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[pre-commit.ci] pre-commit autoupdate

[pre-commit.ci] pre-commit autoupdate #1056

Workflow file for this run

.github/workflows/build_and_test.yml at 0eddc42
# This CI run does core building+testing of OpenMEEG using various OSes
# and options.
name: Test
concurrency:
group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
cancel-in-progress: true
on:
push:
branches: [ main ]
pull_request:
branches: [ main ]
env:
BUILD_TYPE: Release
PYTHONUNBUFFERED: '1'
defaults:
run:
shell: bash -el {0}
jobs:
build:
continue-on-error: true
timeout-minutes: 60
strategy:
matrix:
# By default, all builds use:
# - OpenBLAS
# - dynamic BLAS linking
# - cmake to build Python bindings
# - Python 3.10
# - The oldest supported version of numpy (numpyold)
# - MSVC on Windows (if relevant)
# - No VTK support
# - No slow python tests
#
# Deviations from this are noted by additions to the `include`
# params. Defaults are set up properly in the `env-vars` step,
# whose `output`s should be used by subsequent steps.
#
# MKL is tested on all OSes.
#
# Someday we could use OpenBLAS for Windows once vcpkg sorts things out
# (https://github.com/microsoft/vcpkg/issues/25176), but it's unclear
# if this will really help anything. NumPy/SciPy's OpenBLAS (which
# we use currently) should be well tested already though, so there is
# perhaps no need to switch.
include:
- os: ubuntu-20.04 # wrapping_ubuntu-20.04_cmake_OpenBLAS_dynamic_msvc_3.10_oldest
blas: OpenBLAS
blas_linking: dynamic
python: cmake
numpy: numpyold
slow: false
- os: windows-2019
blas: OpenBLAS
blas_linking: dynamic
python: cmake
windows_compiler: msvc
slow: false
- os: macos-13
blas: OpenBLAS
blas_linking: dynamic
python: cmake
slow: false
# Latest OpenBLAS release
- os: ubuntu-22.04 # wrapping_ubuntu-22.04_cmake_OpenBLAS_dynamic_msvc_3.12_latest
blas: OpenBLAS-latest
python-version: '3.12'
# PyPy build
- os: ubuntu-20.04 # wrapping_ubuntu-20.04_cmake_OpenBLAS_dynamic_msvc_pypy-3.9_latest
blas: OpenBLAS
python-version: 'pypy-3.9'
