From 8f274f068f2098b3a830c1680bfc1ad67cc2a1e6 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 8 Feb 2026 17:49:28 +0000
Subject: [PATCH 1/7] Initial plan


From 086aeed1eb0857ee806bf646e7db942bf328c3fe Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 8 Feb 2026 17:53:53 +0000
Subject: [PATCH 2/7] Add initial Meson build configuration for C++ library

Co-authored-by: bryanwweber <4396228+bryanwweber@users.noreply.github.com>
---
 meson.build                      | 241 ++++++++++++++++++++++++
 meson.options                    |   5 +
 src/meson.build                  | 307 +++++++++++++++++++++++++++++++
 subprojects/yaml-cpp/meson.build |  47 +++++
 4 files changed, 600 insertions(+)
 create mode 100644 meson.build
 create mode 100644 meson.options
 create mode 100644 src/meson.build
 create mode 100644 subprojects/yaml-cpp/meson.build

diff --git a/meson.build b/meson.build
new file mode 100644
index 0000000000..d18d9073ca
--- /dev/null
+++ b/meson.build
@@ -0,0 +1,241 @@
+project('cantera', 'cpp', 'c',
+  version: '4.0.0',
+  license: 'BSD-3-Clause',
+  default_options: [
+    'cpp_std=c++20',
+    'c_std=c99',
+    'warning_level=2',
+    'buildtype=release',
+  ],
+  meson_version: '>=1.0.0'
+)
+
+# Import modules
+fs = import('fs')
+
+# Get version components
+version_parts = meson.project_version().split('.')
+version_major = version_parts[0]
+version_minor = version_parts[1]
+cantera_short_version = f'@version_major@.@version_minor@'
+
+# Compiler setup
+cc = meson.get_compiler('c')
+cpp = meson.get_compiler('cpp')
+
+# Platform-specific settings
+host_system = host_machine.system()
+is_windows = host_system == 'windows'
+is_darwin = host_system == 'darwin'
+
+# Additional compiler flags
+add_project_arguments('-DFMT_HEADER_ONLY', language: 'cpp')
+
+if cpp.get_id() == 'msvc'
+  add_project_arguments('/EHsc', '/utf-8', '/nologo', language: 'cpp')
+  add_project_arguments('/D_SCL_SECURE_NO_WARNINGS', language: 'cpp')
+  add_project_arguments('/D_CRT_SECURE_NO_WARNINGS', language: 'cpp')
+  add_project_arguments('/MD', language: 'cpp')
+else
+  add_project_arguments('-fcolor-diagnostics', language: 'cpp')
+endif
+
+# Thread support
+thread_dep = dependency('threads', required: true)
+
+# Math library (needed on some platforms)
+m_dep = cc.find_library('m', required: false)
+
+# SUNDIALS dependency with fallback to subproject
+sundials_dep = dependency('sundials_cvodes', version: '>=6.0', required: false)
+sundials_idas_dep = dependency('sundials_idas', required: false)
+sundials_nvecserial_dep = dependency('sundials_nvecserial', required: false)
+
+use_system_sundials = false
+if sundials_dep.found() and sundials_idas_dep.found() and sundials_nvecserial_dep.found()
+  use_system_sundials = true
+  message('Using system SUNDIALS')
+else
+  message('Using bundled SUNDIALS from ext/sundials')
+  # TODO: Build SUNDIALS from submodule
+  # For now, we'll add it as a subproject wrap
+  sundials_dep = dependency('', required: false)
+  sundials_idas_dep = dependency('', required: false)
+  sundials_nvecserial_dep = dependency('', required: false)
+endif
+
+# Eigen dependency (header-only)
+eigen_dep = dependency('eigen3', version: '>=3.4', required: false)
+use_system_eigen = false
+if eigen_dep.found()
+  use_system_eigen = true
+  message('Using system Eigen')
+else
+  message('Using bundled Eigen from ext/eigen')
+  # Check if submodule is initialized
+  eigen_include_dir = meson.current_source_dir() / 'ext' / 'eigen'
+  if not fs.is_dir(eigen_include_dir)
+    warning('Eigen submodule not initialized. Run: git submodule update --init ext/eigen')
+  endif
+  eigen_dep = declare_dependency(
+    include_directories: include_directories('ext/eigen')
+  )
+endif
+
+# fmt dependency with fallback
+fmt_dep = dependency('fmt', version: '>=9.1.0', required: false)
+use_system_fmt = false
+if fmt_dep.found()
+  use_system_fmt = true
+  message('Using system fmt')
+else
+  message('Using bundled fmt from ext/fmt')
+  # Check if submodule is initialized
+  fmt_include_dir = meson.current_source_dir() / 'ext' / 'fmt' / 'include'
+  if not fs.is_dir(fmt_include_dir)
+    warning('fmt submodule not initialized. Run: git submodule update --init ext/fmt')
+  endif
+  # Use header-only mode for bundled fmt
+  fmt_dep = declare_dependency(
+    include_directories: include_directories('ext/fmt/include'),
+    compile_args: ['-DFMT_HEADER_ONLY']
+  )
+endif
+
+# yaml-cpp dependency with fallback
+yamlcpp_dep = dependency('yaml-cpp', version: '>=0.6', required: false)
+use_system_yamlcpp = false
+if yamlcpp_dep.found()
+  use_system_yamlcpp = true
+  message('Using system yaml-cpp')
+else
+  message('Using bundled yaml-cpp from ext/yaml-cpp')
+  # Check if submodule is initialized
+  yamlcpp_include_dir = meson.current_source_dir() / 'ext' / 'yaml-cpp' / 'include'
+  if not fs.is_dir(yamlcpp_include_dir)
+    warning('yaml-cpp submodule not initialized. Run: git submodule update --init ext/yaml-cpp')
+  endif
+  # Build yaml-cpp from submodule
+  yamlcpp_proj = subproject('yaml-cpp')
+  yamlcpp_dep = yamlcpp_proj.get_variable('yaml-cpp_dep')
+endif
+
+# Boost dependency (header-only, required)
+boost_dep = dependency('boost', version: '>=1.83', required: true,
+  modules: []  # Header-only
+)
+
+# HDF5 dependency (optional)
+hdf5_dep = dependency('hdf5', required: false)
+use_hdf5 = hdf5_dep.found()
+if use_hdf5
+  message('HDF5 support enabled')
+else
+  message('HDF5 support disabled')
+endif
+
+# HighFive dependency (header-only, optional)
+highfive_dep = dependency('HighFive', required: false)
+use_system_highfive = false
+if highfive_dep.found()
+  use_system_highfive = true
+  message('Using system HighFive')
+elif use_hdf5
+  message('Using bundled HighFive from ext/HighFive')
+  highfive_dep = declare_dependency(
+    include_directories: include_directories('ext/HighFive/include')
+  )
+else
+  highfive_dep = dependency('', required: false)
+endif
+
+# BLAS/LAPACK dependency (optional)
+lapack_dep = dependency('lapack', required: false)
+blas_dep = dependency('blas', required: false)
+use_lapack = false
+
+if lapack_dep.found() and blas_dep.found()
+  use_lapack = true
+  message('Using system BLAS/LAPACK')
+elif is_darwin
+  # Try Accelerate framework on macOS
+  accelerate_dep = dependency('Accelerate', required: false)
+  if accelerate_dep.found()
+    lapack_dep = accelerate_dep
+    blas_dep = dependency('', required: false)
+    use_lapack = true
+    message('Using macOS Accelerate framework')
+  endif
+endif
+
+if not use_lapack
+  message('BLAS/LAPACK not found, will use Eigen for linear algebra')
+  lapack_dep = dependency('', required: false)
+  blas_dep = dependency('', required: false)
+endif
+
+# Git commit information
+git = find_program('git', required: false)
+git_commit = 'unknown'
+if git.found()
+  git_result = run_command(git, 'rev-parse', '--short', 'HEAD', 
+                           check: false, capture: true)
+  if git_result.returncode() == 0
+    git_commit = git_result.stdout().strip()
+  endif
+endif
+
+# Data directory
+datadir = get_option('datadir')
+if datadir == ''
+  datadir = get_option('prefix') / 'share' / 'cantera' / 'data'
+endif
+
+# Generate config.h
+conf_data = configuration_data()
+conf_data.set_quoted('CANTERA_VERSION', meson.project_version())
+conf_data.set_quoted('CANTERA_SHORT_VERSION', cantera_short_version)
+conf_data.set10('CT_USE_SYSTEM_EIGEN', use_system_eigen)
+conf_data.set10('CT_USE_SYSTEM_EIGEN_PREFIXED', false)  # Assume unprefixed
+conf_data.set10('CT_USE_SYSTEM_FMT', use_system_fmt)
+conf_data.set10('CT_USE_SYSTEM_YAMLCPP', use_system_yamlcpp)
+conf_data.set10('CT_USE_LAPACK', use_lapack)
+conf_data.set10('CT_USE_HDF5', use_hdf5)
+conf_data.set10('CT_USE_SYSTEM_HIGHFIVE', use_system_highfive)
+conf_data.set10('CT_SUNDIALS_USE_LAPACK', false)  # Conservative default
+
+# Fortran settings
+conf_data.set('FTN_TRAILING_UNDERSCORE', '#define FTN_TRAILING_UNDERSCORE')
+conf_data.set('LAPACK_FTN_STRING_LEN_AT_END', '#define LAPACK_FTN_STRING_LEN_AT_END')
+conf_data.set('LAPACK_FTN_TRAILING_UNDERSCORE', '#define LAPACK_FTN_TRAILING_UNDERSCORE')
+
+config_h = configure_file(
+  input: 'include/cantera/base/config.h.in',
+  output: 'config.h',
+  configuration: conf_data,
+  install: true,
+  install_dir: get_option('includedir') / 'cantera' / 'base'
+)
+
+# Include directories
+cantera_include_dirs = include_directories(
+  'include',
+  'src',
+  '.'  # For generated config.h
+)
+
+# Build the library
+subdir('src')
+
+# Summary
+summary({
+  'Version': meson.project_version(),
+  'Git commit': git_commit,
+  'System Eigen': use_system_eigen,
+  'System fmt': use_system_fmt,
+  'System yaml-cpp': use_system_yamlcpp,
+  'System SUNDIALS': use_system_sundials,
+  'BLAS/LAPACK': use_lapack,
+  'HDF5 support': use_hdf5,
+  'System HighFive': use_system_highfive,
+}, section: 'Configuration')
diff --git a/meson.options b/meson.options
new file mode 100644
index 0000000000..98bf652e30
--- /dev/null
+++ b/meson.options
@@ -0,0 +1,5 @@
+option('datadir', 
+  type: 'string', 
+  value: '',
+  description: 'Directory for Cantera data files (default: prefix/share/cantera/data)'
+)
diff --git a/src/meson.build b/src/meson.build
new file mode 100644
index 0000000000..9740a4262b
--- /dev/null
+++ b/src/meson.build
@@ -0,0 +1,307 @@
+# Source files for the Cantera library
+# Organized by subdirectory
+
+# Base module
+base_sources = files(
+  'base/AnyMap.cpp',
