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refactor(reaction): refactored to an abstract reaction class in prep for weak reactions

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This commit is contained in:
Emily Boudreaux
2025-08-14 13:33:46 -04:00
parent d920a55ba6
commit 0b77f2e269
81 changed files with 1050041 additions and 913 deletions
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16
src/python/engine/bindings.cpp
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@@ -1,8 +1,6 @@
#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 <iostream>
#include <pybind11/stl_bind.h> // Needed for binding std::vector, std::map etc. if needed directly
#include "bindings.h"
@@ -152,7 +150,7 @@ void register_engine_bindings(py::module &m) {
);
}
void register_base_engine_bindings(pybind11::module &m) {
void register_base_engine_bindings(const pybind11::module &m) {
py::class_<gridfire::StepDerivatives<double>>(m, "StepDerivatives")
.def_readonly("dYdt", &gridfire::StepDerivatives<double>::dydt, "The right-hand side (dY/dt) of the ODE system.")
@@ -165,15 +163,15 @@ void register_base_engine_bindings(pybind11::module &m) {
con_stype_register_graph_engine_bindings(m);
}
void abs_stype_register_engine_bindings(pybind11::module &m) {
void abs_stype_register_engine_bindings(const pybind11::module &m) {
py::class_<gridfire::Engine, PyEngine>(m, "Engine");
}
void abs_stype_register_dynamic_engine_bindings(pybind11::module &m) {
void abs_stype_register_dynamic_engine_bindings(const pybind11::module &m) {
const auto a = py::class_<gridfire::DynamicEngine, PyDynamicEngine>(m, "DynamicEngine");
}
void con_stype_register_graph_engine_bindings(pybind11::module &m) {
void con_stype_register_graph_engine_bindings(const pybind11::module &m) {
py::enum_<gridfire::NetworkBuildDepth>(m, "NetworkBuildDepth")
.value("Full", gridfire::NetworkBuildDepth::Full, "Full network build depth")
.value("Shallow", gridfire::NetworkBuildDepth::Shallow, "Shallow network build depth")
@@ -199,7 +197,7 @@ void con_stype_register_graph_engine_bindings(pybind11::module &m) {
py::arg("depth") = gridfire::NetworkBuildDepth::Full,
"Initialize GraphEngine with a composition, partition function and build depth."
);
py_dynamic_engine_bindings.def(py::init<const gridfire::reaction::LogicalReactionSet &>(),
py_dynamic_engine_bindings.def(py::init<const gridfire::reaction::ReactionSet &>(),
py::arg("reactions"),
"Initialize GraphEngine with a set of reactions."
);
@@ -267,7 +265,7 @@ void con_stype_register_graph_engine_bindings(pybind11::module &m) {
registerDynamicEngineDefs<gridfire::GraphEngine, gridfire::DynamicEngine>(py_dynamic_engine_bindings);
}
void register_engine_view_bindings(pybind11::module &m) {
void register_engine_view_bindings(const pybind11::module &m) {
auto py_defined_engine_view_bindings = py::class_<gridfire::DefinedEngineView, gridfire::DynamicEngine>(m, "DefinedEngineView");
py_defined_engine_view_bindings.def(py::init<std::vector<std::string>, gridfire::DynamicEngine&>(),