# One with latest numpy, plus VTK
- os: ubuntu-22.04
blas: OpenBLAS
numpy: numpydev
slow: true
# Windows mingw64 is disabled because of some path problem where cmake
# cannot find Python3 (!). We don't really need it because wheels and
# conda-forge both use MSVC, things work there, and it's the official
# Windows compiler. So we disable it for now at least (YAGNI).
# There is some stuff below and in cmake_configure.sh we could get rid
# of if we decide to fully drop it later.
# - os: windows-2019
# windows_compiler: mingw64
# MKL on each OS (static unless it has to be dynamic)
- os: windows-2019
blas: mkl-findblas
blas_linking: static
- os: ubuntu-20.04
blas: mkl-findblas
- os: macos-13
blas: mkl-findblas # only available on Intel
blas_linking: static
# One without Python but with VTK (once we fix it!)
- os: ubuntu-22.04
python: no-python
# vtk: vtk9 # TODO: Uncomment and update merge reqs
slow: true
# Windows static
- os: windows-2019
blas: OpenBLAS
blas_linking: static
# Setuptools
- os: ubuntu-20.04
python: setuptools
- os: macos-latest
python: setuptools
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v4
# all subsequent steps should use steps.env-vars.outputs.* instead
# of matrix.* entries
- name: Environment variables
id: env-vars
run: |
echo "os=${{matrix.os}}" >> $GITHUB_OUTPUT
if [[ "${{matrix.numpy}}" == *'dev' ]]; then
echo "numpy_version=dev" >> $GITHUB_OUTPUT
elif [[ "${{matrix.numpy}}" == *'old' ]]; then
echo "numpy_version=oldest" >> $GITHUB_OUTPUT
else
echo "numpy_version=latest" >> $GITHUB_OUTPUT
fi
PYTHON_VERSION="${{ matrix.python-version }}"
if [[ "$PYTHON_VERSION" == "" ]]; then
PYTHON_VERSION="3.10"
fi
echo "python_version=$PYTHON_VERSION" >> $GITHUB_OUTPUT
if [[ "${{matrix.blas_linking}}" == 'static' ]]; then
echo "Enabling static BLAS"
echo "BLA_STATIC_OPT=-DBLA_STATIC=ON" >> $GITHUB_ENV
echo "blas_linking=static" >> $GITHUB_OUTPUT
else
echo "blas_linking=dynamic" >> $GITHUB_OUTPUT
fi
if [[ "${{matrix.python}}" == 'no-python' ]]; then
echo "Disabling Python"
echo "PYTHON_OPT=-DENABLE_PYTHON=OFF" >> $GITHUB_ENV
echo "python=no-python" >> $GITHUB_OUTPUT
echo "python_type=no-python" >> $GITHUB_OUTPUT
else
echo "python=python" >> $GITHUB_OUTPUT
if [[ "${{matrix.python}}" == "" ]] || [[ "${{matrix.python}}" == "cmake" ]]; then
echo "python_type=cmake" >> $GITHUB_OUTPUT
elif [[ "${{matrix.python}}" == "setuptools" ]]; then
echo "python_type=setuptools" >> $GITHUB_OUTPUT
echo "PYTHON_OPT=-DENABLE_PYTHON=OFF" >> $GITHUB_ENV
else
echo "Unknown matrix.python=\"${{matrix.python}}\""
exit 1
fi
fi
if [[ "${{matrix.windows_compiler}}" == "mingw64" ]]; then
echo "windows_compiler=mingw64" >> $GITHUB_OUTPUT
else
echo "windows_compiler=msvc" >> $GITHUB_OUTPUT
fi
if [[ "${{matrix.slow}}" == "true" ]]; then
SLOW_OPT="-DTEST_SLOW_PYTHON=ON"
fi
if [[ "${{matrix.blas}}" == 'mkl'* ]]; then
echo "Setting BLA_IMPLEMENTATION=${{matrix.blas}}"
echo "BLA_IMPL=-DBLA_IMPLEMENTATION=${{matrix.blas}}" >> $GITHUB_ENV
