Add BLAS/LAPACK support for macOS and Linux

.github/workflows/python-package.yml

@@ -157,7 +157,7 @@ jobs:
         # one for each Python version
         os: [ubuntu-latest]
         arch: [aarch64]
-        python: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
         include:
           - os: ubuntu-latest
             arch: x86_64
@@ -166,23 +166,23 @@ jobs:
             boost-arch: x86
             boost-toolset: msvc
             boost-platform-version: 2022
-            boost-version: "1.85.0"
+            boost-version: "1.86.0"
           - os: macos-14
             arch: arm64
             boost-arch: aarch64
             boost-toolset: clang
             # Since we only use the headers, we can use the platform version for this
             # macos version
             boost-platform-version: "14"
-            boost-version: "1.85.0"
+            boost-version: "1.86.0"
           - os: macos-13
             arch: x86_64
             boost-arch: x86
             boost-toolset: clang
             # Since we only use the headers, we can use the platform version for this
             # macos version
             boost-platform-version: "13"
-            boost-version: "1.85.0"
+            boost-version: "1.86.0"
       fail-fast: false
     steps:
       - name: Checkout the repository
@@ -236,8 +236,8 @@ jobs:
         if: runner.os != 'Linux'
         uses: actions/cache@v4
         with:
-          key: ${{ matrix.os }}-${{ matrix.arch }}-0
-          path: ${{ runner.temp }}/cache
+          key: ${{ matrix.os }}-${{ matrix.arch }}-1
+          path: ${{ github.workspace }}/cache
 
       # Windows-only steps
       - name: Set Up Nuget
@@ -247,7 +247,8 @@ jobs:
         with:
           python-version: 3.12
         if: runner.os == 'Windows'
-      - run: bash ./cibw_before_all_windows.sh "${{ runner.temp }}"
+      - name: Build required libraries
+        run: bash ./cibw_before_all_windows.sh "${{ github.workspace }}"
         if: runner.os == 'Windows'
       - name: Set up CIBW environment
         # On Windows, Boost_ROOT needs to have \ replaced by / because that's what
@@ -263,7 +264,7 @@ jobs:
 
       # macOS-only steps
       - name: Build required libraries
-        run: bash ./cibw_before_all_macos.sh "${{ runner.temp }}"
+        run: bash ./cibw_before_all_macos.sh "${{ github.workspace }}"
         if: runner.os == 'macOS'
       # Force installation to resolve Python 3.8 bug (https://github.com/pypa/cibuildwheel/pull/1871#issuecomment-2161613619)
       - name: Hack for 3.8 bug
@@ -280,7 +281,7 @@ jobs:
         if: runner.os == 'macOS'
 
       - name: Build wheels
-        uses: pypa/[email protected].2
+        uses: pypa/[email protected].3
         env:
           CIBW_ENVIRONMENT_LINUX: CT_SKIP_SLOW=1 CANTERA_TEST_DIR=/host/${{ steps.download-test-files.outputs.test-root }}
           CIBW_ENVIRONMENT_WINDOWS: CT_SKIP_SLOW=1 CMAKE_BUILD_PARALLEL_LEVEL=4

.gitignore

@@ -0,0 +1,4 @@
+cache
+hdf5-*
+HighFive-*
+*.tar.gz

cibw_before_all_macos.sh

@@ -36,11 +36,9 @@ set -eo pipefail
 function setup_github_env {
     if [[ "$GITHUB_ENV" != "" ]]; then
         echo "HDF5_DIR=${HDF5_DIR}" | tee -a $GITHUB_ENV
-        echo "LIBAEC_DIR=${LIBAEC_DIR}" | tee -a $GITHUB_ENV
-        echo "ZLIB_DIR=${ZLIB_DIR}" | tee -a $GITHUB_ENV
         echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}" | tee -a $GITHUB_ENV
         echo "MACOSX_DEPLOYMENT_TARGET=${MACOSX_DEPLOYMENT_TARGET}" | tee -a $GITHUB_ENV
-        echo "DYLD_FALLBACK_LIBRARY_PATH=${HDF5_DIR}/lib:${ZLIB_DIR}/lib:${LIBAEC_DIR}/lib" | tee -a $GITHUB_ENV
+        echo "DYLD_FALLBACK_LIBRARY_PATH=${HDF5_DIR}/lib" | tee -a $GITHUB_ENV
     fi
 }
 
