build-test.yml

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 -ev ${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