echo "blas=${{matrix.blas}}" >> $GITHUB_OUTPUT
else
echo "blas=OpenBLAS" >> $GITHUB_OUTPUT
fi
if [[ "${{matrix.blas}}" == *'-latest' ]]; then
echo "Setting blas_version=latest"
echo "blas_version=latest" >> $GITHUB_OUTPUT
fi
# Build docs on Ubuntu, not elsewhere (for speed)
if [[ "${{matrix.os}}" == 'ubuntu'* ]]; then
DOC_OPT="-DBUILD_DOCUMENTATION=ON"
else
DOC_OPT="-DBUILD_DOCUMENTATION=OFF"
fi
# OpenMP doesn't work well on macOS
if [[ "${{matrix.os}}" == 'macos'* ]]; then
OPENMP_OPT="-DUSE_OPENMP=OFF"
fi
if [[ "${{matrix.vtk}}" == 'vtk'* ]]; then
echo "vtk_version=${{matrix.vtk}}" >> $GITHUB_OUTPUT
VTK_OPT="-DUSE_VTK=ON"
else
VTK_OPT="-DUSE_VTK=OFF"
fi
WERROR_OPT="-DENABLE_WERROR=ON"
# On windows, copy the runtime DLLs
if [[ "${{matrix.os}}" == 'windows'* ]]; then
PYTHON_COPY_RUNTIME_DLLS_OPT="-DPYTHON_COPY_RUNTIME_DLLS=ON"
echo "OMP_NUM_THREADS=1" >> $GITHUB_ENV
fi
echo "Using WERROR_OPT=$WERROR_OPT"
echo "SLOW_OPT=$SLOW_OPT" >> $GITHUB_ENV
echo "WERROR_OPT=$WERROR_OPT" >> $GITHUB_ENV
echo "Using DOC_OPT=$DOC_OPT"
echo "DOC_OPT=$DOC_OPT" >> $GITHUB_ENV
echo "Using VTK_OPT=$VTK_OPT"
echo "VTK_OPT=$VTK_OPT" >> $GITHUB_ENV
echo "Using OPENMP_OPT=$OPENMP_OPT"
echo "OPENMP_OPT=$OPENMP_OPT" >> $GITHUB_ENV
echo "Using PYTHON_COPY_RUNTIME_DLLS=$PYTHON_COPY_RUNTIME_DLLS_OPT"
echo "PYTHON_COPY_RUNTIME_DLLS_OPT=$PYTHON_COPY_RUNTIME_DLLS_OPT" >> $GITHUB_ENV
- run: sudo apt update -q
if: startsWith(steps.env-vars.outputs.os,'ubuntu')
- name: Setup ccache
uses: hendrikmuhs/ccache-action@v1.2
with:
key: ${{ github.job }}-${{ steps.env-vars.outputs.os }}
# Use conda for all Python except PyPy
- name: Python via conda
uses: conda-incubator/setup-miniconda@v3
if: startswith(steps.env-vars.outputs.python, 'python') && !startswith(steps.env-vars.outputs.python_version, 'pypy')
with:
activate-environment: "test"
python-version: "${{ steps.env-vars.outputs.python_version }}"
channels: conda-forge
channel-priority: strict
- name: Python via setup-python
uses: actions/setup-python@v5
if: startswith(steps.env-vars.outputs.python, 'python') && startswith(steps.env-vars.outputs.python_version, 'pypy')
with:
python-version: "${{ steps.env-vars.outputs.python_version }}"
- name: Python packages
if: startswith(steps.env-vars.outputs.python, 'python')
run: |
which python
python --version
which pip
pip --version
pip install --upgrade -q pip
if [[ ${{steps.env-vars.outputs.os}} == 'windows'* ]]; then
EXTRA_PIP="delvewheel pytest<8.0.0"
elif [[ ${{steps.env-vars.outputs.os}} == 'macos'* ]]; then
EXTRA_PIP="delocate pytest"
else
EXTRA_PIP="auditwheel pytest"
fi
if [[ "${{steps.env-vars.outputs.numpy_version}}" == 'dev' ]]; then
echo "Installing NumPy main"
pip install --upgrade --pre --only-binary ":all:" --default-timeout=60 -i "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" "numpy>=2.0.0.dev0"
elif [[ "${{steps.env-vars.outputs.numpy_version}}" == 'oldest' ]]; then
pip install --upgrade --only-binary ":all:" "numpy<2"
else
echo "Installing NumPy 2.0"