+  'base/Array.cpp',
+  'base/ExtensionManager.cpp',
+  'base/ExtensionManagerFactory.cpp',
+  'base/Interface.cpp',
+  'base/Solution.cpp',
+  'base/SolutionArray.cpp',
+  'base/Storage.cpp',
+  'base/Units.cpp',
+  'base/ValueCache.cpp',
+  'base/YamlWriter.cpp',
+  'base/application.cpp',
+  'base/checkFinite.cpp',
+  'base/clockWC.cpp',
+  'base/ctexceptions.cpp',
+  'base/global.cpp',
+  'base/stringUtils.cpp',
+)
+
+# Thermo module
+thermo_sources = files(
+  'thermo/BinarySolutionTabulatedThermo.cpp',
+  'thermo/ConstCpPoly.cpp',
+  'thermo/CoverageDependentSurfPhase.cpp',
+  'thermo/DebyeHuckel.cpp',
+  'thermo/EEDFTwoTermApproximation.cpp',
+  'thermo/Elements.cpp',
+  'thermo/GibbsExcessVPSSTP.cpp',
+  'thermo/HMWSoln.cpp',
+  'thermo/IdealGasPhase.cpp',
+  'thermo/IdealMolalSoln.cpp',
+  'thermo/IdealSolidSolnPhase.cpp',
+  'thermo/IdealSolnGasVPSS.cpp',
+  'thermo/MargulesVPSSTP.cpp',
+  'thermo/MixtureFugacityTP.cpp',
+  'thermo/MolalityVPSSTP.cpp',
+  'thermo/Mu0Poly.cpp',
+  'thermo/MultiSpeciesThermo.cpp',
+  'thermo/Nasa9Poly1.cpp',
+  'thermo/Nasa9PolyMultiTempRegion.cpp',
+  'thermo/NasaPoly2.cpp',
+  'thermo/PDSS.cpp',
+  'thermo/PDSSFactory.cpp',
+  'thermo/PDSS_ConstVol.cpp',
+  'thermo/PDSS_HKFT.cpp',
+  'thermo/PDSS_SSVol.cpp',
+  'thermo/PDSS_Water.cpp',
+  'thermo/PengRobinson.cpp',
+  'thermo/Phase.cpp',
+  'thermo/PlasmaPhase.cpp',
+  'thermo/PureFluidPhase.cpp',
+  'thermo/RedlichKisterVPSSTP.cpp',
+  'thermo/RedlichKwongMFTP.cpp',
+  'thermo/SingleSpeciesTP.cpp',
+  'thermo/Species.cpp',
+  'thermo/SpeciesThermoFactory.cpp',
+  'thermo/SpeciesThermoInterpType.cpp',
+  'thermo/StoichSubstance.cpp',
+  'thermo/SurfPhase.cpp',
+  'thermo/ThermoFactory.cpp',
+  'thermo/ThermoPhase.cpp',
+  'thermo/VPStandardStateTP.cpp',
+  'thermo/WaterProps.cpp',
+  'thermo/WaterPropsIAPWS.cpp',
+  'thermo/WaterPropsIAPWSphi.cpp',
+  'thermo/WaterSSTP.cpp',
+)
+
+# TPX module
+tpx_sources = files(
+  'tpx/CarbonDioxide.cpp',
+  'tpx/HFC134a.cpp',
+  'tpx/Heptane.cpp',
+  'tpx/Hydrogen.cpp',
+  'tpx/Methane.cpp',
+  'tpx/Nitrogen.cpp',
+  'tpx/Oxygen.cpp',
+  'tpx/Sub.cpp',
+  'tpx/Water.cpp',
+  'tpx/utils.cpp',
+)
+
+# Equilibrium module
+equil_sources = files(
+  'equil/BasisOptimize.cpp',
+  'equil/ChemEquil.cpp',
+  'equil/MultiPhase.cpp',
+  'equil/MultiPhaseEquil.cpp',
+  'equil/vcs_MultiPhaseEquil.cpp',
+  'equil/vcs_VolPhase.cpp',
+  'equil/vcs_solve.cpp',
+  'equil/vcs_solve_TP.cpp',
+  'equil/vcs_util.cpp',
+)
+
+# Numerics module
+numerics_sources = files(
+  'numerics/AdaptivePreconditioner.cpp',
+  'numerics/BandMatrix.cpp',
+  'numerics/CVodesIntegrator.cpp',
+  'numerics/DenseMatrix.cpp',
+  'numerics/EigenSparseDirectJacobian.cpp',
+  'numerics/EigenSparseJacobian.cpp',
+  'numerics/Func1.cpp',
+  'numerics/Func1Factory.cpp',
+  'numerics/FuncEval.cpp',
+  'numerics/IdasIntegrator.cpp',
+  'numerics/Integrators.cpp',
+  'numerics/SteadyStateSystem.cpp',
+  'numerics/SystemJacobianFactory.cpp',
+  'numerics/funcs.cpp',
+  'numerics/polyfit.cpp',
+)
+
+# Kinetics module
+kinetics_sources = files(
+  'kinetics/Arrhenius.cpp',
+  'kinetics/BlowersMaselRate.cpp',
+  'kinetics/BulkKinetics.cpp',
+  'kinetics/ChebyshevRate.cpp',
+  'kinetics/Custom.cpp',
+  'kinetics/ElectronCollisionPlasmaRate.cpp',
+  'kinetics/Falloff.cpp',
+  'kinetics/Group.cpp',
+  'kinetics/InterfaceKinetics.cpp',
+  'kinetics/InterfaceRate.cpp',
+  'kinetics/Kinetics.cpp',
+  'kinetics/KineticsFactory.cpp',
+  'kinetics/LinearBurkeRate.cpp',
+  'kinetics/PlogRate.cpp',
+  'kinetics/Reaction.cpp',
+  'kinetics/ReactionPath.cpp',
+  'kinetics/ReactionRateDelegator.cpp',
+  'kinetics/ReactionRateFactory.cpp',
+  'kinetics/TwoTempPlasmaRate.cpp',
+)
+
+# Transport module
+transport_sources = files(
+  'transport/DustyGasTransport.cpp',
+  'transport/GasTransport.cpp',
+  'transport/HighPressureGasTransport.cpp',
+  'transport/IonGasTransport.cpp',
+  'transport/MMCollisionInt.cpp',
+  'transport/MixTransport.cpp',
+  'transport/MultiTransport.cpp',
+  'transport/Transport.cpp',
+  'transport/TransportData.cpp',
+  'transport/TransportFactory.cpp',
+  'transport/WaterTransport.cpp',
+)
+
+# OneD module
+oned_sources = files(
+  'oneD/Boundary1D.cpp',
+  'oneD/Domain1D.cpp',
+  'oneD/DomainFactory.cpp',
+  'oneD/Flow1D.cpp',
+  'oneD/IonFlow.cpp',
+  'oneD/MultiJac.cpp',
+  'oneD/MultiNewton.cpp',
+  'oneD/OneDim.cpp',
+  'oneD/Sim1D.cpp',
+  'oneD/refine.cpp',
+)
+
+# ZeroD module
+zerod_sources = files(
+  'zeroD/ConnectorFactory.cpp',
+  'zeroD/ConnectorNode.cpp',
+  'zeroD/ConstPressureMoleReactor.cpp',
+  'zeroD/ConstPressureReactor.cpp',
+  'zeroD/FlowDevice.cpp',
+  'zeroD/FlowReactor.cpp',
+  'zeroD/IdealGasConstPressureMoleReactor.cpp',
+  'zeroD/IdealGasConstPressureReactor.cpp',
+  'zeroD/IdealGasMoleReactor.cpp',
+  'zeroD/IdealGasReactor.cpp',
+  'zeroD/MoleReactor.cpp',
+  'zeroD/Reactor.cpp',
+  'zeroD/ReactorBase.cpp',
+  'zeroD/ReactorFactory.cpp',
+  'zeroD/ReactorNet.cpp',
+  'zeroD/ReactorSurface.cpp',
+  'zeroD/Wall.cpp',
+  'zeroD/flowControllers.cpp',
+)
+
+# Extensions module (minimal for now)
+extensions_sources = files(
+  'extensions/PythonExtensionManager.cpp',
+  'extensions/canteraShared.cpp',
+  'extensions/pythonShim.cpp',
+)
+
+# Combine all sources
+cantera_sources = [
+  base_sources,
+  thermo_sources,
+  tpx_sources,
+  equil_sources,
+  numerics_sources,
+  kinetics_sources,
+  transport_sources,
+  oned_sources,
+  zerod_sources,
+  extensions_sources,
+]
+
+# Additional compile definitions for specific files
+application_cpp_args = ['-DCANTERA_DATA="' + datadir + '"']
+global_cpp_args = ['-DGIT_COMMIT="' + git_commit + '"']
+
+# Build application.cpp with special define
+application_lib = static_library('cantera_application',
+  'base/application.cpp',
+  include_directories: cantera_include_dirs,
+  cpp_args: application_cpp_args,
+  dependencies: [
+    eigen_dep,
+    fmt_dep,
+    yamlcpp_dep,
+    boost_dep,
+    thread_dep,
+    m_dep,
+  ],
+  pic: true,
+)
+
+# Build global.cpp with special define
+global_lib = static_library('cantera_global',
+  'base/global.cpp',
+  include_directories: cantera_include_dirs,
+  cpp_args: global_cpp_args,
+  dependencies: [
+    eigen_dep,
+    fmt_dep,
+    yamlcpp_dep,
+    boost_dep,
+    thread_dep,
+    m_dep,
+  ],
+  pic: true,
+)
+
+# Collect dependencies
+cantera_deps = [
+  eigen_dep,
+  fmt_dep,
+  yamlcpp_dep,
+  boost_dep,
+  thread_dep,
+  m_dep,
+]
+
+if sundials_dep.found()
+  cantera_deps += [sundials_dep, sundials_idas_dep, sundials_nvecserial_dep]
+endif
+
+if use_lapack
+  cantera_deps += [lapack_dep]
+  if blas_dep.found()
+    cantera_deps += [blas_dep]
+  endif
+endif
+
+if use_hdf5
+  cantera_deps += [hdf5_dep, highfive_dep]
+endif
+
+# Build the shared library
+cantera_lib = shared_library('cantera',
+  cantera_sources,
+  include_directories: cantera_include_dirs,
+  dependencies: cantera_deps,
+  link_whole: [application_lib, global_lib],
+  install: true,
+  version: meson.project_version(),
+  soversion: version_major,
+)
+
+# Install headers
+install_subdir('include/cantera',
+  install_dir: get_option('includedir'),
+  strip_directory: false,
+)
+
+# Declare dependency for use by other subprojects
+cantera_dep = declare_dependency(
+  link_with: cantera_lib,
+  include_directories: cantera_include_dirs,
+  dependencies: cantera_deps,
+)
+
+# pkg-config file
+pkg = import('pkgconfig')
+pkg.generate(cantera_lib,
+  name: 'Cantera',
+  description: 'Chemical kinetics, thermodynamics, and transport library',
+  url: 'https://cantera.org',
+  subdirs: 'cantera',
+)
diff --git a/subprojects/yaml-cpp/meson.build b/subprojects/yaml-cpp/meson.build
new file mode 100644
index 0000000000..f90213581f
--- /dev/null
+++ b/subprojects/yaml-cpp/meson.build
@@ -0,0 +1,47 @@
+# Minimal yaml-cpp subproject build file
+# This is a simplified build for Cantera's bundled yaml-cpp
+
+yaml_cpp_sources = files(
+  '../../ext/yaml-cpp/src/binary.cpp',
+  '../../ext/yaml-cpp/src/convert.cpp',
+  '../../ext/yaml-cpp/src/depthguard.cpp',
+  '../../ext/yaml-cpp/src/directives.cpp',
+  '../../ext/yaml-cpp/src/emit.cpp',
+  '../../ext/yaml-cpp/src/emitfromevents.cpp',
+  '../../ext/yaml-cpp/src/emitter.cpp',
+  '../../ext/yaml-cpp/src/emitterstate.cpp',
+  '../../ext/yaml-cpp/src/emitterutils.cpp',
+  '../../ext/yaml-cpp/src/exceptions.cpp',
+  '../../ext/yaml-cpp/src/exp.cpp',
+  '../../ext/yaml-cpp/src/memory.cpp',
+  '../../ext/yaml-cpp/src/node.cpp',
+  '../../ext/yaml-cpp/src/node_data.cpp',
+  '../../ext/yaml-cpp/src/nodebuilder.cpp',
+  '../../ext/yaml-cpp/src/nodeevents.cpp',
+  '../../ext/yaml-cpp/src/null.cpp',
+  '../../ext/yaml-cpp/src/ostream_wrapper.cpp',
+  '../../ext/yaml-cpp/src/parse.cpp',
+  '../../ext/yaml-cpp/src/parser.cpp',
+  '../../ext/yaml-cpp/src/regex_yaml.cpp',
+  '../../ext/yaml-cpp/src/scanner.cpp',
+  '../../ext/yaml-cpp/src/scanscalar.cpp',
+  '../../ext/yaml-cpp/src/scantag.cpp',
+  '../../ext/yaml-cpp/src/scantoken.cpp',
+  '../../ext/yaml-cpp/src/simplekey.cpp',
+  '../../ext/yaml-cpp/src/singledocparser.cpp',
+  '../../ext/yaml-cpp/src/stream.cpp',
+  '../../ext/yaml-cpp/src/tag.cpp',
+)
+
+yaml_cpp_inc = include_directories('../../ext/yaml-cpp/include')
+
+yaml_cpp_lib = static_library('yaml-cpp',
+  yaml_cpp_sources,
+  include_directories: yaml_cpp_inc,
+  pic: true,
+)
+
+yaml_cpp_dep = declare_dependency(
+  link_with: yaml_cpp_lib,
+  include_directories: yaml_cpp_inc,
+)

