build(meson): much more robust build system

benchmarks/Memory/main.cpp

@@ -9,7 +9,7 @@
 
 #include "fourdst/logging/logging.h"
 #include "fourdst/atomic/species.h"
-#include "fourdst/composition/utils.h"
+#include "fourdst/composition/utils/utils.h"
 
 #include "quill/Logger.h"
 #include "quill/Backend.h"

benchmarks/SingleZoneSolver/gf_wall_vs_temp.cpp

@@ -11,7 +11,7 @@
 #include "fourdst/composition/composition.h"
 #include "fourdst/logging/logging.h"
 #include "fourdst/atomic/species.h"
-#include "fourdst/composition/utils.h"
+#include "fourdst/composition/utils/utils.h"
 
 #include "quill/Logger.h"
 #include "quill/Backend.h"

benchmarks/SingleZoneSolver/main.cpp

@@ -11,7 +11,7 @@
 #include "fourdst/composition/composition.h"
 #include "fourdst/logging/logging.h"
 #include "fourdst/atomic/species.h"
-#include "fourdst/composition/utils.h"
+#include "fourdst/composition/utils/utils.h"
 
 #include "quill/Logger.h"
 #include "quill/Backend.h"

benchmarks/Timing/main.cpp

@@ -7,7 +7,7 @@
 
 #include "fourdst/logging/logging.h"
 #include "fourdst/atomic/species.h"
-#include "fourdst/composition/utils.h"
+#include "fourdst/composition/utils/utils.h"
 
 #include "quill/Logger.h"
 #include "quill/Backend.h"

build-config/cppad/meson.build

@@ -7,7 +7,6 @@ cppad_cmake_options.add_cmake_defines({
                                           'include_doc': 'false',
                                           'CMAKE_POSITION_INDEPENDENT_CODE': true
                                       })
-
 cppad_cmake_options.set_install(false)
 
 cppad_sp = cmake.subproject(
@@ -31,13 +30,19 @@ libcppad_static = static_library(
 )
 
 cppad_dep = declare_dependency(
-  link_with: libcppad_static,
     include_directories: cppad_incs
 )
 
-message('Installing CppAD headers to ' + get_option('includedir'))
+message('Staging vendored CppAD headers for ' + gridfire_vendor_includedir)
-install_subdir(
+
-  'subprojects/CppAD-20250000.2/include',
+custom_target(
-  install_dir: get_option('includedir'),
+    'vendor_cppad_headers',
-  strip_directory: true
+    command: copytree_cmd + [
+        meson.project_source_root() / 'subprojects' / 'CppAD-20250000.2' / 'include' / 'cppad',
+        '@OUTPUT@',
+    ],
+    output: 'cppad',
+    depends: libcppad_static,
+    install: true,
+    install_dir: gridfire_vendor_includedir,
 )

build-config/eigen/meson.build

@@ -1,5 +1,13 @@
-eigen_dep = dependency(
+eigen_sp = subproject('eigen')
-    'eigen3',
+eigen_dep = eigen_sp.get_variable('eigen_dep').as_system()
-    version : '>=3.3',
+
-    fallback : ['eigen', 'eigen_dep']
+custom_target(
-).as_system()
+    'vendor_eigen_headers',
+    command: copytree_cmd + [
+        meson.project_source_root() / 'subprojects' / 'eigen-3.4.0' / 'Eigen',
+        '@OUTPUT@',
+    ],
+    output: 'Eigen',
+    install: true,
+    install_dir: gridfire_vendor_includedir,
+)

build-config/fourdst/meson.build

@@ -1,14 +1,11 @@
-# bring in all of the fourdst utility repositories
-
 fourdst_build_lib_all = true
 if not get_option('plugin_support')
     fourdst_build_lib_all=false
     message('Disabling fourdst plugin support as per user request.')
 endif
 
-fourdst_sp = subproject('fourdst',
+fourdst_default_options = [
-                        default_options:
+    'build_tests=' + get_option('build_tests').to_string(),
-                            ['build_tests=' + get_option('build_tests').to_string(),
     'build_python=' + get_option('build_python').to_string(),
     'build_lib_all=' + fourdst_build_lib_all.to_string(),
     'build_lib_comp=true',
@@ -17,7 +14,12 @@ fourdst_sp = subproject('fourdst',
     'build_lib_const=true',
     'pkg_config=' + get_option('pkg_config').to_string(),
 ]
-)
+
+if get_option('build_python')
+    fourdst_default_options += ['default_library=static']
+endif
+
+fourdst_sp = subproject('fourdst', default_options: fourdst_default_options)
 
