From 285c5bc1334b3babfb6340df38b232e6d4a61cef Mon Sep 17 00:00:00 2001 From: Francesco Ballarin Date: Thu, 16 Nov 2023 10:12:44 +0100 Subject: [PATCH] Pin versions for compatibility with dolfinx v0.6.0 --- .github/workflows/ci.yml | 88 +++++----------------------------------- setup.cfg | 14 +++---- 2 files changed, 18 insertions(+), 84 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b068774..35fd175 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -9,6 +9,7 @@ on: - main schedule: - cron: "0 5 * * *" + workflow_call: workflow_dispatch: jobs: @@ -30,18 +31,8 @@ jobs: 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 - - 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" >> $GITHUB_ENV - backend: dolfinx-real - container: dolfinx/dolfinx:nightly + container: ghcr.io/fenics/dolfinx/dolfinx:v0.6.0-r1 setup_container: | . /usr/local/bin/dolfinx-real-mode echo "PETSC_ARCH=$PETSC_ARCH" >> $GITHUB_ENV @@ -49,7 +40,7 @@ jobs: echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV echo "PKG_CONFIG_PATH=$PKG_CONFIG_PATH" >> $GITHUB_ENV - backend: dolfinx-complex - container: dolfinx/dolfinx:nightly + container: ghcr.io/fenics/dolfinx/dolfinx:v0.6.0-r1 setup_container: | . /usr/local/bin/dolfinx-complex-mode echo "PETSC_ARCH=$PETSC_ARCH" >> $GITHUB_ENV @@ -62,102 +53,45 @@ jobs: options: --user root steps: - uses: actions/checkout@v3 + with: + ref: dolfinx-v0.6.0 - 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 --upgrade https://dmf.unicatt.it/ballarin/public/itkwidgets-0.33.0.dev0-py2.py3-none-any.whl - python3 -m pip install .[docs,lint,tests,tutorials] - fi + python3 -m pip install .[docs,lint,tests,tutorials] 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="${{ steps.unit_options.outputs.pytest_options }}" + COVERAGE_UNIT_OMIT="" + PYTEST_UNIT_OPTIONS="" COVERAGE_FILE=.coverage_unit_serial python3 -m coverage run --source=rbnicsx --omit="${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="${{ steps.unit_options.outputs.pytest_options }}" + COVERAGE_UNIT_OMIT="" + PYTEST_UNIT_OPTIONS="" COVERAGE_FILE=.coverage_unit_parallel mpirun -n 2 python3 -m coverage run --source=rbnicsx --parallel-mode --omit="${COVERAGE_UNIT_OMIT}" -m pytest ${PYTEST_UNIT_OPTIONS} tests/unit - name: Combine coverage reports run: | python3 -m coverage combine .coverage* python3 -m coverage report --fail-under=100 --show-missing --skip-covered - - name: Run flake8 and mypy checks on tutorial files - if: startsWith(matrix.backend, 'none') != true - run: | - NO_TESTS_COLLECTED=5 - python3 -m pytest --ipynb-action=create-notebooks tutorials || (($?==$NO_TESTS_COLLECTED)) - python3 -m pytest --ipynb-action=create-notebooks --tag-collapse tutorials || (($?==$NO_TESTS_COLLECTED)) - python3 -m pytest --ipynb-action=create-notebooks --np=2 tutorials || (($?==$NO_TESTS_COLLECTED)) - python3 -m pytest --ipynb-action=create-notebooks --tag-collapse --np=2 tutorials || (($?==$NO_TESTS_COLLECTED)) - python3 -m nbqa flake8 . - python3 -m nbqa mypy . - shell: bash - - name: Check for stray outputs, counts and metadata in tutorial files - if: startsWith(matrix.backend, 'none') != true - uses: RBniCS/check-jupyter-metadata-action@main - with: - pattern: "tutorials/**/*.ipynb" - name: Import modules at least once, so that tutorials duration is not affected by module setup - if: startsWith(matrix.backend, 'none') != true run: | python3 -m pytest --durations=0 --durations-min=1.0 tutorials/.imports.ipynb - name: Run tutorials (serial) - if: startsWith(matrix.backend, 'none') != true run: | python3 -m pytest --tag-collapse --durations=0 --durations-min=1.0 tutorials - name: Run tutorials (parallel) - if: startsWith(matrix.backend, 'none') != true run: | python3 -m pytest --tag-collapse --np=2 --durations=0 --durations-min=1.0 tutorials - name: Upload tutorials logs as an artifact in case of failure - if: startsWith(matrix.backend, 'none') != true && (failure() || cancelled()) + if: failure() || cancelled() uses: actions/upload-artifact@v3 with: name: "tutorials-logs-${{ matrix.backend }}" path: | tutorials/**/.ipynb_pytest/**/*.log* - - name: Warn if scheduled workflow is about to be disabled - if: github.repository == 'RBniCS/RBniCSx' && github.ref == 'refs/heads/main' && github.event_name == 'schedule' - uses: fem-on-colab/warn-workflow-about-to-be-disabled-action@main - with: - workflow-filename: ci.yml - days-elapsed: 55 diff --git a/setup.cfg b/setup.cfg index 9bb0e38..c38b83a 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,9 +51,9 @@ rbnicsx = [options.extras_require] backends = - fenics-dolfinx - multiphenicsx @ git+https://github.com/multiphenics/multiphenicsx.git - ufl4rom @ git+https://github.com/RBniCS/ufl4rom.git + fenics-dolfinx >= 0.6.0, <0.7.0 + multiphenicsx @ git+https://github.com/multiphenics/multiphenicsx.git@dolfinx-v0.6.0 + ufl4rom @ git+https://github.com/RBniCS/ufl4rom.git@7cf5eae docs = sphinx lint = @@ -67,16 +67,16 @@ lint = tests = coverage nbqa - nbvalx[unit_tests] @ git+https://github.com/multiphenics/nbvalx.git + nbvalx[unit_tests] @ git+https://github.com/multiphenics/nbvalx.git@86d9b38 pytest >= 7.0 scipy tutorials = rbnicsx[backends] gmsh - itkwidgets - nbvalx[notebooks] @ git+https://github.com/multiphenics/nbvalx.git + itkwidgets < 0.33 + nbvalx[notebooks] @ git+https://github.com/multiphenics/nbvalx.git@86d9b38 plotly - pyvista + pyvista < 0.38.0 [flake8] max-line-length = 120