Avoid using ufl deprecated finite elements #1034
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| name: RBniCSx CI | |
| on: | |
| push: | |
| branches: | |
| - "**" | |
| pull_request: | |
| branches: | |
| - main | |
| schedule: | |
| - cron: "0 5 * * *" | |
| workflow_dispatch: | |
| jobs: | |
| test: | |
| if: >- | |
| ( | |
| ( | |
| github.event_name == 'schedule' | |
| && github.repository == 'RBniCS/RBniCSx' | |
| ) || ( | |
| github.event_name != 'schedule' | |
| && !( | |
| contains(github.event.head_commit.message, '[ci skip]') | |
| || contains(github.event.head_commit.message, '[skip ci]') | |
| ) | |
| ) | |
| ) | |
| 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/python3.11/site-packages/petsc4py/py.typed | |
| - 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" >> $GITHUB_ENV | |
| rm /usr/local/lib/python3.11/site-packages/petsc4py/py.typed | |
| - backend: dolfinx-real | |
| container: dolfinx/dolfinx:nightly | |
| setup_container: | | |
| . /usr/local/bin/dolfinx-real-mode | |
| echo "PETSC_ARCH=$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" >> $GITHUB_ENV | |
| rm /usr/local/lib/python3.10/dist-packages/petsc4py/py.typed | |
| - backend: dolfinx-complex | |
| container: dolfinx/dolfinx:nightly | |
| setup_container: | | |
| . /usr/local/bin/dolfinx-complex-mode | |
| echo "PETSC_ARCH=$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 | |
| rm /usr/local/lib/python3.10/dist-packages/petsc4py/py.typed | |
| fail-fast: false | |
| container: | |
| image: ${{ matrix.container }} | |
| options: --user root | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup container | |
| run: ${{ matrix.setup_container }} | |
| - name: Install RBniCSx | |
| run: | | |
| if [[ "${{ matrix.backend }}" == none* ]]; then | |
| python3 -m pip install .[docs,lint,tests] | |
| else | |
| python3 -m pip install .[docs,lint,tests,tutorials] | |
| fi | |
| python3 -c "import rbnicsx._cpp" | |
| shell: bash | |
| - name: Update mypy configuration | |
| if: startsWith(matrix.backend, 'none') == true | |
| run: | | |
| echo "[mypy-dolfinx]" >> setup.cfg | |
| echo "ignore_missing_imports = True" >> setup.cfg | |
| echo "[mypy-dolfinx.*]" >> setup.cfg | |
| echo "ignore_missing_imports = True" >> setup.cfg | |
| echo "[mypy-rbnicsx._cpp.default_compiler_options_with_dolfinx]" >> setup.cfg | |
| echo "follow_imports = silent" >> setup.cfg | |
| sed -i 's@exclude = (^\\\.eggs|^build|^dist|conftest\\\.py\$)@exclude = (^\\\.eggs|^build|^dist|conftest\\\.py\$|^rbnicsx/backends|^rbnicsx/_cpp/backends|^rbnicsx/_cpp/default_compiler_options_with_dolfinx\\\.py\$|^tests/unit/backends|^tests/unit/_cpp/backends)@g' setup.cfg | |
| shell: bash | |
| - name: Run flake8 and mypy checks on python files | |
| run: | | |
| python3 -m flake8 . | |
| python3 -m mypy . | |
| - name: Run documentation generation | |
| if: startsWith(matrix.backend, 'none') != true | |
| run: | | |
| cd docs && make html | |
| - 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 ${PYTEST_UNIT_OPTIONS} tests/unit | |
| - name: Combine coverage reports | |
| run: | | |
| python3 -m coverage combine .coverage* | |
| python3 -m coverage report --fail-under=100 --show-missing --skip-covered | |
| - name: Run flake8 and mypy checks on tutorial files | |
| if: startsWith(matrix.backend, 'none') != true | |
| run: | | |
| NO_TESTS_COLLECTED=5 | |
| python3 -m pytest --ipynb-action=create-notebooks tutorials || (($?==$NO_TESTS_COLLECTED)) | |
| python3 -m pytest --ipynb-action=create-notebooks --tag-collapse tutorials || (($?==$NO_TESTS_COLLECTED)) | |
| python3 -m pytest --ipynb-action=create-notebooks --np=2 tutorials || (($?==$NO_TESTS_COLLECTED)) | |
| python3 -m pytest --ipynb-action=create-notebooks --tag-collapse --np=2 tutorials || (($?==$NO_TESTS_COLLECTED)) | |
| python3 -m nbqa flake8 . | |
| python3 -m nbqa mypy . | |
| shell: bash | |
| - name: Check for stray outputs, counts and metadata in tutorial files | |
| if: startsWith(matrix.backend, 'none') != true | |
| uses: RBniCS/check-jupyter-metadata-action@main | |
| with: | |
| pattern: "tutorials/**/*.ipynb" | |
| - name: Import modules at least once, so that tutorials duration is not affected by module setup | |
| if: startsWith(matrix.backend, 'none') != true | |
| run: | | |
| python3 -m pytest --durations=0 --durations-min=1.0 tutorials/.imports.ipynb | |
| - name: Run tutorials (serial) | |
| if: startsWith(matrix.backend, 'none') != true | |
| run: | | |
| python3 -m pytest --tag-collapse --durations=0 --durations-min=1.0 tutorials | |
| - name: Run tutorials (parallel) | |
| if: startsWith(matrix.backend, 'none') != true | |
| run: | | |
| python3 -m pytest --tag-collapse --np=2 --durations=0 --durations-min=1.0 tutorials | |
| - name: Upload tutorials logs as an artifact in case of failure | |
| if: startsWith(matrix.backend, 'none') != true && (failure() || cancelled()) | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: "tutorials-logs-${{ matrix.backend }}" | |
| path: | | |
| tutorials/**/.ipynb_pytest/**/*.log* | |
| warn: | |
| runs-on: ubuntu-latest | |
| if: github.repository == 'RBniCS/RBniCSx' && github.ref == 'refs/heads/main' && github.event_name == 'schedule' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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 |