 composition_dep = fourdst_sp.get_variable('composition_dep')
 log_dep = fourdst_sp.get_variable('log_dep')
@@ -36,3 +38,45 @@ if get_option('plugin_support')
     warning('Including plugin library from fourdst. Note this will bring in minizip-ng and openssl, which can cause build issues with cross compilation due to their complexity.')
     libplugin = fourdst_sp.get_variable('libplugin')
 endif
+
+if get_option('build_python')
+    sp_root = meson.project_source_root() / 'subprojects'
+
+    fourdst_header_trees = [
+
+        ['config',
+         sp_root / 'libconfig' / 'src' / 'config' / 'include' / 'fourdst' / 'config',
+         gridfire_includedir / 'fourdst'],
+        ['composition',
+         sp_root / 'libcomposition' / 'src' / 'composition' / 'include' / 'fourdst' / 'composition',
+         gridfire_includedir / 'fourdst'],
+        ['atomic',
+         sp_root / 'libcomposition' / 'src' / 'composition' / 'include' / 'fourdst' / 'atomic',
+         gridfire_includedir / 'fourdst'],
+        ['constants',
+         sp_root / 'libconstants' / 'src' / 'constants' / 'include' / 'fourdst' / 'constants',
+         gridfire_includedir / 'fourdst'],
+        ['logging',
+         sp_root / 'liblogging' / 'src' / 'logging' / 'include' / 'fourdst' / 'logging',
+         gridfire_includedir / 'fourdst'],
+        ['toml++',
+         sp_root / 'libconfig' / 'build-config' / 'tomlpp' / 'vendor' / 'include' / 'toml++',
+         gridfire_fourdst_vendor_includedir],
+        ['quill',
+         sp_root / 'quill' / 'include' / 'quill',
+         gridfire_fourdst_vendor_includedir],
+        ['CLI',
+         sp_root / 'CLI11-2.6.1' / 'include' / 'CLI',
+         gridfire_fourdst_vendor_includedir],
+    ]
+
+    foreach t : fourdst_header_trees
+        custom_target(
+            'wheel_headers_' + t[0].underscorify(),
+            command: copytree_cmd + [t[1], '@OUTPUT@'],
+            output: t[0],
+            install: true,
+            install_dir: t[2],
+        )
+    endforeach
+endif

build-config/json/meson.build

@@ -1,3 +1,9 @@
 json_dep = declare_dependency(
     include_directories: include_directories('include')
 )
+
+install_subdir(
+    'include',
+    install_dir: gridfire_vendor_includedir,
+    strip_directory: true,
+)

build-config/meson.build

@@ -4,6 +4,41 @@ if get_option('build_python')
   subdir('python')
   subdir('pybind')
 endif
+
+if get_option('build_python')
+  gridfire_pkg_dir    = py_installation.get_install_dir() / 'gridfire'
+  gridfire_includedir = gridfire_pkg_dir / 'include'
+  gridfire_libdir     = gridfire_pkg_dir / 'lib'
+  gridfire_pcdir      = gridfire_libdir / 'pkgconfig'
+else
+  gridfire_includedir = get_option('includedir')
+  gridfire_libdir     = get_option('libdir')
+  gridfire_pcdir      = get_option('libdir') / 'pkgconfig'
+endif
+
+gridfire_vendor_includedir = gridfire_includedir / 'gridfire' / 'vendor'
+
+gridfire_fourdst_vendor_includedir = gridfire_includedir / 'fourdst' / 'vendor'
+
+vendor_py = import('python').find_installation('python3')
+copytree_cmd = [
+  vendor_py, '-c',
+  '''import sys, os, stat, shutil
+src, dst = sys.argv[1], sys.argv[2]
+shutil.rmtree(dst, ignore_errors=True)
+shutil.copytree(src, dst)
+for root, dirs, files in os.walk(dst):
+    os.chmod(root, 0o755)
+    for f in files:
+        p = os.path.join(root, f)
+        os.chmod(p, os.stat(p).st_mode | 0o644)
+''',
+]
+copyfiles_cmd = [
+  vendor_py, '-c',
+  'import sys, shutil; [shutil.copy2(p, sys.argv[-1]) for p in sys.argv[1:-1]]',
+]
+
 subdir('fourdst')
 subdir('sundials')
 
@@ -14,7 +49,6 @@ subdir('eigen')
 subdir('json')
 
 subdir('CLI11')
-subdir('unordered_dense')
 
 if get_option('use_mimalloc')
   subdir('mimalloc')

build-config/python/meson.build

@@ -1,8 +1,7 @@
 py_installation = import('python').find_installation('python3', pure: false)
 
-
 if meson.is_cross_build() and host_machine.system() == 'darwin'
-  py_ver = get_option('python-target-version')
+  py_ver = get_option('python_target_version')
   message('Cross build on Darwin, using python version ' + py_ver)
   py_inc_dir = include_directories('../../cross/python_includes/python-' + py_ver + '/include/python' + py_ver)
   py_dep = declare_dependency(include_directories: py_inc_dir)

build-config/sundials/cvode/meson.build

@@ -1,9 +1,11 @@
 cmake = import('cmake')
 cvode_cmake_options = cmake.subproject_options()
 
+sundials_hidden_flags = '-Wno-deprecated-declarations -fvisibility=hidden -fvisibility-inlines-hidden'
+
 cvode_cmake_options.add_cmake_defines({
-    'CMAKE_CXX_FLAGS'   : '-Wno-deprecated-declarations',
+                                          'CMAKE_CXX_FLAGS'   : sundials_hidden_flags,
-    'CMAKE_C_FLAGS'     : '-Wno-deprecated-declarations',
+                                          'CMAKE_C_FLAGS'     : sundials_hidden_flags,
                                           'BUILD_SHARED_LIBS' : 'OFF',
                                           'BUILD_STATIC_LIBS' : 'ON',
                                           'EXAMPLES_ENABLE_C' : 'OFF',
@@ -62,7 +64,6 @@ cvode_includes = [
     sundials_sunlinsoldense_includes
 ]
 