@@ -51,22 +49,19 @@ if [[ "$1" == "" ]] ; then
     exit 1
 fi
 PROJECT_PATH="$1"
-SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
 ARCH=$(uname -m)
 
+HDF5_VERSION="1.14.5"
 ZLIB_VERSION="1.3.1"
-LIBAEC_VERSION="1.0.6"
-
-HDF5_VERSION="1.14.4.3"
+LIBAEC_VERSION="1.1.3"
+HDF5_PATCH_VERSION=${HDF5_VERSION}
+HIGHFIVE_VERSION="2.10.0"
 # Replace the last dot with a dash because that's what some of the files in this
 # release have done.
-HDF5_PATCH_VERSION=${HDF5_VERSION%.*}-${HDF5_VERSION##*.}
+# HDF5_PATCH_VERSION=${HDF5_VERSION%.*}-${HDF5_VERSION##*.}
 
 HDF5_DIR="${PROJECT_PATH}/cache/hdf5/${HDF5_VERSION}-${ARCH}"
-ZLIB_DIR="${PROJECT_PATH}/cache/zlib/${ZLIB_VERSION}-${ARCH}"
-LIBAEC_DIR="${PROJECT_PATH}/cache/libaec/${LIBAEC_VERSION}-${ARCH}"
-
-LD_LIBRARY_PATH="${ZLIB_DIR}/lib:${LD_LIBRARY_PATH}"
+HIGHFIVE_DIR="${PROJECT_PATH}/cache/highfive/${HIGHFIVE_VERSION}-${ARCH}"
 
 # When compiling HDF5, we should use the minimum across all Python versions for a given
 # arch, for versions see for example a more updated version of the following:
@@ -79,8 +74,9 @@ else
 fi
 
 lib_name=libhdf5.dylib
+inc_name=highfive.hpp
 
-if [ -f ${HDF5_DIR}/lib/${lib_name} ]; then
+if [ -f ${HDF5_DIR}/lib/${lib_name} ] && [ -f ${HIGHFIVE_DIR}/include/highfive/${inc_name} ]; then
     echo "using cached build"
     setup_github_env
     exit 0
@@ -92,50 +88,47 @@ brew install ninja cmake
 
 pushd ${PROJECT_PATH}
 
-curl -fsSLO "https://github.com/madler/zlib/releases/download/v${ZLIB_VERSION}/zlib-${ZLIB_VERSION}.tar.gz"
-tar -xzf zlib-${ZLIB_VERSION}.tar.gz
-
-mkdir -p zlib-${ZLIB_VERSION}/build
-pushd zlib-${ZLIB_VERSION}/build
-cmake -G Ninja \
-    -DCMAKE_INSTALL_PREFIX=${ZLIB_DIR} \
-    -DZLIB_BUILD_EXAMPLES=OFF \
-    ..
-
-ninja install
-popd
-
-curl -fsSLO "https://gitlab.dkrz.de/k202009/libaec/uploads/45b10e42123edd26ab7b3ad92bcf7be2/libaec-${LIBAEC_VERSION}.tar.gz"
-tar -xzf libaec-${LIBAEC_VERSION}.tar.gz
-mkdir -p libaec-${LIBAEC_VERSION}/build
-pushd libaec-${LIBAEC_VERSION}
-patch -p0 < ${SCRIPT_DIR}/libaec_cmakelists.patch
-pushd build
+curl -fsSLO "https://github.com/HDFGroup/hdf5/releases/download/hdf5_${HDF5_VERSION}/hdf5-${HDF5_PATCH_VERSION}.tar.gz"
+tar -xzf hdf5-${HDF5_PATCH_VERSION}.tar.gz
+mkdir -p hdf5-${HDF5_PATCH_VERSION}/build
+pushd hdf5-${HDF5_PATCH_VERSION}/build
 
