feat(reflection): Bring in new libconfig

This version of fourdst (v0.9.14) brings in the version libconfig which
includes reflection based config filed (v2.0.2).

This is a breaking change as any code which used versions of libconfig <
v2.0.0 will no longer function when linked against this version of
fourdst

.gitignore

@@ -75,7 +75,11 @@ subprojects/liblogging/
 subprojects/eigen-*/
 !subprojects/pybind11.wrap
 subprojects/libplugin/
+subprojects/minizip-ng-*
 subprojects/.wraplock
+subprojects/openssl-*
+subprojects/glaze/
+subprojects/tomlplusplus-*/
 
 *.csv
 *.dot
@@ -83,6 +87,10 @@ subprojects/.wraplock
 qhull.wrap
 quill.wrap
 yaml-cpp.wrap
+minizip-ng.wrap
+openssl.wrap
+glaze.wrap
+tomlplusplus.wrap
 
 .vscode/
 

build-config/libcomposition/meson.build

@@ -1,4 +1,9 @@
-composition_p = subproject('libcomposition', default_options: ['pkg-config=' + pkg_config_bool_str])
+composition_p = subproject('libcomposition',
+  default_options: [
+    'pkg_config=' + get_option('pkg_config').to_string(),
+    'build_tests=' + get_option('build_tests').to_string(),
+    'build_examples=false'
+])
 comp_dep  = composition_p.get_variable('composition_dep')
 libcomposition = composition_p.get_variable('libcomposition')
 spw_dep = composition_p.get_variable('species_weight_dep')

build-config/libconfig/meson.build

@@ -1,5 +1,7 @@
-config_p = subproject('libconfig', default_options:['pkg-config=false'])
+config_p = subproject('libconfig',
+  default_options:[
+    'pkg_config=' + get_option('pkg_config').to_string(),
+    'build_tests=' + get_option('build_tests').to_string(),
+    'build_examples=false'
+    ])
 config_dep  = config_p.get_variable('config_dep')
-libconfig = config_p.get_variable('libconfig')
-
-alias_target('build-libconfig', libconfig)

build-config/libconstants/meson.build

@@ -1,4 +1,8 @@
-const_p = subproject('libconstants', default_options: ['pkg-config=' + pkg_config_bool_str])
+const_p = subproject('libconstants', default_options: [
+    'pkg_config=' + get_option('pkg_config').to_string(),
+    'build_tests=' + get_option('build_tests').to_string(),
+    'build_examples=false'
+  ])
 const_dep  = const_p.get_variable('const_dep')
 libconst = const_p.get_variable('libconst')
 

build-config/liblogging/meson.build

@@ -1,4 +1,8 @@
-logging_p = subproject('liblogging', default_options: ['pkg-config=' + pkg_config_bool_str])
+logging_p = subproject('liblogging', default_options: [
+    'pkg_config=' + get_option('pkg_config').to_string(),
+    'build_tests=' + get_option('build_tests').to_string(),
+    'build_examples=false'
+  ])
 liblogging = logging_p.get_variable('liblogging')
 
 logging_dep  = logging_p.get_variable('logging_dep')

build-config/libplugin/meson.build

@@ -1,4 +1,8 @@
-plugin_p = subproject('libplugin', default_options: ['pkg-config=' + pkg_config_bool_str, 'tests=' + get_option('tests').to_string()])
+plugin_p = subproject('libplugin', default_options: [
+                          'pkg-config=' + get_option('pkg_config').to_string(),
+                          'build-tests=' + get_option('build_tests').to_string(),
+                          'python-wheel=' + get_option('build_python').to_string(),
+                      ])
 libplugin = plugin_p.get_variable('libplugin')
 
 plugin_dep  = plugin_p.get_variable('plugin_dep')

build-config/meson.build

@@ -1,6 +1,19 @@
+if get_option('build_lib_comp') or get_option('build_lib_all') or get_option('build_python')
     subdir('libcomposition')
+endif
+if get_option('build_lib_config') or get_option('build_lib_all') or get_option('build_python')
     subdir('libconfig')
+endif
+if get_option('build_lib_const') or get_option('build_lib_all') or get_option('build_python')
     subdir('libconstants')
+endif
+if get_option('build_lib_log') or get_option('build_lib_all')
     subdir('liblogging')
+endif
+if get_option('build_lib_plugin') or get_option('build_lib_all')
     subdir('libplugin')
+endif
+
+if get_option('build_python')
     subdir('pybind')
+endif

build-python/meson.build

@@ -1,8 +1,7 @@
-# --- Python Extension Setup ---
 py_installation = import('python').find_installation('python3', pure: false)
 
