Run mypy on conftest.py files separately to avoid duplicate module error #1323
Workflow file for this run
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| name: multiphenicsx CI | |
| on: | |
| push: | |
| branches: | |
| - "**" | |
| pull_request: | |
| branches: | |
| - main | |
| schedule: | |
| - cron: "0 3 * * *" | |
| workflow_call: | |
| workflow_dispatch: | |
| jobs: | |
| test: | |
| if: >- | |
| ( | |
| ( | |
| github.event_name == 'schedule' | |
| && github.repository == 'multiphenics/multiphenicsx' | |
| ) || ( | |
| github.event_name != 'schedule' | |
| && !( | |
| contains(github.event.head_commit.message, '[ci skip]') | |
| || contains(github.event.head_commit.message, '[skip ci]') | |
| ) | |
| ) | |
| ) | |
| runs-on: ubuntu-latest | |
| container: ghcr.io/fenics/dolfinx/dolfinx:nightly | |
| strategy: | |
| matrix: | |
| petsc_arch: [real, complex] | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup container | |
| run: | | |
| . /usr/local/bin/dolfinx-${{ matrix.petsc_arch }}-mode | |
| echo "PETSC_ARCH=$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" >> $GITHUB_ENV | |
| rm /usr/local/lib/python3.10/dist-packages/petsc4py/py.typed | |
| - name: Install multiphenicsx | |
| run: | | |
| python3 -m pip install --check-build-dependencies --no-build-isolation --config-settings=build-dir="build" --config-settings=cmake.build-type="Debug" --verbose .[docs,lint,tests,tutorials] | |
| - name: Run ruff on python files | |
| run: | | |
| python3 -m ruff . | |
| - name: Run isort on python files | |
| run: | | |
| python3 -m isort --check --diff . | |
| - name: Run mypy on python files | |
| run: | | |
| python3 -m mypy --exclude=conftest.py . | |
| python3 -m mypy tests/unit/conftest.py | |
| python3 -m mypy tutorials/conftest.py | |
| - name: Run yamllint on workflows | |
| run: | | |
| python3 -m yamllint -d "{extends: default, rules: {document-start: {present: false}, line-length: disable, truthy: {check-keys: false}}}" . | |
| - name: Run documentation generation | |
| run: | | |
| cd docs && python3 -m sphinx -W -b html . build/html | |
| - name: Remove source directory to ensure that package from installation directory is used | |
| run: | | |
| rm -rf multiphenicsx | |
| - name: Run unit tests (serial) | |
| run: | | |
| COVERAGE_FILE=.coverage_unit_serial python3 -m coverage run --source=multiphenicsx -m pytest tests/unit | |
| - name: Run unit tests (parallel) | |
| run: | | |
| COVERAGE_FILE=.coverage_unit_parallel mpirun -n 3 python3 -m coverage run --source=multiphenicsx --parallel-mode -m pytest tests/unit | |
| - name: Combine coverage reports | |
| run: | | |
| python3 -m coverage combine .coverage* | |
| python3 -m coverage report --fail-under=100 --show-missing --skip-covered | |
| - name: Generate tutorial files | |
| run: | | |
| NO_TESTS_COLLECTED=5 | |
| python3 -m pytest --ipynb-action=create-notebooks tutorials || (($?==$NO_TESTS_COLLECTED)) | |
| python3 -m pytest --ipynb-action=create-notebooks --np=2 tutorials || (($?==$NO_TESTS_COLLECTED)) | |
| shell: bash | |
| - name: Run ruff on tutorial files | |
| run: | | |
| python3 -m nbqa ruff . | |
| - name: Run isort on tutorial files | |
| run: | | |
| python3 -m nbqa isort --check --diff . | |
| - name: Run mypy on tutorial files | |
| run: | | |
| python3 -m nbqa mypy . | |
| - name: Check for stray outputs, counts and metadata in tutorial files | |
| uses: RBniCS/check-jupyter-metadata-action@main | |
| with: | |
| pattern: "tutorials/**/*.ipynb" | |
| - name: Run tutorials (serial) | |
| run: | | |
| python3 -m pytest tutorials | |
| - name: Run tutorials (parallel) | |
| run: | | |
| python3 -m pytest --np 3 tutorials | |
| - name: Upload tutorials logs as an artifact in case of failure | |
| if: failure() || cancelled() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: "tutorials-logs-${{ matrix.petsc_arch }}" | |
| path: | | |
| tutorials/**/.ipynb_pytest/**/*.log* | |
| warn: | |
| runs-on: ubuntu-latest | |
| if: github.repository == 'multiphenics/multiphenicsx' && 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 |