MAINT: Switch to abi3 mode and unify before_all (openmeeg#708)

.github/workflows/build_and_test.yml

@@ -18,7 +18,7 @@ env:
 
 defaults:
   run:
-    shell: bash -el {0}
+    shell: bash -o pipefail -el {0}
 
 jobs:
 
@@ -61,6 +61,11 @@ jobs:
           python: cmake
           windows_compiler: msvc
           slow: false
+        - os: macos-15
+          blas: OpenBLAS
+          blas_linking: dynamic
+          python: cmake
+          slow: false
         - os: macos-13
           blas: OpenBLAS
           blas_linking: dynamic
@@ -93,9 +98,6 @@ jobs:
           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
@@ -265,7 +267,7 @@ jobs:
             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 setuptools_scm wheel twine threadpoolctl $EXTRA_PIP
+        pip install --upgrade --progress-bar off --only-binary="numpy" -q setuptools setuptools_scm wheel twine threadpoolctl "swig>=4.2" $EXTRA_PIP
 
 
     - name: MKL setup - mkl via conda
@@ -344,12 +346,14 @@ jobs:
       if: startswith(steps.env-vars.outputs.os,'macos')
       run: |
         echo "Installing dependencies with brew"
-        brew update > /dev/null
+        echo "::group::brew update"
+        brew update
+        echo "::endgroup::"
         if [[ "${{steps.env-vars.outputs.blas}}" == "OpenBLAS" ]]; then
           BREW_EXTRA=openblas
         fi
         echo "Installing dependencies with brew"
-        HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 HOMEBREW_NO_AUTO_UPDATE=1 brew install hdf5 libmatio libomp swig $BREW_EXTRA
+        HOMEBREW_NO_AUTO_UPDATE=1 brew install hdf5 libmatio libomp swig zlib $BREW_EXTRA
         echo "brew install complete"
         if [[ "${{steps.env-vars.outputs.blas}}" == "OpenBLAS" ]]; then
           if [[ "$(arch)" == "arm64" ]]; then
@@ -564,26 +568,40 @@ jobs:
         python setup.py bdist_wheel sdist
         echo "Wheels:"
         ls -alR dist/*.whl
-        unzip dist/*.whl -d check
+        FNAME=$(ls dist/*.whl)
+        echo "Processing $FNAME"
+        test -n "$FNAME"
+        test -f "$FNAME"
+        unzip "$FNAME" -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 $DELVEWHEEL_ADD_DLL -w dist dist/*.whl
+          PATH="$(cygpath -w $PWD/openmeeg);$PATH" delvewheel show "$FNAME"
+          PATH="$(cygpath -w $PWD/openmeeg);$PATH" delvewheel repair $DELVEWHEEL_ADD_DLL -w dist "$FNAME"
         elif [[ ${{steps.env-vars.outputs.os}} == 'macos'* ]]; then
-          delocate-wheel -v dist/*.whl
-          delocate-listdeps --all dist/*.whl
+          length=${#FNAME}
+          ORIG_FNAME="${FNAME::length-4}.orig"
+          cp -a "$FNAME" "$ORIG_FNAME"
+          # TODO: This is broken for our abi3 wheel
+          # delocate-wheel -v "$FNAME"
+          # This can change thename of the wheel so we need to re-find it
+          FNAME=$(ls dist/*.whl)
+          test -f "$FNAME"
+          mv "$ORIG_FNAME" "${ORIG_FNAME}.whl"
+          delocate-listdeps --all "$FNAME"
         # This build uses a toolchain that is too new, so skip this on Linux
         # else
-        #   auditwheel show dist/*.whl
-        #   auditwheel repair dist/*.whl
+        #   auditwheel show "$FNAME"
+        #   auditwheel repair "$FNAME"
+        #   FNAME=$(ls dist/*.whl)
+        #   test -f "$FNAME"
         fi
         rm -Rf check
-        unzip dist/*.whl -d check
+        unzip "$FNAME" -d check
         echo "Contents after:"
         ls -alR check/*
         twine check dist/*
-        pip install dist/*.whl --force-reinstall
+        pip install "$FNAME" --force-reinstall
         if [[ "${{ steps.env-vars.outputs.numpy_version }}" == "oldest" ]]; then
           pip install --only-binary "numpy" "numpy<2"
         fi
@@ -597,7 +615,7 @@ jobs:
         fi
 
