remake

Author: TorkelE

src/Catalyst.jl

@@ -91,7 +91,7 @@ export make_empty_network, addspecies!, addparam!, addreaction!, reactionparamsm
 export dependants, dependents, substoichmat, prodstoichmat, netstoichmat
 export conservationlaws, conservedquantities, conservedequations, conservationlaw_constants
 export isequivalent
-export remake_noise_scaling
+export remake_noise_scaling, get_noise_scaling, has_noise_scaling
 
 # depreciated functions to remove in future releases
 export params, numparams

src/reactionsystem.jl

@@ -762,7 +762,8 @@ end
         default_reaction_metadata::Vector{Pair{Symbol, T}} = Vector{Pair{Symbol, Any}}()) where {T}
 
 Takes a `ReactionSystem` and remakes it, returning a modified `ReactionSystem`. Modifications depend
-on which additional arguments are provided. The input `ReactionSystem` is not mutated.
+on which additional arguments are provided. The input `ReactionSystem` is not mutated. Updating
+default reaction metadata is currently the only supported feature.
 
 Arguments:
 - `rs::ReactionSystem`: The `ReactionSystem` which you wish to remake.
@@ -772,11 +773,26 @@ Arguments:
     have their value updated).
 """
 function remake_ReactionSystem_internal(rs::ReactionSystem;  default_reaction_metadata = [])
-    # Updates the metadata for all reactions (equation are ignored).
+    rs = set_default_metadata(rs;  default_reaction_metadata)
+    return rs
+end
+
+# For a `ReactionSystem`, updates all `Reaction`'s default metadata.
+function set_default_metadata(rs::ReactionSystem;  default_reaction_metadata = [])
+    # Updates reaction metadata for for reactions in this specific system.
     eqtransform(eq) = eq isa Reaction ? set_default_metadata(eq, default_reaction_metadata) : eq
     updated_equations = map(eqtransform, get_eqs(rs))
     @set! rs.eqs = updated_equations
     @set! rs.rxs = Reaction[rx for rx in updated_equations if rx isa Reaction]
+    
+    # Updates reaction metadata for all its subsystems.
+    new_sub_systems = similar(get_systems(rs))
+    for (i, sub_system) in enumerate(get_systems(rs))
+        new_sub_systems[i] = set_default_metadata(sub_system; default_reaction_metadata)
+    end
+    @set! rs.systems = new_sub_systems
+
+    # Returns the updated system.
     return rs
 end
 
@@ -790,17 +806,17 @@ end
 set_default_metadata(eq::Equation, default_metadata) = eq
 
 """
-    remake_noise_scaling(rs::ReactionSystem, noise_scaling)
+set_default_noise_scaling(rs::ReactionSystem, noise_scaling)
 
 Creates an updated `ReactionSystem`. This is the old `ReactionSystem`, but each `Reaction` that does
-not have a `Noise_scaling` metadata have its noise_scaling metadata updated. The input `ReactionSystem`
-is not mutated.
+not have a `noise_scaling` metadata have its noise_scaling metadata updated. The input `ReactionSystem`
+is not mutated. Any subsystems of `rs` have their `noise_scaling` metadata updated as well.
 
 Arguments:
 - `rs::ReactionSystem`: The `ReactionSystem` which you wish to remake.
 - `noise_scaling`: The updated noise scaling terms
 """
-function remake_noise_scaling(rs::ReactionSystem, noise_scaling)
+function set_default_noise_scaling(rs::ReactionSystem, noise_scaling)
     return remake_ReactionSystem_internal(rs, default_reaction_metadata = [:noise_scaling => noise_scaling])
 end
 

test/model_simulation/simulate_SDEs.jl

@@ -250,6 +250,28 @@ let
     @test reactions(noise_scaling_network2)[2].metadata == [:noise_scaling => 0.5]
 end
 
+# Tests the `remake_noise_scaling` function on a hierarchical model.
+let
+    # Creates hierarchical model.
+    rn1 = @reaction_network begin
+        p, 0 --> X, [noise_scaling=2.0]
+        d, X --> 0
+    end
+    rn2 = @reaction_network begin
+        k1, X1 --> X2, [noise_scaling=5.0]
+        k2, X2 --> X1
+    end
+    rn = compose(rn1, [rn2])
+
+    # Checks that systems have the correct noise scaling terms.
+    rn = Catalyst.remake_ReactionSystem_internal(rn, default_reaction_metadata = [:noise_scaling => 0.5])
+    rn1_noise_scaling = [get_noise_scaling(rx) for rx in rn.rxs]
+    rn2_noise_scaling = [get_noise_scaling(rx) for rx in Catalyst.get_systems(rn)[1].rxs]
+    rn_noise_scaling = [get_noise_scaling(rx) for rx in reactions(rn)]
+    @test issetequal(rn1_noise_scaling, [2.0, 0.5])
+    @test issetequal(rn2_noise_scaling, [5.0, 0.5])
+    @test issetequal(rn_noise_scaling, [2.0, 0.5, 5.0, 0.5])
+end
 
 ### Checks Simulations Don't Error ###