RBniCSx CI #1621
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: RBniCSx CI | |
| on: | |
| push: | |
| branches: | |
| - "**" | |
| pull_request: | |
| branches: | |
| - main | |
| schedule: | |
| - cron: "0 5 * * *" | |
| workflow_call: | |
| workflow_dispatch: | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| include: | |
| - backend: none-real | |
| container: numericalpdes/base_images:slepc4py-real | |
| setup_container: | | |
| echo "OMPI_ALLOW_RUN_AS_ROOT=1" >> $GITHUB_ENV | |
| echo "OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1" >> $GITHUB_ENV | |
| rm /usr/local/lib/python3.12/site-packages/petsc4py/py.typed | |
| python3 -m pip install nanobind scikit-build-core[pyproject] | |
| - backend: none-complex | |
| container: numericalpdes/base_images:slepc4py-complex | |
| setup_container: | | |
| echo "OMPI_ALLOW_RUN_AS_ROOT=1" >> $GITHUB_ENV | |
| echo "OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1" >> $GITHUB_ENV | |
| rm /usr/local/lib/python3.12/site-packages/petsc4py/py.typed | |
| python3 -m pip install nanobind scikit-build-core[pyproject] | |
| - backend: dolfinx-real | |
| container: ghcr.io/fenics/dolfinx/dolfinx:nightly | |
| setup_container: | | |
| . /usr/local/bin/dolfinx-real-mode | |
| echo "PETSC_ARCH=$PETSC_ARCH" >> $GITHUB_ENV | |
| echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH" >> $GITHUB_ENV | |
| echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV | |
| echo "PKG_CONFIG_PATH=$PKG_CONFIG_PATH" >> $GITHUB_ENV | |
| echo "CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH" >> $GITHUB_ENV | |
| rm /dolfinx-env/lib/python3.12/site-packages/petsc4py/py.typed | |
| - backend: dolfinx-complex | |
| container: ghcr.io/fenics/dolfinx/dolfinx:nightly | |
| setup_container: | | |
| . /usr/local/bin/dolfinx-complex-mode | |
| echo "PETSC_ARCH=$PETSC_ARCH" >> $GITHUB_ENV | |
| echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH" >> $GITHUB_ENV | |
| echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV | |
| echo "PKG_CONFIG_PATH=$PKG_CONFIG_PATH" >> $GITHUB_ENV | |
| echo "CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH" >> $GITHUB_ENV | |
| rm /dolfinx-env/lib/python3.12/site-packages/petsc4py/py.typed | |
| fail-fast: false | |
| container: | |
| image: ${{ matrix.container }} | |
| options: --user root | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup container | |
| run: ${{ matrix.setup_container }} | |
| - name: Install RBniCSx | |
| run: | | |
| if [[ "${{ matrix.backend }}" == none* ]]; then | |
| python3 -m pip install --check-build-dependencies --no-build-isolation --config-settings=build-dir="build" --config-settings=cmake.build-type="Debug" --verbose .[docs,lint,tests] | |
| else | |
| python3 -m pip install --check-build-dependencies --no-build-isolation --config-settings=build-dir="build" --config-settings=cmake.build-type="Debug" --verbose .[docs,lint,tests,tutorials] | |
| fi | |
| shell: bash | |
| - name: Clean build files | |
| run: | | |
| git config --global --add safe.directory $PWD | |
| git clean -xdf | |
| - name: Update mypy configuration | |
| run: | | |
| if [[ "${{ matrix.backend }}" == none* ]]; then | |
| sed -i 's@\[tool\.mypy\]@[tool.mypy]\nexclude = "(^rbnicsx/backends|^tests/unit/backends)"@g' pyproject.toml | |
| sed -i 's@ # "dolfinx",@ "dolfinx",@g' pyproject.toml | |
| sed -i 's@ # "dolfinx.*",@ "dolfinx.*",@g' pyproject.toml | |
| fi | |
| shell: bash | |
| - name: Run ruff on python files | |
| run: | | |
| python3 -m ruff check . | |
| - name: Run isort on python files | |
| run: | | |
| python3 -m isort --check --diff . | |
| - name: Run mypy on python files | |
| run: | | |
| python3 -m mypy --exclude=conftest.py . | |
| python3 -m mypy tests/unit/conftest.py | |
| python3 -m mypy tutorials/conftest.py | |
| - name: Run yamllint on workflows | |
| run: | | |
| python3 -m yamllint -d "{extends: default, rules: {document-start: {present: false}, line-length: disable, truthy: {check-keys: false}}}" . | |
| - name: Run clang-format on C++ files | |
| run: | | |
| wget https://raw.githubusercontent.com/FEniCS/dolfinx/main/.clang-format | |
| find . -type f \( -name "*.cpp" -o -name "*.h" \) | xargs clang-format --dry-run --Werror | |