IS_PYPY=$(python -c "import sys; print(int('pypy' in sys.implementation.name))")
if [[ "$IS_PYPY" == "1" ]]; then
pip install --upgrade numpy
else
pip install --upgrade --pre --only-binary ":all:" "numpy>=2.0.0rc1,<3"
fi
fi
pip install --upgrade --progress-bar off --only-binary="numpy" -q setuptools wheel twine threadpoolctl $EXTRA_PIP
- name: MKL setup - mkl via conda
if: startswith(steps.env-vars.outputs.blas,'mkl')
run: |
# To get a local testing env, you can do for example:
# $ conda create -n openmeeg-mkl -c conda-forge --strict-channel-priority mkl-devel swig libmatio hdf5 numpy
# $ conda activate openmeeg-mkl
#
# On Windows, locally this static build almost works:
# ./build_tools/cmake_configure.sh -DBLA_IMPLEMENTATION=mkl-findblas -DBLA_STATIC=ON -DCMAKE_PREFIX_PATH="$CONDA_PREFIX/Library" -DCMAKE_CXX_FLAGS="-I$CONDA_PREFIX/Library/include" -DENABLE_PYTHON=ON
# cmake --build build --config Release
#
# On Linux, locally this works:
# ./build_tools/cmake_configure.sh -DBLA_IMPLEMENTATION=mkl-findblas -DCMAKE_PREFIX_PATH="$CONDA_PREFIX/lib" -DCMAKE_CXX_FLAGS="-I$CONDA_PREFIX/include" -DENABLE_PYTHON=ON
# cmake --build build --config Release
# cd build && LD_PRELOAD=$CONDA_PREFIX/lib/libmkl_rt.so ctest -C Release
#
conda install -c conda-forge -q mkl-devel
echo "$CONDA_PREFIX/lib/*mkl*:"
if [[ "${{steps.env-vars.outputs.os}}" == 'windows'* ]]; then
ls -alR $(cygpath -u $CONDA_PREFIX)/Library/lib/*mkl*
echo "CMAKE_PREFIX_PATH=$(cygpath -m $CONDA_PREFIX/Library)" >> $GITHUB_ENV
echo "CMAKE_CXX_FLAGS=-I$(cygpath -m $CONDA_PREFIX/Library/include) ${CMAKE_CXX_FLAGS}" >> $GITHUB_ENV
else
ls -alR $CONDA_PREFIX/lib/*mkl*
echo "CMAKE_PREFIX_PATH=$CONDA_PREFIX/lib" >> $GITHUB_ENV
echo "CMAKE_CXX_FLAGS=-I$CONDA_PREFIX/include ${CMAKE_CXX_FLAGS}" >> $GITHUB_ENV
if [[ "${{steps.env-vars.outputs.os}}" == 'ubuntu'* ]]; then
echo "LD_PRELOAD=$CONDA_PREFIX/lib/libmkl_rt.so" >> $GITHUB_ENV
fi
fi
- name: Windows 1 - cache vcpkg
if: startswith(steps.env-vars.outputs.os,'windows')
uses: actions/cache@v4
with:
path: |
vcpkg
build/vcpkg_installed
key: vcpkg-${{ hashFiles('**/vcpkg.json') }}-${{ steps.env-vars.outputs.windows_compiler }}-0
- name: Windows 2 - hdf5 and libmatio via vcpkg
if: startsWith(steps.env-vars.outputs.os,'windows')
id: runvcpkg
run: |
if [[ "${{ steps.env-vars.outputs.windows_compiler }}" == "mingw64" ]]; then
export VCPKG_DEFAULT_TRIPLET="x64-mingw-dynamic"
else
export VCPKG_DEFAULT_TRIPLET="x64-windows-release"
export CMAKE_GENERATOR="Visual Studio 16 2019"
fi
source ./build_tools/setup_vcpkg_compilation.sh
# On Windows, we tell cmake to copy all runtime deps to the build dir,
# and for tests (and Python) to find them, we need to add it to PATH
echo "PATH=$(cygpath -w ${PWD}/build);$PATH" >> $GITHUB_ENV
- name: Windows 3 - OpenBLAS via MacPython download
if: startsWith(steps.env-vars.outputs.blas,'OpenBLAS') && startsWith(steps.env-vars.outputs.os,'windows')
run: |