-
 empty_cvode_file = configure_file(
     output: 'cvode_dummy_ar.cpp',
     command: ['echo'],
@@ -70,7 +71,6 @@ empty_cvode_file = configure_file(
 )
 
 
-
 libcvode_static = static_library(
     'cvode-static',
     empty_cvode_file,
@@ -80,10 +80,6 @@ libcvode_static = static_library(
     install: false
 )
 
-
 cvode_dep = declare_dependency(
-  link_with: libcvode_static,
     include_directories: cvode_includes,
 )
-
-

build-config/sundials/kinsol/meson.build

@@ -3,8 +3,8 @@ cmake = import('cmake')
 kinsol_cmake_options = cmake.subproject_options()
 
 kinsol_cmake_options.add_cmake_defines({
-    'CMAKE_CXX_FLAGS'   : '-Wno-deprecated-declarations',
+                                           'CMAKE_CXX_FLAGS'   : '-Wno-deprecated-declarations -fvisibility=hidden -fvisibility-inlines-hidden',
-    'CMAKE_C_FLAGS'     : '-Wno-deprecated-declarations',
+                                           'CMAKE_C_FLAGS'     : '-Wno-deprecated-declarations -fvisibility=hidden -fvisibility-inlines-hidden',
                                            'BUILD_SHARED_LIBS' : 'OFF',
                                            'BUILD_STATIC_LIBS' : 'ON',
                                            'EXAMPLES_ENABLE_C' : 'OFF',
@@ -48,8 +48,5 @@ libkinsol_static = static_library(
 
 
 kinsol_dep = declare_dependency(
-  link_with: libkinsol_static,
     include_directories: kinsol_includes
 )
-
-

build-config/sundials/meson.build

@@ -7,3 +7,11 @@ sundials_dep = declare_dependency(
         kinsol_dep,
     ],
 )
+
+# Vendor the SUNDIALS public headers (see vendor/meson.build). GridFire's
+# installed public headers #include <sundials/...> etc., so consumers of
+# gridfire.pc must compile against exactly the headers this build used --
+# never whatever SUNDIALS happens to be in /usr/local/include (which may be
+# a different version or configuration, e.g. an MPI-enabled build whose
+# sundials_config.h pulls in <mpi.h>).
+subdir('vendor')

build-config/sundials/vendor/meson.build

@@ -0,0 +1,46 @@
+sundials_src_include = meson.project_source_root() / 'subprojects' / 'cvode-7.5.0' / 'include'
+kinsol_src_include   = meson.project_source_root() / 'subprojects' / 'kinsol-7.5.0' / 'include'
+
+sundials_vendor_dirs = [
+    'sundials',           # core (includes sundials/priv/)
+    'cvode',
+    'nvector',
+    'sunmatrix',
+    'sunlinsol',
+    'sunnonlinsol',
+    'sunmemory',
+    'sunadaptcontroller',
+]
+
+foreach d : sundials_vendor_dirs
+    custom_target(
+        'vendor_sundials_' + d,
+        command: copytree_cmd + [sundials_src_include / d, '@OUTPUT@'],
+        output: d,
+        install: true,
+        install_dir: gridfire_vendor_includedir,
+    )
+endforeach
+
+custom_target(
+    'vendor_sundials_kinsol',
+    command: copytree_cmd + [kinsol_src_include / 'kinsol', '@OUTPUT@'],
+    output: 'kinsol',
+    install: true,
+    install_dir: gridfire_vendor_includedir,
+)
+
+sundials_cmake_include = meson.global_build_root() / 'subprojects' / 'cvode-7.5.0' / '__CMake_build' / 'include' / 'sundials'
+
+custom_target(
+    'vendor_sundials_generated',
+    command: copyfiles_cmd + [
+        sundials_cmake_include / 'sundials_config.h',
+        sundials_cmake_include / 'sundials_export.h',
+        '@OUTDIR@',
+    ],
+    output: ['sundials_config.h', 'sundials_export.h'],
+    depends: libcvode_static,
+    install: true,
+    install_dir: gridfire_vendor_includedir / 'sundials',
+)

build-config/xxHash/meson.build

@@ -1,4 +1,9 @@
-
 xxhash_dep = declare_dependency(
     include_directories: include_directories('include')
 )
+
+install_subdir(
+    'include',
+    install_dir: gridfire_vendor_includedir,
+    strip_directory: true,
+)

build-extra/pkg-config/gridfire-wheel.pc.in

@@ -0,0 +1,9 @@
+prefix=${pcfiledir}/../..
+includedir=${prefix}/include
+libdir=${prefix}/lib
+
+Name: gridfire
+Description: GridFire nuclear reaction network solver (bundled with the gridfire Python wheel)
+Version: @VERSION@
+Cflags: -I${includedir} -I${includedir}/gridfire/vendor -I${includedir}/fourdst/vendor
+Libs: -L${libdir} -lgridfire -Wl,-rpath,${libdir}

