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Split testing workflows (#56)
* split jobs into separate workflows * removed disabled workflow * renamed workflow * try using an action for installing prerequisites * move actions into correct place * forgot to checkout repo * add indent * add default run shell to action * add shell to each run in action * add concurrency settings to tests * run tests only on pull-request into devel-tiny * install Struphy from Github in test
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‎.github/actions/install/psydac-req/action.yml‎

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name: Install prerequisites
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runs:
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using: composite
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steps:
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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cache-dependency-path: |
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pyproject.toml
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requirements.txt
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- name: Install non-Python dependencies on Ubuntu
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if: matrix.os == 'ubuntu-latest'
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uses: awalsh128/cache-apt-pkgs-action@latest
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with:
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packages: gfortran openmpi-bin libopenmpi-dev libhdf5-openmpi-dev g++ liblapack3 cmake cmake-curses-gui zlib1g-dev libnetcdf-dev libnetcdff-dev
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version: 1.0
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execute_install_scripts: true
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# When loading cached apt packages, the default MPI compiler isn't set.
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# Workaround is to 'reinstall' openmpi-bin, which doesn't actually perform
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# installation (since openmpi-bin already exists), but instead reruns
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# `update-alternatives` which fixes the symlinks to mpicc/mpif90.
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- name: Reconfigure non-Python dependencies on Ubuntu
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if: matrix.os == 'ubuntu-latest'
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shell: bash
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run: |
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sudo apt-get update
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sudo apt-get install --reinstall openmpi-bin libhdf5-openmpi-dev liblapack-dev libblas-dev
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- name: Install non-Python dependencies on macOS
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if: matrix.os == 'macos-14'
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shell: bash
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run: |
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brew install make
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brew install open-mpi
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brew install hdf5-mpi
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brew install libomp
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brew update
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brew install python3
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brew install gcc
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brew install openblas
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brew install lapack
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brew install git
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brew install pandoc
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brew install cmake
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brew install netcdf-fortran
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brew install pkgconf
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GFORTRAN_HOME=$(which gfortran || true)
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echo "GFORTRAN_HOME : $GFORTRAN_HOME"
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if [[ ! -f "$GFORTRAN_HOME" ]]; then
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gfort=$(find ${PATH//:/\/ } -name 'gfortran-*' -exec basename {} \; | sort | tail -n 1 || true)
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echo "Found $gfort"
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gfort_path=$(which ${gfort})
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folder=$(dirname ${gfort_path})
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ln -s ${gfort_path} ${folder}/gfortran
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fi
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echo "MPI_OPTS=--oversubscribe" >> $GITHUB_ENV
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echo "/opt/homebrew/opt/make/libexec/gnubin" >> $GITHUB_PATH
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- name: Print information on MPI and HDF5 libraries
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shell: bash
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run: |
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ompi_info
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h5pcc -showconfig -echo || true
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- name: Upgrade pip
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shell: bash
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run: |
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python -m pip install --upgrade pip
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- name: Determine directory of parallel HDF5 library
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shell: bash
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run: |
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if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
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HDF5_DIR=$(dpkg -L libhdf5-openmpi-dev | grep libhdf5.so | xargs dirname)
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elif [[ "${{ matrix.os }}" == "macos-14" ]]; then
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HDF5_DIR=$(brew list hdf5-mpi | grep "libhdf5.dylib" | xargs dirname | xargs dirname)
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fi
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echo $HDF5_DIR
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echo "HDF5_DIR=$HDF5_DIR" >> $GITHUB_ENV
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- name: Cache PETSc
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uses: actions/cache@v4
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id: cache-petsc
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env:
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cache-name: cache-PETSc
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with:
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path: "./petsc"
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key: petsc-${{ matrix.os }}-${{ matrix.python-version }}
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- if: steps.cache-petsc.outputs.cache-hit != 'true'
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name: Download a specific release of PETSc
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shell: bash
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run: |
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git clone --depth 1 --branch v3.23.3 https://gitlab.com/petsc/petsc.git
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- if: steps.cache-petsc.outputs.cache-hit != 'true'
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name: Install PETSc with complex support
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working-directory: ./petsc
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shell: bash
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run: |
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export PETSC_DIR=$(pwd)
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export PETSC_ARCH=petsc-cmplx
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./configure --with-scalar-type=complex --with-fortran-bindings=0 --have-numpy=1 --download-fblaslapack=1
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make all
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echo "PETSC_DIR=$PETSC_DIR" > petsc.env
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echo "PETSC_ARCH=$PETSC_ARCH" >> petsc.env
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# This step is not really necessary and could be combined with PETSc install
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# step; however it's good to verify if the cached PETSc installation really works!
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- name: Test PETSc installation
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working-directory: ./petsc
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shell: bash
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run: |
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source petsc.env
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make check
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echo "PETSC_DIR=$PETSC_DIR" >> $GITHUB_ENV
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echo "PETSC_ARCH=$PETSC_ARCH" >> $GITHUB_ENV
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- name: Install petsc4py
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working-directory: ./petsc
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shell: bash
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run: |
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python -m pip install wheel Cython numpy
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python -m pip install src/binding/petsc4py
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# - name: Check parallel h5py installation
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# run: |
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# python -c "
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# from mpi4py import MPI
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# import h5py
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# # This particular instantiation of h5py.File will fail if parallel h5py isn't installed
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# f = h5py.File('parallel_test.hdf5', 'w', driver='mpio', comm=MPI.COMM_WORLD)
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# print(f)"