# OpenBLAS direct download (too slow to build using vcpkg)
# and renaming to match what cmake wants to see
source ./build_tools/download_openblas.sh windows
echo "OPENBLAS_LIB=$OPENBLAS_LIB" >> $GITHUB_ENV
echo "OPENBLAS_INCLUDE=$OPENBLAS_INCLUDE" >> $GITHUB_ENV
echo "LIB=$LIB" >> $GITHUB_ENV
echo "CMAKE_CXX_FLAGS=$CMAKE_CXX_FLAGS" >> $GITHUB_ENV
- name: macOS - hdf5, libmatio, libomp and (optionally) OpenBLAS via brew
if: startswith(steps.env-vars.outputs.os,'macos')
run: |
echo "Installing dependencies with brew"
brew update > /dev/null
if [[ "${{steps.env-vars.outputs.blas}}" == "OpenBLAS" ]]; then
BREW_EXTRA=openblas
fi
echo "Installing dependencies with brew"
# TODO: Not libmatio 1.5.27 compatible
brew tap-new $USER/local-libmatio
brew tap homebrew/core --force
brew extract --version=1.5.26 libmatio $USER/local-libmatio
HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 HOMEBREW_NO_AUTO_UPDATE=1 brew install hdf5 libmatio@1.5.26 libomp swig $BREW_EXTRA
echo "brew install complete"
if [[ "${{steps.env-vars.outputs.blas}}" == "OpenBLAS" ]]; then
if [[ "$(arch)" == "arm64" ]]; then
BLAS_DIR=/opt/homebrew/opt/openblas
else
BLAS_DIR=/usr/local/opt/openblas
fi
OPENBLAS_INCLUDE=$BLAS_DIR/include
OPENBLAS_LIB=$BLAS_DIR/lib
echo "Checking for $OPENBLAS_INCLUDE"
test -d "$OPENBLAS_INCLUDE"
echo "Checking for LAPACK"
ls -al $OPENBLAS_INCLUDE
test -f "$OPENBLAS_INCLUDE/lapack.h"
ls -al $OPENBLAS_LIB
test -f "$OPENBLAS_LIB/libopenblas.dylib"
echo "OPENBLAS_INCLUDE=$OPENBLAS_INCLUDE" >> $GITHUB_ENV
echo "CMAKE_CXX_FLAGS=-I$OPENBLAS_INCLUDE" >> $GITHUB_ENV
echo "LINKER_OPT=-L$OPENBLAS_LIB" >> $GITHUB_ENV
echo "CMAKE_PREFIX_PATH=$BLAS_DIR" >> $GITHUB_ENV
fi
# Set our version min
echo "SYSTEM_VERSION_OPT=-DCMAKE_OSX_DEPLOYMENT_TARGET=10.15" >> $GITHUB_ENV
- name: Linux - hdf5, libmatio, doxygen, (optionally) vtk, and (optionally) OpenBLAS via apt
if: startsWith(steps.env-vars.outputs.os,'ubuntu')
run: |
APT_EXTRA=""
if [[ "${{ steps.env-vars.outputs.blas }}" == "OpenBLAS" ]] && [[ "${{ steps.env-vars.outputs.blas_version }}" != "latest" ]]; then
APT_EXTRA="$APT_EXTRA libopenblas-dev"
fi
if [[ "${{ steps.env-vars.outputs.blas }}" == "OpenBLAS-latest" ]]; then
APT_EXTRA="$APT_EXTRA g++-12 gcc-12 gfortran-12"
fi
if [[ "${{ steps.env-vars.outputs.vtk_version }}" != "" ]]; then
APT_EXTRA="$APT_EXTRA lib${{ steps.env-vars.outputs.vtk_version }}-dev"
fi
set -x
sudo apt -yq install liblapacke-dev doxygen graphviz libhdf5-dev libmatio-dev lcov $APT_EXTRA
set +x
# Set GCC version
if [[ "${{ steps.env-vars.outputs.blas }}" == "OpenBLAS-latest" ]]; then
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-12 100 --slave /usr/bin/g++ g++ /usr/bin/g++-12 --slave /usr/bin/gcov gcov /usr/bin/gcov-12
fi
gcc --version
- name: Linux - OpenBLAS via GitHub
if: startsWith(steps.env-vars.outputs.os,'ubuntu') && startsWith(steps.env-vars.outputs.blas_version,'latest')
run: |
curl -LO https://github.com/xianyi/OpenBLAS/archive/refs/tags/v0.3.20.tar.gz
tar xzf v0.3.20.tar.gz
ls -al
cd OpenBLAS-0.3.20
ls -alR .
