ci.yml

name: CI

on:
  push:
    branches:
      - "**"
  pull_request:
    branches:
      - main
  schedule:
    - cron: "0 5 * * *"
  workflow_dispatch:
  workflow_call:
    inputs:
      ref:
        description: "The branch, tag or SHA to checkout"
        type: string
      index:
        description: "The package index, e.g. PyPI or TestPyPI, from which to install the package. If empty, the package will not be installed from any package index, but from the current git clone"
        type: string
      index_version:
        description: "The version of the package to be installed from the package index. If empty, the latest compatible version will be installed. Only used when index is non empty."
        type: string
      expected_index_version:
        description: "The expected version of the package when installed from the package index. If emtpy, no check is carried out. Only used when index is non empty."
        type: string

jobs:
  test:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        include:
          - backend: none-real
            container: debian:testing
            petsc_arch: real
          - backend: none-complex
            container: debian:testing
            petsc_arch: complex
          - backend: dolfinx-v0.11.0-real
            container: ghcr.io/fenics/dolfinx/dolfinx:v0.11.0
            petsc_arch: real
          - backend: dolfinx-v0.11.0-complex
            container: ghcr.io/fenics/dolfinx/dolfinx:v0.11.0
            petsc_arch: complex
          - backend: dolfinx-stable-real
            container: ghcr.io/fenics/dolfinx/dolfinx:stable
            petsc_arch: real
          - backend: dolfinx-stable-complex
            container: ghcr.io/fenics/dolfinx/dolfinx:stable
            petsc_arch: complex
          - backend: dolfinx-nightly-real
            container: ghcr.io/fenics/dolfinx/dolfinx:nightly
            petsc_arch: real
          - backend: dolfinx-nightly-complex
            container: ghcr.io/fenics/dolfinx/dolfinx:nightly
            petsc_arch: complex
      fail-fast: false
    container: ${{ matrix.container }}
    steps:
      - name: Install git
        run: |
          export DEBIAN_FRONTEND="noninteractive"
          apt update -y -q
          apt install -y -qq ca-certificates git
      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0  # v7.0.0
        with:
          ref: ${{ inputs.ref }}
      - name: Setup container
        run: |
          export DEBIAN_FRONTEND="noninteractive"
          apt update -y -q
          apt install -y -qq libegl1 libgl1-mesa-dri
          if [[ "${{ matrix.backend }}" == "dolfinx"* ]]; then
            pip install pkgconfig
            HDF5_MPI=ON python3 -m pip install h5py --no-build-isolation --no-binary=h5py
            . /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 -f /dolfinx-env/lib/python3.*/site-packages/ufl/py.typed
          else
            apt install -y -qq cmake gcc g++ python3-mpi4py python3-nanobind python3-dev python3-pip python3-scikit-build-core python3-setuptools wget
            echo "OMPI_ALLOW_RUN_AS_ROOT=1" >> $GITHUB_ENV
            echo "OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1" >> $GITHUB_ENV
            rm /usr/lib/python3.*/EXTERNALLY-MANAGED
            apt install -y -qq libpetsc-${{ matrix.petsc_arch }}-dev libslepc-${{ matrix.petsc_arch }}-dev python3-petsc4py-${{ matrix.petsc_arch }} python3-slepc4py-${{ matrix.petsc_arch }}
            PETSC_DIR=/usr/lib/petscdir/petsc-${{ matrix.petsc_arch }}
            echo "PETSC_DIR=$PETSC_DIR" >> $GITHUB_ENV
            SLEPC_DIR=/usr/lib/slepcdir/slepc-${{ matrix.petsc_arch }}
            echo "SLEPC_DIR=$SLEPC_DIR" >> $GITHUB_ENV
          fi
        shell: bash
      - name: Wait for package index availability (PyPI and TestPyPI only)
        if: inputs.index != '' && inputs.index_version != ''
        run: |
          INDEX=${{ inputs.index }}
          INDEX_VERSION=${{ inputs.index_version }}
          PACKAGE_NAME="RBniCSx"
          if [[ "${INDEX}" == "TestPyPI" ]]; then
            INDEX_URL=https://test.pypi.org
          elif [[ "${INDEX}" == "PyPI" ]]; then
            INDEX_URL=https://pypi.org
          else
            echo "Invalid package index" && exit 1
          fi
          COUNTER=0
          INDEX_VERSION_FOUND=0
          while [[ ${INDEX_VERSION_FOUND} -ne 1 ]]; do
            python3 -m pip install --no-cache-dir --index-url ${INDEX_URL}/simple/ ${PACKAGE_NAME}==0 2> all_${PACKAGE_NAME}_versions || true
            if grep -q ${INDEX_VERSION} all_${PACKAGE_NAME}_versions; then
              INDEX_VERSION_FOUND=1
            fi
            [[ ${INDEX_VERSION_FOUND} -ne 1 && ${COUNTER} -eq 5 ]] && echo "Giving up on finding version ${INDEX_VERSION} on ${INDEX_URL}" && exit 1
            [[ ${INDEX_VERSION_FOUND} -ne 1 ]] && echo "Cannot find version ${INDEX_VERSION} on ${INDEX_URL}, attempt ${COUNTER}: trying again after a short pause" && sleep 10
            [[ ${INDEX_VERSION_FOUND} -eq 1 ]] && echo "Found version ${INDEX_VERSION} on ${INDEX_URL}, attempt ${COUNTER}"
            COUNTER=$((COUNTER+1))
          done
        shell: bash
      - name: Install RBniCSx (PyPI and TestPyPI only)
        if: inputs.index != ''
        run: |
          INDEX=${{ inputs.index }}
          INDEX_VERSION=${{ inputs.index_version }}
