Avoid warnings for jacobians close to zero in the corona model #333
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| cache: pip | |
| - name: Run pre-commit | |
| uses: pre-commit/[email protected] | |
| tests: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| - ubuntu-latest | |
| # - windows-latest Reason: get it running on ubuntu-latest first | |
| # - macOS-latest Reason: get it running on ubuntu-latest first | |
| python-version: ["3.10",] | |
| name: Run tests | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up python | |
| id: setup-python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Poetry | |
| uses: snok/install-poetry@v1 | |
| with: | |
| version: 1.8.3 | |
| virtualenvs-create: true | |
| virtualenvs-in-project: true | |
| installer-parallel: true | |
| - name: Verify poetry installation | |
| run: poetry --version | |
| - name: Install amici dependencies | |
| run: | | |
| sudo apt update | |
| sudo apt install -y swig | |
| sudo apt install -y libblas-dev | |
| sudo apt install -y libatlas-base-dev | |
| sudo apt install -y libhdf5-dev | |
| - name: Load cached venv | |
| id: cached-poetry-dependencies | |
| uses: actions/cache@v4 | |
| with: | |
| path: .venv | |
| key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }} | |
| - name: Install dependencies | |
| run: poetry install --no-interaction --with=dev --extras=sbml | |
| if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' | |
| - name: Prepare cpp test | |
| run: | | |
| sudo apt install -y cmake | |
| sudo apt install -y libeigen3-dev | |
| sudo ln -s /usr/include/eigen3/Eigen /usr/include/Eigen | |
| sudo apt install -y pybind11-dev | |
| source $VENV | |
| cd eulerpi/examples/cpp | |
| mkdir build | |
| cd build | |
| cmake .. | |
| make -j | |
| - name: Run pytest | |
| run: | | |
| source $VENV | |
| pytest -v | |
| # TODO: coverage run creates segmentation fault on Github ci, but not locally. Debug it | |
| # - name: Run coverage | |
| # run: | | |
| # source $VENV | |
| # coverage run -m pytest -v | |
| # coverage report |