 py_mod = py_installation.extension_module(
-    '_phys', # Name of the generated .so/.pyd file (without extension)
+    '_phys',
     sources: [
         meson.project_source_root() + '/src-pybind/bindings.cpp',
         meson.project_source_root() + '/src-pybind/composition/bindings.cpp',
@@ -34,6 +33,7 @@ py_installation.install_sources(
         meson.project_source_root() + '/src-pybind/fourdst/_phys/atomic.pyi',
         meson.project_source_root() + '/src-pybind/fourdst/_phys/config.pyi',
         meson.project_source_root() + '/src-pybind/fourdst/_phys/constants.pyi',
+        meson.project_source_root() + '/src-pybind/fourdst/_phys/exceptions.pyi',
     ),
     subdir: 'fourdst/',
 )

meson.build

@@ -1,19 +1,13 @@
-project('fourdst', 'cpp', version: 'v0.9.6', default_options: ['cpp_std=c++23'], meson_version: '>=1.5.0')
+project('fourdst', 'cpp', version: 'v0.9.14', default_options: ['cpp_std=c++23'], meson_version: '>=1.5.0')
 
 add_project_arguments('-fvisibility=default', language: 'cpp')
 
-pkg_config_bool_str = 'false'
-if get_option('pkg-config')
-    pkg_config_bool_str = 'true'
-endif
-
 
 # Configure vendor libraries
 subdir('build-config')
 
 # Configure python bindings
+if get_option('build_python')
     subdir('build-python')
-
-# Build python bindings
-subdir('src-pybind')
+endif
 

meson_options.txt

@@ -1,3 +1,10 @@
-option('pkg-config', type: 'boolean', value: false, description: 'generate pkg-config file for all libraries and fourdst (defaults to false to allow easy pip building)')
-option('electron-build-py-backend', type: 'boolean', value: false, description: 'use pyinstaller to build the python backend for the electron app')
-option('tests', type: 'boolean', value: false, description: 'compile subproject tests')
+option('pkg_config', type: 'boolean', value: false, description: 'generate pkg-config file for all libraries and fourdst (defaults to false to allow easy pip building)')
+option('electron_build_py_backend', type: 'boolean', value: false, description: 'use pyinstaller to build the python backend for the electron app')
+option('build_tests', type: 'boolean', value: false, description: 'compile subproject tests')
+option('build_lib_all', type: 'boolean', value: true, description: 'build the full fourdst library with all features enabled')
+option('build_lib_comp', type: 'boolean', value: false, description: 'build the minimal fourdst library with only compression and decompression features enabled')
+option('build_lib_config', type: 'boolean', value: false, description: 'build the fourdst library configuration tool only')
+option('build_lib_const', type: 'boolean', value: false, description: 'build the fourdst library constants only')
+option('build_python', type: 'boolean', value: true, description: 'build the python bindings so you can use fourdst from python. This will also build libcomposition, libconfig, and libconstants')
+option('build_lib_log', type: 'boolean', value: false, description: 'build the fourdst library logging features only')
+option('build_lib_plugin', type: 'boolean', value: false, description: 'build the fourdst plugin module only')

pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "mesonpy"
 
 [project]
 name = "fourdst"  # Choose your Python package name
-version = "0.8.5" # Your project's version
+version = "v0.9.11" # Your project's version
 description = "Python interface to the utility fourdst modules from the 4D-STAR project"
 readme = "readme.md"
 license = { file = "LICENSE.txt" } # Reference your license file [cite: 2]

src-pybind/bindings.cpp

@@ -9,6 +9,9 @@
 PYBIND11_MODULE(_phys, m) {
     m.doc() = "Python bindings for the fourdst utility modules which are a part of the 4D-STAR project.";
 
+    auto exceptionMod = m.def_submodule("exceptions", "Exception bindings");
+    register_comp_exceptions(exceptionMod);
+
     auto atomicMod = m.def_submodule("atomic", "Species bindings");
     register_species_bindings(atomicMod);
 
@@ -18,6 +21,6 @@ PYBIND11_MODULE(_phys, m) {
     auto constMod = m.def_submodule("constants", "Constants-module bindings");
     register_const_bindings(constMod);
 
-    auto configMod = m.def_submodule("config", "Configuration-module bindings");
-    register_config_bindings(configMod);
+    const auto configMod = m.def_submodule("config", "Configuration-module bindings");
+    register_config_enums(configMod);
 }

src-pybind/composition/bindings.cpp

@@ -12,6 +12,7 @@
 #include "fourdst/atomic/species.h"
 #include "fourdst/composition/utils.h"
 #include "fourdst/composition/utils/composition_hash.h"
+#include "fourdst/composition/exceptions/exceptions_composition.h"
 
 namespace py = pybind11;
 
