Allow subsetting simulation conditions in simulate_petab (#2199) #6002
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| name: Benchmark Collection | |
| on: | |
| push: | |
| branches: | |
| - develop | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| - develop | |
| merge_group: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '48 4 * * *' | |
| jobs: | |
| build: | |
| name: Benchmark Collection | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [ "3.9" ] | |
| extract_subexpressions: ["true", "false"] | |
| env: | |
| AMICI_EXTRACT_CSE: ${{ matrix.extract_subexpressions }} | |
| steps: | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 20 | |
| # install dependencies | |
| - name: apt | |
| run: | | |
| sudo apt-get update \ | |
| && sudo apt-get install -y swig libatlas-base-dev | |
| - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH | |
| # install AMICI | |
| - name: Create AMICI sdist | |
| run: | | |
| pip3 install build && cd python/sdist && python3 -m build --sdist | |
| - name: Install AMICI sdist | |
| run: | | |
| pip3 install --user petab[vis] && \ | |
| AMICI_PARALLEL_COMPILE=2 pip3 install -v --user \ | |
| $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis] | |
| # retrieve test models | |
| - name: Download and test benchmark collection | |
| run: | | |
| git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \ | |
| && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \ | |
| && AMICI_PARALLEL_COMPILE=2 tests/benchmark-models/test_benchmark_collection.sh | |
| # run gradient checks | |
| - name: Run Gradient Checks | |
| run: | | |
| pip install git+https://github.com/ICB-DCM/fiddy.git \ | |
| && cd tests/benchmark-models && pytest ./test_petab_benchmark.py | |
| # upload results | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: computation times | |
| path: | | |
| tests/benchmark-models/computation_times.csv | |
| tests/benchmark-models/computation_times.png |