Test against apt DOLFINx releases #107
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| name: Test against apt DOLFINx releases | |
| on: | |
| schedule: | |
| - cron: "0 3 * * *" | |
| workflow_dispatch: | |
| jobs: | |
| generate-matrix: | |
| runs-on: ubuntu-latest | |
| env: | |
| MATRIX_JSON_FILE: "matrix.json" | |
| MATRIX_SCRIPT_FILE: "matrix.sh" | |
| PETSC_SCALAR_TYPES: "real complex" | |
| outputs: | |
| matrix: ${{ steps.store-matrix.outputs.matrix }} | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Prepare script to generate json file | |
| run: | | |
| cat << EOF > ${MATRIX_SCRIPT_FILE} | |
| PETSC_SCALAR_TYPES_ARRAY=("" ${PETSC_SCALAR_TYPES}) | |
| CONTAINER_OS="\${1}" | |
| CONTAINER_RELEASE="\${2}" | |
| MOVED_TO_OLD_RELEASES="\${3}" | |
| PYTHON_VERSION="\${4}" | |
| PIP_AND_SETUPTOOLS_TOO_OLD="\${5}" | |
| DOLFINX_VERSION="\${6}" | |
| CPP_WRAPPER_LIBRARY="\${7}" | |
| ADD_PPA="\${8}" | |
| for PETSC_SCALAR_TYPE in "\${PETSC_SCALAR_TYPES_ARRAY[@]}"; do | |
| echo -e "\t\t{" >> ${MATRIX_JSON_FILE} | |
| echo -e "\t\t\t\"container_os\": \"\${CONTAINER_OS}\"," >> ${MATRIX_JSON_FILE} | |
| echo -e "\t\t\t\"container_release\": \"\${CONTAINER_RELEASE}\"," >> ${MATRIX_JSON_FILE} | |
| echo -e "\t\t\t\"moved_to_old_releases\": \${MOVED_TO_OLD_RELEASES}," >> ${MATRIX_JSON_FILE} | |
| echo -e "\t\t\t\"python_version\": \"\${PYTHON_VERSION}\"," >> ${MATRIX_JSON_FILE} | |
| echo -e "\t\t\t\"pip_and_setuptools_too_old\": \${PIP_AND_SETUPTOOLS_TOO_OLD}," >> ${MATRIX_JSON_FILE} | |
| echo -e "\t\t\t\"dolfinx_version\": \"\${DOLFINX_VERSION}\"," >> ${MATRIX_JSON_FILE} | |
| echo -e "\t\t\t\"cpp_wrapper_library\": \"\${CPP_WRAPPER_LIBRARY}\"," >> ${MATRIX_JSON_FILE} | |
| echo -e "\t\t\t\"add_ppa\": \${ADD_PPA}," >> ${MATRIX_JSON_FILE} | |
| echo -e "\t\t\t\"petsc_scalar_type\": \"\${PETSC_SCALAR_TYPE}\"" >> ${MATRIX_JSON_FILE} | |
| echo -e "\t\t}," >> ${MATRIX_JSON_FILE} | |
| done | |
| EOF | |
| - name: Initialize matrix json file | |
| run: | | |
| touch ${MATRIX_JSON_FILE} | |
| echo -e "{" >> ${MATRIX_JSON_FILE} | |
| echo -e "\t\"include\": [" >> ${MATRIX_JSON_FILE} | |
| - name: Add ubuntu 22.04 (without ppa) to matrix json file | |
| run: | | |
| echo "Skipped: ubuntu 22.04 has dolfinx v0.3.0, which is too old" | |
| - name: Add ubuntu 22.04 (with ppa) to matrix json file | |
| run: | | |
| CONTAINER_OS="ubuntu" | |
| CONTAINER_RELEASE="22.04" | |
| MOVED_TO_OLD_RELEASES="false" | |
| PYTHON_VERSION="3.10" | |
| PIP_AND_SETUPTOOLS_TOO_OLD="true" | |
| DOLFINX_VERSION="0.9.0" | |
| CPP_WRAPPER_LIBRARY="nanobind" | |
| ADD_PPA="true" | |
| bash ${MATRIX_SCRIPT_FILE} ${CONTAINER_OS} ${CONTAINER_RELEASE} ${MOVED_TO_OLD_RELEASES} ${PYTHON_VERSION} ${PIP_AND_SETUPTOOLS_TOO_OLD} ${DOLFINX_VERSION} ${CPP_WRAPPER_LIBRARY} ${ADD_PPA} | |
| - name: Add ubuntu 22.10 (without ppa) to matrix json file | |
| run: | | |
| echo "Skipped: ubuntu 22.10 has dolfinx v0.4.1, which fails every unit test for unknown reasons related to pybind11" | |
| - name: Add ubuntu 22.10 (with ppa) to matrix json file | |
| run: | | |
| echo "Skipped: ubuntu 22.10 was removed from the ppa" | |
| - name: Add ubuntu 23.04 (without ppa) to matrix json file | |
