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Merge pull request #30 from InsightSoftwareConsortium/github-actions
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‎.github/workflows/build-test-package.yml‎

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name: Build, test, package
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on: [push,pull_request]
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jobs:
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build-test-cxx:
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runs-on: ${{ matrix.os }}
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strategy:
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max-parallel: 3
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matrix:
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os: [ubuntu-18.04, windows-2019, macos-10.15]
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include:
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- os: ubuntu-18.04
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c-compiler: "gcc"
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cxx-compiler: "g++"
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itk-git-tag: "v5.1.1"
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cmake-build-type: "MinSizeRel"
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- os: windows-2019
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c-compiler: "cl.exe"
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cxx-compiler: "cl.exe"
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itk-git-tag: "v5.1.1"
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cmake-build-type: "Release"
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- os: macos-10.15
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c-compiler: "clang"
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cxx-compiler: "clang++"
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itk-git-tag: "v5.1.1"
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cmake-build-type: "MinSizeRel"
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python 3.7
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uses: actions/setup-python@v1
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with:
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python-version: 3.7
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- name: Install build dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install ninja
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- name: Download ITK
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run: |
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cd ..
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git clone https://github.com/InsightSoftwareConsortium/ITK.git
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cd ITK
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git checkout ${{ matrix.itk-git-tag }}
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- name: Build ITK
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if: matrix.os != 'windows-2019'
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run: |
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cd ..
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mkdir ITK-build
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cd ITK-build
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cmake -DCMAKE_C_COMPILER:FILEPATH="${{ matrix.c-compiler }}" -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE:STRING=${{ matrix.cmake-build-type }} -DBUILD_TESTING:BOOL=OFF -GNinja ../ITK
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ninja
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- name: Build ITK
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if: matrix.os == 'windows-2019'
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run: |
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cd ..
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mkdir ITK-build
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cd ITK-build
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call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
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cmake -DCMAKE_C_COMPILER:FILEPATH="${{ matrix.c-compiler }}" -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE:STRING=${{ matrix.cmake-build-type }} -DBUILD_TESTING:BOOL=OFF -GNinja ../ITK
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ninja
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shell: cmd
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- name: Fetch CTest driver script
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run: |
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curl -L https://raw.githubusercontent.com/InsightSoftwareConsortium/ITK/dashboard/itk_common.cmake -O
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- name: Configure CTest script
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shell: bash
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run: |
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operating_system="${{ matrix.os }}"
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cat > dashboard.cmake << EOF
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set(CTEST_SITE "GitHubActions")
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file(TO_CMAKE_PATH "\$ENV{GITHUB_WORKSPACE}/.." CTEST_DASHBOARD_ROOT)
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file(TO_CMAKE_PATH "\$ENV{GITHUB_WORKSPACE}/" CTEST_SOURCE_DIRECTORY)
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file(TO_CMAKE_PATH "\$ENV{GITHUB_WORKSPACE}/../build" CTEST_BINARY_DIRECTORY)
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set(dashboard_source_name "${GITHUB_REPOSITORY}")
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if(ENV{GITHUB_REF} MATCHES "master")
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set(branch "-master")
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set(dashboard_model "Continuous")
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else()
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set(branch "-${GITHUB_REF}")
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set(dashboard_model "Experimental")
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endif()
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set(CTEST_BUILD_NAME "${GITHUB_REPOSITORY}-${operating_system}-\${branch}")
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set(CTEST_UPDATE_VERSION_ONLY 1)
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set(CTEST_TEST_ARGS \${CTEST_TEST_ARGS} PARALLEL_LEVEL \${PARALLEL_LEVEL})
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set(CTEST_BUILD_CONFIGURATION "Release")
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set(CTEST_CMAKE_GENERATOR "Ninja")
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set(CTEST_CUSTOM_WARNING_EXCEPTION
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\${CTEST_CUSTOM_WARNING_EXCEPTION}
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# macOS Azure VM Warning
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"ld: warning: text-based stub file"
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)
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set(dashboard_no_clean 1)
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set(ENV{CC} ${{ matrix.c-compiler }})
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set(ENV{CXX} ${{ matrix.cxx-compiler }})
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if(WIN32)
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set(ENV{PATH} "\${CTEST_DASHBOARD_ROOT}/ITK-build/bin;\$ENV{PATH}")
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endif()
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set(dashboard_cache "
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ITK_DIR:PATH=\${CTEST_DASHBOARD_ROOT}/ITK-build
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BUILD_TESTING:BOOL=ON
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")
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string(TIMESTAMP build_date "%Y-%m-%d")
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message("CDash Build Identifier: \${build_date} \${CTEST_BUILD_NAME}")
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message("CTEST_SITE = \${CTEST_SITE}")
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include(\${CTEST_SCRIPT_DIRECTORY}/itk_common.cmake)
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EOF
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cat dashboard.cmake
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- name: Build and test
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if: matrix.os != 'windows-2019'
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run: |
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ctest --output-on-failure -j 2 -V -S dashboard.cmake
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- name: Build and test
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if: matrix.os == 'windows-2019'
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run: |
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call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
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ctest --output-on-failure -j 2 -V -S dashboard.cmake
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shell: cmd
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build-linux-python-packages:
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runs-on: ubuntu-18.04
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strategy:
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max-parallel: 2
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matrix:
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python-version: [36, 37, 38, 39]
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include:
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- itk-python-git-tag: "v5.1.1.post1"
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steps:
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- uses: actions/checkout@v2
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- name: 'Free up disk space'
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run: |
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# Workaround for https://github.com/actions/virtual-environments/issues/709
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df -h
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sudo apt-get clean
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sudo rm -rf "/usr/local/share/boost"
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sudo rm -rf "$AGENT_TOOLSDIRECTORY"
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df -h
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- name: 'Fetch build script'
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run: |
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curl -L https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKPythonPackage/master/scripts/dockcross-manylinux-download-cache-and-build-module-wheels.sh -O
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chmod u+x dockcross-manylinux-download-cache-and-build-module-wheels.sh
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- name: 'Build 🐍 Python 📦 package'
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run: |
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export ITK_PACKAGE_VERSION=${{ matrix.itk-python-git-tag }}
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./dockcross-manylinux-download-cache-and-build-module-wheels.sh cp${{ matrix.python-version }}
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- name: Publish Python package as GitHub Artifact
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uses: actions/upload-artifact@v1
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with:
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name: LinuxWheel${{ matrix.python-version }}
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path: dist
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build-macos-python-packages:
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runs-on: macos-10.15
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strategy:
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max-parallel: 2
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matrix:
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include:
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- itk-python-git-tag: "v5.1.1.post1"
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steps:
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- uses: actions/checkout@v2
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- name: 'Fetch build script'
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run: |
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curl -L https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKPythonPackage/master/scripts/macpython-download-cache-and-build-module-wheels.sh -O
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chmod u+x macpython-download-cache-and-build-module-wheels.sh
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- name: 'Build 🐍 Python 📦 package'
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run: |
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export ITK_PACKAGE_VERSION=${{ matrix.itk-python-git-tag }}
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export MACOSX_DEPLOYMENT_TARGET=10.9
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./macpython-download-cache-and-build-module-wheels.sh
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- name: Publish Python package as GitHub Artifact
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uses: actions/upload-artifact@v1
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with:
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name: MacOSWheels
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path: dist
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build-windows-python-packages:
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runs-on: windows-2019
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strategy:
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max-parallel: 2
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matrix:
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python-version-minor: [6, 7, 8, 9]
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include:
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- itk-python-git-tag: "v5.1.1.post1"
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steps:
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- uses: actions/checkout@v2
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with:
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path: "im"
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- name: 'Install Python'
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run: |
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$pythonArch = "64"
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$pythonVersion = "3.${{ matrix.python-version-minor }}"
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iex ((new-object net.webclient).DownloadString('https://raw.githubusercontent.com/scikit-build/scikit-ci-addons/master/windows/install-python.ps1'))
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- name: 'Fetch build dependencies'
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shell: bash
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run: |
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mv im ../../
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cd ../../
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curl -L "https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${{ matrix.itk-python-git-tag }}/ITKPythonBuilds-windows.zip" -o "ITKPythonBuilds-windows.zip"
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7z x ITKPythonBuilds-windows.zip -o/c/P -aoa -r
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curl -L "https://data.kitware.com/api/v1/file/5c0ad59d8d777f2179dd3e9c/download" -o "doxygen-1.8.11.windows.bin.zip"
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7z x doxygen-1.8.11.windows.bin.zip -o/c/P/doxygen -aoa -r
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curl -L "https://data.kitware.com/api/v1/file/5bbf87ba8d777f06b91f27d6/download/grep-win.zip" -o "grep-win.zip"
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7z x grep-win.zip -o/c/P/grep -aoa -r
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- name: 'Build 🐍 Python 📦 package'
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shell: cmd
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run: |
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cd ../../im
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call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
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set PATH="C:\P\grep;%PATH%"
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set CC=cl.exe
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set CXX=cl.exe
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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"
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- name: Publish Python package as GitHub Artifact
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uses: actions/upload-artifact@v1
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with:
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name: WindowWheel3.${{ matrix.python-version-minor }}
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path: ../../im/dist
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publish-python-packages-to-pypi:
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needs:
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- build-linux-python-packages
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- build-macos-python-packages
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- build-windows-python-packages
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runs-on: ubuntu-18.04
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steps:
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- name: Download Python Packages
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uses: actions/download-artifact@v2
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- name: Prepare packages for upload
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run: |
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ls -R
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for d in */; do
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mv ${d}/*.whl .
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done
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mkdir dist
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mv *.whl dist/
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ls dist
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- name: Publish 🐍 Python 📦 package to PyPI
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if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
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uses: pypa/gh-action-pypi-publish@master
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with:
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user: __token__
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password: ${{ secrets.pypi_password }}