build-extra/pkg-config/meson.build

@@ -1,22 +1,29 @@
-if get_option('pkg_config')
+if get_option('build_python')
+    message('Generating wheel-relocatable pkg-config file for GridFire...')
+    wheel_pc_conf = configuration_data()
+    wheel_pc_conf.set('VERSION', meson.project_version())
+    configure_file(
+        input: 'gridfire-wheel.pc.in',
+        output: 'gridfire.pc',
+        configuration: wheel_pc_conf,
+        install: true,
+        install_dir: gridfire_pcdir,
+    )
+elif get_option('pkg_config')
     message('Generating pkg-config file for GridFire...')
     pkg = import('pkgconfig')
     pkg.generate(
+        libgridfire,
         name: 'gridfire',
         description: 'GridFire nuclear reaction network solver',
-        version: meson.project_version(),
-        libraries: [
-            libgridfire,
-            libcomposition,
-            libconst,
-            liblogging,
-            libcppad_static,
-            libcvode_static,
-            libkinsol_static
-            
-        ],
-        subdirs: ['gridfire'],
         filebase: 'gridfire',
-        install_dir: join_paths(get_option('libdir'), 'pkgconfig')
+        subdirs: ['gridfire'],
+        requires: [
+            'fourdst_composition',
+            'fourdst_config',
+            'fourdst_constants',
+            'fourdst_logging',
+        ],
+        extra_cflags: ['-I${includedir}' / 'gridfire' / 'vendor'],
     )
 endif

build-python/meson.build

@@ -4,12 +4,15 @@ if get_option('build_python')
     gridfire_py_deps = [
         py_dep,
         pybind11_dep,
-      const_dep,
-      config_dep,
-      composition_dep,
         gridfire_dep
     ]
 
+    if host_machine.system() == 'darwin'
+        gridfire_ext_rpath = '@loader_path/lib'
+    else
+        gridfire_ext_rpath = '$ORIGIN/lib'
+    endif
+
     py_sources =  [
         meson.project_source_root() + '/src/python/bindings.cpp',
         meson.project_source_root() + '/src/python/types/bindings.cpp',
@@ -41,14 +44,16 @@ if get_option('build_python')
             name_prefix: '',
             name_suffix: 'so',
             install: true,
+            install_rpath: gridfire_ext_rpath,
             install_dir: py_installation.get_install_dir() + '/gridfire'
         )
     else
         py_mod = py_installation.extension_module(
-        '_gridfire', # Name of the generated .so/.pyd file (without extension)
+            '_gridfire',
             sources: py_sources,
             dependencies : gridfire_py_deps,
             install : true,
+            install_rpath: gridfire_ext_rpath,
             subdir: 'gridfire',
         )
     endif

meson_options.txt

@@ -1,4 +1,4 @@
-option('log_level', type: 'combo', choices: ['traceL3', 'traceL2', 'traceL1', 'debug', 'info', 'warning', 'error', 'critial'], value: 'info', description: 'Set the log level for the GridFire library')
+option('log_level', type: 'combo', choices: ['traceL3', 'traceL2', 'traceL1', 'debug', 'info', 'warning', 'error', 'critical'], value: 'info', description: 'Set the log level for the GridFire library')
 option('pkg_config', type: 'boolean', value: true, description: 'generate pkg-config file for GridFire (gridfire.pc)')
 option('build_python', type: 'boolean', value: false, description: 'build the python bindings so you can use GridFire from python')
 option('build_tests', type: 'boolean', value: true, description: 'build the test suite')

pip_install_mac_patch.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# pip_install_mac.sh - Temporary workaround for meson-python duplicate RPATH bug on macOS
+# pip_install_mac_patch.sh - Workaround for meson-python duplicate RPATH bug on macOS
 
 set -e
 
@@ -9,26 +9,30 @@ YELLOW='\033[1;33m'
 GREEN='\033[0;32m'
 NC='\033[0m' # No Color
 
+# Returns 0 if the Mach-O binary at $1 has duplicate LC_RPATH entries.
+has_duplicate_rpaths() {
+    local binary="$1"
+    local rpaths dup
+    rpaths=$(otool -l "$binary" | awk '/cmd LC_RPATH/{getline; getline; print $2}')
+    dup=$(printf '%s\n' "$rpaths" | sort | uniq -d)
+    [ -n "$dup" ]
+}
+
 echo -e "${YELLOW}"
 echo "========================================================================="
-echo "                    TEMPORARY INSTALLATION WORKAROUND"
+echo "          INSTALLATION + DUPLICATE-RPATH SAFETY NET (macOS)"
 echo "========================================================================="
 echo -e "${NC}"
 echo ""
-echo -e "${YELLOW}WARNING:${NC} This script applies a temporary patch to fix a known issue with"
+echo "This script installs gridfire with pip and then checks the installed"
-echo "meson-python that causes duplicate RPATH entries in built Python extensions"
+echo "extension modules for duplicate LC_RPATH entries (a meson-python bug"
-echo "on macOS, preventing module imports."
+echo "exposed by macOS 26.1, see:"
+echo "  https://github.com/mesonbuild/meson-python/issues/813 )."
 echo ""
-echo "This workaround will:"
+echo "With the current self-contained wheel layout the bug should not"
-echo "  1. Install fourdst using pip"
+echo "trigger; binaries are only patched if duplicates are actually found."
-echo "  2. Locate the installed extension module"
-echo "  3. Remove duplicate RPATH entries using install_name_tool"
 echo ""
-echo "This is a temporary solution while the meson-python team resolves the"
+echo -e "${YELLOW}Continue? [y/N]${NC} "
-echo "duplicate RPATH bug. For more information, see:"
-echo "  https://github.com/mesonbuild/meson-python/issues/813"
-echo ""
-echo -e "${YELLOW}Do you understand and wish to continue? [y/N]${NC} "
 read -r response
 
