feat(bindings): ported most bindings over from serif

src-pybind/bindings.cpp

@@ -0,0 +1,23 @@
+#include <pybind11/pybind11.h>
+
+#include <string>
+
+#include "constants/bindings.h"
+#include "composition/bindings.h"
+#include "config/bindings.h"
+
+PYBIND11_MODULE(fourdst, m) {
+    m.doc() = "Python bindings for the fourdst utility modules which are a part of the 4D-STAR project.";
+
+    auto compMod  = m.def_submodule("composition", "Composition-module bindings");
+    register_comp_bindings(compMod);
+
+    auto atomicMod = m.def_submodule("atomic", "Species bindings");
+    register_species_bindings(atomicMod);
+
+    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);
+}

src-pybind/composition/bindings.cpp

@@ -0,0 +1,163 @@
+#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 "fourdst/composition/composition.h"
+#include "fourdst/composition/atomicSpecies.h"
+
+#include "bindings.h"
+
+#include "fourdst/composition/species.h"
+
+namespace py = pybind11;
+
+std::string sv_to_string(std::string_view sv) {
+    return std::string(sv);
+}
+
+std::string get_ostream_str(const fourdst::composition::Composition& comp) {
+     std::ostringstream oss;
+     oss << comp;
+     return oss.str();
+}
+
+
+void register_comp_bindings(pybind11::module &comp_submodule) {
+    // --- Bindings for composition and species module ---
+    py::class_<fourdst::composition::GlobalComposition>(comp_submodule, "GlobalComposition")
+        .def_readonly("specificNumberDensity", &fourdst::composition::GlobalComposition::specificNumberDensity)
+        .def_readonly("meanParticleMass", &fourdst::composition::GlobalComposition::meanParticleMass)
+        .def("__repr__", // Add a string representation for easy printing in Python
+             [](const fourdst::composition::GlobalComposition &gc) {
+                 return "<GlobalComposition(specNumDens=" + std::to_string(gc.specificNumberDensity) +
+                        ", meanMass=" + std::to_string(gc.meanParticleMass) + ")>";
+             });
+
+    py::class_<fourdst::composition::CompositionEntry>(comp_submodule, "CompositionEntry")
+        .def("symbol", &fourdst::composition::CompositionEntry::symbol)
+        .def("mass_fraction",
+             py::overload_cast<>(&fourdst::composition::CompositionEntry::mass_fraction, py::const_),
+             "Gets the mass fraction of the species.")
+        .def("mass_fraction",
+             py::overload_cast<double>(&fourdst::composition::CompositionEntry::mass_fraction, py::const_),
+             py::arg("meanMolarMass"), // Name the argument in Python
+             "Gets the mass fraction of the species given the mean molar mass.")
+        .def("number_fraction",
+              py::overload_cast<>(&fourdst::composition::CompositionEntry::number_fraction, py::const_),
+              "Gets the number fraction of the species.")
+        .def("number_fraction",
+              py::overload_cast<double>(&fourdst::composition::CompositionEntry::number_fraction, py::const_),
+              py::arg("totalMoles"),
+              "Gets the number fraction of the species given the total moles.")
+
+        .def("rel_abundance", &fourdst::composition::CompositionEntry::rel_abundance)
+        .def("isotope", &fourdst::composition::CompositionEntry::isotope) // Assuming Species is bound or convertible
+        .def("getMassFracMode", &fourdst::composition::CompositionEntry::getMassFracMode)
+
+        .def("__repr__", // Optional: nice string representation
+            [](const fourdst::composition::CompositionEntry &ce) {
+                // You might want to include more info here now
+                return "<CompositionEntry(symbol='" + ce.symbol() + "', " +
+                    "mass_frac=" + std::to_string(ce.mass_fraction()) + ", " +
+                    "num_frac=" + std::to_string(ce.number_fraction()) + ")>";
+            });
+
+        // --- Binding for the main Composition class ---
+    py::class_<fourdst::composition::Composition>(comp_submodule, "Composition")
+        // Constructors
+        .def(py::init<>(), "Default constructor")
+        .def(py::init<const std::vector<std::string>&>(),
+             py::arg("symbols"),
+             "Constructor taking a list of symbols to register (defaults to mass fraction mode)")
+        // .def(py::init<const std::set<std::string>&>(), py::arg("symbols")) // Binding std::set constructor is possible but often less convenient from Python
+        .def(py::init<const std::vector<std::string>&, const std::vector<double>&, bool>(),
+             py::arg("symbols"), py::arg("fractions"), py::arg("massFracMode") = true,
+             "Constructor taking symbols, fractions, and mode (True=Mass, False=Number)")
+
+        // Methods
+        .def("finalize", &fourdst::composition::Composition::finalize, py::arg("norm") = false,
+             "Finalize the composition, optionally normalizing fractions to sum to 1.")
+
+        .def("registerSymbol", py::overload_cast<const std::string&, bool>(&fourdst::composition::Composition::registerSymbol),
+             py::arg("symbol"), py::arg("massFracMode") = true, "Register a single symbol.")
+        .def("registerSymbol", py::overload_cast<const std::vector<std::string>&, bool>(&fourdst::composition::Composition::registerSymbol),
+             py::arg("symbols"), py::arg("massFracMode") = true, "Register multiple symbols.")
+
+        .def("getRegisteredSymbols", &fourdst::composition::Composition::getRegisteredSymbols,
