c-cpp.yml

name: native
on:
  push:
    branches: [master]
    paths-ignore:
    - 'docker/Dockerfile'
    - 'docker/docker*.yml'
    - '**.md'
    - 'VirtualBox/**'
    - '.github/workflows/*docker*'
    - 'CITATION.cff'
    - '.mailmap'
    - 'NOTICE.txt'
    - 'LICENSE.txt'
  pull_request:
    branches: [master]
    paths-ignore:
    - 'docker/Dockerfile'
    - 'docker/docker*.yml'
    - '**.md'
    - 'VirtualBox/**'
    - '.github/workflows/*docker*'
    - 'CITATION.cff'
    - '.mailmap'
    - 'NOTICE.txt'
    - 'LICENSE.txt'
  workflow_dispatch:
    inputs:
      tmate:
        description: Debug with tmate ssh session
        type: boolean
        default: false
        required: true
jobs:
  test:
    runs-on: ${{ matrix.os }}
    defaults: {run: {shell: 'bash -el {0}'}}
    env:
      COMPILER: gcc
      BUILD_TYPE: Release
    strategy:
      matrix:
        include:
        - cxx-ver: 9
          flags: -devel -armadillo -boost -fftw3 +hdf5 -swig
          os: ubuntu-22.04
        - cxx-ver: 9
          flags: -devel -armadillo -boost +fftw3 +hdf5 +swig
          os: ubuntu-22.04
        #- cxx-ver: 9
        #  flags: -devel -armadillo +boost -fftw3 +hdf5 -swig
        #  os: ubuntu-latest
        - cxx-ver: 9
          flags: -devel -armadillo -boost -fftw3 +hdf5 -swig +gtest
          os: ubuntu-22.04
        - cxx-ver: 11
          flags: +devel +armadillo -boost -fftw3 +hdf5 -swig -root
          os: ubuntu-22.04
        - cxx-ver: 11
          flags: -devel +armadillo -boost -fftw3 +hdf5 -swig -root
          os: ubuntu-22.04
      fail-fast: false # don't terminate matrix if one job fails
    steps:
    - uses: actions/checkout@v6
    - if: contains(matrix.os, fromJSON('["ubuntu","macos"]'))
      name: increase disk space
      run: sudo .github/workflows/GHA_increase_disk_space.sh
    - uses: conda-incubator/setup-miniconda@v4
      with:
        auto-activate: true
        activate-environment: ""
        channels: conda-forge,defaults
        mamba-version: "*"
    - id: deps
      name: install dependencies
      working-directory: docker
      run: |
        conda env update -n base -f requirements.yml
        echo "Python_ROOT_DIR=$CONDA_PREFIX" >> $GITHUB_ENV
        echo "Python3_ROOT_DIR=$CONDA_PREFIX" >> $GITHUB_ENV
        sudo ./raw-ubuntu.sh
        sudo ./build_system-ubuntu.sh
        sudo ./build_essential-ubuntu.sh
        sudo ./build_gadgetron-ubuntu.sh
    - name: optionally install ROOT
      run: |
        sh -ex
        if [[ " ${{ matrix.flags }} " =~ " -root " ]]; then
            # Install ROOT (warning: currently only valid on Ubuntu)
            ROOT_file=root_v6.28.12.Linux-ubuntu20-x86_64-gcc9.4.tar.gz
            wget https://root.cern/download/"$ROOT_file"
            tar -xzf "$ROOT_file"
            rm "$ROOT_file"
            source root/bin/thisroot.sh
            echo ROOT_DIR="$ROOTSYS/cmake" >> $GITHUB_ENV
            echo ROOTSYS="$ROOTSYS" >> $GITHUB_ENV
            echo
            # work-around problem with problem with Vdt for ROOT version pre-6.30.04 as per https://github.com/root-project/root/pull/14178
            echo Vdt_ROOT="$ROOTSYS" >> $GITHUB_ENV
            # thisroot modifies the following
            case ${{matrix.os}} in
             (ubuntu*)
                echo LD_LIBRARY_PATH="${CMAKE_INSTALL_PREFIX}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
                echo PATH="$PATH" >> $GITHUB_ENV
                ;;
              (macOS*) # future-proof
                echo DYLD_FALLBACK_LIBRARY_PATH="${CMAKE_INSTALL_PREFIX}/lib:$DYLD_FALLBACK_LIBRARY_PATH" >> $GITHUB_ENV
                echo PATH="$PATH" >> $GITHUB_ENV
                ;;
              (windows*) # future-proof
                echo PATH="${CMAKE_INSTALL_PREFIX}/lib:${CMAKE_INSTALL_PREFIX}/bin:$PATH" >> $GITHUB_ENV
                ;;
            esac
        fi
    - uses: hendrikmuhs/ccache-action@v1
      with:
        key: ${{ matrix.os }}-${{ env.COMPILER }}-${{ matrix.cxx-ver }}-${{ env.BUILD_TYPE }}-${{ github.ref_name }}-${{ github.run_id }}
        restore-keys: |
          ${{ matrix.os }}-${{ env.COMPILER }}-${{ matrix.cxx-ver }}-${{ env.BUILD_TYPE }}-${{ github.ref_name }}
          ${{ matrix.os }}-${{ env.COMPILER }}-${{ matrix.cxx-ver }}-${{ env.BUILD_TYPE }}
        append-timestamp: false
    - name: export CC CXX
      run: |
        set -ex
        if test '${{ env.COMPILER }}' = clang; then
          CC=clang
          CXX=clang++
        elif test '${{ env.COMPILER }}' = gcc; then
          CC=gcc
          CXX=g++
        fi
        if test -n '${{ matrix.cxx-ver }}'; then
          CC=${CC}-${{ matrix.cxx-ver }}
          CXX=${CXX}-${{ matrix.cxx-ver }}
          sudo apt install -yq ${CXX} ${CC}
        fi
        # make available to jobs below
        echo "CC=$CC" >> $GITHUB_ENV
        echo "CXX=$CXX" >> $GITHUB_ENV
    - name: cmake -S .
