Aragog P-S refactor: PALEOS, JAX, energy-formulation, CI, PROTEUS integration #213
Workflow file for this run
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| name: Aragog CI Test Suite | |
| on: | |
| push: | |
| pull_request: | |
| branches: | |
| - main | |
| types: | |
| - opened | |
| - reopened | |
| - synchronize | |
| - ready_for_review | |
| workflow_dispatch: | |
| # Push and PR CI: unit tests only, on ubuntu + macos x py 3.11/3.12/3.13. | |
| # Targets <5 min wall. Slow tests (full multi-Myr CVODE solves) live in | |
| # the scheduled nightly workflow `nightly.yml` instead, alongside coverage | |
| # enforcement against the 85% floor. Running the slow suite or coverage | |
| # instrumentation on every push burns ~10 min CI time per commit and gives | |
| # no bug-finding signal that the unit suite doesn't already cover. | |
| # | |
| # Uses micromamba + conda-forge for the env so SUNDIALS, gfortran, and the | |
| # scikits-odes binary stack come prebuilt instead of being compiled from | |
| # source against stock apt/brew (which lag the SUNDIALS major version | |
| # scikits-odes-sundials 3.x requires). | |
| permissions: | |
| contents: read | |
| jobs: | |
| test-fast: | |
| name: Aragog-check (${{ matrix.os }}, py${{ matrix.python-version }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ["3.11", "3.12", "3.13"] | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v5 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up conda env (sundials from conda-forge) | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-name: aragog-test | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| sundials | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - name: Install pip-only test deps (scikits-odes-sundials builds against conda SUNDIALS) | |
| run: | | |
| pip install pytest pytest-xdist pytest-dependency ruff | |
| # Install scikits-odes-sundials directly (skip the scikits-odes | |
| # metapackage). This avoids scikits-odes-daepack, which is a | |
| # transitive Fortran dep with f2py incompatibility with numpy | |
| # 2.3+ and needs gfortran on macOS. aragog imports CVODE | |
| # directly from scikits_odes_sundials.cvode and has no use for | |
| # the DAE solvers in the metapackage. | |
| pip install scikits-odes-sundials jax equinox | |
| - name: Install aragog | |
| run: | | |
| pip install -e . | |
| - name: Fetch SPIDER EOS test data | |
| run: | | |
| mkdir -p /tmp/aragog-test-data | |
| curl -sL -o /tmp/spider_eos.tar.gz \ | |
| https://github.com/FormingWorlds/aragog/releases/download/test-data-v1/spider_eos_test_data.tar.gz | |
| tar xzf /tmp/spider_eos.tar.gz -C /tmp/aragog-test-data/ | |
| echo "ARAGOG_TEST_EOS_DIR=/tmp/aragog-test-data/spider_eos" >> $GITHUB_ENV | |
| - name: Lint with Ruff | |
| run: | | |
| ruff check src/ tests/ | |
| ruff format --check src/ tests/ | |
| - name: Run unit tests | |
| run: | | |
| pytest -m "unit and not slow" -n auto -o "addopts=" \ | |
| -o "junit_family=legacy" --junitxml=junit.xml | |
| - name: Upload test results to Codecov | |
| if: ${{ !cancelled() && matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12' }} | |
| uses: codecov/test-results-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| slug: FormingWorlds/Aragog | |
| files: junit.xml |