@@ -335,7 +336,7 @@ void register_comp_bindings(pybind11::module &m) {
 
 }
 
-void register_species_bindings(const pybind11::module &chem_submodule) {
+void register_species_bindings(pybind11::module &chem_submodule) {
      // --- Bindings for species module ---
      py::class_<fourdst::atomic::Species>(chem_submodule, "Species")
           .def("mass", &fourdst::atomic::Species::mass, "Get atomic mass (amu)")
@@ -372,4 +373,35 @@ void register_species_bindings(const pybind11::module &chem_submodule) {
 
 
      chem_submodule.attr("species") = py::cast(fourdst::atomic::species); // Expose the species map
+
+     auto replace_dash_with_underscore = [](const std::string& str) {
+          std::string result = str;
+          std::ranges::replace(result, '-', '_');
+          return result;
+     };
+
+     for (const auto& [name, species] : fourdst::atomic::species) {
+          chem_submodule.attr(replace_dash_with_underscore(name).c_str()) = py::cast(species);
+     }
+
+     chem_submodule.def("az_to_species",
+          [](const int a, const int z) {
+               const auto result = fourdst::atomic::az_to_species(a, z);
+               if (!result) {
+                    throw fourdst::composition::exceptions::SpeciesError(std::format("Species with A={} and Z={} not found.", a, z));
+               }
+               return result.value();
+          },
+          py::arg("a"),
+          py::arg("z"),
+          "Get Species object from proton number (Z) and mass number (A)."
+     );
+}
+
+void register_comp_exceptions(pybind11::module &m) {
+     py::register_exception<fourdst::composition::exceptions::CompositionError>(m, "CompositionError");
+     py::register_exception<fourdst::composition::exceptions::InvalidCompositionError>(m, "InvalidCompositionError", m.attr("CompositionError"));
+     py::register_exception<fourdst::composition::exceptions::SpeciesError>(m, "SpeciesError");
+     py::register_exception<fourdst::composition::exceptions::UnknownSymbolError>(m, "UnknownSymbolError", m.attr("SpeciesError"));
+     py::register_exception<fourdst::composition::exceptions::UnregisteredSymbolError>(m, "UnregisteredSymbolError", m.attr("SpeciesError"));
 }

src-pybind/composition/bindings.h

@@ -2,5 +2,7 @@
 
 #include <pybind11/pybind11.h>
 
+void register_comp_exceptions(pybind11::module &m);
+void register_species_bindings(pybind11::module &m);
 void register_comp_bindings(pybind11::module &m);
-void register_species_bindings(const pybind11::module &m);
+

src-pybind/config/bindings.cpp

@@ -1,55 +1,17 @@
-#include <pybind11/pybind11.h>
-#include <pybind11/stl.h> // Needed for vectors, maps, sets, strings
-#include <pybind11/stl_bind.h> // Needed for binding std::vector, std::map etc if needed directly
-
-#include <string>
 #include "bindings.h"
 
+#include <pybind11/pybind11.h>
 #include "fourdst/config/config.h"
 
-namespace py = pybind11;
+void register_config_enums(const pybind11::module_& m) {
+    using namespace fourdst::config;
+    pybind11::enum_<ConfigState>(m, "ConfigState")
+        .value("DEFAULT", ConfigState::DEFAULT)
+        .value("LOADED_FROM_FILE", ConfigState::LOADED_FROM_FILE)
+        .export_values();
 
-// Helper function template for binding Config::get
-template <typename T>
-void def_config_get(py::module &m) {
-    m.def("get",
-          [](const std::string &key, T defaultValue) {
-              return fourdst::config::Config::getInstance().get<T>(key, defaultValue);
-          },
-          py::arg("key"), py::arg("defaultValue"),
-          "Get configuration value (type inferred from default)");
-}
-
-void register_config_bindings(pybind11::module &config_submodule) {
-    def_config_get<int>(config_submodule);
-    def_config_get<double>(config_submodule);
-    def_config_get<std::string>(config_submodule);
-    def_config_get<bool>(config_submodule);
-
-    config_submodule.def("loadConfig",
-        [](const std::string& configFilePath) {
-            return fourdst::config::Config::getInstance().loadConfig(configFilePath);
-        },
-        py::arg("configFilePath"),
-        "Load configuration from a YAML file.");
-
-    config_submodule.def("has",
-        [](const std::string &key) {
-            return fourdst::config::Config::getInstance().has(key);
-        },
-        py::arg("key"),
-        "Check if a key exists in the configuration.");
-
-    config_submodule.def("keys",
-        []() {
-            return py::cast(fourdst::config::Config::getInstance().keys());
-        },
-        "Get a list of all configuration keys.");
-
-    config_submodule.def("__repr__",
-        []() {
-            std::ostringstream oss;
-            oss << fourdst::config::Config::getInstance(); // Use the existing operator<<
-            return std::string("<fourdsse_bindings.config module accessing C++ Singleton>\n") + oss.str();
-        });
+    pybind11::enum_<RootNameLoadPolicy>(m, "RootNameLoadPolicy")
+        .value("FROM_FILE", RootNameLoadPolicy::FROM_FILE)
+        .value("KEEP_CURRENT", RootNameLoadPolicy::KEEP_CURRENT)
+        .export_values();
 }

