ElastixGitHubActions.yml

name: Elastix

on: [push, pull_request]
  
jobs:
  build:
    # The CMake configure and build commands are platform agnostic and should work equally
    # well on Windows or Mac.  You can convert this to a matrix build if you need
    # cross-platform coverage.
    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix

    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++"
            itk-git-tag: "v5.4.0"
            cmake-build-type: "Release"
            ANNLib: "libANNlib-5.2.so"
            ANNLib2: "libANNlib-5.2.so.1"
          - os: windows-2022
            c-compiler: "cl.exe"
            cxx-compiler: "cl.exe"
            itk-git-tag: "v5.4.0"
            cmake-build-type: "Release"
            ANNLib: "ANNlib-5.2.dll"
            vcvars64: "C:/Program Files/Microsoft Visual Studio/2022/Enterprise/VC/Auxiliary/Build/vcvars64.bat"
          - os: macos-12
            c-compiler: "clang"  
            cxx-compiler: "clang++"
            itk-git-tag: "v5.4.0"
            cmake-build-type: "Release"
            ANNLib: "libANNlib-5.2.1.dylib"
            ANNLib2: "libANNlib-5.2.dylib"

    steps:
    - uses: actions/checkout@v3
    
    - name: Make directory structure
      run: |
        items=(*)
        mkdir Elastix-source
        mv ${items[*]} Elastix-source
        mv .editorconfig Elastix-source
        mv .clang-format Elastix-source
        mv Elastix-source/Dockerfile .
      shell: bash
      
    - uses: actions/cache@v3
      id: cache
      with:
        path: |
          ITK-build
          ITK-source
        key: ${{ matrix.itk-git-tag }}-${{ matrix.os }}-${{ matrix.cmake-build-type }} 
        
    - name: Set up Python
      uses: actions/setup-python@v3
      with:
        python-version: 3.8

    - name: Install build dependencies
      run: |
        python -m pip install --upgrade pip
        python -m pip install ninja
        
    - name: Get specific version of CMake, Ninja
      uses: lukka/get-cmake@v3.24.2
      
    - name: Download ITK
      if: steps.cache.outputs.cache-hit != 'true'
      run: |
        git clone https://github.com/InsightSoftwareConsortium/ITK.git ITK-source
        cd ITK-source
        git checkout ${{ matrix.itk-git-tag }}
   
    - name: Build ITK
      if: ${{ steps.cache.outputs.cache-hit != 'true' && !startsWith(matrix.os, 'windows') }}
      run: |
        mkdir ITK-build
        cd ITK-build
        cmake -DCMAKE_C_COMPILER:FILEPATH="${{ matrix.c-compiler }}" -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE:STRING=${{ matrix.cmake-build-type }} -DBUILD_EXAMPLES=OFF -DBUILD_TESTING:BOOL=OFF -DITK_LEGACY_REMOVE=ON -GNinja ../ITK-source
        ninja
        
    - name: Build ITK
      if: steps.cache.outputs.cache-hit != 'true' && startsWith(matrix.os, 'windows')
      run: |
        mkdir ITK-build
        cd ITK-build
        call "${{ matrix.vcvars64 }}"
        cmake -DCMAKE_C_COMPILER:FILEPATH="${{ matrix.c-compiler }}" -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE:STRING=${{ matrix.cmake-build-type }} -DBUILD_EXAMPLES=OFF -DBUILD_TESTING:BOOL=OFF -GNinja ../ITK-source
        ninja
      shell: cmd
      
    - name: Install requirements of PythonTests
      run: |
        python -m pip install -r ${{ github.workspace }}/Elastix-source/Testing/PythonTests/requirements.txt

    - name: Configure CTest script
      shell: bash
      run: |
        operating_system="${{ matrix.os }}"
        cat > dashboard.cmake << EOF
        set(CTEST_SITE "GitHubActions")
        file(TO_CMAKE_PATH "\$ENV{GITHUB_WORKSPACE}" CTEST_DASHBOARD_ROOT)
        file(TO_CMAKE_PATH "\$ENV{GITHUB_WORKSPACE}/Elastix-source" CTEST_SOURCE_DIRECTORY)
        file(TO_CMAKE_PATH "\$ENV{GITHUB_WORKSPACE}/Elastix-build" CTEST_BINARY_DIRECTORY)
        set(dashboard_source_name "${GITHUB_REPOSITORY}")
        set(branch "${GITHUB_REF#refs/heads/}")
        set(sha "${GITHUB_SHA}")
        set(dashboard_model "Experimental")
        set(CTEST_BUILD_NAME "${GITHUB_REPOSITORY}-${operating_system}-\${branch}-\${sha}")
        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(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
        ELASTIX_USE_GTEST:BOOL=ON
        USE_ALL_COMPONENTS:BOOL=ON
        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_SOURCE_DIRECTORY}/Testing/Dashboard/elxCommonCDash.cmake)
        EOF
        cat dashboard.cmake