‎.github/workflows/compile-with-pyccel-devel.yml‎

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name: Compile psydac w. pyccel devel
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on:
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pull_request:
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branches: [devel-tiny]
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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compile-with-pyccel-devel:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ ubuntu-latest ]
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# TODO: Make sure that struphy works with python > 3.11, keep the lower bound to 3.10
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python-version: [ '3.10', '3.12', '3.13' ]
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compile_language: ['c', 'fortran']
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isMerge:
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- ${{ github.event_name == 'push' && github.ref == 'refs/heads/devel' }}
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# exclude:
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# - { isMerge: false, python-version: '3.10' }
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# - { isMerge: false, python-version: '3.11' }
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# include:
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# - os: macos-14
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# python-version: '3.10'
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# - os: macos-14
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# python-version: '3.13'
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name: Compile psydac w. pyccel devel on ${{ matrix.os }} / Python ${{ matrix.python-version }} / ${{ matrix.compile_language }}
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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- name: Install prerequisites
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uses: ./.github/actions/install/psydac-req
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- name: Install project
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run: |
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python -m pip install ".[test]" --no-cache-dir
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python -m pip freeze
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- name: Set up environment variables
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run: |
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echo "PSYDAC_DIR=$GITHUB_WORKSPACE" >> $GITHUB_ENV
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echo "PYCCEL_DIR=$GITHUB_WORKSPACE/pyccel" >> $GITHUB_ENV
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- name: Clone pyccel from Github (devel branch)
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run: |
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git clone --recurse-submodules https://github.com/pyccel/pyccel.git $PYCCEL_DIR
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- name: Install pyccel
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working-directory: ${{ env.PYCCEL_DIR }}
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run: |
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echo "Pyccel location for this branch"
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pip show pyccel
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pip uninstall pyccel -y
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python -m pip install ".[test]" --no-cache-dir
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echo "Pyccel location after reinstalling"
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pip show pyccel
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- name: Compile psydac kernels
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run: |
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psydac-accelerate --language ${{ matrix.compile_language }}

‎.github/workflows/documentation.yml.disabled‎

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This file was deleted.

‎.github/workflows/test-psydac.yml‎

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name: Test psydac
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on:
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pull_request:
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branches: [devel-tiny]
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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test_psydac:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ ubuntu-latest ]
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# TODO: Make sure that struphy works with python > 3.11, keep the lower bound to 3.10
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python-version: [ '3.10', '3.12', '3.13' ]
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compile_language: ['c', 'fortran']
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isMerge:
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- ${{ github.event_name == 'push' && github.ref == 'refs/heads/devel' }}
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# exclude:
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# - { isMerge: false, python-version: '3.10' }
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# - { isMerge: false, python-version: '3.11' }
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# include:
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# - os: macos-14
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# python-version: '3.10'
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# - os: macos-14
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# python-version: '3.13'
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name: Test Psydac on ${{ matrix.os }} / Python ${{ matrix.python-version }} / ${{ matrix.compile_language }}
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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- name: Install prerequisites
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uses: ./.github/actions/install/psydac-req
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- name: Install project without mpi
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run: |
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python -m pip install ".[test]" --no-cache-dir
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python -m pip freeze
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- name: Compile psydac kernels
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run: |
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psydac-accelerate --language ${{ matrix.compile_language }}
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# - name: Test Pyccel optimization flags
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# run: |
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# pytest --pyargs psydac -m pyccel --capture=no
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- name: Initialize test directory
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run: |
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mkdir pytest
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cp mpi_tester.py pytest
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- name: Run coverage tests on macOS
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if: matrix.os == 'macos-14'
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working-directory: ./pytest
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run: >-
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python -m pytest -n auto
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--cov psydac
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--cov-config $GITHUB_WORKSPACE/pyproject.toml
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--cov-report xml
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--pyargs psydac -m "not parallel and not petsc"
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- name: Run single-process tests with Pytest on Ubuntu
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if: matrix.os == 'ubuntu-latest'
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working-directory: ./pytest
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run: |
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python -m pytest -n auto --pyargs psydac -m "not parallel and not petsc"
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- name: Run single-process PETSc tests with Pytest
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working-directory: ./pytest
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run: |
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python -m pytest -n auto --pyargs psydac -m "not parallel and petsc"
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- name: Install project with mpi
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run: |
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python -m pip install ".[mpi]"
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python -m pip freeze
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- name: Run MPI tests with Pytest
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working-directory: ./pytest
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run: |
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python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and not petsc"
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- name: Run MPI PETSc tests with Pytest
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working-directory: ./pytest
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run: |
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python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and petsc"
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- name: Remove test directory
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if: always()
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run: |
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rm -rf pytest
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