     - name: Upload wrapped Python lib
-      if: startswith(steps.env-vars.outputs.python, 'python')
+      if: startswith(steps.env-vars.outputs.python, 'python') && (success() || failure())
       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 }}
@@ -621,3 +639,4 @@ jobs:
       if: startsWith(steps.env-vars.outputs.os,'ubuntu')
       with:
         files: coverage.info
+        token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/cibuildwheel_apps.yml

@@ -72,11 +72,11 @@ jobs:
           output-dir: installers
         env:
           CIBW_ENVIRONMENT_LINUX: ""
-          CIBW_ENVIRONMENT_MACOS: "OPENMEEG_MACOS_WHEEL_PURE=false"
+          CIBW_ENVIRONMENT_MACOS: ""
           CIBW_ENVIRONMENT_WINDOWS: ""
-          CIBW_BUILD: "cp310-*"
+          CIBW_BUILD: "cp310-*"  # same as default, but just in case we add PyPy in the future
           CIBW_BUILD_FRONTEND: "pip"
-          CIBW_BEFORE_ALL: "bash {project}/build_tools/cibw_before_all_apps.sh {project}"
+          CIBW_BEFORE_ALL: "bash {project}/build_tools/cibw_before_all.sh {project} app"
           CIBW_BEFORE_BUILD_WINDOWS: ""
           CIBW_REPAIR_WHEEL_COMMAND_LINUX: ""
           CIBW_REPAIR_WHEEL_COMMAND_MACOS: ""

.github/workflows/codeql-analysis.yml

@@ -34,7 +34,7 @@ jobs:
         gcc --version
     - name: Install NumPy
       run: |
-        pip install --upgrade --user --pre "numpy>=2.0.0b1,<3" setuptools setuptools_scm
+        pip install --upgrade --user --pre "numpy>=2.0.0b1,<3" setuptools setuptools_scm "swig>=4.2"
     - name: Configure
       run: |
         export DISABLE_CCACHE=1

.gitignore

@@ -18,3 +18,5 @@ coverage.info
 .vscode/
 Testing/
 .ccache/
+installers/
+wheelhouse/

CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required (VERSION 3.14)
-project (OpenMEEG VERSION 2.5.12 LANGUAGES C CXX)
+project (OpenMEEG VERSION 2.5.13 LANGUAGES C CXX)
 
 set(CMAKE_CXX_STANDARD 17)  # use c++17
 

build_tools/cibw_before_all.sh

@@ -8,9 +8,22 @@ if [[ "$1" == "" ]]; then
     echo "Usage: $0 <PROJECT_PATH>"
     exit 1
 fi
+KIND=$2
+if [[ "$KIND" == "" ]]; then
+    KIND=wheel
+fi
+if [[ "$KIND" != "wheel" ]] && [[ "$KIND" != "app" ]]; then
+    echo "Usage $0 <PROJECT_PATH> <KIND>"
+    echo "Got KIND=\"$KIND\", should be \"wheel\" or \"app\""
+    exit 1
+fi
 cd $1
 ROOT=$(pwd)
-echo "Using project root \"${ROOT}\" on RUNNER_OS=\"${RUNNER_OS}\""
+if [ -z "$RUNNER_OS" ]; then
+    echo "RUNNER_OS is empty, it must be present in the environment"
+    exit 1
+fi
+echo "Using project root \"${ROOT}\" on RUNNER_OS=\"${RUNNER_OS}\" to set up KIND=\"$KIND\""
 
 # Let's have NumPy help us out
 if [[ "$RUNNER_OS" == "macOS" ]] && [[ $(uname -m) == 'arm64' ]]; then
@@ -29,8 +42,11 @@ rm -Rf numpy numpy-1.23.1 tools
 echo "Using NumPy PLATFORM=\"${PLATFORM}\""
 git config --global --add safe.directory "$ROOT"
 git checkout LICENSE.txt  # This file is modified by NumPy
+if [[ "$KIND" == "app" ]]; then
+    rm -Rf .ccache gfortran.dmg gfortran-darwin-arm64.tar.gz openblas-v*.zip
+fi
 git status --porcelain --untracked-files=no
-test -z "$(git status --porcelain --untracked-files=no)"
+test -z "$(git status --porcelain --untracked-files=no)" || test "$CHECK_PORCELAIN" == "false"
 