 if [[ ! "$response" =~ ^[Yy]$ ]]; then
@@ -39,7 +43,6 @@ fi
 echo ""
 echo -e "${GREEN}Step 1: Finding current Python environment...${NC}"
 
-# Get the current Python executable
 PYTHON_BIN=$(which python3)
 if [ -z "$PYTHON_BIN" ]; then
     echo -e "${RED}Error: python3 not found in PATH${NC}"
@@ -50,12 +53,11 @@ echo "Using Python: $PYTHON_BIN"
 PYTHON_VERSION=$($PYTHON_BIN --version)
 echo "Python version: $PYTHON_VERSION"
 
-# Get site-packages directory
 SITE_PACKAGES=$($PYTHON_BIN -c "import site; print(site.getsitepackages()[0])")
 echo "Site packages: $SITE_PACKAGES"
 echo ""
 
-echo -e "${GREEN}Step 2: Installing fourdst with pip...${NC}"
+echo -e "${GREEN}Step 2: Installing gridfire with pip...${NC}"
 $PYTHON_BIN -m pip install . -v --no-build-isolation
 
 if [ $? -ne 0 ]; then
@@ -64,80 +66,43 @@ if [ $? -ne 0 ]; then
 fi
 echo ""
 
-echo -e "${GREEN}Step 3: Locating installed gridfire extension module...${NC}"
+FIX_SCRIPT="build-python/fix_rpaths.py"
 
-# Find the .so file
+check_and_fix() {
-SO_FILE=$(find "$SITE_PACKAGES/gridfire" -name "_gridfire.cpython-*-darwin.so" 2>/dev/null | head -n 1)
+    local label="$1" so_file="$2"
 
-if [ -z "$SO_FILE" ]; then
+    if [ -z "$so_file" ]; then
-    echo -e "${RED}Error: Could not find _gridfire.cpython-*-darwin.so in $SITE_PACKAGES/gridfire${NC}"
+        echo -e "${YELLOW}Skipping ${label}: extension module not found (package may not be installed).${NC}"
-    echo "Installation may have failed or the file is in an unexpected location."
+        return 0
-    exit 1
     fi
 
-echo "Found gridfire extension module: $SO_FILE"
+    echo "Found ${label} extension module: $so_file"
-echo ""
+    if has_duplicate_rpaths "$so_file"; then
-
+        echo -e "${YELLOW}Duplicate LC_RPATH entries detected in ${label}; applying fix...${NC}"
-echo -e "${GREEN}Step 4: Running RPATH fix script for gridfire extension module...${NC}"
-
-# Check if fix_rpath.py exists
-FIX_SCRIPT="build-python/fix_rpaths.py"
         if [ ! -f "$FIX_SCRIPT" ]; then
             echo -e "${RED}Error: $FIX_SCRIPT not found${NC}"
-    echo "Please ensure you're running this script from the project root directory."
+            echo "Please run this script from the project root directory."
             exit 1
         fi
-
+        $PYTHON_BIN "$FIX_SCRIPT" "$so_file"
-# Run the fix script
+    else
-$PYTHON_BIN "$FIX_SCRIPT" "$SO_FILE"
+        echo -e "${GREEN}No duplicate LC_RPATH entries in ${label}; no patch needed.${NC}"
-
-if [ $? -ne 0 ]; then
-    echo -e "${RED}Error: RPATH fix script failed for gridfire extension module${NC}"
-    exit 1
     fi
-
-echo -e "${GREEN}Step 5: Locating installed fourdst extension module...${NC}"
-
-# Find the .so file
-SO_FILE=$(find "$SITE_PACKAGES/fourdst" -name "_phys.cpython-*-darwin.so" 2>/dev/null | head -n 1)
-
-if [ -z "$SO_FILE" ]; then
-    echo -e "${RED}Error: Could not find _phys.cpython-*-darwin.so in $SITE_PACKAGES/fourdst${NC}"
-    echo "Installation may have failed or the file is in an unexpected location."
-    exit 1
-fi
-
-echo "Found fourdst extension module: $SO_FILE"
     echo ""
+}
 
-echo -e "${GREEN}Step 6: Running RPATH fix script for fourdst extension module...${NC}"
+echo -e "${GREEN}Step 3: Checking installed extension modules...${NC}"
 
-# Check if fix_rpath.py exists
+GRIDFIRE_SO=$(find "$SITE_PACKAGES/gridfire" -name "_gridfire.cpython-*-darwin.so" 2>/dev/null | head -n 1)
-FIX_SCRIPT="build-python/fix_rpaths.py"
+check_and_fix "gridfire" "$GRIDFIRE_SO"
-if [ ! -f "$FIX_SCRIPT" ]; then
-    echo -e "${RED}Error: $FIX_SCRIPT not found${NC}"
-    echo "Please ensure you're running this script from the project root directory."
-    exit 1
-fi
 