+             "Get the set of registered symbols.")
+
+        .def("setMassFraction", py::overload_cast<const std::string&, const double&>(&fourdst::composition::Composition::setMassFraction),
+             py::arg("symbol"), py::arg("mass_fraction"), "Set mass fraction for a single symbol (requires massFracMode). Returns old value.")
+        .def("setMassFraction", py::overload_cast<const std::vector<std::string>&, const std::vector<double>&>(&fourdst::composition::Composition::setMassFraction),
+             py::arg("symbols"), py::arg("mass_fractions"), "Set mass fractions for multiple symbols (requires massFracMode). Returns list of old values.")
+
+        .def("setNumberFraction", py::overload_cast<const std::string&, const double&>(&fourdst::composition::Composition::setNumberFraction),
+             py::arg("symbol"), py::arg("number_fraction"), "Set number fraction for a single symbol (requires !massFracMode). Returns old value.")
+        .def("setNumberFraction", py::overload_cast<const std::vector<std::string>&, const std::vector<double>&>(&fourdst::composition::Composition::setNumberFraction),
+             py::arg("symbols"), py::arg("number_fractions"), "Set number fractions for multiple symbols (requires !massFracMode). Returns list of old values.")
+
+        .def("mix", &fourdst::composition::Composition::mix, py::arg("other"), py::arg("fraction"),
+             "Mix with another composition. Returns new Composition.")
+
+        .def("getMassFraction", py::overload_cast<const std::string&>(&fourdst::composition::Composition::getMassFraction, py::const_),
+             py::arg("symbol"), "Get mass fraction for a symbol (calculates if needed). Requires finalization.")
+        .def("getMassFraction", py::overload_cast<>(&fourdst::composition::Composition::getMassFraction, py::const_),
+             "Get dictionary of all mass fractions. Requires finalization.")
+
+        .def("getNumberFraction", py::overload_cast<const std::string&>(&fourdst::composition::Composition::getNumberFraction, py::const_),
+             py::arg("symbol"), "Get number fraction for a symbol (calculates if needed). Requires finalization.")
+        .def("getNumberFraction", py::overload_cast<>(&fourdst::composition::Composition::getNumberFraction, py::const_),
+             "Get dictionary of all number fractions. Requires finalization.")
+
+        // Note: pybind11 automatically converts std::pair to a Python tuple
+        .def("getComposition", py::overload_cast<const std::string&>(&fourdst::composition::Composition::getComposition, py::const_),
+             py::arg("symbol"), "Returns a tuple (CompositionEntry, GlobalComposition) for the symbol. Requires finalization.")
+        // Binding the version returning map<string, Entry> requires a bit more care or helper function
+        // to convert the map to a Python dict if needed directly. Let's bind the pair version for now.
+         .def("getComposition", py::overload_cast<>(&fourdst::composition::Composition::getComposition, py::const_),
+             "Returns a tuple (dict[str, CompositionEntry], GlobalComposition) for all symbols. Requires finalization.")
+
+
+        .def("subset", &fourdst::composition::Composition::subset, py::arg("symbols"), py::arg("method") = "norm",
+             "Create a new Composition containing only the specified symbols.")
+        .def("hasSymbol", &fourdst::composition::Composition::hasSymbol, py::arg("symbol"),
+             "Check if a symbol is registered.")
+        .def("setCompositionMode", &fourdst::composition::Composition::setCompositionMode, py::arg("massFracMode"),
+             "Set the mode (True=Mass, False=Number). Requires finalization before switching.")
+
+        // Operator overload
+        .def(py::self + py::self, "Mix equally with another composition.") // Binds operator+
+
+        // Add __repr__ or __str__
+         .def("__repr__", [](const fourdst::composition::Composition &comp) {
+             return get_ostream_str(comp); // Use helper for C++ operator<<
+         });
+
+}
+
+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)")
+         .def("massUnc", &fourdst::atomic::Species::massUnc, "Get atomic mass uncertainty (amu)")
+         .def("bindingEnergy", &fourdst::atomic::Species::bindingEnergy, "Get binding energy (keV/nucleon?)") // Check units
+         .def("betaDecayEnergy", &fourdst::atomic::Species::betaDecayEnergy, "Get beta decay energy (keV?)") // Check units
+         .def("betaCode", [](const fourdst::atomic::Species& s){ return sv_to_string(s.betaCode()); }, "Get beta decay code") // Convert string_view
+         .def("name", [](const fourdst::atomic::Species& s){ return sv_to_string(s.name()); }, "Get species name (e.g., 'H-1')") // Convert string_view
+         .def("el", [](const fourdst::atomic::Species& s){ return sv_to_string(s.el()); }, "Get element symbol (e.g., 'H')") // Convert string_view
+         .def("nz", &fourdst::atomic::Species::nz, "Get NZ value")
+         .def("n", &fourdst::atomic::Species::n, "Get neutron number N")
+         .def("z", &fourdst::atomic::Species::z, "Get proton number Z")
+         .def("a", &fourdst::atomic::Species::a, "Get mass number A")
+
+     .def("__repr__",
+          [](const fourdst::atomic::Species &s) {
+              std::ostringstream oss;
+              oss << s;
+              return oss.str();
+          });
+
+     chem_submodule.attr("species") = py::cast(fourdst::atomic::species); // Expose the species map
+}

