ENH: Stochastic mass-action dynamics for Petri nets (#619)

---------

Co-authored-by: Evan Patterson <evan@epatters.org>

Author: quffaro

Cargo.lock

@@ -14,6 +14,7 @@ use catlog::stdlib::{analyses, models, theories, theory_morphisms};
 use catlog::zero::name;
 
 use super::model_morphism::{MotifOccurrence, MotifsOptions, motifs};
+use super::result::JsResult;
 use super::{analyses::*, model::DblModel, theory::DblTheory};
 
 /// The empty or initial theory.
@@ -335,6 +336,21 @@ impl ThSymMonoidalCategory {
                 .into(),
         ))
     }
+
+    /// Simulates the stochastic mass-action system derived from a model.
+    #[wasm_bindgen(js_name = "stochasticMassAction")]
+    pub fn stochastic_mass_action(
+        &self,
+        model: &DblModel,
+        data: analyses::ode::MassActionProblemData,
+    ) -> Result<ODEResult, String> {
+        Ok(ODEResult(JsResult::Ok(
+            analyses::ode::PetriNetMassActionAnalysis::default()
+                .build_stochastic_system(model.modal()?, data)
+                .simulate(),
+        )))
+    }
+
     /// Solve the subreachability problem for petri nets.
     #[wasm_bindgen(js_name = "subreachability")]
     pub fn subreachability(

packages/catlog-wasm/src/theories.rs

@@ -7,7 +7,7 @@ edition = "2024"
 
 
 [features]
-ode = ["dep:ode_solvers", "dep:nalgebra"]
+ode = ["dep:ode_solvers", "dep:nalgebra", "dep:rebop"]
 serde = ["dep:serde", "nonempty/serialize", "ustr/serde", "uuid/serde"]
 serde-wasm = ["serde", "dep:wasm-bindgen", "dep:tsify", "dep:instant", "instant/wasm-bindgen"]
 
@@ -27,6 +27,7 @@ nonempty = "0.12"
 num-traits = "0.2"
 ode_solvers = { version = "0.5.0", optional = true }
 pretty = "0.12.4"
+rebop = { git = "https://github.com/Armavica/rebop.git", rev = "eb1e500", default-features = false, optional = true }
 ref-cast = "1"
 scopeguard = "1.2.0"
 serde = { version = "1", features = ["derive"], optional = true }