From 30bc375e6200458f1ef19f6d8f5d9f849319a238 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 8 Feb 2026 18:04:11 +0000
Subject: [PATCH 3/7] Fix Meson config and build most of C++ library

- Configure config.h generation with proper defines
- Create symlinks for ext dependencies (fmt, yaml-cpp, Eigen)
- Build yaml-cpp from ext/ submodule
- Use system Eigen3, Boost
- Use header-only fmt from ext/
- Fix compiler flags for GCC
- Build progresses to ~117/192 targets before hitting SUNDIALS requirement

Co-authored-by: bryanwweber <4396228+bryanwweber@users.noreply.github.com>
---
 ext/fmt                                |  2 +-
 ext/yaml-cpp                           |  2 +-
 include/cantera/base/config.h.meson.in | 56 ++++++++++++++++
 meson.build                            | 88 ++++++++++++++++++++------
 meson.options => meson_options.txt     |  2 +-
 src/meson.build                        | 10 +--
 subprojects/yaml-cpp/meson.build       |  2 +
 7 files changed, 134 insertions(+), 28 deletions(-)
 create mode 100644 include/cantera/base/config.h.meson.in
 rename meson.options => meson_options.txt (81%)

diff --git a/ext/fmt b/ext/fmt
index a33701196a..2d7dc922c6 160000
--- a/ext/fmt
+++ b/ext/fmt
@@ -1 +1 @@
-Subproject commit a33701196adfad74917046096bf5a2aa0ab0bb50
+Subproject commit 2d7dc922c66338b4dc6654fcd9ba6ecb2d09b914
diff --git a/ext/yaml-cpp b/ext/yaml-cpp
index 0579ae3d97..2e6383d272 160000
--- a/ext/yaml-cpp
+++ b/ext/yaml-cpp
@@ -1 +1 @@
-Subproject commit 0579ae3d976091d7d664aa9d2527e0d0cff25763
+Subproject commit 2e6383d272f676e1ad28ae5c47016045cbaff938
diff --git a/include/cantera/base/config.h.meson.in b/include/cantera/base/config.h.meson.in
new file mode 100644
index 0000000000..81c0b27da3
--- /dev/null
+++ b/include/cantera/base/config.h.meson.in
@@ -0,0 +1,56 @@
+#ifndef CT_CONFIG_H
+#define CT_CONFIG_H
+
+//---------------------------- Version Flags ------------------//
+// Cantera version -> this will be a double-quoted string value
+@CANTERA_VERSION@
+
+// Just the major + minor version (that is, 2.2 instead of 2.2.0)
+@CANTERA_SHORT_VERSION@
+
+//------------------------ Fortran settings -------------------//
+
+// define types doublereal, integer, and ftnlen to match the
+// corresponding Fortran data types on your system. The defaults
+// are OK for most systems
+
+typedef double doublereal;   // Fortran double precision
+typedef int integer;      // Fortran integer
+typedef int ftnlen;       // Fortran hidden string length type
+
+// Fortran compilers pass character strings in argument lists by
+// adding a hidden argument with the length of the string. Some
+// compilers add the hidden length argument immediately after the
+// CHARACTER variable being passed, while others put all of the hidden
+// length arguments at the end of the argument list. Define this if
+// the lengths are at the end of the argument list. This is usually the
+// case for most unix Fortran compilers, but is (by default) false for
+// Visual Fortran under Windows.
+#define STRING_LEN_AT_END
+
+// Define this if Fortran adds a trailing underscore to names in object files.
+// For linux and most unix systems, this is the case.
+@FTN_TRAILING_UNDERSCORE@
+
+//-------- LAPACK / BLAS ---------
+
+@LAPACK_FTN_STRING_LEN_AT_END@
+@LAPACK_FTN_TRAILING_UNDERSCORE@
+@CT_USE_LAPACK@
+
+@CT_USE_SYSTEM_EIGEN@
+@CT_USE_SYSTEM_EIGEN_PREFIXED@
+@CT_USE_SYSTEM_FMT@
+@CT_USE_SYSTEM_YAMLCPP@
+
+//-------------- Optional Cantera Capabilities ----------------------
+
+// Enable Sundials to use an external BLAS/LAPACK library if it was
+// built to use this option
+@CT_SUNDIALS_USE_LAPACK@
+
+// Enable export/import of HDF data via C++ HighFive
+@CT_USE_HDF5@
+@CT_USE_SYSTEM_HIGHFIVE@
+
+#endif
diff --git a/meson.build b/meson.build
index d18d9073ca..5913615597 100644
--- a/meson.build
+++ b/meson.build
@@ -36,7 +36,7 @@ if cpp.get_id() == 'msvc'
   add_project_arguments('/D_SCL_SECURE_NO_WARNINGS', language: 'cpp')
   add_project_arguments('/D_CRT_SECURE_NO_WARNINGS', language: 'cpp')
   add_project_arguments('/MD', language: 'cpp')
-else
+elif cpp.get_id() == 'clang'
   add_project_arguments('-fcolor-diagnostics', language: 'cpp')
 endif
 
@@ -112,12 +112,55 @@ else
   message('Using bundled yaml-cpp from ext/yaml-cpp')
   # Check if submodule is initialized
   yamlcpp_include_dir = meson.current_source_dir() / 'ext' / 'yaml-cpp' / 'include'
-  if not fs.is_dir(yamlcpp_include_dir)
+  yamlcpp_src_dir = meson.current_source_dir() / 'ext' / 'yaml-cpp' / 'src'
+  if not fs.is_dir(yamlcpp_include_dir) or not fs.is_dir(yamlcpp_src_dir)
     warning('yaml-cpp submodule not initialized. Run: git submodule update --init ext/yaml-cpp')
   endif
-  # Build yaml-cpp from submodule
-  yamlcpp_proj = subproject('yaml-cpp')
-  yamlcpp_dep = yamlcpp_proj.get_variable('yaml-cpp_dep')
+  
+  # Build yaml-cpp directly in main build
+  yamlcpp_sources = files(
+    'ext/yaml-cpp/src/binary.cpp',
+    'ext/yaml-cpp/src/convert.cpp',
+    'ext/yaml-cpp/src/depthguard.cpp',
+    'ext/yaml-cpp/src/directives.cpp',
+    'ext/yaml-cpp/src/emit.cpp',
+    'ext/yaml-cpp/src/emitfromevents.cpp',
+    'ext/yaml-cpp/src/emitter.cpp',
+    'ext/yaml-cpp/src/emitterstate.cpp',
+    'ext/yaml-cpp/src/emitterutils.cpp',
+    'ext/yaml-cpp/src/exceptions.cpp',
+    'ext/yaml-cpp/src/exp.cpp',
+    'ext/yaml-cpp/src/memory.cpp',
+    'ext/yaml-cpp/src/node.cpp',
+    'ext/yaml-cpp/src/node_data.cpp',
+    'ext/yaml-cpp/src/nodebuilder.cpp',
+    'ext/yaml-cpp/src/nodeevents.cpp',
+    'ext/yaml-cpp/src/null.cpp',
+    'ext/yaml-cpp/src/ostream_wrapper.cpp',
+    'ext/yaml-cpp/src/parse.cpp',
+    'ext/yaml-cpp/src/parser.cpp',
+    'ext/yaml-cpp/src/regex_yaml.cpp',
+    'ext/yaml-cpp/src/scanner.cpp',
+    'ext/yaml-cpp/src/scanscalar.cpp',
+    'ext/yaml-cpp/src/scantag.cpp',
+    'ext/yaml-cpp/src/scantoken.cpp',
+    'ext/yaml-cpp/src/simplekey.cpp',
+    'ext/yaml-cpp/src/singledocparser.cpp',
+    'ext/yaml-cpp/src/stream.cpp',
+    'ext/yaml-cpp/src/tag.cpp',
+  )
+  
+  yamlcpp_inc = include_directories('ext/yaml-cpp/include')
+  yamlcpp_lib = static_library('yaml-cpp-bundled',
+    yamlcpp_sources,
+    include_directories: yamlcpp_inc,
+    pic: true,
+  )
+  
+  yamlcpp_dep = declare_dependency(
+    link_with: yamlcpp_lib,
+    include_directories: yamlcpp_inc,
+  )
 endif
 
 # Boost dependency (header-only, required)
@@ -186,23 +229,23 @@ if git.found()
 endif
 
 # Data directory
-datadir = get_option('datadir')
-if datadir == ''
-  datadir = get_option('prefix') / 'share' / 'cantera' / 'data'
+ct_datadir = get_option('cantera_datadir')
+if ct_datadir == ''
+  ct_datadir = get_option('prefix') / 'share' / 'cantera' / 'data'
 endif
 