‎.github/workflows/clang-format-linter.yml‎

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name: clang-format linter
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on: [push,pull_request]
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jobs:
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lint:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v1
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with:
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fetch-depth: 1
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- uses: InsightSoftwareConsortium/ITKClangFormatLinterAction@master

‎README.rst‎

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11
ITKLabelErodeDilate
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===================
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.. image:: https://github.com/InsightSoftwareConsortium/ITKLabelErodeDilate/workflows/Build,%20test,%20package/badge.svg
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.. |CircleCI| image:: https://circleci.com/gh/InsightSoftwareConsortium/ITKLabelErodeDilate.svg?style=shield
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:target: https://circleci.com/gh/InsightSoftwareConsortium/ITKLabelErodeDilate
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‎include/itkLabelSetDilateImageFilter.hxx‎

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@@ -32,31 +32,32 @@ namespace itk
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template <typename TInputImage, typename TOutputImage>
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void
3434
LabelSetDilateImageFilter<TInputImage, TOutputImage>::ThreadedGenerateData(
35-
const OutputImageRegionType & outputRegionForThread, ThreadIdType threadId)
35+
const OutputImageRegionType & outputRegionForThread,
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ThreadIdType threadId)
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{
37-
// compute the number of rows first, so we can setup a progress reporter
38-
typename std::vector< unsigned int > NumberOfRows;
39-
InputSizeType size = outputRegionForThread.GetSize();
38+
// compute the number of rows first, so we can setup a progress reporter
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typename std::vector<unsigned int> NumberOfRows;
40+
InputSizeType size = outputRegionForThread.GetSize();
4041