      env:
        CMAKE_BUILD_TYPE: ${{ env.BUILD_TYPE }}
      run: |
        set -ex
        export PATH="/usr/lib/ccache:/usr/local/opt/ccache/libexec:$PATH"
        export superbuild=`pwd`
        BUILD_FLAGS="-DCMAKE_INSTALL_PREFIX=~/install -DPYVER=3 -DUSE_SYSTEM_RocksDB:BOOL=OFF -DBUILD_TESTING_Gadgetron:BOOL=ON -DSTIR_DISABLE_HDF5:BOOL=ON -DUSE_ITK:BOOL=ON -DBUILD_CIL:BOOL=ON -DBUILD_siemens_to_ismrmrd:BOOL=ON"
        [[ " ${{ matrix.flags }} " =~ " +armadillo " ]] && BUILD_FLAGS="${BUILD_FLAGS} -DUSE_SYSTEM_Armadillo:BOOL=OFF"
        [[ " ${{ matrix.flags }} " =~ " -armadillo " ]] && BUILD_FLAGS="${BUILD_FLAGS} -DUSE_SYSTEM_Armadillo:BOOL=ON"
        [[ " ${{ matrix.flags }} " =~ " +boost " ]] && BUILD_FLAGS="${BUILD_FLAGS} -DUSE_SYSTEM_Boost:BOOL=OFF"
        [[ " ${{ matrix.flags }} " =~ " -boost " ]] && BUILD_FLAGS="${BUILD_FLAGS} -DUSE_SYSTEM_Boost:BOOL=ON"
        [[ " ${{ matrix.flags }} " =~ " +fftw3 " ]] && BUILD_FLAGS="${BUILD_FLAGS} -DUSE_SYSTEM_FFTW3:BOOL=OFF"
        [[ " ${{ matrix.flags }} " =~ " -fftw3 " ]] && BUILD_FLAGS="${BUILD_FLAGS} -DUSE_SYSTEM_FFTW3:BOOL=ON"
        [[ " ${{ matrix.flags }} " =~ " +hdf5 " ]] && BUILD_FLAGS="${BUILD_FLAGS} -DUSE_SYSTEM_HDF5:BOOL=OFF"
        [[ " ${{ matrix.flags }} " =~ " -hdf5 " ]] && BUILD_FLAGS="${BUILD_FLAGS} -DUSE_SYSTEM_HDF5:BOOL=ON"
        [[ " ${{ matrix.flags }} " =~ " +swig " ]] && BUILD_FLAGS="${BUILD_FLAGS} -DUSE_SYSTEM_SWIG:BOOL=OFF"
        [[ " ${{ matrix.flags }} " =~ " -swig " ]] && BUILD_FLAGS="${BUILD_FLAGS} -DUSE_SYSTEM_SWIG:BOOL=ON"
        [[ " ${{ matrix.flags }} " =~ " +gtest " ]] && BUILD_FLAGS="${BUILD_FLAGS} -DUSE_SYSTEM_GTest:BOOL=OFF"
        [[ " ${{ matrix.flags }} " =~ " -gtest " ]] && BUILD_FLAGS="${BUILD_FLAGS} -DUSE_SYSTEM_GTest:BOOL=ON"
        # note: SIRF needs CMP0074 with older versions of pre-built ROOT (see above)
        [[ " ${{ matrix.flags }} " =~ " -root " ]] && BUILD_FLAGS="${BUILD_FLAGS} -DUSE_ROOT:BOOL=ON -DUSE_SYSTEM_ROOT:BOOL=ON -DSIRF_EXTRA_CMAKE_ARGS=-DCMAKE_POLICY_DEFAULT_CMP0074=NEW"
        [[ " ${{ matrix.flags }} " =~ " +devel " ]] && BUILD_FLAGS="${BUILD_FLAGS} -DDEVEL_BUILD:BOOL=ON"
        [[ " ${{ matrix.flags }} " =~ " -devel " ]] && BUILD_FLAGS="${BUILD_FLAGS} -DDEVEL_BUILD:BOOL=OFF"
        cmake -G Ninja -S ${GITHUB_WORKSPACE} -B ./build ${BUILD_FLAGS}
    - run: cmake --build ./build
    # tmate ssh debugging
    - if: github.event_name == 'workflow_dispatch' && github.event.inputs.tmate == 'true'
      uses: mxschmitt/action-tmate@v3
      timeout-minutes: 15
    - if: failure()
      name: Upload build log files for debugging
      uses: actions/upload-artifact@v7
      with:
        name: logs-${{ matrix.cxx-ver }}-${{ matrix.flags }}-${{ matrix.os }}
        path: ${{ github.workspace }}/build/**/*.log
        retention-days: 7
    - name: pip install torch
      run: pip install torch --index-url https://download.pytorch.org/whl/cpu
    - name: ctest
      run: ./docker/ctest_sirf.sh