 # PLATFORM can be:
 # linux-x86_64
@@ -40,15 +56,31 @@ test -z "$(git status --porcelain --untracked-files=no)"
 # win-amd64
 
 if [[ "$PLATFORM" == 'linux-'* ]]; then
+    echo "::group::yum"
     rpm --import https://repo.almalinux.org/almalinux/RPM-GPG-KEY-AlmaLinux
     yum -y install epel-release
-    yum -y install hdf5-devel matio-devel
-    export OPENBLAS_INCLUDE=/usr/local/include
-    export OPENBLAS_LIB=/usr/local/lib
+    yum -y install hdf5-devel matio-devel curl zip unzip tar ninja-build
+    echo "::endgroup::"
+    BLAS_DIR=/usr/local
+    export OPENBLAS_INCLUDE=$BLAS_DIR/include
+    export OPENBLAS_LIB=$BLAS_DIR/lib
     export CMAKE_CXX_FLAGS="-I$OPENBLAS_INCLUDE"
     export LINKER_OPT="-lgfortran -lpthread"
     export DISABLE_CCACHE=1
     SHARED_OPT="-DBUILD_SHARED_LIBS=OFF"
+    if [[ "$KIND" == "app" ]]; then
+        if [[ "$PLATFORM" == "linux-x86_64" ]]; then
+            export VCPKG_DEFAULT_TRIPLET="x64-linux"
+        elif [[ "$PLATFORM" == "linux-aarch64" ]]; then
+            export VCPKG_DEFAULT_TRIPLET="arm64-linux"
+        else
+            echo "Unknown PLATFORM=\"$PLATFORM\""
+            exit 1
+        fi
+        source ./build_tools/setup_vcpkg_compilation.sh
+        LAPACK_LIBRARIES_OPT="-DLAPACK_LIBRARIES=/usr/local/lib/libopenblas.a"
+        LIBDIR_OPT="-DCMAKE_INSTALL_LIBDIR=lib"
+    fi
 elif [[ "$PLATFORM" == 'macosx-'* ]]; then
     BLAS_DIR=/usr/local
     OPENBLAS_INCLUDE=$BLAS_DIR/include
@@ -57,60 +89,134 @@ elif [[ "$PLATFORM" == 'macosx-'* ]]; then
     export CMAKE_PREFIX_PATH="$BLAS_DIR"
     export LINKER_OPT="-L$OPENBLAS_LIB"
     if [[ "$PLATFORM" == "macosx-x86_64" ]]; then
-        export VCPKG_DEFAULT_TRIPLET="x64-osx-release-10.15"
-        export SYSTEM_VERSION_OPT="-DCMAKE_OSX_DEPLOYMENT_TARGET=10.15"
+        VC_NAME="x64"
+        MIN_VER="10.15"
+        LIBGFORTRAN="/usr/local/gfortran/lib/libgfortran.3.dylib"
     elif [[ "$PLATFORM" == "macosx-arm64" ]]; then
-        export VCPKG_DEFAULT_TRIPLET="arm64-osx-release-11.0"
-        export SYSTEM_VERSION_OPT="-DCMAKE_OSX_DEPLOYMENT_TARGET=11.0"
+        VC_NAME="arm64"
+        MIN_VER="11.0"
+        LIBGFORTRAN="$(find /opt/gfortran-darwin-arm64/lib -name libgfortran.dylib)"
     else
         echo "Unknown PLATFORM=\"$PLATFORM\""
         exit 1
     fi
+    export VCPKG_DEFAULT_TRIPLET="${VC_NAME}-osx-release-${MIN_VER}"
+    export SYSTEM_VERSION_OPT="-DCMAKE_OSX_DEPLOYMENT_TARGET=${MIN_VER}"
     source ./build_tools/setup_vcpkg_compilation.sh
     # libomp can cause segfaults on macos... maybe from version conflicts with OpenBLAS, or from being too recent?
     export OPENMP_OPT="-DUSE_OPENMP=OFF"
-    # need SWIG for Python bindings
-    brew install swig
+    if [[ "$KIND" == "app" ]]; then
+        GFORTRAN_LIB=$(dirname $LIBGFORTRAN)
+        GFORTRAN_NAME=$(basename $LIBGFORTRAN)
+        sudo chmod -R a+w $GFORTRAN_LIB
+        otool -L $LIBGFORTRAN
+        install_name_tool -id "@rpath/${GFORTRAN_NAME}" $LIBGFORTRAN
+        LIBRARIES_INSTALL_OPT="-DEXTRA_INSTALL_LIBRARIES=$LIBGFORTRAN"
+        if [[ "$PLATFORM" == "macosx-x86_64" ]]; then
+            PACKAGE_ARCH_SUFFIX="_Intel"
+            install_name_tool -change "${GFORTRAN_LIB}/libgcc_s.1.dylib" "@rpath/libgcc_s.1.dylib" ${LIBGFORTRAN}
+            install_name_tool -change "${GFORTRAN_LIB}/libquadmath.0.dylib" "@rpath/libquadmath.0.dylib" ${LIBGFORTRAN}
+            LIBRARIES_INSTALL_OPT="$LIBRARIES_INSTALL_OPT;$GFORTRAN_LIB/libgcc_s.1.dylib;$GFORTRAN_LIB/libquadmath.0.dylib"
+        else