make NO_FORTRAN=0 NO_STATIC=0 NO_DYNAMIC=0 NUM_THREADS=24 NO_WARMUP=1
sudo make install PREFIX=/usr/local
- name: Configure
run: |
if [[ "${{steps.env-vars.outputs.os}}" == 'windows'* ]]; then
export EXTRA_UCRT="-DCMAKE_INSTALL_UCRT_LIBRARIES=TRUE"
elif [[ "${{steps.env-vars.outputs.os}}" == 'ubuntu'* ]]; then
export EXTRA_COV="-DENABLE_COVERAGE=ON"
fi
EXT_SUFFIX=$(python -c "import sysconfig;print(sysconfig.get_config_var('EXT_SUFFIX'))")
which cmake
cmake --version
source ./build_tools/cmake_configure.sh --install-prefix=$PWD/install -DCMAKE_VERBOSE_MAKEFILE=ON $EXTRA_UCRT $EXTRA_COV -DPython3_EXT_SUFFIX=$EXT_SUFFIX -DPYTHON_FORCE_EXT_SUFFIX=ON
- name: Build
run: |
cmake --build build --config ${{env.BUILD_TYPE}}
ls -al build
if [ -d build/wrapping/python/openmeeg ]; then
ls -alR build/wrapping/python/openmeeg
else
echo "No Python wrapping found"
fi
- name: Install
run: |
cmake --build build --target install --config Release
- name: Prepare for delocate
if: startswith(steps.env-vars.outputs.python, 'python')
# Let's make it easy for delvewheel to find the stuff it might need
run: |
cd build
if [[ "${{steps.env-vars.outputs.os}}" == 'windows'* ]]; then
echo "All:"
find . -type f -iname "*.dll"
echo "Data:"
find . -type f -name "Head1.geom"
echo "Before:"
ls -al *.dll || true
if [[ "${{steps.env-vars.outputs.blas}}" == "OpenBLAS" ]]; then
#if [[ "${{ steps.env-vars.outputs.blas_linking }}" != "static" ]]; then
if [[ "{{ steps.env-vars.outputs.windows_compiler }}" != "msvc"* ]]; then
strip $OPENBLAS_LIB/libopenblas_v*.dll
fi
cp $OPENBLAS_LIB/libopenblas_v*.dll .
cp $OPENBLAS_LIB/libopenblas_v*.dll openblas.dll
#fi
# TODO: if this is static it shouldn't be necessary, but it seems to be...
elif [[ "${{steps.env-vars.outputs.blas}}" == 'mkl'* ]]; then
ls -alR $(cygpath -u $CONDA_PREFIX)/Library/bin
cp $(cygpath -u $CONDA_PREFIX)/Library/bin/*mkl*.dll .
echo "DELVEWHEEL_ADD_DLL=--add-dll=mkl_intel_thread.2.dll" >> $GITHUB_ENV
fi
if [[ "{{ steps.env-vars.outputs.windows_compiler }}" != "msvc"* ]]; then
cp /c/Strawberry/c/bin/libquadmath-0.dll .
cp /mingw64/bin/libgcc_s_seh-1.dll .
cp /mingw64/bin/libwinpthread-1.dll .
cp /mingw64/bin/libstdc++-6.dll .
strip libstdc++-6.dll
cp /c/Strawberry/c/bin/libgomp-1.dll .
cp /mingw64/bin/zlib1.dll .
