Python Tests #394
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| name: Python Tests | |
| on: | |
| push: | |
| branches: | |
| - develop | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '48 4 * * *' | |
| jobs: | |
| build: | |
| name: Python Version Matrix | |
| runs-on: ubuntu-22.04 | |
| continue-on-error: ${{ matrix.experimental }} | |
| env: | |
| AMICI_SKIP_CMAKE_TESTS: "TRUE" | |
| AMICI_PARALLEL_COMPILE: "" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - python-version: '3.10' | |
| experimental: false | |
| - python-version: '3.11' | |
| experimental: false | |
| - python-version: '3.12' | |
| experimental: false | |
| - python-version: '3.13' | |
| experimental: false | |
| steps: | |
| - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV | |
| - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 20 | |
| - name: Install apt dependencies | |
| uses: ./.github/actions/install-apt-dependencies | |
| - name: Build BNGL | |
| run: scripts/buildBNGL.sh | |
| - name: Install python package | |
| run: scripts/installAmiciSource.sh | |
| # install pysb before sympy to allow for sympy>=1.12 (https://github.com/pysb/pysb/commit/e83937cb8c74afc9b2fa96595b68464946745f33) | |
| - run: source venv/bin/activate && pip3 install git+https://github.com/pysb/pysb | |
| - run: source venv/bin/activate && pip3 install "sympy>1.12" | |
| - name: Get Pooch Cache Directory | |
| id: get-pooch-cache | |
| run: | | |
| echo "pooch-cache=$(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: | | |
| source venv/bin/activate \ | |
| && python3 -m pytest \ | |
| --durations=10 \ | |
| --ignore-glob=*petab* \ | |
| --ignore-glob=*test_splines.py ${AMICI_DIR}/python/tests |