AMICI: Fix potential out-of-bounds read in Model::checkFinite #1003
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| # 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 | |
| - name: Install AMICI deps | |
| run: | | |
| cd $AMICI_PATH \ | |
| && scripts/buildSuiteSparse.sh \ | |
| && scripts/buildSundials.sh | |
| - name: Install AMICI | |
| run: | | |
| cmake \ | |
| -S ${AMICI_PATH} \ | |
| -B ${AMICI_PATH}/build \ | |
| -DCMAKE_BUILD_TYPE=Debug \ | |
| -DENABLE_PYTHON=ON \ | |
| -DBUILD_TESTS=OFF \ | |
| && cmake --build "${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@v3 | |
| 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 |