Support for PEtab SciML in jax #11398
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| name: C++/Python Tests | |
| on: | |
| push: | |
| merge_group: | |
| workflow_dispatch: | |
| pull_request: | |
| branches: | |
| - master | |
| - develop | |
| jobs: | |
| ubuntu-cpp-python-tests: | |
| name: C++/Python tests Ubuntu | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| python-version: [ "3.11" ] | |
| steps: | |
| - name: Cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.cache/pooch | |
| key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }} | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/checkout@v4 | |
| - run: git fetch --prune --unshallow | |
| - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV | |
| - name: Set up AMICI C++ libraries | |
| uses: ./.github/actions/setup-amici-cpp | |
| - name: Install libsuitesparse-dev | |
| # We don't need libsuitesparse-dev, but let's have it installed, | |
| # to ensure that its presence does not break the build | |
| run: sudo apt-get install -y libsuitesparse-dev | |
| - name: C++ tests | |
| run: scripts/run-cpp-tests.sh | |
| - name: Install python package | |
| run: scripts/installAmiciSource.sh | |
| - name: Check OpenMP support | |
| run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())" | |
| - name: Python tests (part 1) | |
| run: | | |
| source venv/bin/activate \ | |
| && pytest \ | |
| --ignore-glob=*petab* \ | |
| --ignore-glob=*test_splines.py \ | |
| --ignore-glob=*test_splines_short.py \ | |
| --ignore-glob=*test_pysb.py \ | |
| --cov=amici \ | |
| --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \ | |
| --cov-append \ | |
| --durations=10 \ | |
| ${AMICI_DIR}/python/tests | |
| - name: Python tests splines | |
| if: ${{ github.base_ref == 'master' || github.event.merge_group.base_ref == 'master'}} | |
| run: | | |
| source venv/bin/activate \ | |
| && pytest \ | |
| --cov=amici \ | |
| --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \ | |
| --cov-append \ | |
| --durations=10 \ | |
| ${AMICI_DIR}/python/tests/test_splines.py | |
| - 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: build/coverage_py.xml | |
| flags: python | |
| fail_ci_if_error: true | |
| verbose: true | |
| - name: Capture coverage info (lcov) | |
| run: | | |
| lcov --compat-libtool --no-external \ | |
| -d ${AMICI_DIR}/build/CMakeFiles/amici.dir/src \ | |
| -b ${AMICI_DIR} -c -o coverage_cpp.info \ | |
| && lcov --compat-libtool --no-external \ | |
| -d ${AMICI_DIR}/python/sdist/build/temp_amici/CMakeFiles/amici.dir/src \ | |
| -b ${AMICI_DIR}/python/sdist -c -o coverage_py.info \ | |
| && lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info | |
| - name: Codecov CPP | |
| if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev' | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: coverage.info | |
| flags: cpp | |
| fail_ci_if_error: true | |
| - name: Run sonar-scanner | |
| if: ${{ env.SONAR_TOKEN != '' }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} | |
| run: | | |
| sonar-scanner \ | |
| -Dsonar.cfamily.build-wrapper-output=bw-output \ | |
| -Dsonar.projectVersion="$(git describe --abbrev=4 --dirty=-dirty --always --tags | tr -d '\n')" | |
| ubuntu-python-tests: | |
| name: Python tests Ubuntu | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| python-version: [ "3.10" ] | |
| steps: | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.cache/pooch | |
| key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }} | |
| - uses: actions/checkout@v4 | |
| - run: git fetch --prune --unshallow | |
| - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV | |
| - name: Set up AMICI C++ libraries | |
| uses: ./.github/actions/setup-amici-cpp | |
| - name: Install python package | |
| run: scripts/installAmiciSource.sh | |
| - name: Python tests | |
| run: | | |
| source venv/bin/activate \ | |
| && pytest \ | |
| --cov=amici \ | |
| --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \ | |
| --cov-append \ | |
| --durations=10 \ | |
| ${AMICI_DIR}/python/tests/test_pysb.py \ | |
| ${AMICI_DIR}/python/tests/test_splines_short.py | |
| - 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: build/coverage_py.xml | |
| flags: python | |
| fail_ci_if_error: true | |
| verbose: true | |
| - name: Capture coverage info (lcov) | |
| run: | | |
| lcov --compat-libtool --no-external \ | |
| -d ${AMICI_DIR}/build/CMakeFiles/amici.dir/src \ | |
| -b ${AMICI_DIR} -c -o coverage_cpp.info \ | |
| && lcov --compat-libtool --no-external \ | |
| -d ${AMICI_DIR}/python/sdist/build/temp_amici/CMakeFiles/amici.dir/src \ | |