          EXPECTED_INDEX_VERSION=${{ inputs.expected_index_version }}
          PACKAGE_NAME="RBniCSx"
          if [[ "${INDEX}" == "TestPyPI" ]]; then
            INDEX_FLAGS="--no-cache-dir --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/"
          elif [[ "${INDEX}" == "PyPI" ]]; then
            INDEX_FLAGS="--no-cache-dir"
          else
            echo "Invalid package index" && exit 1
          fi
          if [[ -n "${INDEX_VERSION}" ]]; then
            PACKAGE_VERSION="==${INDEX_VERSION}"
            echo "Installing version ${INDEX_VERSION} from ${INDEX}"
          else
            PACKAGE_VERSION=""
            echo "Installing latest compatible version from ${INDEX}"
          fi
          if [[ "${{ matrix.backend }}" == "dolfinx"* ]]; then
            PACKAGE_EXTRAS="docs,lint,tests,tutorials"
          else
            PACKAGE_EXTRAS="docs,lint,tests"
          fi
          python3 -m pip install ${INDEX_FLAGS} --no-build-isolation --config-settings=build-dir="build" --config-settings=cmake.build-type="Debug" --verbose ${PACKAGE_NAME}[${PACKAGE_EXTRAS}]${PACKAGE_VERSION}
          if [[ -n "${EXPECTED_INDEX_VERSION}" ]]; then
            ACTUAL_INDEX_VERSION=$(python3 -c 'import importlib.metadata; print(importlib.metadata.version("RBniCSx"))')
            if [[ "${ACTUAL_INDEX_VERSION}" != "${EXPECTED_INDEX_VERSION}" ]]; then
              echo "Error: installed ${PACKAGE_NAME} version is ${ACTUAL_INDEX_VERSION}, while expected version is ${EXPECTED_INDEX_VERSION}"
              exit 1
            fi
          fi
        shell: bash
      - name: Install RBniCSx (git clone only)
        if: inputs.index == ''
        run: |
          if [[ "${{ matrix.backend }}" == "dolfinx"* ]]; then
            PACKAGE_EXTRAS="docs,lint,tests,tutorials"
          else
            PACKAGE_EXTRAS="docs,lint,tests"
          fi
          python3 -m pip install --check-build-dependencies --no-build-isolation --config-settings=build-dir="build" --config-settings=cmake.build-type="Debug" --verbose .[${PACKAGE_EXTRAS}]
        shell: bash
      - name: Clean build files (git clone only)
        if: inputs.index == ''
        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
        if: startsWith(matrix.backend, 'dolfinx') == true
        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 [[ "${{ matrix.backend }}" == none* ]]; then
            sed -i "s@rbnicsx.backends@@g" api.rst
          fi
          python3 -m sphinx -W -b html . build/html
        shell: bash
      - name: Remove source directory to ensure that package from installation directory is used
        run: |
          rm -rf rbnicsx
      - name: Determine coverage and pytest options for unit tests
        id: unit_options
        run: |
          if [[ "${{ 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 ${PYTEST_UNIT_OPTIONS} tests/unit
      - name: Combine coverage reports
        run: |
          python3 -m coverage combine .coverage*
          python3 -m coverage report --fail-under=100 --show-missing --skip-covered
      - name: Generate tutorial files
        if: startsWith(matrix.backend, 'dolfinx') == true
        run: |
          NO_TESTS_COLLECTED=5
          python3 -m pytest --ipynb-action=create-notebooks tutorials || (($?==$NO_TESTS_COLLECTED))
          python3 -m pytest --ipynb-action=create-notebooks --collapse tutorials || (($?==$NO_TESTS_COLLECTED))
          python3 -m pytest --ipynb-action=create-notebooks --np=2 tutorials || (($?==$NO_TESTS_COLLECTED))
          python3 -m pytest --ipynb-action=create-notebooks --collapse --np=2 tutorials || (($?==$NO_TESTS_COLLECTED))
        shell: bash
      - name: Run ruff on tutorial files
        if: startsWith(matrix.backend, 'dolfinx') == true
        run: |
          python3 -m nbqa ruff .
      - name: Run isort on tutorial files
        if: startsWith(matrix.backend, 'dolfinx') == true
        run: |
          python3 -m nbqa isort --check --diff .
      - name: Run mypy on tutorial files
        if: startsWith(matrix.backend, 'dolfinx') == true
        run: |
          python3 -m nbqa mypy .
      - name: Check for stray outputs, counts and metadata in tutorial files
        if: startsWith(matrix.backend, 'dolfinx') == true
        uses: RBniCS/check-jupyter-metadata-action@6df653e5d45f7620d888c6a1bd85d07b4f903045  # v1.0.0
        with:
          pattern: "tutorials/**/*.ipynb"
      - name: Run tutorials (serial)
        if: startsWith(matrix.backend, 'dolfinx') == true
        run: |
          VISKEX_PYVISTA_BACKEND="static" python3 -m pytest --collapse --durations=0 --durations-min=1.0 tutorials
      - name: Run tutorials (parallel)
        if: startsWith(matrix.backend, 'dolfinx') == true
        run: |
          VISKEX_PYVISTA_BACKEND="static" python3 -m pytest --collapse --np=2 --durations=0 --durations-min=1.0 tutorials
      - name: Upload tutorials logs as an artifact in case of failure
        if: startsWith(matrix.backend, 'dolfinx') == true && (failure() || cancelled())
        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
        with:
          name: "tutorials-logs-${{ 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@58c6022d9aeb22accfa8df9bf5b58c3d8867208c  # v1.0.0
        with:
          workflow-filename: ci.yml
          days-elapsed: 55