/[email protected] | |
| - uses: actions/checkout@v3 | |
| with: | |
| path: "im" | |
| - name: 'Reduce source path length' | |
| shell: bash | |
| run: | | |
| # Move checked-out source to a shorter path to avoid Windows path length issues | |
| mv im ../../ | |
| - name: 'Install Python' | |
| run: | | |
| $pythonArch = "64" | |
| $pythonVersion = "3.${{ matrix.python-version-minor }}" | |
| iex ((new-object net.webclient).DownloadString('https://raw.githubusercontent.com/scikit-build/scikit-ci-addons/master/windows/install-python.ps1')) | |
| - uses: shogo82148/actions-setup-perl@v1 | |
| - uses: ilammy/setup-nasm@v1 | |
| - name: 'Fetch build dependencies' | |
| shell: bash | |
| run: | | |
| cd ../../im | |
| curl -L "https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${{ env.itk-wheel-tag }}/ITKPythonBuilds-windows.zip" -o "ITKPythonBuilds-windows.zip" | |
| 7z x ITKPythonBuilds-windows.zip -o/c/P -aoa -r | |
| curl -L "https://data.kitware.com/api/v1/file/5c0ad59d8d777f2179dd3e9c/download" -o "doxygen-1.8.11.windows.bin.zip" | |
| 7z x doxygen-1.8.11.windows.bin.zip -o/c/P/doxygen -aoa -r | |
| curl -L "https://data.kitware.com/api/v1/file/5bbf87ba8d777f06b91f27d6/download/grep-win.zip" -o "grep-win.zip" | |
| 7z x grep-win.zip -o/c/P/grep -aoa -r | |
| if [[ -n ${{ env.ITKPythonPackage-git-tag }} ]]; then | |
| echo "Updating ITKPythonPackage build scripts to ${{ env.ITKPythonPackage-git-tag }}" | |
| pushd /c/P/IPP | |
| git remote add InsightSoftwareConsortium https://github.com/InsightSoftwareConsortium/ITKPythonPackage.git --tags | |
| git fetch InsightSoftwareConsortium | |
| git checkout ${{ env.ITKPythonPackage-git-tag }} | |
| git status | |
| popd | |
| else | |
| echo "Using ITKPythonPackage scripts included with ITKPythonBuilds archive" | |
| fi | |
| - name: 'Build 🐍 Python 📦 package' | |
| shell: cmd | |
| run: | | |
| cd ../../im | |
| call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat" | |
| set PATH=C:\P\grep;%PATH% | |
| set CC=cl.exe | |
| set CXX=cl.exe | |
| pwd | |
| C:\Python3${{ matrix.python-version-minor }}-x64\python.exe C:\P\IPP\scripts\windows_build_module_wheels.py --py-envs "3${{ matrix.python-version-minor }}-x64" --no-cleanup | |
| mkdir ${{ github.workspace }}\dist | |
| copy dist\*.whl ${{ github.workspace }}\dist | |
| - name: Publish Python package as GitHub Artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: WindowsWheel3.${{ matrix.python-version-minor }} | |
| path: dist/*.whl | |
| publish-python-packages-to-pypi: | |
| needs: | |
| - build-linux-py | |
| - build-macos-py | |
| - build-windows-py | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Download Python Packages | |
| uses: actions/download-artifact@v3 | |
| - name: Prepare packages for upload | |
| run: | | |
| ls -R | |
| for d in */; do | |
| mv ${d}/*.whl . | |
| done | |
| mkdir dist | |
| mv *.whl dist/ | |
| ls dist | |
| - name: Publish 🐍 Python 📦 package to PyPI | |
| if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') | |
| uses: pypa/gh-action-pypi-publish@master | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.pypi_password }} |