+            PACKAGE_ARCH_SUFFIX="_M1"
+            install_name_tool -change "${GFORTRAN_LIB}/libgcc_s.2.dylib" "@rpath/libgcc_s.2.dylib" ${LIBGFORTRAN}
+            LIBRARIES_INSTALL_OPT="$LIBRARIES_INSTALL_OPT;$GFORTRAN_LIB/libgcc_s.2.dylib"
+            # Doesn't seem like this should be necessary but it is for the arm64 build
+            codesign --force -s - $GFORTRAN_LIB/libgcc_s.2.dylib
+        fi
+        # Need to fix the now-broken signature via ad-hoc signing (at least on arm)
+        # https://github.com/matthew-brett/delocate/blob/de38e09acd86b27c795c3d342d132031c45b1aff/delocate/tools.py#L660
+        codesign --force -s - $LIBGFORTRAN
+        # Set LINKER_OPT after vckpg_compilation.sh because it also sets LINKER_OPT
+        export LINKER_OPT="$LINKER_OPT -lgfortran -L$GFORTRAN_LIB"
+        PACKAGE_ARCH_OPT="-DPACKAGE_ARCH_SUFFIX=$PACKAGE_ARCH_SUFFIX"
+    fi
 elif [[ "$PLATFORM" == "win-amd64" ]]; then
     export VCPKG_DEFAULT_TRIPLET="x64-windows-release-static"
     export CMAKE_GENERATOR="Visual Studio 17 2022"
     source ./build_tools/setup_vcpkg_compilation.sh
     source ./build_tools/download_openblas.sh windows  # NumPy doesn't install the headers for Windows
     pip install delvewheel "pefile!=2024.8.26"
     export SYSTEM_VERSION_OPT="-DCMAKE_SYSTEM_VERSION=7"
+    if [[ "$KIND" == "app" ]]; then
+        OPENBLAS_DLL=$(ls $OPENBLAS_LIB/libopenblas*.dll)
+        echo "OPENBLAS_DLL=\"${OPENBLAS_DLL}\""
+        test -f $OPENBLAS_DLL
+        LIBRARIES_INSTALL_OPT="-DEXTRA_INSTALL_LIBRARIES=$(cygpath -m ${OPENBLAS_DLL})"
+    fi
 else
     echo "Unknown platform: ${PLATFORM}"
     exit 1
 fi
 export PYTHON_OPT="-DENABLE_PYTHON=OFF"
 export BLA_IMPLEMENTATION="OpenBLAS"
 export WERROR_OPT="-DENABLE_WERROR=ON"
-pip install cmake
-./build_tools/cmake_configure.sh -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=${ROOT}/install ${CMAKE_PREFIX_PATH_OPT} -DENABLE_APPS=OFF ${SHARED_OPT} -DCMAKE_INSTALL_UCRT_LIBRARIES=TRUE ${BLAS_LIBRARIES_OPT} ${LAPACK_LIBRARIES_OPT}
-cmake --build build --target install --target package --config release
+echo "::group::pip"
+pip install --upgrade cmake "swig>=4.2"
+echo "::endgroup::"
+if [[ "${KIND}" == "wheel" ]]; then
+    ./build_tools/cmake_configure.sh -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=${ROOT}/install ${CMAKE_PREFIX_PATH_OPT} -DENABLE_APPS=OFF ${SHARED_OPT} -DCMAKE_INSTALL_UCRT_LIBRARIES=TRUE ${BLAS_LIBRARIES_OPT} ${LAPACK_LIBRARIES_OPT}
+    echo "::group::cmake --build"
+    cmake --build build --target install --target package --config release
+    echo "::endgroup::"
+else
+    export BLA_STATIC_OPT="-DBLA_STATIC=ON"
+    ./build_tools/cmake_configure.sh -DCMAKE_WARN_DEPRECATED=FALSE -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=${ROOT}/install ${LIBDIR_OPT} ${LIBRARIES_INSTALL_OPT} ${PACKAGE_ARCH_OPT} ${CMAKE_PREFIX_PATH_OPT} -DENABLE_APPS=ON ${SHARED_OPT} -DCMAKE_INSTALL_UCRT_LIBRARIES=TRUE ${BLAS_LIBRARIES_OPT} ${LAPACK_LIBRARIES_OPT}
+    echo "::group::cmake --build"
+    cmake --build build --config release
+    if [[ "${PLATFORM}" == 'macosx-'* ]]; then
+        for name in OpenMEEG OpenMEEGMaths; do
+            install_name_tool -change "${LIBGFORTRAN}" "@rpath/${GFORTRAN_NAME}" ./build/${name}/lib${name}.1.1.0.dylib
+        done
+    fi
+    echo "::endgroup::"
+    echo "::group::cmake --target package"
+    cmake --build build --target package --target install --config release
+    mkdir -p installers
+    cp -av build/OpenMEEG-*-*.* installers/
+    echo "::endgroup::"
+fi
 
