parpe_tests.yml

# https://help.github.com/en/actions/reference/workflow-syntax-for-github-actions
# https://help.github.com/en/actions/configuring-and-managing-workflows/using-environment-variables
name: parPE tests
on:
  push:
  pull_request:
  workflow_dispatch:
  schedule:
    - cron:  '48 4 * * *'

jobs:
  container:
    runs-on: ubuntu-latest
    container: ghcr.io/icb-dcm/custom_ci_image:master
    name: parPE tests
    env:
      # mpiexec prefix for running tests
      # If we are running in docker, we generally don't have SYS_PTRACE
      #  permissions  and thus, cannot use vader. Also disable Infiniband.
      PARPE_TESTS_MPIEXEC: mpiexec -n 5 --oversubscribe --allow-run-as-root --mca btl_vader_single_copy_mechanism none --mca btl ^openib --mca oob_tcp_if_include lo --mca btl_tcp_if_include lo --mca orte_base_help_aggregate 0

    steps:
    - uses: actions/checkout@master
    - name: chown checkout directory
      # https://github.com/actions/runner/issues/2033
      run: chown -R $(id -u):$(id -g) $PWD
    - run: git fetch --prune --unshallow

    - run: echo "PARPE_BASE=$(pwd)" >> $GITHUB_ENV
    - run: echo "PARPE_BUILD=${PARPE_BASE}/build" >> $GITHUB_ENV
    - run: echo "AMICI_PATH=${PARPE_BASE}/deps/AMICI/" >> $GITHUB_ENV

    # sonar cloud
    - run: echo "SONAR_SCANNER_VERSION=5.0.1.3006" >> $GITHUB_ENV
    - run: echo "SONAR_SCANNER_HOME=/root/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
    - run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
    - run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH
    - run: echo "/root/.sonar/build-wrapper-linux-x86" >> $GITHUB_PATH

    - name: Info
      run: lsb_release -a && printenv

      # Build dependencies
    - run: sudo apt-get update && sudo apt-get install -y pipx && pipx install cmake
    - run: echo "$HOME/.local/bin" >> $GITHUB_PATH
    - name: Install AMICI deps
      run: |
        cd $AMICI_PATH \
          && scripts/buildSuiteSparse.sh \
          && scripts/buildSundials.sh

    - name: Install AMICI
      run: |
        cmake \
          -S ${AMICI_PATH} \
          -B ${AMICI_PATH}/build \
          -DCMAKE_BUILD_TYPE=Debug \
          -DENABLE_PYTHON=ON \
          -DBUILD_TESTS=OFF \
          -DCMAKE_PREFIX_PATH="${CMAKE_PREFIX_PATH};${AMICI_PATH}/ThirdParty/SuiteSparse/install" \
          && cmake --build "${AMICI_PATH}/build" --parallel -- VERBOSE=1

    - name: Install parPE Python deps
      run: |
        pip install -r ${PARPE_BASE}/python/requirements.txt \
          && sudo apt install lcov

    - name: "Install parPE deps: fides"
      run: |
        sudo apt install libspdlog-dev && ${PARPE_BASE}/ThirdParty/installFides.sh

    - name: Configure parPE
      run: |
        cmake \
          -S"${PARPE_BASE}" \
          -B"${PARPE_BUILD}" \
          -DCMAKE_CXX_FLAGS="-Wall -Wextra -Werror -Wno-deprecated-copy" \
          -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \
          -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
          -DGCOV_REPORT=TRUE \
          -DBUILD_TESTING=TRUE \
          -DPARPE_ENABLE_FIDES=TRUE

    - name: Build parPE
      # with sonar build wrapper
      run: |
        build-wrapper-linux-x86-64 --out-dir bw-output \
          cmake --build "${PARPE_BUILD}" --parallel -- VERBOSE=1

    - name: Run parPE python unittests
      run: |
        $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \
          pip install pytest-cov \
        && $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \
          pytest \
            --cov-report=xml:$PARPE_BUILD/coverage_py.xml \
            --cov=parpe --cov-append \
            $PARPE_BASE/python/tests/

    # Redundant with parpe_coverage_cobertura
    #- name: Run CTEST
    #  run: cd ${PARPE_BUILD} && CTEST_OUTPUT_ON_FAILURE=1 make test

    - name: Create coverage report
      run: |
        cd ${PARPE_BUILD} \
          && CTEST_OUTPUT_ON_FAILURE=1 make parpe_coverage \
          && make ExperimentalCoverage

    - name: Cache sonar files
      id: cache-sonar
      uses: actions/cache@v4
      with:
        path: sonar_cache
        key: ${{ runner.os }}-sonar_cache

    - name: Run sonar-scanner
      if: ${{ env.SONAR_TOKEN != '' }}
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
      run: |
        sonar-scanner \
         -Dsonar.cfamily.build-wrapper-output=bw-output \
         -Dsonar.projectVersion="$(git describe --abbrev=4 --dirty=-dirty --always --tags | tr -d '\n')"

    - name: Run example notebooks
      run: |
        misc/run_notebook.sh \
          examples/parpeamici/steadystate/parpeExampleSteadystateBasic.ipynb \
          examples/parpeamici/steadystate/parpeExampleSteadystateHierarchical.ipynb

    - name: Run valgrind
      run: |
        cd ${PARPE_BUILD} \
          && if (CTEST_OUTPUT_ON_FAILURE=1 make ExperimentalMemCheck); \
              then cat Testing/Temporary/MemoryChecker.*.log; \
              else cat Testing/Temporary/MemoryChecker.*.log; exit 1; fi