 cmake -G Ninja \
     -DCMAKE_BUILD_TYPE=Release \
-    -DCMAKE_INSTALL_PREFIX=${LIBAEC_DIR} \
-    -DBUILD_TESTING=OFF \
+    -DCMAKE_INSTALL_PREFIX=${HDF5_DIR} \
+    -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON \
+    -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=ON \
+    -DHDF5_BUILD_EXAMPLES:BOOL=OFF \
+    -DHDF5_BUILD_TOOLS:BOOL=OFF \
+    -DBUILD_TESTING:BOOL=OFF \
+    -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=TGZ \
+    -DZLIB_PACKAGE_NAME:STRING=zlib \
+    -DZLIB_TGZ_NAME:STRING=zlib-${ZLIB_VERSION}.tar.gz \
+    -DZLIB_TGZ_ORIGPATH:STRING=https://github.com/madler/zlib/releases/download/v${ZLIB_VERSION} \
+    -DZLIB_USE_LOCALCONTENT:BOOL=OFF \
+    -DLIBAEC_PACKAGE_NAME:STRING=libaec \
+    -DLIBAEC_TGZ_NAME:STRING=libaec-${LIBAEC_VERSION}.tar.gz \
+    -DLIBAEC_TGZ_ORIGPATH:STRING=https://github.com/MathisRosenhauer/libaec/releases/download/v${LIBAEC_VERSION} \
+    -DLIBAEC_USE_LOCALCONTENT:BOOL=OFF \
+    -DHDF_PACKAGE_NAMESPACE:STRING=ct_ \
     ..
 
 ninja install
 popd
-popd
 
-curl -fsSLO "https://github.com/HDFGroup/hdf5/releases/download/hdf5_${HDF5_VERSION}/hdf5-${HDF5_PATCH_VERSION}.tar.gz"
-tar -xzf hdf5-${HDF5_PATCH_VERSION}.tar.gz
-mkdir -p hdf5-${HDF5_PATCH_VERSION}/build
-pushd hdf5-${HDF5_PATCH_VERSION}/build
+curl -fsSLO https://github.com/BlueBrain/HighFive/archive/refs/tags/v${HIGHFIVE_VERSION}.tar.gz
+tar -xzf v${HIGHFIVE_VERSION}.tar.gz
+mkdir -p HighFive-${HIGHFIVE_VERSION}/build
+pushd HighFive-${HIGHFIVE_VERSION}/build
 
 cmake -G Ninja \
     -DCMAKE_BUILD_TYPE=Release \
-    -DZLIB_ROOT=${ZLIB_DIR} \
-    -Dlibaec_ROOT=${LIBAEC_DIR} \
-    -DCMAKE_INSTALL_PREFIX=${HDF5_DIR} \
-    -DHDF5_ENABLE_Z_LIB_SUPPORT=ON \
-    -DHDF5_ENABLE_SZIP_SUPPORT=ON \
-    -DHDF5_BUILD_EXAMPLES=OFF \
-    -DBUILD_TESTING=OFF \
+    -DHDF5_ROOT=${HDF5_DIR} \
+    -DCMAKE_INSTALL_PREFIX=${HIGHFIVE_DIR} \
+    -DHIGHFIVE_USE_BOOST:BOOL=OFF \
+    -DHIGHFIVE_UNIT_TESTS:BOOL=OFF \
+    -DHIGHFIVE_EXAMPLES:BOOL=OFF \
+    -DHIGHFIVE_BUILD_DOCS:BOOL=OFF \
     ..
 
