Fix pSTIR python tests #876
Workflow file for this run
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| name: Build-test CI | |
| on: | |
| push: | |
| branches: [ master ] | |
| paths-ignore: | |
| - '**.md' | |
| - LICENSE.txt | |
| - NOTICE.txt | |
| - .mailmap | |
| - CITATION.cff | |
| pull_request: | |
| branches: [ master ] | |
| paths-ignore: | |
| - '**.md' | |
| - LICENSE.txt | |
| - NOTICE.txt | |
| - .mailmap | |
| - CITATION.cff | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| include: | |
| # remove Ubuntu 20.04 until #1179 | |
| # - os: ubuntu-20.04 | |
| # compiler: gcc | |
| # compiler_version: 8 | |
| # DEVEL_BUILD: "OFF" | |
| # EXTRA_BUILD_FLAGS: "-DUSE_ITK=ON" | |
| # CMAKE_BUILD_TYPE: "Release" | |
| - os: ubuntu-latest | |
| compiler: gcc | |
| compiler_version: 9 | |
| DEVEL_BUILD: "OFF" | |
| EXTRA_BUILD_FLAGS: "-DUSE_ITK=ON" | |
| CMAKE_BUILD_TYPE: "Release" | |
| - os: ubuntu-latest | |
| compiler: gcc | |
| compiler_version: 9 | |
| DEVEL_BUILD: "ON" | |
| EXTRA_BUILD_FLAGS: "-DUSE_ITK=ON" | |
| CMAKE_BUILD_TYPE: "Release" | |
| # need to upgrade Gadgetron before we can enable gcc 10 | |
| #- os: ubuntu-latest | |
| # compiler: gcc | |
| # compiler_version: 10 | |
| # DEVEL_BUILD: "ON" | |
| # EXTRA_BUILD_FLAGS: "-DUSE_ITK=ON" | |
| # CMAKE_BUILD_TYPE: "Release" | |
| # let's run all of them, as opposed to aborting when one fails | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| - name: install_dependencies | |
| run: | |
| cd ${GITHUB_WORKSPACE}; | |
| git clone https://github.com/SyneRBI/SIRF-SuperBuild --recursive -b master; | |
| cd SIRF-SuperBuild/docker; | |
| sudo bash raw-ubuntu.sh; | |
| sudo bash build_essential-ubuntu.sh; | |
| sudo bash build_python-ubuntu.sh; | |
| sudo bash build_gadgetron-ubuntu.sh; | |
| sudo bash build_system-ubuntu.sh; | |
| PYTHON_EXECUTABLE=python3 PYTHON_INSTALL_DIR=~/virtualenv bash user_python-ubuntu.sh; | |
| - name: ccache | |
| uses: hendrikmuhs/ccache-action@v1 | |
| with: | |
| key: ${{ matrix.os }}-${{ matrix.CMAKE_BUILD_TYPE }}-${{ matrix.DEVEL_BUILD }} | |
| - name: set_compiler_variables | |
| shell: bash | |
| run: | | |
| set -ex | |
| if test 'XX${{ matrix.compiler }}' = 'XXclang'; then | |
| CC="clang" | |
| CXX="clang++" | |
| elif test 'XX${{ matrix.compiler }}' = 'XXgcc'; then | |
| CC="gcc" | |
| CXX="g++" | |
| fi | |
| if test 'XX${{ matrix.compiler_version }}' != 'XX'; then | |
| CC=${CC}-${{ matrix.compiler_version }} | |
| CXX=${CXX}-${{ matrix.compiler_version }} | |
| sudo apt install -yq ${CXX} ${CC} | |
| fi | |
| export CC CXX | |
| # make available to jobs below | |
| echo CC="$CC" >> $GITHUB_ENV | |
| echo CXX="$CXX" >> $GITHUB_ENV | |
| - name: configure | |
| shell: bash | |
| run: | | |
| set -ex; | |
| export PATH="/usr/lib/ccache:/usr/local/opt/ccache/libexec:$PATH" | |
| cmake --version | |
| #echo "cmake flags ${{ matrix.CMAKE_BUILD_TYPE }} ${{ matrix.EXTRA_BUILD_FLAGS }}" | |
| BUILD_FLAGS="-DCMAKE_BUILD_TYPE=${{ matrix.CMAKE_BUILD_TYPE }} -DUSE_SYSTEM_ACE=ON -DUSE_SYSTEM_Armadillo=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DBUILD_siemens_to_ismrmrd=ON -DUSE_SYSTEM_SWIG=ON -DCMAKE_INSTALL_PREFIX=~/install -DPYVER=3"; | |
| BUILD_FLAGS="$BUILD_FLAGS -DSIRF_SOURCE_DIR:PATH=${GITHUB_WORKSPACE} -DDISABLE_GIT_CHECKOUT_SIRF=ON" | |
| # only test SIRF (others are tested in the SIRF-SuperBuild action) | |
| BUILD_FLAGS="$BUILD_FLAGS -DBUILD_TESTING_GADGETRON=OFF -DBUILD_TESTING_ISMRMRD=OFF" | |
| DEVEL_BUILD="-DDEVEL_BUILD=${{ matrix.DEVEL_BUILD }}" | |
| mkdir -p build/; | |
| cd build; | |
| source ~/virtualenv/bin/activate; | |
| cmake -S ../SIRF-SuperBuild ${BUILD_FLAGS} ${{ matrix.EXTRA_BUILD_FLAGS }} ${DEVEL_BUILD}; | |
| - name: build | |
| shell: bash | |
| run: | |
| cd ${GITHUB_WORKSPACE}/build; | |
| source ~/virtualenv/bin/activate; | |
| source ~/install/bin/env_sirf.sh; | |
| cmake --build . -j 2; | |
| - name: tests | |
| shell: bash | |
| run: | |
| bash -v ${GITHUB_WORKSPACE}/SIRF-SuperBuild/docker/ctest_sirf.sh | |
| - name: Coverage | |
| shell: bash | |
| run: | | |
| pwd | |
| source ~/virtualenv/bin/activate | |
| coverage combine .coverage-* | |
| coverage report | |
| - name: Coveralls | |
| uses: AndreMiras/coveralls-python-action@develop | |
| with: | |
| parallel: true | |
| flag-name: python test | |
| debug: true | |
| coveralls_finish: | |
| needs: build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Coveralls Finished | |
| uses: AndreMiras/coveralls-python-action@develop | |
| with: | |
| parallel-finished: true |