 # Generate config.h
 conf_data = configuration_data()
-conf_data.set_quoted('CANTERA_VERSION', meson.project_version())
-conf_data.set_quoted('CANTERA_SHORT_VERSION', cantera_short_version)
-conf_data.set10('CT_USE_SYSTEM_EIGEN', use_system_eigen)
-conf_data.set10('CT_USE_SYSTEM_EIGEN_PREFIXED', false)  # Assume unprefixed
-conf_data.set10('CT_USE_SYSTEM_FMT', use_system_fmt)
-conf_data.set10('CT_USE_SYSTEM_YAMLCPP', use_system_yamlcpp)
-conf_data.set10('CT_USE_LAPACK', use_lapack)
-conf_data.set10('CT_USE_HDF5', use_hdf5)
-conf_data.set10('CT_USE_SYSTEM_HIGHFIVE', use_system_highfive)
-conf_data.set10('CT_SUNDIALS_USE_LAPACK', false)  # Conservative default
+conf_data.set('CANTERA_VERSION', '#define CANTERA_VERSION "' + meson.project_version() + '"')
+conf_data.set('CANTERA_SHORT_VERSION', '#define CANTERA_SHORT_VERSION "' + cantera_short_version + '"')
+conf_data.set('CT_USE_SYSTEM_EIGEN', use_system_eigen ? '#define CT_USE_SYSTEM_EIGEN 1' : '/* #undef CT_USE_SYSTEM_EIGEN */')
+conf_data.set('CT_USE_SYSTEM_EIGEN_PREFIXED', '/* #undef CT_USE_SYSTEM_EIGEN_PREFIXED */')
+conf_data.set('CT_USE_SYSTEM_FMT', use_system_fmt ? '#define CT_USE_SYSTEM_FMT 1' : '/* #undef CT_USE_SYSTEM_FMT */')
+conf_data.set('CT_USE_SYSTEM_YAMLCPP', use_system_yamlcpp ? '#define CT_USE_SYSTEM_YAMLCPP 1' : '/* #undef CT_USE_SYSTEM_YAMLCPP */')
+conf_data.set('CT_USE_LAPACK', use_lapack ? '#define CT_USE_LAPACK 1' : '/* #undef CT_USE_LAPACK */')
+conf_data.set('CT_USE_HDF5', use_hdf5 ? '#define CT_USE_HDF5 1' : '/* #undef CT_USE_HDF5 */')
+conf_data.set('CT_USE_SYSTEM_HIGHFIVE', use_system_highfive ? '#define CT_USE_SYSTEM_HIGHFIVE 1' : '/* #undef CT_USE_SYSTEM_HIGHFIVE */')
+conf_data.set('CT_SUNDIALS_USE_LAPACK', '/* #undef CT_SUNDIALS_USE_LAPACK */')
 
 # Fortran settings
 conf_data.set('FTN_TRAILING_UNDERSCORE', '#define FTN_TRAILING_UNDERSCORE')
@@ -210,20 +253,25 @@ conf_data.set('LAPACK_FTN_STRING_LEN_AT_END', '#define LAPACK_FTN_STRING_LEN_AT_
 conf_data.set('LAPACK_FTN_TRAILING_UNDERSCORE', '#define LAPACK_FTN_TRAILING_UNDERSCORE')
 
 config_h = configure_file(
-  input: 'include/cantera/base/config.h.in',
+  input: 'include/cantera/base/config.h.meson.in',
   output: 'config.h',
   configuration: conf_data,
   install: true,
   install_dir: get_option('includedir') / 'cantera' / 'base'
 )
 
+# Create symlink for config.h in build directory so it's found at cantera/base/config.h
+meson.add_postconf_script('sh', '-c', 'mkdir -p "$MESON_BUILD_ROOT/cantera/base" && ln -sf "$MESON_BUILD_ROOT/config.h" "$MESON_BUILD_ROOT/cantera/base/config.h"'.replace('$MESON_BUILD_ROOT', meson.current_build_dir()))
+
 # Include directories
 cantera_include_dirs = include_directories(
   'include',
   'src',
-  '.'  # For generated config.h
 )
 
+# Build directory for generated files (contains config.h)
+cantera_build_include = include_directories('.')
+
 # Build the library
 subdir('src')
 
diff --git a/meson.options b/meson_options.txt
similarity index 81%
rename from meson.options
rename to meson_options.txt
index 98bf652e30..f276783933 100644
--- a/meson.options
+++ b/meson_options.txt
@@ -1,4 +1,4 @@
-option('datadir', 
+option('cantera_datadir', 
   type: 'string', 
   value: '',
   description: 'Directory for Cantera data files (default: prefix/share/cantera/data)'
diff --git a/src/meson.build b/src/meson.build
index 9740a4262b..4855a59599 100644
--- a/src/meson.build
+++ b/src/meson.build
@@ -213,13 +213,13 @@ cantera_sources = [
 ]
 
 # Additional compile definitions for specific files
-application_cpp_args = ['-DCANTERA_DATA="' + datadir + '"']
+application_cpp_args = ['-DCANTERA_DATA="' + ct_datadir + '"']
 global_cpp_args = ['-DGIT_COMMIT="' + git_commit + '"']
 
 # Build application.cpp with special define
 application_lib = static_library('cantera_application',
   'base/application.cpp',
-  include_directories: cantera_include_dirs,
+  include_directories: [cantera_include_dirs, cantera_build_include],
   cpp_args: application_cpp_args,
   dependencies: [
     eigen_dep,
@@ -235,7 +235,7 @@ application_lib = static_library('cantera_application',
 # Build global.cpp with special define
 global_lib = static_library('cantera_global',
   'base/global.cpp',
-  include_directories: cantera_include_dirs,
+  include_directories: [cantera_include_dirs, cantera_build_include],
   cpp_args: global_cpp_args,
   dependencies: [
     eigen_dep,
@@ -276,7 +276,7 @@ endif
 # Build the shared library
 cantera_lib = shared_library('cantera',
   cantera_sources,
-  include_directories: cantera_include_dirs,
+  include_directories: [cantera_include_dirs, cantera_build_include],
   dependencies: cantera_deps,
   link_whole: [application_lib, global_lib],
   install: true,
@@ -293,7 +293,7 @@ install_subdir('include/cantera',
 # Declare dependency for use by other subprojects
 cantera_dep = declare_dependency(
   link_with: cantera_lib,
-  include_directories: cantera_include_dirs,
+  include_directories: [cantera_include_dirs, cantera_build_include],
   dependencies: cantera_deps,
 )
 
diff --git a/subprojects/yaml-cpp/meson.build b/subprojects/yaml-cpp/meson.build
index f90213581f..57264aa9d3 100644
--- a/subprojects/yaml-cpp/meson.build
+++ b/subprojects/yaml-cpp/meson.build
@@ -1,3 +1,5 @@
+project('yaml-cpp', 'cpp', version: '0.8.0')
+
 # Minimal yaml-cpp subproject build file
 # This is a simplified build for Cantera's bundled yaml-cpp
 

From 21b25ac5f529e81422e052f9dd9e90ed98ce4155 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 8 Feb 2026 18:05:05 +0000
Subject: [PATCH 4/7] Add Meson build documentation and ext symlinks

- Add MESON_BUILD.md with usage instructions
- Add symlinks for ext dependencies in include/cantera/ext/
- Document workaround for fmt join.h compatibility

Co-authored-by: bryanwweber <4396228+bryanwweber@users.noreply.github.com>
---
 MESON_BUILD.md               | 101 +++++++++++++++++++++++++++++++++++
 include/cantera/ext/Eigen    |   1 +
 include/cantera/ext/fmt      |   1 +
 include/cantera/ext/yaml-cpp |   1 +
 4 files changed, 104 insertions(+)
 create mode 100644 MESON_BUILD.md
 create mode 120000 include/cantera/ext/Eigen
 create mode 120000 include/cantera/ext/fmt
 create mode 120000 include/cantera/ext/yaml-cpp

diff --git a/MESON_BUILD.md b/MESON_BUILD.md
new file mode 100644
index 0000000000..7abc2967fe
--- /dev/null
+++ b/MESON_BUILD.md
@@ -0,0 +1,101 @@
+# Meson Build System for Cantera
+
+This directory contains the initial Meson build configuration for Cantera's C++ library.
+
+## Status
+
+The Meson build system is under development and currently builds most of the C++ library (117/192 targets). The build is blocked by the SUNDIALS dependency which needs to be added as a subproject or installed system-wide.
+
+## Quick Start
+
+### Prerequisites
+
+- Meson >= 1.0.0
+- Ninja build system
+- C++20 compatible compiler (GCC, Clang, or MSVC)
+- System dependencies:
+  - Eigen3 >= 3.4 (or will use ext/eigen submodule)
+  - Boost >= 1.83 (required, must be system-installed)
+  - Optional: HDF5, BLAS/LAPACK
+
+### Building
+
+1. Initialize required submodules:
+   ```bash
+   git submodule update --init ext/fmt ext/yaml-cpp
+   ```
+
+2. Create a compatibility symlink for fmt (required for older fmt references):
+   ```bash
+   cd ext/fmt/include/fmt && ln -s ranges.h join.h
+   ```
+
+3. Configure the build:
+   ```bash
+   meson setup builddir
+   ```
+
+4. Compile:
+   ```bash
+   meson compile -C builddir
+   ```
+
+5. Install (optional):
+   ```bash
+   meson install -C builddir
+   ```
+
+## Dependencies
+
+### Required
+- **Boost** (>= 1.83): Header-only, must be system-installed
+- **Eigen3** (>= 3.4): Uses system if available, otherwise ext/eigen submodule
+- **fmt** (>= 9.1.0): Uses system if available, otherwise ext/fmt (header-only mode)
+- **yaml-cpp** (>= 0.6): Uses system if available, otherwise builds from ext/yaml-cpp
+
+### Optional
+- **SUNDIALS** (>= 6.0): Required for ODE/DAE integration (not yet implemented)
+- **HDF5**: For HDF5 data file support
+- **BLAS/LAPACK**: For optimized linear algebra (falls back to Eigen)
+- **HighFive**: C++ wrapper for HDF5
+
+## Configuration Options
+
+- `cantera_datadir`: Directory for Cantera data files (default: `prefix/share/cantera/data`)
+
+Example:
+```bash
+meson setup builddir -Dcantera_datadir=/opt/cantera/data
+```
+
+## Known Limitations
+
+1. **SUNDIALS not yet supported**: The SUNDIALS dependency needs to be implemented as a Meson subproject or made available system-wide
+2. **No Python bindings**: Only C++ library is currently supported
+3. **No Fortran interface**: F90 interface not yet implemented
+4. **Limited testing**: Build system needs more testing across platforms
+
+## Comparison with SCons
+
+The Meson build aims to eventually replace the SCons build system with these benefits:
+- Faster build times with better parallelization
+- Better IDE integration
+- Standard pkg-config support
+- Simpler dependency management
+- Cross-compilation support
+
+## Contributing
+
+This is initial work to replace the SCons build system. Contributions are welcome to:
+- Add SUNDIALS subproject support
+- Improve dependency detection
+- Add testing infrastructure
+- Port more configuration options from SCons
+
+## Files
+
+- `meson.build`: Root build configuration
+- `meson_options.txt`: Build options
+- `src/meson.build`: C++ source compilation
+- `include/cantera/base/config.h.meson.in`: Configuration header template
+- `subprojects/`: Fallback dependencies (currently only yaml-cpp)
diff --git a/include/cantera/ext/Eigen b/include/cantera/ext/Eigen
new file mode 120000
index 0000000000..4691a45985
--- /dev/null
+++ b/include/cantera/ext/Eigen
@@ -0,0 +1 @@
+../../../ext/eigen/Eigen
\ No newline at end of file
diff --git a/include/cantera/ext/fmt b/include/cantera/ext/fmt
new file mode 120000
index 0000000000..e3ea0d0edd
--- /dev/null
+++ b/include/cantera/ext/fmt
@@ -0,0 +1 @@
+../../../ext/fmt/include/fmt
\ No newline at end of file
diff --git a/include/cantera/ext/yaml-cpp b/include/cantera/ext/yaml-cpp
new file mode 120000
index 0000000000..4c41e6ced5
--- /dev/null
+++ b/include/cantera/ext/yaml-cpp
@@ -0,0 +1 @@
+../../../ext/yaml-cpp/include/yaml-cpp
\ No newline at end of file

From f363fa1d7a62b7b48126737e1e155992e2da7b05 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 8 Feb 2026 18:16:49 +0000
Subject: [PATCH 5/7] Refactor to use glob patterns and avoid listing
 individual files

- Use find command with Meson run_command to auto-discover .cpp files
- Remove manual listing of 150+ source files in src/meson.build
- Auto-discover yaml-cpp source files instead of listing them
- Update documentation to explain glob pattern approach
- Follows SCons multi_glob pattern for automatic source discovery

Co-authored-by: bryanwweber <4396228+bryanwweber@users.noreply.github.com>
---
 MESON_BUILD.md                   |  33 +++-
 meson.build                      |  58 +++----
 src/meson.build                  | 282 +++++++++----------------------
 subprojects/yaml-cpp/meson.build |  49 ------
 4 files changed, 133 insertions(+), 289 deletions(-)
 delete mode 100644 subprojects/yaml-cpp/meson.build

diff --git a/MESON_BUILD.md b/MESON_BUILD.md
index 7abc2967fe..7c9b6ccc7e 100644
--- a/MESON_BUILD.md
+++ b/MESON_BUILD.md
@@ -4,7 +4,7 @@ This directory contains the initial Meson build configuration for Cantera's C++
 
 ## Status
 
-The Meson build system is under development and currently builds most of the C++ library (117/192 targets). The build is blocked by the SUNDIALS dependency which needs to be added as a subproject or installed system-wide.
+The Meson build system is under development and currently builds most of the C++ library (~60% of targets). The build is blocked by the SUNDIALS dependency which needs to be added as a subproject or installed system-wide.
 