 ninja install

cibw_before_all_windows.sh

@@ -48,7 +48,7 @@ export LINK="/LIBPATH:$PROJECT_PATH\zlib-msvc-x64\build\native\lib_release"
 export ZLIB_ROOT="$PROJECT_PATH\zlib-msvc-x64\build\native"
 
 # HDF5
-export HDF5_VERSION="1.14.4.3"
+export HDF5_VERSION="1.14.5"
 export HDF5_VSVERSION="17-64"
 export HDF5_DIR="$PROJECT_PATH/cache/hdf5/$HDF5_VERSION"
 

get_hdf5_win.py

@@ -48,30 +48,23 @@
 import requests
 
 HDF5_URL = "https://github.com/HDFGroup/hdf5/releases/download/hdf5_{dotted_version}/hdf5-{dashed_version}.zip"
-ZLIB_ROOT = environ.get("ZLIB_ROOT")
 
 CMAKE_CONFIGURE_CMD = [
     "cmake",
     "-DBUILD_SHARED_LIBS:BOOL=ON",
     "-DCMAKE_BUILD_TYPE:STRING=RELEASE",
     "-DHDF5_BUILD_CPP_LIB=OFF",
-    "-DHDF5_BUILD_HL_LIB=ON",
+    "-DHDF5_BUILD_HL_LIB=OFF",
     "-DHDF5_BUILD_TOOLS:BOOL=OFF",
     "-DBUILD_TESTING:BOOL=OFF",
+    "-DHDF5_BUILD_EXAMPLES:BOOL=OFF",
 ]
-if ZLIB_ROOT:
-    CMAKE_CONFIGURE_CMD += [
-        "-DHDF5_ENABLE_Z_LIB_SUPPORT=ON",
-        f"-DZLIB_INCLUDE_DIR={ZLIB_ROOT}\\include",
-        f"-DZLIB_LIBRARY_RELEASE={ZLIB_ROOT}\\lib_release\\zlib.lib",
-        f"-DZLIB_LIBRARY_DEBUG={ZLIB_ROOT}\\lib_debug\\zlibd.lib",
-    ]
 CMAKE_BUILD_CMD = ["cmake", "--build"]
 CMAKE_INSTALL_ARG = ["--target", "install", "--config", "Release"]
 CMAKE_INSTALL_PATH_ARG = "-DCMAKE_INSTALL_PREFIX={install_path}"
-CMAKE_HDF5_LIBRARY_PREFIX = ["-DHDF5_EXTERNAL_LIB_PREFIX=h5py_"]
+CMAKE_HDF5_LIBRARY_PREFIX = ["-DHDF5_EXTERNAL_LIB_PREFIX=ct_"]
 REL_PATH_TO_CMAKE_CFG = "hdf5-{version}"
-DEFAULT_VERSION = "1.14.3.3"
+DEFAULT_VERSION = "1.14.5"
 VSVERSION_TO_GENERATOR = {
     "9": "Visual Studio 9 2008",
     "10": "Visual Studio 10 2010",
@@ -190,7 +183,7 @@ def main():
     install_path = environ.get("HDF5_DIR")
     version = environ.get("HDF5_VERSION", DEFAULT_VERSION)
     vs_version = environ.get("HDF5_VSVERSION")
-    use_prefix = True if environ.get("H5PY_USE_PREFIX") is not None else False
+    use_prefix = True if environ.get("HDF5_USE_PREFIX") is not None else False
 
     if install_path is not None:
         if not exists(install_path):
@@ -208,7 +201,7 @@ def main():
         print("using cached hdf5", file=stderr)
     if install_path is not None:
         print("hdf5 files: ", file=stderr)
-        for dirpath, dirnames, filenames in walk(install_path):
+        for dirpath, _, filenames in walk(install_path):
             for file in filenames:
                 print(" * " + pjoin(dirpath, file))