src-pybind/config/bindings.h

@@ -1,5 +1,26 @@
 #pragma once
 
 #include <pybind11/pybind11.h>
+#include "fourdst/config/config.h"
 
-void register_config_bindings(pybind11::module &config_submodule);
+#include <string>
+#include <format>
+
+void register_config_enums(const pybind11::module_& m);
+
+template <typename ConfigType>
+pybind11::class_<ConfigType> bind_config_specialization(pybind11::module_& m , const std::string& name) {
+    return pybind11::class_<ConfigType>(m, name.c_str())
+        .def(pybind11::init<>())
+        .def("load", &ConfigType::load, pybind11::arg("file_path"), "Load configuration from a file.")
+        .def("save", &ConfigType::save, pybind11::arg("file_path") = "config_output.toml", "Save configuration to a file.")
+        .def("save_schema", &ConfigType::save_schema, pybind11::arg("directory") = ".", "Save the configuration schema to a directory.")
+        .def("get_state", &ConfigType::get_state, "Get the current state of the configuration.")
+        .def("describe_state", &ConfigType::describe_state, "Get the current state of the configuration.")
+        .def("__repr__",
+             [](const ConfigType &cfg) -> std::string {
+                return std::format("{}", cfg);
+             }
+        );
+
+}

src-pybind/fourdst/__init__.py

@@ -11,4 +11,4 @@ sys.modules['fourdst.config'] = config
 
 __all__ = ['atomic', 'composition', 'constants', 'config', 'core', 'cli']
 
-__version__ = 'v0.9.6'
+__version__ = 'v0.9.11'

src-pybind/fourdst/_phys/__init__.pyi

@@ -6,4 +6,5 @@ from . import atomic
 from . import composition
 from . import config
 from . import constants
-__all__: list[str] = ['atomic', 'composition', 'config', 'constants']
+from . import exceptions
+__all__: list[str] = ['atomic', 'composition', 'config', 'constants', 'exceptions']

src-pybind/fourdst/_phys/exceptions.pyi

@@ -0,0 +1,15 @@
+"""
+Exception bindings
+"""
+from __future__ import annotations
+__all__: list[str] = ['CompositionError', 'InvalidCompositionError', 'SpeciesError', 'UnknownSymbolError', 'UnregisteredSymbolError']
+class CompositionError(Exception):
+    pass
+class InvalidCompositionError(CompositionError):
+    pass
+class SpeciesError(Exception):
+    pass
+class UnknownSymbolError(SpeciesError):
+    pass
+class UnregisteredSymbolError(SpeciesError):
+    pass

src-pybind/meson.build

@@ -1,4 +0,0 @@
-subdir('composition')
-subdir('constants')
-subdir('config')
-

subprojects/libcomposition.wrap

@@ -1,4 +1,4 @@
 [wrap-git]
 url = https://github.com/4D-STAR/libcomposition.git
-revision = v2.2.0
+revision = v2.2.4
 depth = 1

subprojects/libconfig.wrap

@@ -1,4 +1,4 @@
 [wrap-git]
 url = https://github.com/4D-STAR/libconfig.git
-revision = v1.1.3
+revision = v2.0.2
 depth = 1

subprojects/libconstants.wrap

@@ -1,4 +1,4 @@
 [wrap-git]
 url = https://github.com/4D-STAR/libconstants.git
-revision = v1.1.0
+revision = v1.1.1
 depth = 1

subprojects/liblogging.wrap

@@ -1,4 +1,4 @@
 [wrap-git]
 url = https://github.com/4D-STAR/liblogging.git
-revision = v1.1.0
+revision = v1.1.1
 depth = 1

subprojects/libplugin.wrap

@@ -1,4 +1,4 @@
 [wrap-git]
 url = https://github.com/4D-STAR/libplugin.git
-revision = v0.3.4
+revision = v0.3.7
 depth = 1