    - name: Test MacOs
      if: startsWith(matrix.os, 'macos')
      run: |
       ctest --output-on-failure -VV -j 2 -E "elastix_run_example_COMPARE_IM|elastix_run_3DCT_lung.MI.bspline.ASGD.001_COMPARE_TP|elastix_run_3DCT_lung.NMI.bspline.ASGD.001_COMPARE_TP" -S dashboard.cmake
      
    - name: Test Windows
      if: startsWith(matrix.os, 'windows')
      run: |
        call "${{ matrix.vcvars64 }}"
        ctest --output-on-failure -VV -j 2 -E "elastix_run_example_COMPARE_IM|elastix_run_3DCT_lung.MI.bspline.ASGD.001_COMPARE_TP" -S dashboard.cmake
      shell: cmd

    - name: Test Ubuntu
      if: startsWith(matrix.os, 'ubuntu')
      run: |
        ctest --output-on-failure -VV -j 2 -E "elastix_run_example_COMPARE_IM|elastix_run_3DCT_lung.MI.bspline.ASGD.001_COMPARE_TP" -S dashboard.cmake
      
    - name: Build externalproject example
      if: ${{ !startsWith(matrix.os, 'windows') }}
      run: |
        mkdir externalproject-build
        cd externalproject-build
        cmake -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DElastix_DIR=${{ github.workspace }}/Elastix-build -GNinja ../Elastix-source/dox/externalproject
        ninja
        
    - name: Build externalproject example
      if: startsWith(matrix.os, 'windows')
      run: |
        mkdir externalproject-build
        cd externalproject-build
        call "${{ matrix.vcvars64 }}"
        cmake -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DElastix_DIR=${{ github.workspace }}/Elastix-build -GNinja ../Elastix-source/dox/externalproject
        ninja
      shell: cmd

    - name: Run externalproject example
      if: ${{ !startsWith(matrix.os, 'windows') }}
      run: |
        externalproject-build/elastix_translation_example

    - name: Run externalproject example
      if: startsWith(matrix.os, 'windows')
      run: |
        set path=${{ github.workspace }}\Elastix-build\bin
        externalproject-build\elastix_translation_example.exe
      shell: cmd
      
    - name: Prepare Artifacts Unix
      if: ${{ !startsWith(matrix.os, 'windows') }}
      shell: bash
      run: |
        mkdir bin
        mkdir lib
        mkdir uploads
        mv Elastix-build/bin/elastix bin
        mv Elastix-build/bin/transformix bin
        mv Elastix-build/bin/${{ matrix.ANNLib }} lib
        mv Elastix-build/bin/${{ matrix.ANNLib2 }} lib
        mv Elastix-source/NOTICE uploads
        mv Elastix-source/LICENSE uploads
        mv bin uploads
        mv lib uploads
      
    - name: Prepare Artifacts Windows
      if: startsWith(matrix.os, 'windows')
      shell: bash
      run: |
        mkdir uploads
        mv Elastix-source/NOTICE uploads
        mv Elastix-source/LICENSE uploads
        mv Elastix-build/bin/elastix.exe uploads
        mv Elastix-build/bin/transformix.exe uploads
        mv Elastix-build/bin/${{ matrix.ANNLib }} uploads
  
    - name: Publish Artifacts
      uses: actions/upload-artifact@v3
      with: 
        name: "${{ matrix.os }}"
        path: uploads
        
    - name: Login to Docker Hub
      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') && startsWith(matrix.os, 'ubuntu')
      uses: docker/login-action@v1
      with:
        username: ${{ secrets.DOCKER_HUB_USERNAME }}
        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

    - name: Build and push
      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') && startsWith(matrix.os, 'ubuntu')     
      run: |
        mkdir output
        docker build -t superelastix/elastix:${GITHUB_REF#refs/tags/} .
        docker run -u $UID:$GROUPS --mount type=bind,source="$(pwd)"/output,target=/out -v "$(pwd)"/Elastix-source/Testing/Data:/elastix/ superelastix/elastix:${GITHUB_REF#refs/tags/} elastix -out /out/ -p /elastix/parameters.3D.NC.euler.ASGD.001.txt -f /elastix/3DCT_lung_baseline.mha -m /elastix/3DCT_lung_followup.mha
        docker push superelastix/elastix:${GITHUB_REF#refs/tags/}