Support for PEtab SciML in jax #6944
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| name: PEtab | |
| on: | |
| push: | |
| branches: | |
| - develop | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| - develop | |
| merge_group: | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| name: PEtab Testsuite | |
| runs-on: ubuntu-latest | |
| env: | |
| ENABLE_GCOV_COVERAGE: TRUE | |
| strategy: | |
| matrix: | |
| python-version: ["3.11"] | |
| steps: | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 20 | |
| - name: Install apt dependencies | |
| uses: ./.github/actions/install-apt-dependencies | |
| # install dependencies | |
| - name: apt | |
| run: | | |
| sudo apt-get update \ | |
| && sudo apt-get install -y python3-venv | |
| - name: Build BNGL | |
| run: scripts/buildBNGL.sh | |
| - run: | | |
| echo "${HOME}/.local/bin/" >> $GITHUB_PATH | |
| echo "${GITHUB_WORKSPACE}/tests/performance/" >> $GITHUB_PATH | |
| echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV | |
| # install AMICI | |
| - name: Install python package | |
| run: scripts/installAmiciSource.sh | |
| - name: Install petab | |
| run: | | |
| source ./venv/bin/activate \ | |
| && pip3 install wheel pytest shyaml pytest-cov pysb>=1.16 | |
| # retrieve test models | |
| - name: Download and install PEtab test suite | |
| run: | | |
| git clone --depth 1 --branch main \ | |
| https://github.com/PEtab-dev/petab_test_suite \ | |
| && source ./venv/bin/activate \ | |
| && cd petab_test_suite && pip3 install -e . | |
| - name: Install PEtab benchmark collection | |
| run: | | |
| git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \ | |
| && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \ | |
| && source venv/bin/activate && python -m pip install -e $BENCHMARK_COLLECTION/../src/python | |
| - name: Install petab | |
| run: | | |
| source ./venv/bin/activate \ | |
| && python3 -m pip uninstall -y petab \ | |
| && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@develop \ | |
| && python3 -m pip install git+https://github.com/pysb/pysb@master \ | |
| && python3 -m pip install sympy>=1.12.1 | |
| - name: Run PEtab-related unit tests | |
| run: | | |
| source ./venv/bin/activate \ | |
| && pytest --cov-report=xml:coverage.xml \ | |
| --cov=./ python/tests/test_*petab*.py python/tests/petab_/ | |
| # run test models | |
| - name: Run PEtab test suite | |
| run: | | |
| source ./venv/bin/activate \ | |
| && AMICI_PARALLEL_COMPILE="" pytest -v \ | |
| --cov-report=xml:coverage.xml \ | |
| --cov-append \ | |
| --cov=amici \ | |
| tests/petab_test_suite/ | |
| - name: Codecov | |
| if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev' | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: coverage.xml | |
| flags: petab | |
| fail_ci_if_error: true |