RBniCSx CI #1760
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| 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: debian:testing | |
| setup_git: | | |
| export DEBIAN_FRONTEND="noninteractive" | |
| apt update -y -q | |
| apt install -y -qq git | |
| setup_container: | | |
| export DEBIAN_FRONTEND="noninteractive" | |
| apt update -y -q | |
| apt install -y -qq cmake libpetsc-real-dev libslepc-real-dev python3-mpi4py python3-nanobind python3-petsc4py-real python3-scikit-build-core python3-setuptools python3-slepc4py-real python3-pip wget | |
| echo "OMPI_ALLOW_RUN_AS_ROOT=1" >> $GITHUB_ENV | |
| echo "OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1" >> $GITHUB_ENV | |
| rm /usr/lib/python3.*/EXTERNALLY-MANAGED | |
| PETSC_DIR=/usr/lib/petscdir/petsc-real | |
| rm $PETSC_DIR/lib/python3/dist-packages/petsc4py/py.typed | |
| echo "PETSC_DIR=$PETSC_DIR" >> $GITHUB_ENV | |
| SLEPC_DIR=/usr/lib/slepcdir/slepc-real | |
| echo "SLEPC_DIR=$SLEPC_DIR" >> $GITHUB_ENV | |
| - backend: none-complex | |
| container: debian:testing | |
| setup_git: | | |
| export DEBIAN_FRONTEND="noninteractive" | |
| apt update -y -q | |
| apt install -y -qq git | |
| setup_container: | | |
| export DEBIAN_FRONTEND="noninteractive" | |
| apt update -y -q | |
| apt install -y -qq cmake libpetsc-complex-dev libslepc-complex-dev python3-mpi4py python3-nanobind python3-petsc4py-complex python3-scikit-build-core python3-setuptools python3-slepc4py-complex python3-pip wget | |
| echo "OMPI_ALLOW_RUN_AS_ROOT=1" >> $GITHUB_ENV | |
| echo "OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1" >> $GITHUB_ENV | |
| rm /usr/lib/python3.*/EXTERNALLY-MANAGED | |
| PETSC_DIR=/usr/lib/petscdir/petsc-complex | |
| rm $PETSC_DIR/lib/python3/dist-packages/petsc4py/py.typed | |
| echo "PETSC_DIR=$PETSC_DIR" >> $GITHUB_ENV | |
| SLEPC_DIR=/usr/lib/slepcdir/slepc-complex | |
| echo "SLEPC_DIR=$SLEPC_DIR" >> $GITHUB_ENV | |
| - backend: dolfinx-real | |
| container: ghcr.io/fenics/dolfinx/dolfinx:nightly | |
| setup_git: "" | |
| setup_container: | | |
| . /usr/local/bin/dolfinx-real-mode | |
| echo "PETSC_ARCH=$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" >> $GITHUB_ENV | |
| rm /dolfinx-env/lib/python3.12/site-packages/petsc4py/py.typed | |
| - backend: dolfinx-complex | |
| container: ghcr.io/fenics/dolfinx/dolfinx:nightly | |
| setup_git: "" | |
| setup_container: | | |
| . /usr/local/bin/dolfinx-complex-mode | |
| echo "PETSC_ARCH=$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: | |
| - name: Setup git | |
| run: ${{ matrix.setup_git }} | |
| - 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 [[ "${{ matrix.backend }}" == none* ]]; then | |
| sed -i "[email protected]@@g" api.rst | |
| fi | |
| python3 -m sphinx -W -b html . build/html | |
| shell: bash | |
| - name: Remove source directory to ensure that package from installation directory is used | |
| run: | | |
| rm -rf rbnicsx | |
| - name: Determine coverage and pytest options for unit tests | |
| id: unit_options | |
| run: | | |
| if [[ "${{ 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 ${PYTEST_UNIT_OPTIONS} tests/unit | |
| - name: Combine coverage reports | |
| run: | | |
| python3 -m coverage combine .coverage* | |
| python3 -m coverage report --fail-under=100 --show-missing --skip-covered | |
| - name: Generate tutorial files | |
| if: startsWith(matrix.backend, 'dolfinx') == true | |
| run: | | |
| NO_TESTS_COLLECTED=5 | |
| python3 -m pytest --ipynb-action=create-notebooks tutorials || (($?==$NO_TESTS_COLLECTED)) | |
| python3 -m pytest --ipynb-action=create-notebooks --tag-collapse tutorials || (($?==$NO_TESTS_COLLECTED)) | |
| python3 -m pytest --ipynb-action=create-notebooks --np=2 tutorials || (($?==$NO_TESTS_COLLECTED)) | |
| python3 -m pytest --ipynb-action=create-notebooks --tag-collapse --np=2 tutorials || (($?==$NO_TESTS_COLLECTED)) | |
| shell: bash | |
| - name: Run ruff on tutorial files | |
| if: startsWith(matrix.backend, 'dolfinx') == true | |
| run: | | |
| python3 -m nbqa ruff . | |
| - name: Run isort on tutorial files | |
| if: startsWith(matrix.backend, 'dolfinx') == true | |
| run: | | |
| python3 -m nbqa isort --check --diff . | |
| - name: Run mypy on tutorial files | |
| if: startsWith(matrix.backend, 'dolfinx') == true | |
| run: | | |
| python3 -m nbqa mypy . | |
| - name: Check for stray outputs, counts and metadata in tutorial files | |
| if: startsWith(matrix.backend, 'dolfinx') == true | |
| uses: RBniCS/check-jupyter-metadata-action@main | |
| with: | |
| pattern: "tutorials/**/*.ipynb" | |
| - name: Run tutorials (serial) | |
| if: startsWith(matrix.backend, 'dolfinx') == true | |
| run: | | |
| python3 -m pytest --tag-collapse --durations=0 --durations-min=1.0 tutorials | |
| - name: Run tutorials (parallel) | |
| if: startsWith(matrix.backend, 'dolfinx') == true | |
| run: | | |
| python3 -m pytest --tag-collapse --np=2 --durations=0 --durations-min=1.0 tutorials | |
| - name: Upload tutorials logs as an artifact in case of failure | |
| if: startsWith(matrix.backend, 'dolfinx') == true && (failure() || cancelled()) | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: "tutorials-logs-${{ 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 |