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Simplify CI workflow file by moving tutorial skip inside conftest.py #1210

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Simplify CI workflow file by moving tutorial skip inside conftest.py

Simplify CI workflow file by moving tutorial skip inside conftest.py #1210

Workflow file for this run

.github/workflows/ci.yml at 8d43910
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/python3.11/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" >> $GITHUB_ENV
rm /usr/local/lib/python3.11/site-packages/petsc4py/py.typed
python3 -m pip install nanobind scikit-build-core[pyproject]
- backend: dolfinx-real
container: ghcr.io/fenics/dolfinx/dolfinx:nightly
setup_container: |
. /usr/local/bin/dolfinx-real-mode
echo "PETSC_ARCH=$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" >> $GITHUB_ENV
rm /usr/local/lib/python3.10/dist-packages/petsc4py/py.typed
- backend: dolfinx-complex
container: ghcr.io/fenics/dolfinx/dolfinx:nightly
setup_container: |
. /usr/local/bin/dolfinx-complex-mode
echo "PETSC_ARCH=$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 /usr/local/lib/python3.10/dist-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 .
- 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 [[ "${{ matrix.backend }}" == none* ]]; then
sed -i "[email protected]@@g" api.rst
fi
python3 -m sphinx -W -b html . build/html
- name: Remove source directory to ensure that package from installation directory is used
run: |
rm -rf rbnicsx
- name: Determine coverage and pytest options for unit tests
id: unit_options
run: |
if [[ "${{ 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@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:
- 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