Update AMICI to v0.27.0 #1304
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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: PEtab test suite | |
| on: [push, pull_request, workflow_dispatch] | |
| jobs: | |
| container: | |
| runs-on: ubuntu-latest | |
| container: ghcr.io/icb-dcm/custom_ci_image:master | |
| name: PEtab test suite | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: chown checkout directory | |
| # https://github.com/actions/runner/issues/2033 | |
| run: chown -R $(id -u):$(id -g) $PWD | |
| - run: echo "PARPE_BASE=$(pwd)" >> $GITHUB_ENV | |
| - run: echo "PARPE_BUILD=${PARPE_BASE}/build" >> $GITHUB_ENV | |
| - run: echo "AMICI_PATH=${PARPE_BASE}/deps/AMICI/" >> $GITHUB_ENV | |
| # 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 ${AMICI_PATH}/build \ | |
| -DCMAKE_BUILD_TYPE=Debug \ | |
| -DENABLE_PYTHON=ON \ | |
| -DBUILD_TESTS=OFF \ | |
| -DCMAKE_PREFIX_PATH="${CMAKE_PREFIX_PATH};${AMICI_PATH}/ThirdParty/SuiteSparse/install" \ | |
| && cmake --build "${AMICI_PATH}/build" --parallel -- VERBOSE=1 | |
| - name: Configure parpe | |
| run: | | |
| cmake \ | |
| -S"${PARPE_BASE}" \ | |
| -B"${PARPE_BUILD}" \ | |
| -DPARPE_ENABLE_CERES=OFF \ | |
| -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \ | |
| -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \ | |
| -DGCOVR_REPORT=TRUE \ | |
| -DBUILD_TESTING=FALSE | |
| - name: Build parPE | |
| run: | | |
| cmake --build "${PARPE_BUILD}" --parallel -- VERBOSE=1 | |
| # Actual PEtab test suite | |
| - name: PEtab test suite --- requirements | |
| run: | | |
| $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \ | |
| pip3 install pytest-xdist | |
| - name: PEtab test suite --- repository | |
| env: | |
| PETAB_TEST_URL: https://github.com/PEtab-dev/petab_test_suite.git | |
| run: | | |
| cd $PARPE_BASE/ \ | |
| && git clone --depth 1 --branch main $PETAB_TEST_URL \ | |
| && $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \ | |
| pip3 install -e petab_test_suite | |
| - name: PEtab test suite --- tests | |
| run: | | |
| $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \ | |
| pytest -v -n 2 $PARPE_BASE/tests/petab-test-suite |