| run: | | |
| echo "Skipped: ubuntu 23.04 has dolfinx v0.5.2, which has a custom patch for dolfinx.mesh.Mesh wrapping that breaks plotting" | |
| - name: Add ubuntu 23.04 (with ppa) to matrix json file | |
| run: | | |
| echo "Skipped: ubuntu 23.04 was removed from the ppa" | |
| - name: Add ubuntu 23.10 (without ppa) to matrix json file | |
| run: | | |
| echo "Skipped: ubuntu 23.10 has dolfinx v0.6.0, which has a custom patch for dolfinx.mesh.Mesh wrapping that breaks plotting" | |
| - name: Add ubuntu 23.10 (with ppa) to matrix json file | |
| run: | | |
| CONTAINER_OS="ubuntu" | |
| CONTAINER_RELEASE="23.10" | |
| MOVED_TO_OLD_RELEASES="true" | |
| PYTHON_VERSION="3.11" | |
| PIP_AND_SETUPTOOLS_TOO_OLD="false" | |
| DOLFINX_VERSION="0.8.0" | |
| CPP_WRAPPER_LIBRARY="nanobind" | |
| ADD_PPA="true" | |
| bash ${MATRIX_SCRIPT_FILE} ${CONTAINER_OS} ${CONTAINER_RELEASE} ${MOVED_TO_OLD_RELEASES} ${PYTHON_VERSION} ${PIP_AND_SETUPTOOLS_TOO_OLD} ${DOLFINX_VERSION} ${CPP_WRAPPER_LIBRARY} ${ADD_PPA} | |
| - name: Add ubuntu 24.04 (without ppa) to matrix json file | |
| run: | | |
| echo "Skipped: ubuntu 24.04 does not have dolfinx" | |
| - name: Add ubuntu 24.04 (with ppa) to matrix json file | |
| run: | | |
| CONTAINER_OS="ubuntu" | |
| CONTAINER_RELEASE="24.04" | |
| MOVED_TO_OLD_RELEASES="false" | |
| PYTHON_VERSION="3.12" | |
| PIP_AND_SETUPTOOLS_TOO_OLD="false" | |
| DOLFINX_VERSION="0.9.0" | |
| CPP_WRAPPER_LIBRARY="nanobind" | |
| ADD_PPA="true" | |
| bash ${MATRIX_SCRIPT_FILE} ${CONTAINER_OS} ${CONTAINER_RELEASE} ${MOVED_TO_OLD_RELEASES} ${PYTHON_VERSION} ${PIP_AND_SETUPTOOLS_TOO_OLD} ${DOLFINX_VERSION} ${CPP_WRAPPER_LIBRARY} ${ADD_PPA} | |
| - name: Add ubuntu 24.10 (without ppa) to matrix json file | |
| run: | | |
| echo "Skipped: ubuntu 24.10 does not have dolfinx" | |
| - name: Add ubuntu 24.10 (with ppa) to matrix json file | |
| run: | | |
| CONTAINER_OS="ubuntu" | |
| CONTAINER_RELEASE="24.10" | |
| MOVED_TO_OLD_RELEASES="false" | |
| PYTHON_VERSION="3.12" | |
| PIP_AND_SETUPTOOLS_TOO_OLD="false" | |
| DOLFINX_VERSION="0.9.0" | |
| CPP_WRAPPER_LIBRARY="nanobind" | |
| ADD_PPA="true" | |
| bash ${MATRIX_SCRIPT_FILE} ${CONTAINER_OS} ${CONTAINER_RELEASE} ${MOVED_TO_OLD_RELEASES} ${PYTHON_VERSION} ${PIP_AND_SETUPTOOLS_TOO_OLD} ${DOLFINX_VERSION} ${CPP_WRAPPER_LIBRARY} ${ADD_PPA} | |
| - name: Add debian 12 to matrix json file | |
| run: | | |
| echo "Skipped: debian 12 has dolfinx v0.5.2, which has a custom patch for dolfinx.mesh.Mesh wrapping that breaks plotting" | |
| - name: Add debian unstable to matrix json file | |
| run: | | |
| CONTAINER_OS="debian" | |
| CONTAINER_RELEASE="unstable" | |
| MOVED_TO_OLD_RELEASES="false" | |
| PYTHON_VERSION="3.13" | |
| PIP_AND_SETUPTOOLS_TOO_OLD="false" | |
| DOLFINX_VERSION="0.9.0" | |
| CPP_WRAPPER_LIBRARY="nanobind" | |
| ADD_PPA="false" | |
| echo "Temporarily disabled because pypi does not provide wheels for vtk 9.3 compatible with python 3.13, and apt install python3-vtk9 does not get picked up by pip show vtk" | |
| # bash ${MATRIX_SCRIPT_FILE} ${CONTAINER_OS} ${CONTAINER_RELEASE} ${MOVED_TO_OLD_RELEASES} ${PYTHON_VERSION} ${PIP_AND_SETUPTOOLS_TOO_OLD} ${DOLFINX_VERSION} ${CPP_WRAPPER_LIBRARY} ${ADD_PPA} | |
| - name: Finalize matrix json file | |
| run: | | |
| sed -i '$s/,//' ${MATRIX_JSON_FILE} | |
| echo -e "\t]" >> ${MATRIX_JSON_FILE} | |
| echo -e "}" >> ${MATRIX_JSON_FILE} | |
| - name: Display matrix json file | |
| run: | | |
| cat ${MATRIX_JSON_FILE} | |
| - name: Store matrix json file content in the output variable | |
| id: store-matrix | |
| run: | | |
| echo "matrix=$(cat ${MATRIX_JSON_FILE} | tr -d ' \t\n\r')" >> ${GITHUB_OUTPUT} | |
| test: | |
| runs-on: ubuntu-latest | |
| needs: generate-matrix | |
| strategy: | |
| matrix: ${{ fromJson(needs.generate-matrix.outputs.matrix) }} | |
| fail-fast: false | |
| container: ${{ matrix.container_os }}:${{ matrix.container_release }} | |
| name: "test (${{ matrix.container_os }}:${{ matrix.container_release }}, ppa: ${{ matrix.add_ppa }}, v${{ matrix.dolfinx_version }}, py${{ matrix.python_version }}, ${{ matrix.petsc_scalar_type }})" | |
| env: | |
| OMPI_ALLOW_RUN_AS_ROOT: "1" | |
| OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: "1" | |
| OMPI_MCA_rmaps_base_oversubscribe: "1" | |
| PRTE_MCA_rmaps_default_mapping_policy: ":oversubscribe" | |
| steps: | |
| - name: Update apt sources file | |
| if: matrix.container_os == 'ubuntu' && matrix.moved_to_old_releases == true | |
| run: | | |
| sed -i -re 's/([a-z]{2}\.)?archive.ubuntu.com|security.ubuntu.com/old-releases.ubuntu.com/g' /etc/apt/sources.list | |
| - name: Install git | |
| run: | | |
| export DEBIAN_FRONTEND="noninteractive" | |
| apt update | |
| apt install -y git | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: dolfinx-v${{ matrix.dolfinx_version }} | |
| - name: Add FEniCS PPA | |
| if: matrix.container_os == 'ubuntu' && matrix.add_ppa == true | |
| run: | | |
| export DEBIAN_FRONTEND="noninteractive" | |
| apt install -y software-properties-common | |
| add-apt-repository ppa:fenics-packages/fenics | |
| apt update | |
| - name: Install DOLFINx | |
| run: | | |
| export DEBIAN_FRONTEND="noninteractive" | |
| PETSC_SCALAR_TYPE=${{ matrix.petsc_scalar_type }} | |
| if [[ -n "${PETSC_SCALAR_TYPE}" ]]; then | |
| apt install -y python3-dolfinx-${PETSC_SCALAR_TYPE} | |
| else | |
| apt install -y python3-dolfinx-real | |
| fi | |
| shell: bash | |
| - name: Ensure python version correctness | |
| run: | | |
| EXPECTED_PYTHON_VERSION=${{ matrix.python_version }} | |
| ACTUAL_PYTHON_VERSION=$(python3 -c 'import sys; print("{}.{}".format(sys.version_info.major, sys.version_info.minor))') | |
| if [[ "${EXPECTED_PYTHON_VERSION}" != "${ACTUAL_PYTHON_VERSION}" ]]; then | |
| echo "Invalid python version: expected ${EXPECTED_PYTHON_VERSION}, got ${ACTUAL_PYTHON_VERSION}" | |
| exit 1 | |
| fi | |
| shell: bash | |
| - name: Set PETSC_DIR and SLEPC_DIR | |
| run: | | |
| PETSC_SCALAR_TYPE=${{ matrix.petsc_scalar_type }} | |
| if [[ -n "${PETSC_SCALAR_TYPE}" ]]; then | |
| PETSC_BASE_DIR=/usr/lib/petscdir | |
| SLEPC_BASE_DIR=/usr/lib/slepcdir | |
| PETSC_DIR=$(find ${PETSC_BASE_DIR} -type d -name "x86_64-linux-gnu-${PETSC_SCALAR_TYPE}") | |
| SLEPC_DIR=$(find ${SLEPC_BASE_DIR} -type d -name "x86_64-linux-gnu-${PETSC_SCALAR_TYPE}") | |
| echo "PETSC_DIR=${PETSC_DIR}" >> $GITHUB_ENV | |
| echo "SLPEC_DIR=${SLEPC_DIR}" >> $GITHUB_ENV | |
| fi | |
| shell: bash | |
| - name: Ensure dolfinx version correctness | |
| run: | | |
| EXPECTED_DOLFINX_VERSION=${{ matrix.dolfinx_version }} | |
| ACTUAL_DOLFINX_VERSION=$(python3 -c 'import dolfinx; print(".".join(dolfinx.__version__.split(".")[:3]))') | |
| if [[ "${EXPECTED_DOLFINX_VERSION}" != "${ACTUAL_DOLFINX_VERSION}" ]]; then | |
| echo "Invalid dolfinx version: expected ${EXPECTED_DOLFINX_VERSION}, got ${ACTUAL_DOLFINX_VERSION}" | |
| exit 1 | |
| fi | |
| shell: bash | |
| - name: Install pip | |
| run: | | |
| export DEBIAN_FRONTEND="noninteractive" | |
| apt update | |
| apt install -y python3-pip | |
| - name: Upgrade pip and setuptools | |
| if: matrix.pip_and_setuptools_too_old == true | |
| run: | | |
| python3 -m pip install --upgrade packaging pip setuptools wheel | |
| - name: Install multiphenicsx core dependencies | |
| run: | | |
| CPP_WRAPPER_LIBRARY=${{ matrix.cpp_wrapper_library }} | |
| if [[ "${CPP_WRAPPER_LIBRARY}" == "pybind11" ]]; then | |
| apt install -y python3-pybind11 | |
| else | |
| apt install -y python3-exceptiongroup python3-nanobind python3-pathspec python3-pyproject-metadata python3-scikit-build-core | |
| fi | |
| shell: bash | |
| - name: Install multiphenicsx test dependencies | |
| run: | | |
| apt install -y python3-gmsh python3-matplotlib python3-scipy python3-sympy | |
| - name: Remove externally managed marker | |
| run: | | |
| rm -f /usr/lib/python3.*/EXTERNALLY-MANAGED | |
| - name: Install multiphenicsx | |
| run: | | |
| CPP_WRAPPER_LIBRARY=${{ matrix.cpp_wrapper_library }} | |
| if [[ "${CPP_WRAPPER_LIBRARY}" == "pybind11" ]]; then | |
| python3 -m pip install .[tests,tutorials] | |
| else | |
| python3 -m pip install --check-build-dependencies --no-build-isolation .[tests,tutorials] | |
| fi | |
| shell: bash | |
| - name: Remove source directory to ensure that package from installation directory is used | |
| run: | | |
| rm -rf multiphenicsx | |
| - name: Run unit tests (serial) | |
| run: | | |
| python3 -m pytest tests/unit | |
| - name: Run unit tests (parallel) | |
| run: | | |
| mpirun -n 3 python3 -m pytest tests/unit | |
| - name: Drop tutorials which are flaky with apt provided dolfinx | |
| run: | | |
| PETSC_SCALAR_TYPE=${{ matrix.petsc_scalar_type }} | |
| if [[ "${PETSC_SCALAR_TYPE}" == "complex" ]]; then | |
| rm -rf tutorials/04_eigenvalue_problems | |
| fi | |
| shell: bash | |
| - name: Run tutorials (serial) | |
| run: | | |
| python3 -m pytest tutorials | |
| - name: Run tutorials (parallel) | |
| run: | | |
| python3 -m pytest --np 3 tutorials | |
| - name: Upload tutorials logs as an artifact in case of failure | |
| if: failure() || cancelled() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: "tutorials-logs-${{ matrix.container_os }}-${{ matrix.container_release }}-ppa-${{ matrix.add_ppa }}-v${{ matrix.dolfinx_version }}-py${{ matrix.python_version }}-${{ matrix.petsc_scalar_type }}" | |
| path: | | |
| tutorials/**/.ipynb_pytest/**/*.log* | |
| include-hidden-files: true | |
| 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: apt_against_releases.yml | |
| days-elapsed: 55 |