| -b ${AMICI_DIR}/python/sdist -c -o coverage_py.info \ | |
| && lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info | |
| - name: Codecov CPP | |
| if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev' | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: coverage.info | |
| flags: cpp_python | |
| fail_ci_if_error: true | |
| - name: Run sonar-scanner | |
| if: ${{ env.SONAR_TOKEN != '' }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} | |
| run: | | |
| sonar-scanner \ | |
| -Dsonar.cfamily.build-wrapper-output=bw-output \ | |
| -Dsonar.projectVersion="$(git describe --abbrev=4 --dirty=-dirty --always --tags | tr -d '\n')" | |
| ubuntu-notebook-tests: | |
| name: Notebook tests Ubuntu | |
| runs-on: ubuntu-22.04 | |
| 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 }} | |
| - name: Cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.cache/pooch | |
| key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }} | |
| - uses: actions/checkout@v4 | |
| - run: git fetch --prune --unshallow | |
| - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV | |
| - name: Set up AMICI C++ libraries | |
| uses: ./.github/actions/setup-amici-cpp | |
| - name: Install python package | |
| run: scripts/installAmiciSource.sh | |
| - name: example notebooks | |
| run: scripts/runNotebook.sh python/examples/example_*/ | |
| - name: doc notebooks | |
| run: scripts/runNotebook.sh documentation/GettingStarted.ipynb | |
| # TODO: Include notebooks in coverage report | |
| macos_cpp_py: | |
| name: Tests MacOS C++/Python | |
| runs-on: macos-latest | |
| env: | |
| PYTHONFAULTHANDLER: "1" | |
| steps: | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: actions/checkout@v4 | |
| - run: git fetch --prune --unshallow | |
| - name: Install dependencies | |
| uses: ./.github/actions/install-macos-dependencies | |
| - name: homebrew | |
| run: brew install cppcheck | |
| - name: Build AMICI | |
| run: scripts/buildAll.sh | |
| - name: Install python package | |
| run: scripts/installAmiciSource.sh | |
| - name: Check OpenMP support | |
| run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())" | |
| - name: cppcheck | |
| run: scripts/run-cppcheck.sh | |
| - name: C++ tests | |
| run: scripts/run-cpp-tests.sh | |
| - name: Get Pooch Cache Directory | |
| id: get-pooch-cache | |
| run: | | |
| echo "pooch-cache=$(source venv/bin/activate && python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV | |
| - name: Cache Pooch Directory | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.pooch-cache }} | |
| key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }} | |
| - name: Python tests | |
| run: | | |
| # ignore warnings until https://github.com/swig/swig/issues/3061 is resolved | |
| scripts/run-python-tests.sh -W ignore:: \ | |
| test_pregenerated_models.py \ | |
| test_splines_short.py \ | |
| test_misc.py | |
| macos_python: | |
| name: Tests MacOS Python | |
| runs-on: macos-latest | |
| env: | |
| PYTHONFAULTHANDLER: "1" | |
| steps: | |
| - name: Cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/Library/Caches/pooch | |
| key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }} | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: actions/checkout@v4 | |
| - run: git fetch --prune --unshallow | |
| - name: Install dependencies | |
| uses: ./.github/actions/install-macos-dependencies | |
| - name: Install python package | |
| run: | | |
| pip show numpy > /dev/null || python3 -m pip install numpy | |
| scripts/installAmiciSource.sh | |
| - name: Check OpenMP support | |
| run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())" | |
| - name: Get BioNetGen | |
| run: scripts/buildBNGL.sh | |
| - name: Get Pooch Cache Directory | |
| id: get-pooch-cache | |
| run: | | |
| echo "pooch-cache=$(source venv/bin/activate && python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV | |
| - name: Cache Pooch Directory | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.pooch-cache }} | |
| key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }} | |
| - name: Install PEtab benchmark collection | |
| run: | | |
| git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \ | |
| && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \ | |
| && source venv/bin/activate && python -m pip install -e $BENCHMARK_COLLECTION/../src/python | |
| - name: Python tests | |
| run: | | |
| # ignore warnings until https://github.com/swig/swig/issues/3061 is resolved | |
| scripts/run-python-tests.sh -W ignore:: \ | |
| --ignore=test_pregenerated_models.py \ | |
| --ignore=test_splines_short.py \ | |
| --ignore=test_misc.py |