 # Put DLLs where they can be found
 if [[ "$PLATFORM" == 'linux'* ]]; then
-    ls -al install/lib64/*.so*
-    cp -av install/lib64/*.so* /usr/local/lib/
-elif [[ "$PLATFORM" == 'macosx-arm64' ]]; then
-    # https://matthew-brett.github.io/docosx/mac_runtime_link.html
-    #cp -av $ROOT/vcpkg_installed/arm64-osx-release-11.0/lib/libomp* $ROOT/install/lib/
-    otool -L $ROOT/install/lib/libOpenMEEG.1.1.0.dylib
-    # install_name_tool -change "@@HOMEBREW_PREFIX@@/opt/libomp/lib/libomp.dylib" "@loader_path/libomp.dylib" $ROOT/install/lib/libOpenMEEG.1.1.0.dylib
-    # otool -L $ROOT/install/lib/libOpenMEEG.1.1.0.dylib
+    mkdir -p /output
+    if [[ "$KIND" == "wheel" ]]; then
+        ls -al install/lib64/*.so*
+        cp -av install/lib64/*.so* /usr/local/lib/
+    else
+        cp -av build/OpenMEEG-*-*.* /output/
+    fi
+elif [[ "$PLATFORM" == 'macosx-'* ]]; then
+    if [[ "$KIND" == "app" ]]; then
+        otool -L $ROOT/build/OpenMEEG/libOpenMEEG.1.1.0.dylib
+        otool -L $ROOT/install/lib/libgfortran*.dylib
+    else
+        if [[ "$PLATFORM" == 'macosx-arm64' ]]; then
+            # https://matthew-brett.github.io/docosx/mac_runtime_link.html
+            #cp -av $ROOT/vcpkg_installed/arm64-osx-release-11.0/lib/libomp* $ROOT/install/lib/
+            otool -L $ROOT/install/lib/libOpenMEEG.1.1.0.dylib
+            # install_name_tool -change "@@HOMEBREW_PREFIX@@/opt/libomp/lib/libomp.dylib" "@loader_path/libomp.dylib" $ROOT/install/lib/libOpenMEEG.1.1.0.dylib
+            # otool -L $ROOT/install/lib/libOpenMEEG.1.1.0.dylib
+        fi
+    fi
 elif [[ "$PLATFORM" == 'win'* ]]; then
-    cp -av $OPENBLAS_LIB/libopenblas_v0.3.20-140-gbfd9c1b5-gcc_8_1_0.dll install/bin/
+    if [[ "$KIND" == "wheel" ]]; then
+        cp -av $OPENBLAS_LIB/libopenblas_v0.3.20-140-gbfd9c1b5-gcc_8_1_0.dll install/bin/
+    else
+        ./build_tools/install_dependency_walker.sh
+    fi
 fi
 
-# TODO: This is only necessary because SWIG does not work outside cmake yet,
-# and we want this on windows
-if [[ "$PLATFORM" == 'win'* ]]; then
-    mv build build_nopython
+if [[ "$KIND" == "wheel" ]]; then
+    # TODO: This is only necessary because SWIG does not work outside cmake yet,
+    # and we want this on windows
+    if [[ "$PLATFORM" == 'win'* ]]; then
+        mv build build_nopython
+    fi
+    echo "ls -al $PWD:"
+    ls -al
 fi
-echo "ls -al $PWD:"
-ls -al
 
 echo "git status:"
 git status --porcelain --untracked-files=no
-test -z "$(git status --porcelain --untracked-files=no)"
+test -z "$(git status --porcelain --untracked-files=no)" || test "$CHECK_PORCELAIN" == "false"