fi
if [[ -f "./OpenMEEGMaths/libmatio.dll" ]]; then
cp ./OpenMEEGMaths/libmatio.dll .
elif [[ -f "./OpenMEEGMaths/Release/libmatio.dll" ]]; then
cp ./OpenMEEGMaths/Release/libmatio.dll .
cp ./OpenMEEGMaths/Release/zlib1.dll .
cp ./OpenMEEGMaths/Release/hdf5.dll .
fi
echo "After:"
ls -al *.dll || true
if [[ "${{steps.env-vars.outputs.python_type}}" == 'cmake' ]]; then
cp -a *.dll wrapping/python/openmeeg
else
cp -a *.dll ../wrapping/python/openmeeg
fi
fi
cat OpenMEEGConfigure.h
- name: Check installed binaries and Python wrapper
run: |
ls -alR ./install/bin ./install/lib
if [[ "${{steps.env-vars.outputs.os}}" == 'windows'* ]]; then
export PATH="$PWD/build:$PWD/install/bin:$(cygpath -u $CONDA_PREFIX)/Library:$PATH"
echo "PATH=$PATH"
elif [[ "${{steps.env-vars.outputs.os}}" == 'macos'* ]]; then
export DYLD_LIBRARY_PATH="$CONDA_PREFIX/lib:$PWD/install/lib:$DYLD_LIBRARY_PATH"
echo "DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH"
else
export LD_LIBRARY_PATH="$CONDA_PREFIX/lib:$PWD/install/lib:/usr/local/lib:LD_LIBRARY_PATH"
echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
fi
./install/bin/om_minverser --help
if [[ "${{steps.env-vars.outputs.python_type}}" == 'cmake' ]]; then
PYVER=$(python -c "import sys; print('.'.join(sys.version.split('.')[:2]))")
PYNAME=$(python -c "import sys; print('pypy' if 'pypy' in sys.implementation.name else 'python')")
if [[ "${{steps.env-vars.outputs.os}}" == 'windows'* ]]; then
export PYTHONPATH=$PWD/install/lib/site-packages
./build_tools/install_dependency_walker.sh
# Ideally this would not be necessary but it makes things work
cp build/*.dll $PWD/install/lib/site-packages/openmeeg/
./Dependencies/Dependencies.exe -modules $PWD/install/lib/site-packages/openmeeg/_openmeeg*.pyd
else
export PYTHONPATH=$PWD/install/lib/${PYNAME}${PYVER}/site-packages
fi
echo "PYTHONPATH=$PYTHONPATH"
python -c "import openmeeg._openmeeg_wrapper as _omc; print(_omc.sqr(4)); assert _omc.sqr(4) == 16"
echo "pip show openmeeg:"
pip show openmeeg
fi
- name: Create, delocate, check, install, and test wheel
if: startswith(steps.env-vars.outputs.python, 'python')
id: wheel
run: |
if [[ "${{steps.env-vars.outputs.python_type}}" == 'setuptools' ]]; then
export OPENMEEG_INCLUDE=$PWD/install/include/OpenMEEG
export OPENMEEG_LIB=$PWD/install/lib
export OPENMEEG_USE_SWIG=1
if [[ "${{steps.env-vars.outputs.os}}" == 'windows'* ]]; then
export PATH="$PWD/build:$PWD/install/bin:$(cygpath -u $CONDA_PREFIX)/Library:$(cygpath -u $CONDA_PREFIX)/Library/lib:$PATH"
export OPENMEEG_LIB=$(cygpath -w $OPENMEEG_LIB)
export OPENMEEG_INCLUDE=$(cygpath -w $OPENMEEG_INCLUDE)
if [[ "${{steps.env-vars.outputs.windows_compiler}}" == 'msvc'* ]]; then
export CL="/std:c++17"
fi
export SWIG_FLAGS="msvc"
echo "PATH=$PATH"
echo "CL=$CL"
elif [[ "${{steps.env-vars.outputs.os}}" == 'macos'* ]]; then
