PEtab: Fix initial state from condition table #1387
Workflow file for this run
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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: Test benchmark collection models | |
| on: [push, pull_request, workflow_dispatch] | |
| jobs: | |
| container: | |
| runs-on: ubuntu-latest | |
| container: ghcr.io/icb-dcm/custom_ci_image:master | |
| name: benchmark models | |
| 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 Benchmark model tests | |
| - name: Benchmark models --- requirements | |
| run: | | |
| sudo apt install bc \ | |
| && $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \ | |
| pip3 install shyaml | |
| - name: Benchmark models --- repository | |
| env: | |
| BM_REPO_URL: https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git | |
| run: | | |
| cd $PARPE_BASE/benchmark_collection \ | |
| && git clone --depth 1 $BM_REPO_URL \ | |
| && echo "BENCHMARK_COLLECTION=$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" >> $GITHUB_ENV \ | |
| && . $PARPE_BASE/build/venv/bin/activate \ | |
| && python -m pip install -e Benchmark-Models-PEtab/src/python | |
| - name: Benchmark models --- tests | |
| run: | | |
| cd $PARPE_BASE/benchmark_collection \ | |
| && . $PARPE_BASE/build/venv/bin/activate \ | |
| && python -m pip uninstall -y petab \ | |
| && python -m pip install https://github.com/PEtab-dev/libpetab-python/archive/develop.zip \ | |
| && python priors_to_measurements.py \ | |
| && AMICI_PARALLEL_COMPILE="" ./all.sh |