src-pybind/composition/bindings.h

@@ -0,0 +1,6 @@
+#pragma once
+
+#include <pybind11/pybind11.h>
+
+void register_comp_bindings(pybind11::module &m);
+void register_species_bindings(pybind11::module &m);

src-pybind/composition/meson.build

@@ -0,0 +1,17 @@
+# Define the library
+bindings_sources = files('bindings.cpp')
+bindings_headers = files('bindings.h')
+
+dependencies = [
+    composition_dep,
+    python3_dep,
+    pybind11_dep,
+]
+
+shared_module('py_composition',
+    bindings_sources,
+    cpp_args: ['-fvisibility=default'],
+    install : true,
+    dependencies: dependencies,
+    include_directories: include_directories('.')
+)

src-pybind/config/bindings.cpp

@@ -0,0 +1,55 @@
+#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 "fourdst/config/config.h"
+
+namespace py = pybind11;
+
+// 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();
+        });
+}

src-pybind/config/bindings.h

@@ -0,0 +1,5 @@
+#pragma once
+
+#include <pybind11/pybind11.h>
+
+void register_config_bindings(pybind11::module &config_submodule);

src-pybind/config/meson.build

@@ -0,0 +1,17 @@
+# Define the library
+bindings_sources = files('bindings.cpp')
+bindings_headers = files('bindings.h')
+
+dependencies = [
+    config_dep,
+    python3_dep,
+    pybind11_dep,
+]
+
+shared_module('py_config',
+              bindings_sources,
+              include_directories: include_directories('.'),
+              cpp_args: ['-fvisibility=default'],
+              install : true,
+              dependencies: dependencies,
+)

src-pybind/constants/bindings.cpp

@@ -0,0 +1,54 @@
+#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 "fourdst/constants/const.h"
+#include "bindings.h"
+
+namespace py = pybind11;
+
+
+void register_const_bindings(pybind11::module &const_submodule) {
+    py::class_<fourdst::constant::Constant>(const_submodule, "Constant")
+        .def_readonly("name", &fourdst::constant::Constant::name)
+        .def_readonly("value", &fourdst::constant::Constant::value)
+        .def_readonly("uncertainty", &fourdst::constant::Constant::uncertainty)
+        .def_readonly("unit", &fourdst::constant::Constant::unit)
+        .def_readonly("reference", &fourdst::constant::Constant::reference)
+        .def("__repr__", [](const fourdst::constant::Constant &c) {
+            return "<Constant(name='" + c.name + "', value=" + std::to_string(c.value) +
+                   ", uncertainty=" + std::to_string(c.uncertainty) +
+                   ", unit='" + c.unit + "')>";
+        });
+
+    py::class_<fourdst::constant::Constants>(const_submodule, "Constants")
+        .def_property_readonly("loaded", &fourdst::constant::Constants::isLoaded)
+        .def_static("get",
+            [](const std::string &name) {
+                return py::cast(
+                    fourdst::constant::Constants::getInstance().get(name)
+                );
+            },
+            "Get a constant by name. Returns None if not found."
+        )
+        .def_static("has",
+            [](const std::string &name) {
+                return fourdst::constant::Constants::getInstance().has(name);
+            },
+            "Check if a constant exists by name.")
+        .def_static("keys",
+            []() {
+                return py::cast(
+                    fourdst::constant::Constants::getInstance().keys()
+                );
+            },
+            "Get a list of all constant names.")
+        .def_static("__class_getitem__",
+         [](const std::string &name) {
+             return py::cast(
+                 fourdst::constant::Constants::getInstance().get(name)
+             );
+         });
+
+}

src-pybind/constants/bindings.h

@@ -0,0 +1,5 @@
+#pragma once
+
+#include <pybind11/pybind11.h>
+
+void register_const_bindings(pybind11::module &const_submodule);

src-pybind/constants/meson.build

@@ -0,0 +1,17 @@
+# Define the library
+bindings_sources = files('bindings.cpp')
+bindings_headers = files('bindings.h')
+
+dependencies = [
+    const_dep,
+    python3_dep,
+    pybind11_dep,
+]
+
+shared_module('py_const',
+    bindings_sources,
+    include_directories: include_directories('.'),
+    cpp_args: ['-fvisibility=default'],
+    install : true,
+    dependencies: dependencies,
+)

src-pybind/meson.build

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