41-
for ( unsigned int i = 0; i < InputImageDimension; i++ )
42+
for (unsigned int i = 0; i < InputImageDimension; i++)
43+
{
44+
NumberOfRows.push_back(1);
45+
for (unsigned int d = 0; d < InputImageDimension; d++)
4246
{
43-
NumberOfRows.push_back(1);
44-
for ( unsigned int d = 0; d < InputImageDimension; d++ )
45-
{
46-
if ( d != i )
47-
{
48-
NumberOfRows[i] *= size[d];
49-
}
50-
}
47+
if (d != i)
48+
{
49+
NumberOfRows[i] *= size[d];
50+
}
5151
}
52-
float progressPerDimension = 1.0 / ImageDimension;
53-
54-
auto *progress = new ProgressReporter(this,
55-
threadId,
56-
NumberOfRows[this->m_CurrentDimension],
57-
30,
58-
this->m_CurrentDimension * progressPerDimension,
59-
progressPerDimension);
52+
}
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float progressPerDimension = 1.0 / ImageDimension;
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auto * progress = new ProgressReporter(this,
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threadId,
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NumberOfRows[this->m_CurrentDimension],
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30,
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this->m_CurrentDimension * progressPerDimension,
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progressPerDimension);
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// this is where the work happens. We use a distance image with
6263
// floating point pixel to perform the parabolic operations. The

‎include/itkLabelSetErodeImageFilter.hxx‎

Lines changed: 17 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,8 @@ namespace itk
3232
template <typename TInputImage, typename TOutputImage>
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void
3434
LabelSetErodeImageFilter<TInputImage, TOutputImage>::ThreadedGenerateData(
35-
const OutputImageRegionType & outputRegionForThread, ThreadIdType threadId)
35+
const OutputImageRegionType & outputRegionForThread,
36+
ThreadIdType threadId)
3637
{
3738
// this is where the work happens. We use a distance image with
3839
// floating point pixel to perform the parabolic operations. The
@@ -43,28 +44,28 @@ LabelSetErodeImageFilter<TInputImage, TOutputImage>::ThreadedGenerateData(
4344
// Similarly, the thresholding on output needs to be integrated
4445
// with the last processing stage.
4546

46-
typename std::vector< unsigned int > NumberOfRows;
47-
InputSizeType size = outputRegionForThread.GetSize();
47+
typename std::vector<unsigned int> NumberOfRows;
48+
InputSizeType size = outputRegionForThread.GetSize();
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49-
for ( unsigned int i = 0; i < InputImageDimension; i++ )
50+
for (unsigned int i = 0; i < InputImageDimension; i++)
5051
{
51-
NumberOfRows.push_back(1);
52-
for ( unsigned int d = 0; d < InputImageDimension; d++ )
52+
NumberOfRows.push_back(1);
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for (unsigned int d = 0; d < InputImageDimension; d++)
54+
{
55+
if (d != i)
5356
{
54-
if ( d != i )
55-
{
56-
NumberOfRows[i] *= size[d];
57-
}
57+
NumberOfRows[i] *= size[d];
5858
}
59+
}
5960
}
6061
float progressPerDimension = 1.0 / ImageDimension;
6162

62-
auto *progress = new ProgressReporter(this,
63-
threadId,
64-
NumberOfRows[this->m_CurrentDimension],
65-
30,
66-
this->m_CurrentDimension * progressPerDimension,
67-
progressPerDimension);
63+
auto * progress = new ProgressReporter(this,
64+
threadId,
65+
NumberOfRows[this->m_CurrentDimension],
66+
30,
67+
this->m_CurrentDimension * progressPerDimension,
68+
progressPerDimension);
6869

6970
using InputConstIteratorType = ImageLinearConstIteratorWithIndex<TInputImage>;
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using OutputIteratorType = ImageLinearIteratorWithIndex<TOutputImage>;

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