export DYLD_LIBRARY_PATH="$CONDA_PREFIX/lib:$PWD/install/lib:$DYLD_LIBRARY_PATH"
export CPATH="$OPENBLAS_INCLUDE:$CPATH"
echo "DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH"
echo "CPATH=$CPATH"
else
export LD_LIBRARY_PATH="$CONDA_PREFIX/lib:$PWD/install/lib:/usr/local/lib:LD_LIBRARY_PATH"
export LIBRARY_PATH="$CONDA_PREFIX/lib:$PWD/install/lib:/usr/local/lib:LIBRARY_PATH"
echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
fi
cd wrapping/python # in root
echo "path=wrapping/python/dist/*.whl" >> $GITHUB_OUTPUT
else
cd build/wrapping/python # in build subdirectory
echo "path=build/wrapping/python/dist/*.whl" >> $GITHUB_OUTPUT
fi
pwd
python setup.py bdist_wheel sdist
echo "Wheels:"
ls -alR dist/*.whl
unzip dist/*.whl -d check
echo "Contents before:"
ls -alR check/*
if [[ ${{steps.env-vars.outputs.os}} == 'windows'* ]]; then
PATH="$(cygpath -w $PWD/openmeeg);$PATH" delvewheel show dist/*.whl
PATH="$(cygpath -w $PWD/openmeeg);$PATH" delvewheel repair $DELVEWHEEL_ADD_DLL -w dist dist/*.whl
elif [[ ${{steps.env-vars.outputs.os}} == 'macos'* ]]; then
delocate-wheel -v dist/*.whl
delocate-listdeps --all dist/*.whl
# This build uses a toolchain that is too new, so skip this on Linux
# else
# auditwheel show dist/*.whl
# auditwheel repair dist/*.whl
fi
rm -Rf check
unzip dist/*.whl -d check
echo "Contents after:"
ls -alR check/*
twine check dist/*
pip install dist/*.whl --force-reinstall
cd ~
python -c "import openmeeg; print(openmeeg.__version__)"
${GITHUB_WORKSPACE}/build_tools/cibw_test_command.sh ${GITHUB_WORKSPACE}
pip uninstall -yq openmeeg
# Now make it so our tests can find the libs
if [[ ${{steps.env-vars.outputs.os}} == 'windows'* ]]; then
echo "PYTHONPATH=$(cygpath -w ${PWD}/build);$PYTHONPATH" >> $GITHUB_ENV
fi
- name: Upload wrapped Python lib
if: startswith(steps.env-vars.outputs.python, 'python')
uses: actions/upload-artifact@v4
with:
name: wrapping_${{ steps.env-vars.outputs.os }}_${{ steps.env-vars.outputs.python_type }}_${{ steps.env-vars.outputs.blas }}_${{ steps.env-vars.outputs.blas_linking }}_${{ steps.env-vars.outputs.windows_compiler }}_${{ steps.env-vars.outputs.python_version }}_${{ steps.env-vars.outputs.numpy_version }}
path: ${{ steps.wheel.outputs.path }}
- name: Test
working-directory: ${{github.workspace}}/build
run: |
ctest -C $BUILD_TYPE || ctest -C $BUILD_TYPE --rerun-failed --output-on-failure
- name: Prepare coverage
if: startsWith(steps.env-vars.outputs.os,'ubuntu')
run: |
lcov --directory . --capture --output-file coverage.info # capture coverage info
lcov --remove coverage.info '/usr/*' --output-file coverage.info # filter out system
lcov --remove coverage.info '*numpy/*' --output-file coverage.info # filter out NumPy
lcov --list coverage.info
- name: Upload coverage to CodeCov
uses: codecov/codecov-action@v4
if: startsWith(steps.env-vars.outputs.os,'ubuntu')
with:
files: coverage.info