-# Run the fix script
+FOURDST_SO=$(find "$SITE_PACKAGES/fourdst" -name "_phys.cpython-*-darwin.so" 2>/dev/null | head -n 1)
-$PYTHON_BIN "$FIX_SCRIPT" "$SO_FILE"
+check_and_fix "fourdst" "$FOURDST_SO"
 
-if [ $? -ne 0 ]; then
-    echo -e "${RED}Error: RPATH fix script failed for fourdst extension module${NC}"
-    exit 1
-fi
-
-echo ""
 echo -e "${GREEN}=========================================================================${NC}"
 echo -e "${GREEN}                    Installation Complete!${NC}"
 echo -e "${GREEN}=========================================================================${NC}"
 echo ""
-echo "You can now use fourdst in your Python environment."
-echo ""
 echo "Test the installation with:"
 echo "  $PYTHON_BIN -c 'import gridfire; print(gridfire.__version__)'"
 echo ""
-echo -e "${YELLOW}Note:${NC} If you reinstall or upgrade fourdst, you will need to run this"
-echo "script again to apply the RPATH fix."
-echo ""

pyproject.toml

@@ -1,17 +1,17 @@
 [build-system]
 requires = [
-    "meson-python>=0.15.0", # Use a recent version
+    "meson-python>=0.19.0",
-    "meson==1.9.1",        # Specify your Meson version requirement
+    "meson>=1.9.1",
-    "pybind11>=2.10"       # pybind11 headers needed at build time
+    "pybind11>=2.10"
 ]
 build-backend = "mesonpy"
 
 [project]
-name = "gridfire"  # Choose your Python package name
+name = "gridfire"
-version = "v0.7.6rc4.2" # Your project's version
+version = "v0.7.6rc4.2"
 description = "Python interface to the GridFire nuclear network code"
 readme = "README.md"
-license = { file = "LICENSE.txt" } # Reference your license file [cite: 2]
+license = { file = "LICENSE.txt" }
 
 authors = [
     {name = "Emily M. Boudreaux", email = "emily@boudreauxmail.com"},
@@ -22,4 +22,20 @@ maintainers = [
 ]
 
 [tool.meson-python.args]
-setup = ['-Dpkg_config=false', '-Dbuildtype=release', '-Dopenmp_support=true', '-Dasan=false', '-Dlog_level=error', '-Dbuild_tests=false', '-Dbuild_c_api=false', '-Dbuild_examples=false', '-Dbuild_benchmarks=false', '-Dbuild_tools=false', '-Dplugin_support=false', '-Duse_mimalloc=false', '-Dbuild_python=true']
+setup = [
+    '-Ddefault_library=static',
+    '-Dpkg_config=false',
+    '-Dbuildtype=release',
+    '-Dopenmp_support=true',
+    '-Dasan=false',
+    '-Dlog_level=error',
+    '-Dbuild_tests=false',
+    '-Dbuild_c_api=false',
+    '-Dbuild_examples=false',
+    '-Dbuild_benchmarks=false',
+    '-Dbuild_tools=false',
+    '-Dplugin_support=false',
+    '-Duse_mimalloc=false',
+    '-Dbuild_python=true'
+]
+install = ['--skip-subprojects']

src/include/gridfire/engine/engine_graph.h

@@ -16,8 +16,6 @@
 
 #include "gridfire/engine/scratchpads/blob.h"
 
-#include "ankerl/unordered_dense.h"
-
 #include <string>
 #include <unordered_map>
 #include <vector>

src/include/gridfire/solver/strategies/PointSolver.h

@@ -15,6 +15,8 @@
 #include <string>
 #include <vector>
 #include <tuple>
+#include <span>
+#include <optional>
 
 // SUNDIALS/CVODE headers
 #include <cvode/cvode.h>
@@ -80,6 +82,24 @@ namespace gridfire::solver {
             [[nodiscard]] std::vector<std::tuple<std::string, std::string>> describe() const override;
 
             [[nodiscard]] fourdst::composition::Composition getPhysicalComposition() const;
+
+            /**
+             * @brief Zero-copy view of the raw solver state vector.
+             *
+             * Layout: [y_0, ..., y_{N-1}, eps] where y_i are molar abundances in
+             * networkSpecies order and eps is the accumulated specific energy.
+             * The view is only valid for the duration of the callback.
+             */
+            [[nodiscard]] std::span<const double> rawState() const;
+
+            /// Abundance of the species at @p species_index (solver state indexing).
+            [[nodiscard]] double abundance(size_t species_index) const;
+
+            /// Abundance of @p sp, or std::nullopt if it is not in the active network.
+            [[nodiscard]] std::optional<double> abundance(const fourdst::atomic::Species& sp) const;
+
+            /// Accumulated specific energy [erg/g] (the trailing state entry).
+            [[nodiscard]] double accumulatedSpecificEnergy() const;
         };
 
     using TimestepCallback = std::function<void(const PointSolverTimestepContext& context)>; ///< Type alias for a timestep callback function.

