up

Author: TorkelE

src/Catalyst.jl

@@ -91,6 +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
 
 # depreciated functions to remove in future releases
 export params, numparams

src/expression_utils.jl

@@ -96,7 +96,9 @@ end
 
 ### Generic Expression Handling ###
 
-# Convert an expression with equal signs (e.g. :(a=1.0, b=2.0)) to one with pairs (e.g. :(a=>1.0, b=>2.0))
+# Convert an expression that is a vector with symbols that have values assigned using `=` to vector 
+# where the assignment instead uses pairs (e.g. :([a=1.0, b=2.0])). Used to e.g. convert default 
+# reaction metadata to a form that can be evaluated as actual code.
 function expr_equal_vector_to_pairs(expr_vec)
     pair_vector = :([])
     foreach(arg -> push!(pair_vector.args, arg.args[1] => arg.args[2]), expr_vec.args) 

src/reaction_network.jl

@@ -643,7 +643,6 @@ end
 
 # Takes a reaction line and creates reaction(s) from it and pushes those to the reaction array.
 # Used to create multiple reactions from, for instance, `k, (X,Y) --> 0`.
-# Handles metadata, e.g. `1.0, Z --> 0, [noise_scaling=η]`.
 function push_reactions!(reactions::Vector{ReactionStruct}, sub_line::ExprValues, prod_line::ExprValues, 
                          rate::ExprValues, metadata::ExprValues, arrow::Symbol)  
     # The rates, substrates, products, and metadata may be in a tupple form (e.g. `k, (X,Y) --> 0`).

src/reactionsystem.jl

@@ -761,32 +761,48 @@ end
     remake_ReactionSystem_internal(rs::ReactionSystem; 
         default_reaction_metadata::Vector{Pair{Symbol, T}} = Vector{Pair{Symbol, Any}}()) where {T}
 
-Takes a reaction systems and reameks it, returning a modified reaction system. