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Implement apt workflow
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@francesco-ballarin
francesco-ballarin committed Jan 11, 2025
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238 changes: 238 additions & 0 deletions .github/workflows/apt_against_releases.yml
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Expand Up @@ -6,10 +6,248 @@ on:
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="\${1}"
MOVED_TO_OLD_RELEASES="\${2}"
PYTHON_VERSION="\${3}"
PIP_AND_SETUPTOOLS_TOO_OLD="\${4}"
DOLFINX_VERSION="\${5}"
CPP_WRAPPER_LIBRARY="\${6}"
for PETSC_SCALAR_TYPE in "\${PETSC_SCALAR_TYPES_ARRAY[@]}"; do
echo -e "\t\t{" >> ${MATRIX_JSON_FILE}
echo -e "\t\t\t\"container\": \"\${CONTAINER}\"," >> ${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\"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 to matrix json file
run: |
CONTAINER="ubuntu: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"
bash ${MATRIX_SCRIPT_FILE} ${CONTAINER} ${MOVED_TO_OLD_RELEASES} ${PYTHON_VERSION} ${PIP_AND_SETUPTOOLS_TOO_OLD} ${DOLFINX_VERSION} ${CPP_WRAPPER_LIBRARY}
- name: Add ubuntu 22.10 to matrix json file
run: |
CONTAINER="ubuntu:22.10"
MOVED_TO_OLD_RELEASES="true"
PYTHON_VERSION="3.10"
PIP_AND_SETUPTOOLS_TOO_OLD="false"
DOLFINX_VERSION="0.6.0"
CPP_WRAPPER_LIBRARY="pybind11"
bash ${MATRIX_SCRIPT_FILE} ${CONTAINER} ${MOVED_TO_OLD_RELEASES} ${PYTHON_VERSION} ${PIP_AND_SETUPTOOLS_TOO_OLD} ${DOLFINX_VERSION} ${CPP_WRAPPER_LIBRARY}
- name: Add ubuntu 23.04 to matrix json file
run: |
CONTAINER="ubuntu:23.04"
MOVED_TO_OLD_RELEASES="false"
PYTHON_VERSION="3.11"
PIP_AND_SETUPTOOLS_TOO_OLD="false"
DOLFINX_VERSION="0.7.3"
CPP_WRAPPER_LIBRARY="pybind11"
bash ${MATRIX_SCRIPT_FILE} ${CONTAINER} ${MOVED_TO_OLD_RELEASES} ${PYTHON_VERSION} ${PIP_AND_SETUPTOOLS_TOO_OLD} ${DOLFINX_VERSION} ${CPP_WRAPPER_LIBRARY}
- name: Add ubuntu 23.10 to matrix json file
run: |
CONTAINER="ubuntu:23.10"
MOVED_TO_OLD_RELEASES="false"
PYTHON_VERSION="3.11"
PIP_AND_SETUPTOOLS_TOO_OLD="false"
DOLFINX_VERSION="0.8.0"
CPP_WRAPPER_LIBRARY="nanobind"
bash ${MATRIX_SCRIPT_FILE} ${CONTAINER} ${MOVED_TO_OLD_RELEASES} ${PYTHON_VERSION} ${PIP_AND_SETUPTOOLS_TOO_OLD} ${DOLFINX_VERSION} ${CPP_WRAPPER_LIBRARY}
- name: Add ubuntu 24.04 to matrix json file
run: |
CONTAINER="ubuntu: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"
bash ${MATRIX_SCRIPT_FILE} ${CONTAINER} ${MOVED_TO_OLD_RELEASES} ${PYTHON_VERSION} ${PIP_AND_SETUPTOOLS_TOO_OLD} ${DOLFINX_VERSION} ${CPP_WRAPPER_LIBRARY}
- name: Add ubuntu 24.10 to matrix json file
run: |
CONTAINER="ubuntu: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"
bash ${MATRIX_SCRIPT_FILE} ${CONTAINER} ${MOVED_TO_OLD_RELEASES} ${PYTHON_VERSION} ${PIP_AND_SETUPTOOLS_TOO_OLD} ${DOLFINX_VERSION} ${CPP_WRAPPER_LIBRARY}
- name: Add debian 12 to matrix json file
run: |
CONTAINER="debian:12"
MOVED_TO_OLD_RELEASES="false"
PYTHON_VERSION="3.11"
PIP_AND_SETUPTOOLS_TOO_OLD="false"
DOLFINX_VERSION="0.5.2"
CPP_WRAPPER_LIBRARY="pybind11"
bash ${MATRIX_SCRIPT_FILE} ${CONTAINER} ${MOVED_TO_OLD_RELEASES} ${PYTHON_VERSION} ${PIP_AND_SETUPTOOLS_TOO_OLD} ${DOLFINX_VERSION} ${CPP_WRAPPER_LIBRARY}
- name: Add debian unstable to matrix json file
run: |
CONTAINER="debian:unstable"
MOVED_TO_OLD_RELEASES="false"
PYTHON_VERSION="3.12"
PIP_AND_SETUPTOOLS_TOO_OLD="false"
DOLFINX_VERSION="0.9.0"
CPP_WRAPPER_LIBRARY="nanobind"
bash ${MATRIX_SCRIPT_FILE} ${CONTAINER} ${MOVED_TO_OLD_RELEASES} ${PYTHON_VERSION} ${PIP_AND_SETUPTOOLS_TOO_OLD} ${DOLFINX_VERSION} ${CPP_WRAPPER_LIBRARY}
- name: Finalize matrix json file
run: |
sed -i '$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: ${{ matrix.container }}
name: test (${{ matrix.container }}, v${{ matrix.dolfinx_version }}, py${{ matrix.python_version }}, ${{ matrix.petsc_scalar_type }})
steps:
- name: Update apt sources file
if: startsWith(matrix.container, 'ubuntu') == true && matrix.moved_to_old_releases == true
run: |
sed -i -re 's/([a-z]{2}\.)?archive.ubuntu.com|security.ubuntu.com/old-releases.ubuntu.com/g' /etc/apt/sources.list
- name: Install git
run: |
export DEBIAN_FRONTEND="noninteractive"
apt update
apt install -y git
- uses: actions/checkout@v4
with:
ref: dolfinx-v${{ matrix.dolfinx_version }}
- name: Add FEniCS PPA
if: startsWith(matrix.container, 'ubuntu') == 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"
apt install -y fenicsx
PETSC_SCALAR_TYPE=${{ matrix.petsc_scalar_type }}
if [[ -n "${PETSC_SCALAR_TYPE}" ]]; then
apt install -y python3-dolfinx-${PETSC_SCALAR_TYPE}
fi
shell: bash
- name: Ensure python version correctness
run: |
EXPECTED_PYTHON_VERSION=${{ 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 ${ACTUAL_PYTHON_VERSION}"
exit 1
fi
shell: bash
- name: Ensure dolfinx version correctness
run: |
EXPECTED_DOLFINX_VERSION=${{ matrix.dolfinx_version }}
ACTUAL_DOLFINX_VERSION=$(python3 -c 'import dolfinx; print(dolfinx.__version__)')
if [[ "${EXPECTED_DOLFINX_VERSION}" != "${ACTUAL_DOLFINX_VERSION}" ]]; then
echo "Invalid dolfinx version: expected ${EXPECTED_DOLFINX_VERSION}, got ${ACTUAL_DOLFINX_VERSION}"
exit 1
fi
shell: bash
- name: Install pip
run: |
export DEBIAN_FRONTEND="noninteractive"
apt update
apt install -y python3-pip
- name: Upgrade pip and setuptools
if: matrix.pip_and_setuptools_too_old == true
run: |
python3 -m pip install --upgrade pip setuptools
- name: Install multiphenicsx core dependencies
run: |
CPP_WRAPPER_LIBRARY=${{ matrix.cpp_wrapper_library }}
if [[ "${CPP_WRAPPER_LIBRARY}" == "pybind11" ]]; then
apt install -y python3-pybind11
else
apt install -y python3-exceptiongroup python3-nanobind python3-pathspec python3-pyproject-metadata python3-scikit-build-core
fi
shell: bash
- name: Install multiphenicsx test dependencies
run: |
apt install -y python3-gmsh python3-scipy python3-sympy
- name: Remove externally managed marker
run: |
rm -f /usr/lib/python3.*/EXTERNALLY-MANAGED
- name: Install multiphenicsx
run: |
CPP_WRAPPER_LIBRARY=${{ matrix.cpp_wrapper_library }}
if [[ "${CPP_WRAPPER_LIBRARY}" == "pybind11" ]]; then
python3 -m pip install .[tests,tutorials]
else
python3 -m pip install --check-build-dependencies --no-build-isolation .[tests,tutorials]
fi
shell: bash
- name: Remove source directory to ensure that package from installation directory is used
run: |
rm -rf multiphenicsx
- name: Set PETSC_DIR
run: |
PETSC_SCALAR_TYPE=${{ matrix.petsc_scalar_type }}
if [[ -n "${PETSC_SCALAR_TYPE}" ]]; then
echo "PETSC_DIR=/usr/lib/petscdir/petsc-${PETSC_SCALAR_TYPE}" >> $GITHUB_ENV
fi
shell: bash
- name: Run unit tests (serial)
run: |
python3 -m pytest tests/unit
- name: Run unit tests (parallel)
run: |
mpirun -n 3 python3 -m pytest tests/unit
- name: Run tutorials (serial)
run: |
python3 -m pytest tutorials
- name: Run tutorials (parallel)
run: |
python3 -m pytest --np 3 tutorials
- name: Upload tutorials logs as an artifact in case of failure
if: failure() || cancelled()
uses: actions/upload-artifact@v4
with:
name: "tutorials-logs-${{ matrix.dolfinx_version }}-${{ matrix.petsc_scalar_type }}-${{ matrix.python_version }}"
path: |
tutorials/**/.ipynb_pytest/**/*.log*
include-hidden-files: true

warn:
runs-on: ubuntu-latest
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