src/include/gridfire/utils/meson.build

@@ -26,16 +26,10 @@ message('  Minor: ' + ver_parts[1])
 message('  Patch: ' + ver_parts[2])
 message('  Tag:   ' + ver_parts[3])
 
-do_install_version_file = true
-if get_option('build_python')
-    message('Not installing version file since we are building the Python extension. The version information will be included in the Python module instead.')
-    do_install_version_file = false
-endif
-
 configure_file(
     input : 'config.h.in',
     output : 'config.h',
     configuration : conf_data,
-    install : do_install_version_file,
+    install : true,
-    install_dir : get_option('includedir') / 'gridfire/utils'
+    install_dir : gridfire_includedir / 'gridfire/utils'
 )

src/lib/engine/procedures/priming.cpp

@@ -1,7 +1,7 @@
 #include "gridfire/engine/procedures/priming.h"
 
 #include "fourdst/atomic/species.h"
-#include "fourdst/composition/utils.h"
+#include "fourdst/composition/utils/utils.h"
 #include "gridfire/solver/solver.h"
 
 #include "gridfire/engine/engine_abstract.h"

src/lib/policy/stellar_policy.cpp

@@ -14,7 +14,7 @@
 #include "gridfire/engine/scratchpads/engine_multiscale_scratchpad.h"
 
 #include "fourdst/atomic/species.h"
-#include "fourdst/composition/utils.h"
+#include "fourdst/composition/utils/utils.h"
 
 namespace {
     std::set<fourdst::atomic::Species> initialize_seed_species() {

src/lib/solver/strategies/PointSolver.cpp

@@ -88,6 +88,28 @@ namespace gridfire::solver {
         return engine.collectComposition(state_ctx, base_comp, T9, rho);
     }
 
+    static_assert(std::is_same_v<sunrealtype, double>, "PointSolverTimestepContext accessors assume SUNDIALS is built with double precision");
+    std::span<const double> PointSolverTimestepContext::rawState() const {
+        return { N_VGetArrayPointer(state),
+                 static_cast<std::size_t>(N_VGetLength(state)) };
+    }
+
+    double PointSolverTimestepContext::abundance(const size_t species_index) const {
+        return N_VGetArrayPointer(state)[species_index];
+    }
+
+    std::optional<double> PointSolverTimestepContext::abundance(const fourdst::atomic::Species& sp) const {
+        const auto& species = engine.getNetworkSpecies(state_ctx);
+        if (std::ranges::find(species, sp) == species.end()) {
+            return std::nullopt;
+        }
+        return abundance(engine.getSpeciesIndex(state_ctx, sp));
+    }
+
+    double PointSolverTimestepContext::accumulatedSpecificEnergy() const {
+        return N_VGetArrayPointer(state)[networkSpecies.size()];
+    }
+
     void PointSolverContext::init() {
         reset_all();
         init_context();

src/meson.build

@@ -1,5 +1,6 @@
-# Define the library
+subdir('include/gridfire/utils')
-subdir('include/gridfire/utils') # Generate the version header file first
+
+cpp = meson.get_compiler('cpp')
 
 gridfire_sources = files(
     'lib/engine/engine_graph.cpp',
@@ -44,7 +45,6 @@ gridfire_build_dependencies = [
     eigen_dep,
     sundials_dep,
     json_dep,
-    uod_dep,
 ]
 
 if get_option('use_mimalloc')
@@ -60,34 +60,63 @@ if get_option('openmp_support')
     gridfire_build_dependencies += [openmp_dep]
 endif
 
-# Define the libnetwork library so it can be linked against by other parts of the build system
+gridfire_link_whole = [libcvode_static, libkinsol_static, libcppad_static]
+
+gridfire_link_args = cpp.get_supported_link_arguments(
+    '-Wl,--exclude-libs,libcvode-static.a:libkinsol_static.a'
+)
+
 if get_option('build_python')
-    libgridfire = static_library('gridfire',
+    gridfire_link_whole += [libcomposition, libconst, liblogging]
+    if get_option('plugin_support')
+        gridfire_link_whole += [libplugin]
+    endif
+    libgridfire = shared_library('gridfire',
                                  gridfire_sources,
                                  include_directories: include_directories('include'),
                                  dependencies: gridfire_build_dependencies,
                                  cpp_args: gridfire_args,
-        objects: [cvode_objs, kinsol_objs],
+                                 link_whole: gridfire_link_whole,
-        install : false)
+                                 link_args: gridfire_link_args,
+                                 install: true,
+                                 install_dir: gridfire_libdir)
 else
     libgridfire = library('gridfire',
                           gridfire_sources,
                           include_directories: include_directories('include'),
                           dependencies: gridfire_build_dependencies,
-                          objects: [cvode_objs, kinsol_objs],
+                          link_whole: gridfire_link_whole,
+                          link_args: gridfire_link_args,
                           cpp_args: gridfire_args,
                           install : true)
 endif
 