 ## Quick Start
 
@@ -51,7 +51,7 @@ The Meson build system is under development and currently builds most of the C++
 - **Boost** (>= 1.83): Header-only, must be system-installed
 - **Eigen3** (>= 3.4): Uses system if available, otherwise ext/eigen submodule
 - **fmt** (>= 9.1.0): Uses system if available, otherwise ext/fmt (header-only mode)
-- **yaml-cpp** (>= 0.6): Uses system if available, otherwise builds from ext/yaml-cpp
+- **yaml-cpp** (>= 0.6): Uses system if available, otherwise auto-discovers and builds from ext/yaml-cpp
 
 ### Optional
 - **SUNDIALS** (>= 6.0): Required for ODE/DAE integration (not yet implemented)
@@ -68,6 +68,30 @@ Example:
 meson setup builddir -Dcantera_datadir=/opt/cantera/data
 ```
 
+## Build Features
+
+### Automatic Source Discovery
+
+The Meson build automatically discovers source files using glob patterns, similar to how SCons uses `multi_glob()`:
+
+```meson
+# Automatically find all .cpp files in each module directory
+base_files = run_command(find, 'base', '-name', '*.cpp', ...)
+foreach f : base_files
+  base_sources += files('base' / f)
+endforeach
+```
+
+This eliminates the need to manually list individual source files.
+
+### Dependency Management
+
+Dependencies are tried in order:
+1. **System packages** (via pkg-config/CMake) 
+2. **Bundled sources** (from ext/ submodules with automatic file discovery)
+
+For yaml-cpp, Meson automatically discovers all source files from `ext/yaml-cpp/src` instead of using the CMake build (which has issues with symlinked subprojects).
+
 ## Known Limitations
 
 1. **SUNDIALS not yet supported**: The SUNDIALS dependency needs to be implemented as a Meson subproject or made available system-wide
@@ -83,6 +107,7 @@ The Meson build aims to eventually replace the SCons build system with these ben
 - Standard pkg-config support
 - Simpler dependency management
 - Cross-compilation support
+- **Automatic source discovery** like SCons `multi_glob()`
 
 ## Contributing
 
@@ -96,6 +121,6 @@ This is initial work to replace the SCons build system. Contributions are welcom
 
 - `meson.build`: Root build configuration
 - `meson_options.txt`: Build options
-- `src/meson.build`: C++ source compilation
+- `src/meson.build`: C++ source compilation with automatic file discovery
 - `include/cantera/base/config.h.meson.in`: Configuration header template
-- `subprojects/`: Fallback dependencies (currently only yaml-cpp)
+- `include/cantera/ext/`: Symlinks to submodule headers (fmt, yaml-cpp, Eigen)
diff --git a/meson.build b/meson.build
index 5913615597..216fd0a0ba 100644
--- a/meson.build
+++ b/meson.build
@@ -103,6 +103,8 @@ else
 endif
 
 # yaml-cpp dependency with fallback
+# Note: CMake integration has issues with Meson detecting source files correctly
+# when the subproject is a symlink. Using direct file specification instead.
 yamlcpp_dep = dependency('yaml-cpp', version: '>=0.6', required: false)
 use_system_yamlcpp = false
 if yamlcpp_dep.found()
@@ -111,48 +113,32 @@ if yamlcpp_dep.found()
 else
   message('Using bundled yaml-cpp from ext/yaml-cpp')
   # Check if submodule is initialized
-  yamlcpp_include_dir = meson.current_source_dir() / 'ext' / 'yaml-cpp' / 'include'
-  yamlcpp_src_dir = meson.current_source_dir() / 'ext' / 'yaml-cpp' / 'src'
-  if not fs.is_dir(yamlcpp_include_dir) or not fs.is_dir(yamlcpp_src_dir)
+  yamlcpp_cmake = meson.current_source_dir() / 'ext' / 'yaml-cpp' / 'CMakeLists.txt'
+  if not fs.exists(yamlcpp_cmake)
     warning('yaml-cpp submodule not initialized. Run: git submodule update --init ext/yaml-cpp')
   endif
   
-  # Build yaml-cpp directly in main build
-  yamlcpp_sources = files(
-    'ext/yaml-cpp/src/binary.cpp',
-    'ext/yaml-cpp/src/convert.cpp',
-    'ext/yaml-cpp/src/depthguard.cpp',
-    'ext/yaml-cpp/src/directives.cpp',
-    'ext/yaml-cpp/src/emit.cpp',
-    'ext/yaml-cpp/src/emitfromevents.cpp',
-    'ext/yaml-cpp/src/emitter.cpp',
-    'ext/yaml-cpp/src/emitterstate.cpp',
-    'ext/yaml-cpp/src/emitterutils.cpp',
-    'ext/yaml-cpp/src/exceptions.cpp',
-    'ext/yaml-cpp/src/exp.cpp',
-    'ext/yaml-cpp/src/memory.cpp',
-    'ext/yaml-cpp/src/node.cpp',
-    'ext/yaml-cpp/src/node_data.cpp',
-    'ext/yaml-cpp/src/nodebuilder.cpp',
-    'ext/yaml-cpp/src/nodeevents.cpp',
-    'ext/yaml-cpp/src/null.cpp',
-    'ext/yaml-cpp/src/ostream_wrapper.cpp',
-    'ext/yaml-cpp/src/parse.cpp',
-    'ext/yaml-cpp/src/parser.cpp',
-    'ext/yaml-cpp/src/regex_yaml.cpp',
-    'ext/yaml-cpp/src/scanner.cpp',
-    'ext/yaml-cpp/src/scanscalar.cpp',
-    'ext/yaml-cpp/src/scantag.cpp',
-    'ext/yaml-cpp/src/scantoken.cpp',
-    'ext/yaml-cpp/src/simplekey.cpp',
-    'ext/yaml-cpp/src/singledocparser.cpp',
-    'ext/yaml-cpp/src/stream.cpp',
-    'ext/yaml-cpp/src/tag.cpp',
-  )
+  # Build yaml-cpp from discovered source files
+  yaml_cpp_src_dir = 'ext/yaml-cpp/src'
+  yaml_cpp_sources = run_command(
+    find_program('find'),
+    yaml_cpp_src_dir,
+    '-name', '*.cpp',
+    '-printf', '%P\n',
+    check: true,
+    capture: true
+  ).stdout().strip().split('\n')
+  
+  yaml_cpp_files = []
+  foreach f : yaml_cpp_sources
+    if f != ''
+      yaml_cpp_files += files(yaml_cpp_src_dir / f)
+    endif
+  endforeach
   
   yamlcpp_inc = include_directories('ext/yaml-cpp/include')
   yamlcpp_lib = static_library('yaml-cpp-bundled',
-    yamlcpp_sources,
+    yaml_cpp_files,
     include_directories: yamlcpp_inc,
     pic: true,
   )
diff --git a/src/meson.build b/src/meson.build
index 4855a59599..bf71cd76eb 100644
--- a/src/meson.build
+++ b/src/meson.build
@@ -1,216 +1,98 @@
 # Source files for the Cantera library
-# Organized by subdirectory
+# Using run_command to automatically discover source files via find
 
-# Base module
-base_sources = files(
-  'base/AnyMap.cpp',
-  'base/Array.cpp',
-  'base/ExtensionManager.cpp',
-  'base/ExtensionManagerFactory.cpp',
-  'base/Interface.cpp',
-  'base/Solution.cpp',
-  'base/SolutionArray.cpp',
-  'base/Storage.cpp',
-  'base/Units.cpp',
-  'base/ValueCache.cpp',
-  'base/YamlWriter.cpp',
-  'base/application.cpp',
-  'base/checkFinite.cpp',
-  'base/clockWC.cpp',
-  'base/ctexceptions.cpp',
-  'base/global.cpp',
-  'base/stringUtils.cpp',
-)
+# Helper to get cpp files from a directory
+find_cpp = find_program('find')
 
-# Thermo module
-thermo_sources = files(
-  'thermo/BinarySolutionTabulatedThermo.cpp',
-  'thermo/ConstCpPoly.cpp',
-  'thermo/CoverageDependentSurfPhase.cpp',
-  'thermo/DebyeHuckel.cpp',
-  'thermo/EEDFTwoTermApproximation.cpp',
-  'thermo/Elements.cpp',
-  'thermo/GibbsExcessVPSSTP.cpp',
-  'thermo/HMWSoln.cpp',
-  'thermo/IdealGasPhase.cpp',
-  'thermo/IdealMolalSoln.cpp',
-  'thermo/IdealSolidSolnPhase.cpp',
-  'thermo/IdealSolnGasVPSS.cpp',
-  'thermo/MargulesVPSSTP.cpp',
-  'thermo/MixtureFugacityTP.cpp',
-  'thermo/MolalityVPSSTP.cpp',
-  'thermo/Mu0Poly.cpp',
-  'thermo/MultiSpeciesThermo.cpp',
-  'thermo/Nasa9Poly1.cpp',
-  'thermo/Nasa9PolyMultiTempRegion.cpp',
-  'thermo/NasaPoly2.cpp',
-  'thermo/PDSS.cpp',
-  'thermo/PDSSFactory.cpp',
-  'thermo/PDSS_ConstVol.cpp',
-  'thermo/PDSS_HKFT.cpp',
-  'thermo/PDSS_SSVol.cpp',
-  'thermo/PDSS_Water.cpp',
-  'thermo/PengRobinson.cpp',
-  'thermo/Phase.cpp',
-  'thermo/PlasmaPhase.cpp',
-  'thermo/PureFluidPhase.cpp',
-  'thermo/RedlichKisterVPSSTP.cpp',
-  'thermo/RedlichKwongMFTP.cpp',
-  'thermo/SingleSpeciesTP.cpp',
-  'thermo/Species.cpp',
-  'thermo/SpeciesThermoFactory.cpp',
-  'thermo/SpeciesThermoInterpType.cpp',
-  'thermo/StoichSubstance.cpp',
-  'thermo/SurfPhase.cpp',
-  'thermo/ThermoFactory.cpp',
-  'thermo/ThermoPhase.cpp',
-  'thermo/VPStandardStateTP.cpp',
-  'thermo/WaterProps.cpp',
-  'thermo/WaterPropsIAPWS.cpp',
-  'thermo/WaterPropsIAPWSphi.cpp',
-  'thermo/WaterSSTP.cpp',
-)
+# Gather all .cpp files from each module subdirectory
+base_files = run_command(find_cpp, 'base', '-maxdepth', '1', '-name', '*.cpp', '-printf', '%f\n', check: true, capture: true).stdout().strip().split('\n')
+base_sources = []
+foreach f : base_files
+  if f != ''
+    base_sources += files('base' / f)
+  endif
+endforeach
 
-# TPX module
-tpx_sources = files(
-  'tpx/CarbonDioxide.cpp',
-  'tpx/HFC134a.cpp',
-  'tpx/Heptane.cpp',
-  'tpx/Hydrogen.cpp',
-  'tpx/Methane.cpp',
-  'tpx/Nitrogen.cpp',
-  'tpx/Oxygen.cpp',
-  'tpx/Sub.cpp',
-  'tpx/Water.cpp',
-  'tpx/utils.cpp',
-)
+thermo_files = run_command(find_cpp, 'thermo', '-maxdepth', '1', '-name', '*.cpp', '-printf', '%f\n', check: true, capture: true).stdout().strip().split('\n')
+thermo_sources = []
+foreach f : thermo_files
+  if f != ''
+    thermo_sources += files('thermo' / f)
+  endif
+endforeach
 
-# Equilibrium module
-equil_sources = files(
-  'equil/BasisOptimize.cpp',
-  'equil/ChemEquil.cpp',
-  'equil/MultiPhase.cpp',
-  'equil/MultiPhaseEquil.cpp',
-  'equil/vcs_MultiPhaseEquil.cpp',
-  'equil/vcs_VolPhase.cpp',
-  'equil/vcs_solve.cpp',
-  'equil/vcs_solve_TP.cpp',
-  'equil/vcs_util.cpp',
-)
+tpx_files = run_command(find_cpp, 'tpx', '-maxdepth', '1', '-name', '*.cpp', '-printf', '%f\n', check: true, capture: true).stdout().strip().split('\n')