| - name: Run cmake-format on cmake files | |
| run: | | |
| wget https://raw.githubusercontent.com/FEniCS/dolfinx/main/.cmake-format | |
| find . -type f \( -name "*.cmake" -o -name "*.cmake.in" -o -name "CMakeLists.txt" \) | xargs cmake-format --check | |
| - name: Run documentation generation | |
| run: | | |
| cd docs | |
| if [[ "${{ matrix.backend }}" == none* ]]; then | |
| sed -i "s@rbnicsx.backends@@g" api.rst | |
| fi | |
| python3 -m sphinx -W -b html . build/html | |
| shell: bash | |
| - name: Remove source directory to ensure that package from installation directory is used | |
| run: | | |
| rm -rf rbnicsx | |
| - name: Determine coverage and pytest options for unit tests | |
| id: unit_options | |
| run: | | |
| if [[ "${{ matrix.backend }}" == none* ]]; then | |
| COVERAGE_UNIT_OMIT="*/rbnicsx/backends/*.py,*/rbnicsx/_cpp/backends/*.py" | |
| PYTEST_UNIT_OPTIONS="--skip-backends" | |
| else | |
| COVERAGE_UNIT_OMIT="" | |
| PYTEST_UNIT_OPTIONS="" | |
| fi | |
| echo "coverage_omit=${COVERAGE_UNIT_OMIT}" >> ${GITHUB_OUTPUT} | |
| echo "pytest_options=${PYTEST_UNIT_OPTIONS}" >> ${GITHUB_OUTPUT} | |
| shell: bash | |
| - name: Run unit tests (serial) | |
| run: | | |
| COVERAGE_UNIT_OMIT="${{ steps.unit_options.outputs.coverage_omit }}" | |
| PYTEST_UNIT_OPTIONS="${{ steps.unit_options.outputs.pytest_options }}" | |
| COVERAGE_FILE=.coverage_unit_serial python3 -m coverage run --source=rbnicsx --omit="${COVERAGE_UNIT_OMIT}" -m pytest ${PYTEST_UNIT_OPTIONS} tests/unit | |
| - name: Run unit tests (parallel) | |
| run: | | |
| COVERAGE_UNIT_OMIT="${{ steps.unit_options.outputs.coverage_omit }}" | |
| PYTEST_UNIT_OPTIONS="${{ steps.unit_options.outputs.pytest_options }}" | |
| COVERAGE_FILE=.coverage_unit_parallel mpirun -n 2 python3 -m coverage run --source=rbnicsx --parallel-mode --omit="${COVERAGE_UNIT_OMIT}" -m pytest ${PYTEST_UNIT_OPTIONS} tests/unit | |
| - name: Combine coverage reports | |
| run: | | |
| python3 -m coverage combine .coverage* | |
| python3 -m coverage report --fail-under=100 --show-missing --skip-covered | |
| - name: Generate tutorial files | |
| run: | | |
| NO_TESTS_COLLECTED=5 | |
| python3 -m pytest --ipynb-action=create-notebooks tutorials || (($?==$NO_TESTS_COLLECTED)) | |
| python3 -m pytest --ipynb-action=create-notebooks --tag-collapse tutorials || (($?==$NO_TESTS_COLLECTED)) | |
| python3 -m pytest --ipynb-action=create-notebooks --np=2 tutorials || (($?==$NO_TESTS_COLLECTED)) | |
| python3 -m pytest --ipynb-action=create-notebooks --tag-collapse --np=2 tutorials || (($?==$NO_TESTS_COLLECTED)) | |
| shell: bash | |
| - name: Update mypy configuration | |
| run: | | |
| if [[ "${{ matrix.backend }}" == none* ]]; then | |
| echo "[tool.nbqa.exclude]" >> pyproject.toml | |
| echo "ruff = \"(^tutorials)\"" >> pyproject.toml | |
| echo "mypy = \"(^tutorials)\"" >> pyproject.toml | |
| fi | |
| shell: bash | |
| - name: Run ruff on tutorial files | |
| run: | | |
| python3 -m nbqa ruff . | |
| - name: Run isort on tutorial files | |
| run: | | |
| python3 -m nbqa isort --check --diff . | |
| - name: Run mypy on tutorial files | |
| run: | | |
| python3 -m nbqa mypy . | |
| - name: Check for stray outputs, counts and metadata in tutorial files | |
| uses: RBniCS/check-jupyter-metadata-action@main | |
| with: | |
| pattern: "tutorials/**/*.ipynb" | |
| - name: Run tutorials (serial) | |
| run: | | |
| python3 -m pytest --tag-collapse --durations=0 --durations-min=1.0 tutorials | |
| - name: Run tutorials (parallel) | |
| run: | | |
| python3 -m pytest --tag-collapse --np=2 --durations=0 --durations-min=1.0 tutorials | |
| - name: Upload tutorials logs as an artifact in case of failure | |
| if: failure() || cancelled() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: "tutorials-logs-${{ matrix.backend }}" | |
| path: | | |
| tutorials/**/.ipynb_pytest/**/*.log* | |
| include-hidden-files: true | |
| warn: | |
| runs-on: ubuntu-latest | |
| if: github.repository == 'RBniCS/RBniCSx' && github.ref == 'refs/heads/main' && github.event_name == 'schedule' | |
| steps: | |
| - name: Warn if scheduled workflow is about to be disabled | |
| uses: fem-on-colab/warn-workflow-about-to-be-disabled-action@main | |
| with: | |
| workflow-filename: ci.yml | |
| days-elapsed: 55 |