+if get_option('build_python')
+    gridfire_iface_deps = []
+    foreach d : gridfire_build_dependencies
+        gridfire_iface_deps += d.partial_dependency(compile_args: true, includes: true)
+    endforeach
+    gridfire_dep = declare_dependency(
+        include_directories: include_directories('include'),
+        link_with: libgridfire,
+        dependencies: gridfire_iface_deps,
+        compile_args: gridfire_args,
+    )
+else
     gridfire_dep = declare_dependency(
         include_directories: include_directories('include'),
         link_with: libgridfire,
-    sources: gridfire_sources,
         dependencies: gridfire_build_dependencies,
         compile_args: gridfire_args,
     )
+endif
 
-install_subdir('include/gridfire', install_dir: get_option('includedir'))
+meson.override_dependency('gridfire', gridfire_dep)
+
+install_subdir('include/gridfire',
+               install_dir: gridfire_includedir,
+               exclude_files: ['utils/config.h.in'],
+)
 
 
 if not get_option('build_c_api') and get_option('build_fortran')
@@ -97,3 +126,4 @@ if get_option('build_c_api')
     message('Configuring C API...')
     subdir('extern')
 endif
+

subprojects/fourdst.wrap

@@ -1,4 +1,4 @@
 [wrap-git]
 url = https://github.com/4D-STAR/fourdst
-revision = v0.9.22
+revision = v0.10.1
 depth = 1

tests/graphnet_sandbox/main.cpp

@@ -9,7 +9,7 @@
 
 #include "fourdst/logging/logging.h"
 #include "fourdst/atomic/species.h"
-#include "fourdst/composition/utils.h"
+#include "fourdst/composition/utils/utils.h"
 
 #include "quill/Logger.h"
 #include "quill/Backend.h"

tools/gf_bbn/main.cpp

@@ -10,7 +10,7 @@
 #include "fourdst/composition/composition.h"
 #include "fourdst/logging/logging.h"
 #include "fourdst/atomic/species.h"
-#include "fourdst/composition/utils.h"
+#include "fourdst/composition/utils/utils.h"
 
 #include "quill/Logger.h"
 #include "quill/Backend.h"
@@ -156,8 +156,8 @@ void record_abundance_history_callback(const gridfire::solver::PointSolverTimest
     std::vector<double> Y;
     for (const auto& species : engine.getNetworkSpecies(ctx.state_ctx)) {
         const size_t sid = engine.getSpeciesIndex(ctx.state_ctx, species);
-        double y =  N_VGetArrayPointer(ctx.state)[sid];
+        const double y = ctx.abundance(sid);
-        Y.push_back(y > 0.0 ? y : 0.0); // Regularize tiny negative abundances to zero
+        Y.push_back(y > 0.0 ? y : 0.0);
     }
 
     const fourdst::composition::Composition comp(engine.getNetworkSpecies(ctx.state_ctx), Y);

tools/gf_multi/main.cpp

@@ -11,7 +11,7 @@
 #include "fourdst/composition/composition.h"
 #include "fourdst/logging/logging.h"
 #include "fourdst/atomic/species.h"
-#include "fourdst/composition/utils.h"
+#include "fourdst/composition/utils/utils.h"
 
 #include "quill/Logger.h"
 #include "quill/Backend.h"
@@ -226,14 +226,12 @@ void log_results(const gridfire::NetOut& netOut, const gridfire::NetIn& netIn) {
 void record_abundance_history_callback(const gridfire::solver::PointSolverTimestepContext& ctx) {
     s_wrote_abundance_history = true;
     const auto& engine = ctx.engine;
-    // std::unordered_map<std::string, std::pair<double, double>> abundances;
     std::vector<double> Y;
     for (const auto& species : engine.getNetworkSpecies(ctx.state_ctx)) {
         const size_t sid = engine.getSpeciesIndex(ctx.state_ctx, species);
-        double y =  N_VGetArrayPointer(ctx.state)[sid];
+        const double y = ctx.abundance(sid);
-        Y.push_back(y > 0.0 ? y : 0.0); // Regularize tiny negative abundances to zero
+        Y.push_back(y > 0.0 ? y : 0.0);
     }
-
     fourdst::composition::Composition comp(engine.getNetworkSpecies(ctx.state_ctx), Y);
 
 

tools/gf_quick/main.cpp

@@ -11,7 +11,7 @@
 #include "fourdst/composition/composition.h"
 #include "fourdst/logging/logging.h"
 #include "fourdst/atomic/species.h"
-#include "fourdst/composition/utils.h"
+#include "fourdst/composition/utils/utils.h"
 
 #include "quill/Logger.h"
 #include "quill/Backend.h"
@@ -157,10 +157,9 @@ void record_abundance_history_callback(const gridfire::solver::PointSolverTimest
     std::vector<double> Y;
     for (const auto& species : engine.getNetworkSpecies(ctx.state_ctx)) {
         const size_t sid = engine.getSpeciesIndex(ctx.state_ctx, species);
-        double y =  N_VGetArrayPointer(ctx.state)[sid];
+        const double y = ctx.abundance(sid);
-        Y.push_back(y > 0.0 ? y : 0.0); // Regularize tiny negative abundances to zero
+        Y.push_back(y > 0.0 ? y : 0.0);
     }
-
     const fourdst::composition::Composition comp(engine.getNetworkSpecies(ctx.state_ctx), Y);
     IntermediateResult stepResult;
     stepResult.comp = comp;