+tpx_sources = []
+foreach f : tpx_files
+  if f != ''
+    tpx_sources += files('tpx' / f)
+  endif
+endforeach
+
+equil_files_cpp = run_command(find_cpp, 'equil', '-maxdepth', '1', '-name', '*.cpp', '-printf', '%f\n', check: true, capture: true).stdout().strip().split('\n')
+equil_files_c = run_command(find_cpp, 'equil', '-maxdepth', '1', '-name', '*.c', '-printf', '%f\n', check: false, capture: true).stdout().strip().split('\n')
+equil_sources = []
+foreach f : equil_files_cpp
+  if f != ''
+    equil_sources += files('equil' / f)
+  endif
+endforeach
+foreach f : equil_files_c
+  if f != ''
+    equil_sources += files('equil' / f)
+  endif
+endforeach
 
-# Numerics module
-numerics_sources = files(
-  'numerics/AdaptivePreconditioner.cpp',
-  'numerics/BandMatrix.cpp',
-  'numerics/CVodesIntegrator.cpp',
-  'numerics/DenseMatrix.cpp',
-  'numerics/EigenSparseDirectJacobian.cpp',
-  'numerics/EigenSparseJacobian.cpp',
-  'numerics/Func1.cpp',
-  'numerics/Func1Factory.cpp',
-  'numerics/FuncEval.cpp',
-  'numerics/IdasIntegrator.cpp',
-  'numerics/Integrators.cpp',
-  'numerics/SteadyStateSystem.cpp',
-  'numerics/SystemJacobianFactory.cpp',
-  'numerics/funcs.cpp',
-  'numerics/polyfit.cpp',
-)
+numerics_files = run_command(find_cpp, 'numerics', '-maxdepth', '1', '-name', '*.cpp', '-printf', '%f\n', check: true, capture: true).stdout().strip().split('\n')
+numerics_sources = []
+foreach f : numerics_files
+  if f != ''
+    numerics_sources += files('numerics' / f)
+  endif
+endforeach
 
-# Kinetics module
-kinetics_sources = files(
-  'kinetics/Arrhenius.cpp',
-  'kinetics/BlowersMaselRate.cpp',
-  'kinetics/BulkKinetics.cpp',
-  'kinetics/ChebyshevRate.cpp',
-  'kinetics/Custom.cpp',
-  'kinetics/ElectronCollisionPlasmaRate.cpp',
-  'kinetics/Falloff.cpp',
-  'kinetics/Group.cpp',
-  'kinetics/InterfaceKinetics.cpp',
-  'kinetics/InterfaceRate.cpp',
-  'kinetics/Kinetics.cpp',
-  'kinetics/KineticsFactory.cpp',
-  'kinetics/LinearBurkeRate.cpp',
-  'kinetics/PlogRate.cpp',
-  'kinetics/Reaction.cpp',
-  'kinetics/ReactionPath.cpp',
-  'kinetics/ReactionRateDelegator.cpp',
-  'kinetics/ReactionRateFactory.cpp',
-  'kinetics/TwoTempPlasmaRate.cpp',
-)
+kinetics_files = run_command(find_cpp, 'kinetics', '-maxdepth', '1', '-name', '*.cpp', '-printf', '%f\n', check: true, capture: true).stdout().strip().split('\n')
+kinetics_sources = []
+foreach f : kinetics_files
+  if f != ''
+    kinetics_sources += files('kinetics' / f)
+  endif
+endforeach
 
-# Transport module
-transport_sources = files(
-  'transport/DustyGasTransport.cpp',
-  'transport/GasTransport.cpp',
-  'transport/HighPressureGasTransport.cpp',
-  'transport/IonGasTransport.cpp',
-  'transport/MMCollisionInt.cpp',
-  'transport/MixTransport.cpp',
-  'transport/MultiTransport.cpp',
-  'transport/Transport.cpp',
-  'transport/TransportData.cpp',
-  'transport/TransportFactory.cpp',
-  'transport/WaterTransport.cpp',
-)
+transport_files = run_command(find_cpp, 'transport', '-maxdepth', '1', '-name', '*.cpp', '-printf', '%f\n', check: true, capture: true).stdout().strip().split('\n')
+transport_sources = []
+foreach f : transport_files
+  if f != ''
+    transport_sources += files('transport' / f)
+  endif
+endforeach
 
-# OneD module
-oned_sources = files(
-  'oneD/Boundary1D.cpp',
-  'oneD/Domain1D.cpp',
-  'oneD/DomainFactory.cpp',
-  'oneD/Flow1D.cpp',
-  'oneD/IonFlow.cpp',
-  'oneD/MultiJac.cpp',
-  'oneD/MultiNewton.cpp',
-  'oneD/OneDim.cpp',
-  'oneD/Sim1D.cpp',
-  'oneD/refine.cpp',
-)
+oned_files = run_command(find_cpp, 'oneD', '-maxdepth', '1', '-name', '*.cpp', '-printf', '%f\n', check: true, capture: true).stdout().strip().split('\n')
+oned_sources = []
+foreach f : oned_files
+  if f != ''
+    oned_sources += files('oneD' / f)
+  endif
+endforeach
 
-# ZeroD module
-zerod_sources = files(
-  'zeroD/ConnectorFactory.cpp',
-  'zeroD/ConnectorNode.cpp',
-  'zeroD/ConstPressureMoleReactor.cpp',
-  'zeroD/ConstPressureReactor.cpp',
-  'zeroD/FlowDevice.cpp',
-  'zeroD/FlowReactor.cpp',
-  'zeroD/IdealGasConstPressureMoleReactor.cpp',
-  'zeroD/IdealGasConstPressureReactor.cpp',
-  'zeroD/IdealGasMoleReactor.cpp',
-  'zeroD/IdealGasReactor.cpp',
-  'zeroD/MoleReactor.cpp',
-  'zeroD/Reactor.cpp',
-  'zeroD/ReactorBase.cpp',
-  'zeroD/ReactorFactory.cpp',
-  'zeroD/ReactorNet.cpp',
-  'zeroD/ReactorSurface.cpp',
-  'zeroD/Wall.cpp',
-  'zeroD/flowControllers.cpp',
-)
+zerod_files = run_command(find_cpp, 'zeroD', '-maxdepth', '1', '-name', '*.cpp', '-printf', '%f\n', check: true, capture: true).stdout().strip().split('\n')
+zerod_sources = []
+foreach f : zerod_files
+  if f != ''
+    zerod_sources += files('zeroD' / f)
+  endif
+endforeach
 
-# Extensions module (minimal for now)
-extensions_sources = files(
-  'extensions/PythonExtensionManager.cpp',
-  'extensions/canteraShared.cpp',
-  'extensions/pythonShim.cpp',
-)
+extensions_files = run_command(find_cpp, 'extensions', '-maxdepth', '1', '-name', '*.cpp', '-printf', '%f\n', check: true, capture: true).stdout().strip().split('\n')
+extensions_sources = []
+foreach f : extensions_files
+  if f != ''
+    extensions_sources += files('extensions' / f)
+  endif
+endforeach
 
 # Combine all sources
-cantera_sources = [
-  base_sources,
-  thermo_sources,
-  tpx_sources,
-  equil_sources,
-  numerics_sources,
-  kinetics_sources,
-  transport_sources,
-  oned_sources,
-  zerod_sources,
-  extensions_sources,
-]
+cantera_sources = base_sources + thermo_sources + tpx_sources + equil_sources + numerics_sources + kinetics_sources + transport_sources + oned_sources + zerod_sources + extensions_sources
 
 # Additional compile definitions for specific files
 application_cpp_args = ['-DCANTERA_DATA="' + ct_datadir + '"']
diff --git a/subprojects/yaml-cpp/meson.build b/subprojects/yaml-cpp/meson.build
deleted file mode 100644
index 57264aa9d3..0000000000
--- a/subprojects/yaml-cpp/meson.build
+++ /dev/null
@@ -1,49 +0,0 @@
-project('yaml-cpp', 'cpp', version: '0.8.0')
-
-# Minimal yaml-cpp subproject build file
-# This is a simplified build for Cantera's bundled yaml-cpp
-
-yaml_cpp_sources = files(
-  '../../ext/yaml-cpp/src/binary.cpp',
-  '../../ext/yaml-cpp/src/convert.cpp',
-  '../../ext/yaml-cpp/src/depthguard.cpp',
-  '../../ext/yaml-cpp/src/directives.cpp',
-  '../../ext/yaml-cpp/src/emit.cpp',
-  '../../ext/yaml-cpp/src/emitfromevents.cpp',
-  '../../ext/yaml-cpp/src/emitter.cpp',
-  '../../ext/yaml-cpp/src/emitterstate.cpp',
-  '../../ext/yaml-cpp/src/emitterutils.cpp',
-  '../../ext/yaml-cpp/src/exceptions.cpp',
-  '../../ext/yaml-cpp/src/exp.cpp',
-  '../../ext/yaml-cpp/src/memory.cpp',
-  '../../ext/yaml-cpp/src/node.cpp',
-  '../../ext/yaml-cpp/src/node_data.cpp',
-  '../../ext/yaml-cpp/src/nodebuilder.cpp',
-  '../../ext/yaml-cpp/src/nodeevents.cpp',
-  '../../ext/yaml-cpp/src/null.cpp',
-  '../../ext/yaml-cpp/src/ostream_wrapper.cpp',
-  '../../ext/yaml-cpp/src/parse.cpp',
-  '../../ext/yaml-cpp/src/parser.cpp',
-  '../../ext/yaml-cpp/src/regex_yaml.cpp',
-  '../../ext/yaml-cpp/src/scanner.cpp',
-  '../../ext/yaml-cpp/src/scanscalar.cpp',
-  '../../ext/yaml-cpp/src/scantag.cpp',
-  '../../ext/yaml-cpp/src/scantoken.cpp',
-  '../../ext/yaml-cpp/src/simplekey.cpp',
-  '../../ext/yaml-cpp/src/singledocparser.cpp',
-  '../../ext/yaml-cpp/src/stream.cpp',
-  '../../ext/yaml-cpp/src/tag.cpp',
-)
-
-yaml_cpp_inc = include_directories('../../ext/yaml-cpp/include')
-
-yaml_cpp_lib = static_library('yaml-cpp',
-  yaml_cpp_sources,
-  include_directories: yaml_cpp_inc,
-  pic: true,
-)
-
-yaml_cpp_dep = declare_dependency(
-  link_with: yaml_cpp_lib,
-  include_directories: yaml_cpp_inc,
-)

From 03f5694687fc90119d86889048a95aafdbe1d439 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 8 Feb 2026 23:21:31 +0000
Subject: [PATCH 6/7] Add Meson CI job to test build system

- Add new 'meson-build' job in CI workflow
- Runs on ubuntu-24.04 with system dependencies
- Tests Meson build configuration and compilation
- Reports build status (partial or complete)
- Runs in parallel with existing SCons jobs
- Update MESON_BUILD.md to clarify SUNDIALS requirement

Co-authored-by: bryanwweber <4396228+bryanwweber@users.noreply.github.com>
---
 .github/workflows/main.yml | 50 ++++++++++++++++++++++++++++++++++++++
 MESON_BUILD.md             |  4 ++-
 2 files changed, 53 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 7b46b929c1..f6b2b2c35b 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -193,6 +193,56 @@ jobs:
     - name: Run sample demo
       run: python3 `which scons` test-clib-demo --debug=time
 
+  meson-build:
+    name: Meson build system test
+    runs-on: ubuntu-24.04
+    timeout-minutes: 60
+    steps:
+    - uses: actions/checkout@v6
+      name: Checkout the repository
+      with:
+        submodules: recursive
+        persist-credentials: false
+    - name: Setup Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.13'
+        architecture: x64
+    - name: Install Apt dependencies
+      run: |
+        sudo apt update
+        sudo apt install -y meson ninja-build libboost-dev libeigen3-dev \
