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ElastixGitHubActions.yml
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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: [macos-10.15, ubuntu-18.04, windows-2019]
include:
- os: ubuntu-18.04
c-compiler: "gcc"
cxx-compiler: "g++"
itk-git-tag: "v5.2.0"
cmake-build-type: "Release"
ANNLib: "libANNlib-5.0.so"
ANNLib2: "libANNlib-5.0.so.1"
- os: windows-2019
c-compiler: "cl.exe"
cxx-compiler: "cl.exe"
itk-git-tag: "v5.2.0"
cmake-build-type: "Release"
ANNLib: "ANNlib-5.0.dll"
vcvars64: "C:/Program Files (x86)/Microsoft Visual Studio/2019/Enterprise/VC/Auxiliary/Build/vcvars64.bat"
- os: macos-10.15
c-compiler: "clang"
cxx-compiler: "clang++"
itk-git-tag: "v5.2.0"
cmake-build-type: "Release"
ANNLib: "libANNlib-5.0.1.dylib"
ANNLib2: "libANNlib-5.0.dylib"
steps:
- uses: actions/checkout@v2
- 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@v2
id: cache
with:
path: |
ITK-build
ITK-source
key: ${{ matrix.itk-git-tag }}-${{ matrix.os }}-${{ matrix.cmake-build-type }}
- name: Set up Python 3.7
uses: actions/setup-python@v1
with:
python-version: 3.7
- 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/[email protected]
- 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 ${{ matrix.itk-git-tag }}
- name: Build ITK
if: steps.cache.outputs.cache-hit != 'true' && matrix.os != 'windows-2019'
run: |
mkdir ITK-build
cd ITK-build
cmake -DCMAKE_C_COMPILER:FILEPATH="${{ 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' && matrix.os == 'windows-2019'
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: 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} ${{ matrix.cxx-compiler }})
if(WIN32)
set(ENV{PATH} "\${CTEST_DASHBOARD_ROOT}/ITK-build/bin;\$ENV{PATH}")
endif()
set(dashboard_cache "
ITK_DIR:PATH=\${CTEST_DASHBOARD_ROOT}/ITK-build
ELASTIX_USE_GTEST:BOOL=ON
USE_ALL_COMPONENTS:BOOL=ON
BUILD_TESTING:BOOL=ON
")
string(TIMESTAMP build_date "%Y-%m-%d")
message("CDash Build Identifier: \${build_date} \${CTEST_BUILD_NAME}")
message("CTEST_SITE= \${CTEST_SITE}")
include(\${CTEST_SOURCE_DIRECTORY}/Testing/Dashboard/elxCommonCDash.cmake)
EOF
cat dashboard.cmake
- name: Test MacOs
if: matrix.os == 'macos-10.15'
run: |
ctest --output-on-failure -VV -j 2 -E "elastix_run_example_COMPARE_IM|elastix_run_3DCT_lung.MI.bspline.ASGD.001_COMPARE_TP|elastix_run_3DCT_lung.NMI.bspline.ASGD.001_COMPARE_TP" -S dashboard.cmake
- name: Test Windows
if: matrix.os == 'windows-2019'
run: |
call "${{ 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: matrix.os == 'ubuntu-18.04'
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: matrix.os != 'windows-2019'
run: |
mkdir externalproject-build
cd externalproject-build
cmake -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DElastix_DIR=${{ github.workspace }}/Elastix-build -GNinja ../Elastix-source/dox/externalproject
ninja
- name: Build externalproject example
if: matrix.os == 'windows-2019'
run: |
mkdir externalproject-build
cd externalproject-build
call "${{ matrix.vcvars64 }}"
cmake -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DElastix_DIR=${{ github.workspace }}/Elastix-build -GNinja ../Elastix-source/dox/externalproject
ninja
shell: cmd
- name: Run externalproject example
if: matrix.os != 'windows-2019'
run: |
externalproject-build/elastix_translation_example
- name: Run externalproject example
if: matrix.os == 'windows-2019'
run: |
set path=${{ github.workspace }}\Elastix-build\bin
externalproject-build\elastix_translation_example.exe
shell: cmd
- name: Prepare Artifacts Unix
if: matrix.os != 'windows-2019'
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: matrix.os == 'windows-2019'
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/${{ matrix.ANNLib }} uploads
- name: Publish Artifacts
uses: actions/upload-artifact@v2
with:
name: "${{ matrix.os }}"
path: uploads
- name: Login to Docker Hub
if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') && matrix.os == 'ubuntu-18.04'
uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKER_HUB_USERNAME }}
password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
- name: Build and push
if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') && matrix.os == 'ubuntu-18.04'
run: |
mkdir output
docker build -t superelastix/elastix:${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/}