Support for PEtab SciML in jax #7942
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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: [ "3.11" ] | |
| extract_subexpressions: ["true", "false"] | |
| env: | |
| AMICI_EXTRACT_CSE: ${{ matrix.extract_subexpressions }} | |
| steps: | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 20 | |
| - name: Install apt dependencies | |
| uses: ./.github/actions/install-apt-dependencies | |
| - run: echo "${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="" pip3 install -v --user \ | |
| $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis,jax] | |
| - name: Install test dependencies | |
| run: | | |
| python3 -m pip uninstall -y petab && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@develop \ | |
| && python3 -m pip install -U sympy \ | |
| && python3 -m pip install git+https://github.com/ICB-DCM/fiddy.git | |
| - name: Download benchmark collection | |
| run: | | |
| pip install git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python | |
| - name: Run tests | |
| env: | |
| AMICI_PARALLEL_COMPILE: "" | |
| run: | | |
| cd tests/benchmark-models && pytest \ | |
| --durations=10 | |
| --cov=amici \ | |
| --cov-report=xml:"coverage_py.xml" \ | |
| --cov-append \ | |
| - name: Codecov Python | |
| if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev' | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: coverage_py.xml | |
| flags: python | |
| fail_ci_if_error: true | |
| verbose: true | |
| # collect & upload results | |
| - name: Aggregate results | |
| run: | | |
| cd tests/benchmark-models && python3 evaluate_benchmark.py | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: computation-times-${{ matrix.python-version }}-${{ matrix.extract_subexpressions }} | |
| path: | | |
| tests/benchmark-models/computation_times.csv | |
| tests/benchmark-models/computation_times.png |