From 7df3481ff41596cee757359a7a876faa1fe3fe11 Mon Sep 17 00:00:00 2001
From: Emily Boudreaux <thomas@boudreauxmail.com>
Date: Mon, 5 May 2025 12:00:40 -0400
Subject: [PATCH] refactor(python/composition): updated python comp bindings to
 use register model

---
 src/python/composition/bindings.cpp | 57 +++++++++++++++--------------
 src/python/composition/bindings.h   |  6 +++
 2 files changed, 35 insertions(+), 28 deletions(-)
 create mode 100644 src/python/composition/bindings.h

diff --git a/src/python/composition/bindings.cpp b/src/python/composition/bindings.cpp
index 8658fc6..a7bf817 100644
--- a/src/python/composition/bindings.cpp
+++ b/src/python/composition/bindings.cpp
@@ -7,6 +7,8 @@
 #include "composition.h"
 #include "atomicSpecies.h"
 
+#include "bindings.h"
+
 namespace py = pybind11;
 
 std::string sv_to_string(std::string_view sv) {
@@ -19,12 +21,8 @@ std::string get_ostream_str(const composition::Composition& comp) {
      return oss.str();
 }
 
-PYBIND11_MODULE(fourdsse_bindings, m) { // Module name must match meson.build
-    m.doc() = "Python bindings for the 4DSSE project"; // Optional module docstring
-
-    auto comp_submodule = m.def_submodule("composition", "Bindings for the Composition module");
-    auto chem_submodule = m.def_submodule("species", "Bindings for the Chemical Species module");
 
+void register_comp_bindings(pybind11::module &comp_submodule) {
     // --- Bindings for composition and species module ---
     py::class_<composition::GlobalComposition>(comp_submodule, "GlobalComposition")
         .def_readonly("specificNumberDensity", &composition::GlobalComposition::specificNumberDensity)
@@ -135,28 +133,31 @@ PYBIND11_MODULE(fourdsse_bindings, m) { // Module name must match meson.build
              return get_ostream_str(comp); // Use helper for C++ operator<<
          });
 
-    // --- Bindings for species module ---
-        py::class_<chemSpecies::Species>(chem_submodule, "Species")
-            .def("mass", &chemSpecies::Species::mass, "Get atomic mass (amu)")
-            .def("massUnc", &chemSpecies::Species::massUnc, "Get atomic mass uncertainty (amu)")
-            .def("bindingEnergy", &chemSpecies::Species::bindingEnergy, "Get binding energy (keV/nucleon?)") // Check units
-            .def("betaDecayEnergy", &chemSpecies::Species::betaDecayEnergy, "Get beta decay energy (keV?)") // Check units
-            .def("betaCode", [](const chemSpecies::Species& s){ return sv_to_string(s.betaCode()); }, "Get beta decay code") // Convert string_view
-            .def("name", [](const chemSpecies::Species& s){ return sv_to_string(s.name()); }, "Get species name (e.g., 'H-1')") // Convert string_view
-            .def("el", [](const chemSpecies::Species& s){ return sv_to_string(s.el()); }, "Get element symbol (e.g., 'H')") // Convert string_view
-            .def("nz", &chemSpecies::Species::nz, "Get NZ value")
-            .def("n", &chemSpecies::Species::n, "Get neutron number N")
-            .def("z", &chemSpecies::Species::z, "Get proton number Z")
-            .def("a", &chemSpecies::Species::a, "Get mass number A")
-
-        .def("__repr__",
-             [](const chemSpecies::Species &s) {
-                 std::ostringstream oss;
-                 oss << s;
-                 return oss.str();
-             });
-
-        chem_submodule.attr("species") = py::cast(chemSpecies::species); // Expose the species map
 
 
-}
\ No newline at end of file
+}
+
+void register_species_bindings(pybind11::module &chem_submodule) {
+     // --- Bindings for species module ---
+     py::class_<chemSpecies::Species>(chem_submodule, "Species")
+         .def("mass", &chemSpecies::Species::mass, "Get atomic mass (amu)")
+         .def("massUnc", &chemSpecies::Species::massUnc, "Get atomic mass uncertainty (amu)")
+         .def("bindingEnergy", &chemSpecies::Species::bindingEnergy, "Get binding energy (keV/nucleon?)") // Check units
+         .def("betaDecayEnergy", &chemSpecies::Species::betaDecayEnergy, "Get beta decay energy (keV?)") // Check units
+         .def("betaCode", [](const chemSpecies::Species& s){ return sv_to_string(s.betaCode()); }, "Get beta decay code") // Convert string_view
+         .def("name", [](const chemSpecies::Species& s){ return sv_to_string(s.name()); }, "Get species name (e.g., 'H-1')") // Convert string_view
+         .def("el", [](const chemSpecies::Species& s){ return sv_to_string(s.el()); }, "Get element symbol (e.g., 'H')") // Convert string_view
+         .def("nz", &chemSpecies::Species::nz, "Get NZ value")
+         .def("n", &chemSpecies::Species::n, "Get neutron number N")
+         .def("z", &chemSpecies::Species::z, "Get proton number Z")
+         .def("a", &chemSpecies::Species::a, "Get mass number A")
+
+     .def("__repr__",
+          [](const chemSpecies::Species &s) {
+              std::ostringstream oss;
+              oss << s;
+              return oss.str();
+          });
+
+     chem_submodule.attr("species") = py::cast(chemSpecies::species); // Expose the species map
+}
diff --git a/src/python/composition/bindings.h b/src/python/composition/bindings.h
new file mode 100644
index 0000000..5d0f02a
--- /dev/null
+++ b/src/python/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);
\ No newline at end of file