+          libsundials-dev libhdf5-dev libfmt-dev libyaml-cpp-dev
+    - name: Initialize submodules for bundled dependencies
+      run: |
+        # Initialize fmt and yaml-cpp in case system versions are too old
+        git submodule update --init --depth=1 ext/fmt ext/yaml-cpp
+        # Create compatibility symlink for fmt
+        cd ext/fmt/include/fmt && ln -sf ranges.h join.h
+    - name: Configure with Meson
+      run: meson setup builddir
+    - name: Compile with Meson
+      run: meson compile -C builddir
+    - name: Show build summary
+      run: |
+        echo "Meson build completed successfully!"
+        echo "Build directory contents:"
+        ls -lh builddir/src/
+    - name: Report Meson build status
+      if: always()
+      run: |
+        if [ -f builddir/build.ninja ]; then
+          echo "✓ Meson configuration successful"
+        else
+          echo "✗ Meson configuration failed"
+        fi
+        if [ -f builddir/src/libcantera.so* ]; then
+          echo "✓ Cantera library built successfully"
+          ls -lh builddir/src/libcantera.so*
+        else
+          echo "⚠ Cantera library not found (build may be partial)"
+        fi
+
   macos-multiple-pythons:
     name: ${{ matrix.macos-version }} with Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.macos-version }}
diff --git a/MESON_BUILD.md b/MESON_BUILD.md
index 7c9b6ccc7e..25f9ff53d4 100644
--- a/MESON_BUILD.md
+++ b/MESON_BUILD.md
@@ -53,8 +53,10 @@ The Meson build system is under development and currently builds most of the C++
 - **fmt** (>= 9.1.0): Uses system if available, otherwise ext/fmt (header-only mode)
 - **yaml-cpp** (>= 0.6): Uses system if available, otherwise auto-discovers and builds from ext/yaml-cpp
 
+### For Full Build (including numerics module)
+- **SUNDIALS** (>= 6.0): Required for ODE/DAE integration. Currently requires system installation (e.g., `libsundials-dev` on Ubuntu). Without SUNDIALS, builds ~60% of C++ library (all modules except numerics).
+
 ### Optional
-- **SUNDIALS** (>= 6.0): Required for ODE/DAE integration (not yet implemented)
 - **HDF5**: For HDF5 data file support
 - **BLAS/LAPACK**: For optimized linear algebra (falls back to Eigen)
 - **HighFive**: C++ wrapper for HDF5

From ba525e3d084c0032f9218746c22cd4dd68ab547f Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 8 Feb 2026 23:36:34 +0000
Subject: [PATCH 7/7] Remove submodule fallback support, require system
 packages only

- Update meson.build to require all dependencies as system packages:
  * Eigen3, fmt, yaml-cpp, SUNDIALS now required (no fallbacks)
  * HighFive optional but system-only (no fallback)
  * Remove all ext/ submodule checks and fallback logic
  * Simplify config.h generation (all system flags set to 1)
  * Clean up summary output

- Update CI workflow:
  * Remove submodule checkout (submodules: false)
  * Remove submodule initialization step
  * Remove fmt join.h symlink creation
  * Keep system package installation

- Update MESON_BUILD.md:
  * Remove all submodule references and instructions
  * Document all dependencies as system-required
  * Add installation commands for Ubuntu, macOS, Fedora
  * Update build steps (no submodule init needed)
  * Update limitations and contributing sections

This simplifies the build by requiring system package managers instead of
maintaining complex fallback logic for bundled dependencies.

Co-authored-by: bryanwweber <4396228+bryanwweber@users.noreply.github.com>
---
 .github/workflows/main.yml |   8 +--
 MESON_BUILD.md             |  91 +++++++++++++-----------
 meson.build                | 141 +++++++------------------------------
 3 files changed, 74 insertions(+), 166 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index f6b2b2c35b..133f3063bb 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -201,7 +201,7 @@ jobs:
     - uses: actions/checkout@v6
       name: Checkout the repository
       with:
-        submodules: recursive
+        submodules: false
         persist-credentials: false
     - name: Setup Python
       uses: actions/setup-python@v6
@@ -213,12 +213,6 @@ jobs:
         sudo apt update
         sudo apt install -y meson ninja-build libboost-dev libeigen3-dev \
           libsundials-dev libhdf5-dev libfmt-dev libyaml-cpp-dev
-    - name: Initialize submodules for bundled dependencies
-      run: |
-        # Initialize fmt and yaml-cpp in case system versions are too old
-        git submodule update --init --depth=1 ext/fmt ext/yaml-cpp
-        # Create compatibility symlink for fmt
-        cd ext/fmt/include/fmt && ln -sf ranges.h join.h
     - name: Configure with Meson
       run: meson setup builddir
     - name: Compile with Meson
diff --git a/MESON_BUILD.md b/MESON_BUILD.md
index 25f9ff53d4..19d9dfcc89 100644
--- a/MESON_BUILD.md
+++ b/MESON_BUILD.md
@@ -1,10 +1,10 @@
 # Meson Build System for Cantera
 
-This directory contains the initial Meson build configuration for Cantera's C++ library.
+This directory contains the Meson build configuration for Cantera's C++ library.
 
 ## Status
 
-The Meson build system is under development and currently builds most of the C++ library (~60% of targets). The build is blocked by the SUNDIALS dependency which needs to be added as a subproject or installed system-wide.
+The Meson build system builds the complete C++ library using system-installed dependencies only.
 
 ## Quick Start
 
@@ -13,53 +13,48 @@ The Meson build system is under development and currently builds most of the C++
 - Meson >= 1.0.0
 - Ninja build system
 - C++20 compatible compiler (GCC, Clang, or MSVC)
-- System dependencies:
-  - Eigen3 >= 3.4 (or will use ext/eigen submodule)
-  - Boost >= 1.83 (required, must be system-installed)
-  - Optional: HDF5, BLAS/LAPACK
+- System dependencies (all required):
+  - Eigen3 >= 3.4
+  - Boost >= 1.83
+  - fmt >= 9.1.0
+  - yaml-cpp >= 0.6
+  - SUNDIALS >= 6.0 (cvodes, idas, nvecserial)
+  - Optional: HDF5, BLAS/LAPACK, HighFive
 
 ### Building
 
-1. Initialize required submodules:
-   ```bash
-   git submodule update --init ext/fmt ext/yaml-cpp
-   ```
-
-2. Create a compatibility symlink for fmt (required for older fmt references):
-   ```bash
-   cd ext/fmt/include/fmt && ln -s ranges.h join.h
-   ```
-
-3. Configure the build:
+1. Configure the build:
    ```bash
    meson setup builddir
    ```
 
-4. Compile:
+2. Compile:
    ```bash
    meson compile -C builddir
    ```
 
-5. Install (optional):
+3. Install (optional):
    ```bash
    meson install -C builddir
    ```
 
 ## Dependencies
 
-### Required
-- **Boost** (>= 1.83): Header-only, must be system-installed
-- **Eigen3** (>= 3.4): Uses system if available, otherwise ext/eigen submodule
-- **fmt** (>= 9.1.0): Uses system if available, otherwise ext/fmt (header-only mode)
-- **yaml-cpp** (>= 0.6): Uses system if available, otherwise auto-discovers and builds from ext/yaml-cpp
+All dependencies must be installed as system packages. The Meson build does not support fallback to bundled libraries in ext/ submodules.
+
+### Required System Packages
+
+- **Boost** (>= 1.83): Header-only library
+- **Eigen3** (>= 3.4): Header-only library for linear algebra
+- **fmt** (>= 9.1.0): Formatting library
+- **yaml-cpp** (>= 0.6): YAML parser/emitter
+- **SUNDIALS** (>= 6.0): ODE/DAE solvers (cvodes, idas, nvecserial components required)
 
-### For Full Build (including numerics module)
-- **SUNDIALS** (>= 6.0): Required for ODE/DAE integration. Currently requires system installation (e.g., `libsundials-dev` on Ubuntu). Without SUNDIALS, builds ~60% of C++ library (all modules except numerics).
+### Optional System Packages
 
-### Optional
 - **HDF5**: For HDF5 data file support
-- **BLAS/LAPACK**: For optimized linear algebra (falls back to Eigen)
-- **HighFive**: C++ wrapper for HDF5
+- **BLAS/LAPACK**: For optimized linear algebra (falls back to Eigen if not available)
+- **HighFive**: C++ wrapper for HDF5 (required if HDF5 support is desired)
 
 ## Configuration Options
 
@@ -86,20 +81,31 @@ endforeach
 
 This eliminates the need to manually list individual source files.
 
-### Dependency Management
+### Installation
 
-Dependencies are tried in order:
-1. **System packages** (via pkg-config/CMake) 
-2. **Bundled sources** (from ext/ submodules with automatic file discovery)
+On Ubuntu/Debian:
+```bash
+sudo apt install meson ninja-build libboost-dev libeigen3-dev \
+  libfmt-dev libyaml-cpp-dev libsundials-dev
+```
 
-For yaml-cpp, Meson automatically discovers all source files from `ext/yaml-cpp/src` instead of using the CMake build (which has issues with symlinked subprojects).
+On macOS with Homebrew:
+```bash
+brew install meson ninja boost eigen fmt yaml-cpp sundials
+```
+
+On Fedora/RHEL:
+```bash
+sudo dnf install meson ninja-build boost-devel eigen3-devel \
+  fmt-devel yaml-cpp-devel sundials-devel
+```
 
 ## Known Limitations
 
-1. **SUNDIALS not yet supported**: The SUNDIALS dependency needs to be implemented as a Meson subproject or made available system-wide
-2. **No Python bindings**: Only C++ library is currently supported
-3. **No Fortran interface**: F90 interface not yet implemented
-4. **Limited testing**: Build system needs more testing across platforms
+1. **No Python bindings**: Only C++ library is currently supported
+2. **No Fortran interface**: F90 interface not yet implemented
+3. **Limited testing**: Build system needs more testing across platforms
+4. **System packages required**: No support for bundled ext/ submodules
 
 ## Comparison with SCons
 
@@ -107,17 +113,17 @@ The Meson build aims to eventually replace the SCons build system with these ben
 - Faster build times with better parallelization
 - Better IDE integration
 - Standard pkg-config support
-- Simpler dependency management
+- Simpler dependency management (system packages only)
 - Cross-compilation support
 - **Automatic source discovery** like SCons `multi_glob()`
 
 ## Contributing
 
-This is initial work to replace the SCons build system. Contributions are welcome to:
-- Add SUNDIALS subproject support
-- Improve dependency detection
+Contributions are welcome to:
+- Add Python bindings support
 - Add testing infrastructure
 - Port more configuration options from SCons
+- Test on more platforms
 
 ## Files
 
@@ -125,4 +131,3 @@ This is initial work to replace the SCons build system. Contributions are welcom
 - `meson_options.txt`: Build options
 - `src/meson.build`: C++ source compilation with automatic file discovery
 - `include/cantera/base/config.h.meson.in`: Configuration header template
-- `include/cantera/ext/`: Symlinks to submodule headers (fmt, yaml-cpp, Eigen)
diff --git a/meson.build b/meson.build
index 216fd0a0ba..d54b88be7f 100644
--- a/meson.build
+++ b/meson.build
@@ -46,108 +46,23 @@ thread_dep = dependency('threads', required: true)
 # Math library (needed on some platforms)
 m_dep = cc.find_library('m', required: false)
 
-# SUNDIALS dependency with fallback to subproject
-sundials_dep = dependency('sundials_cvodes', version: '>=6.0', required: false)
-sundials_idas_dep = dependency('sundials_idas', required: false)
-sundials_nvecserial_dep = dependency('sundials_nvecserial', required: false)
+# SUNDIALS dependency - required system package
+sundials_cvodes_dep = dependency('sundials_cvodes', version: '>=6.0', required: true)
+sundials_idas_dep = dependency('sundials_idas', required: true)
+sundials_nvecserial_dep = dependency('sundials_nvecserial', required: true)
+message('Using system SUNDIALS')
 
-use_system_sundials = false
-if sundials_dep.found() and sundials_idas_dep.found() and sundials_nvecserial_dep.found()
-  use_system_sundials = true
-  message('Using system SUNDIALS')
-else
-  message('Using bundled SUNDIALS from ext/sundials')
-  # TODO: Build SUNDIALS from submodule
-  # For now, we'll add it as a subproject wrap
-  sundials_dep = dependency('', required: false)
-  sundials_idas_dep = dependency('', required: false)
-  sundials_nvecserial_dep = dependency('', required: false)
-endif
+# Eigen dependency (header-only) - required system package
+eigen_dep = dependency('eigen3', version: '>=3.4', required: true)
+message('Using system Eigen')
 
-# Eigen dependency (header-only)
-eigen_dep = dependency('eigen3', version: '>=3.4', required: false)
-use_system_eigen = false
-if eigen_dep.found()
-  use_system_eigen = true
-  message('Using system Eigen')
-else
-  message('Using bundled Eigen from ext/eigen')
-  # Check if submodule is initialized
-  eigen_include_dir = meson.current_source_dir() / 'ext' / 'eigen'
-  if not fs.is_dir(eigen_include_dir)
-    warning('Eigen submodule not initialized. Run: git submodule update --init ext/eigen')
-  endif
-  eigen_dep = declare_dependency(
-    include_directories: include_directories('ext/eigen')
-  )
-endif
+# fmt dependency - required system package
+fmt_dep = dependency('fmt', version: '>=9.1.0', required: true)
+message('Using system fmt')
 
-# fmt dependency with fallback
-fmt_dep = dependency('fmt', version: '>=9.1.0', required: false)
-use_system_fmt = false
-if fmt_dep.found()
-  use_system_fmt = true
-  message('Using system fmt')
-else
-  message('Using bundled fmt from ext/fmt')
-  # Check if submodule is initialized
-  fmt_include_dir = meson.current_source_dir() / 'ext' / 'fmt' / 'include'
-  if not fs.is_dir(fmt_include_dir)
-    warning('fmt submodule not initialized. Run: git submodule update --init ext/fmt')
-  endif
-  # Use header-only mode for bundled fmt
-  fmt_dep = declare_dependency(
-    include_directories: include_directories('ext/fmt/include'),
-    compile_args: ['-DFMT_HEADER_ONLY']
-  )
-endif
-
-# yaml-cpp dependency with fallback
-# Note: CMake integration has issues with Meson detecting source files correctly
-# when the subproject is a symlink. Using direct file specification instead.
-yamlcpp_dep = dependency('yaml-cpp', version: '>=0.6', required: false)
-use_system_yamlcpp = false
-if yamlcpp_dep.found()
-  use_system_yamlcpp = true
-  message('Using system yaml-cpp')
-else
-  message('Using bundled yaml-cpp from ext/yaml-cpp')
-  # Check if submodule is initialized
-  yamlcpp_cmake = meson.current_source_dir() / 'ext' / 'yaml-cpp' / 'CMakeLists.txt'
-  if not fs.exists(yamlcpp_cmake)
-    warning('yaml-cpp submodule not initialized. Run: git submodule update --init ext/yaml-cpp')
-  endif
-  
-  # Build yaml-cpp from discovered source files
-  yaml_cpp_src_dir = 'ext/yaml-cpp/src'
-  yaml_cpp_sources = run_command(
-    find_program('find'),
-    yaml_cpp_src_dir,
-    '-name', '*.cpp',
-    '-printf', '%P\n',
-    check: true,
-    capture: true
-  ).stdout().strip().split('\n')
-  
-  yaml_cpp_files = []
-  foreach f : yaml_cpp_sources
-    if f != ''
-      yaml_cpp_files += files(yaml_cpp_src_dir / f)
-    endif
-  endforeach
-  
-  yamlcpp_inc = include_directories('ext/yaml-cpp/include')
-  yamlcpp_lib = static_library('yaml-cpp-bundled',
-    yaml_cpp_files,
-    include_directories: yamlcpp_inc,
-    pic: true,
-  )
-  
-  yamlcpp_dep = declare_dependency(
-    link_with: yamlcpp_lib,
-    include_directories: yamlcpp_inc,
-  )
-endif
+# yaml-cpp dependency - required system package
+yamlcpp_dep = dependency('yaml-cpp', version: '>=0.6', required: true)
+message('Using system yaml-cpp')
 
 # Boost dependency (header-only, required)
 boost_dep = dependency('boost', version: '>=1.83', required: true,
@@ -164,18 +79,15 @@ else
 endif
 
 # HighFive dependency (header-only, optional)
+# Only use system package, no fallback to submodule
 highfive_dep = dependency('HighFive', required: false)
-use_system_highfive = false
-if highfive_dep.found()
-  use_system_highfive = true
+if highfive_dep.found() and use_hdf5
   message('Using system HighFive')
-elif use_hdf5
-  message('Using bundled HighFive from ext/HighFive')
-  highfive_dep = declare_dependency(
-    include_directories: include_directories('ext/HighFive/include')
-  )
 else
   highfive_dep = dependency('', required: false)
+  if use_hdf5
+    warning('HighFive not found. HDF5 support will be limited. Install HighFive package for full HDF5 support.')
+  endif
 endif
 
 # BLAS/LAPACK dependency (optional)
@@ -224,13 +136,14 @@ endif
 conf_data = configuration_data()
 conf_data.set('CANTERA_VERSION', '#define CANTERA_VERSION "' + meson.project_version() + '"')
 conf_data.set('CANTERA_SHORT_VERSION', '#define CANTERA_SHORT_VERSION "' + cantera_short_version + '"')
-conf_data.set('CT_USE_SYSTEM_EIGEN', use_system_eigen ? '#define CT_USE_SYSTEM_EIGEN 1' : '/* #undef CT_USE_SYSTEM_EIGEN */')
+# All dependencies are now system packages
+conf_data.set('CT_USE_SYSTEM_EIGEN', '#define CT_USE_SYSTEM_EIGEN 1')
 conf_data.set('CT_USE_SYSTEM_EIGEN_PREFIXED', '/* #undef CT_USE_SYSTEM_EIGEN_PREFIXED */')
-conf_data.set('CT_USE_SYSTEM_FMT', use_system_fmt ? '#define CT_USE_SYSTEM_FMT 1' : '/* #undef CT_USE_SYSTEM_FMT */')
-conf_data.set('CT_USE_SYSTEM_YAMLCPP', use_system_yamlcpp ? '#define CT_USE_SYSTEM_YAMLCPP 1' : '/* #undef CT_USE_SYSTEM_YAMLCPP */')
+conf_data.set('CT_USE_SYSTEM_FMT', '#define CT_USE_SYSTEM_FMT 1')
+conf_data.set('CT_USE_SYSTEM_YAMLCPP', '#define CT_USE_SYSTEM_YAMLCPP 1')
 conf_data.set('CT_USE_LAPACK', use_lapack ? '#define CT_USE_LAPACK 1' : '/* #undef CT_USE_LAPACK */')
 conf_data.set('CT_USE_HDF5', use_hdf5 ? '#define CT_USE_HDF5 1' : '/* #undef CT_USE_HDF5 */')
-conf_data.set('CT_USE_SYSTEM_HIGHFIVE', use_system_highfive ? '#define CT_USE_SYSTEM_HIGHFIVE 1' : '/* #undef CT_USE_SYSTEM_HIGHFIVE */')
+conf_data.set('CT_USE_SYSTEM_HIGHFIVE', highfive_dep.found() ? '#define CT_USE_SYSTEM_HIGHFIVE 1' : '/* #undef CT_USE_SYSTEM_HIGHFIVE */')
 conf_data.set('CT_SUNDIALS_USE_LAPACK', '/* #undef CT_SUNDIALS_USE_LAPACK */')
 
 # Fortran settings
@@ -265,11 +178,7 @@ subdir('src')
 summary({
   'Version': meson.project_version(),
   'Git commit': git_commit,
-  'System Eigen': use_system_eigen,
-  'System fmt': use_system_fmt,
-  'System yaml-cpp': use_system_yamlcpp,
-  'System SUNDIALS': use_system_sundials,
   'BLAS/LAPACK': use_lapack,
   'HDF5 support': use_hdf5,
-  'System HighFive': use_system_highfive,
+  'HighFive': highfive_dep.found(),
 }, section: 'Configuration')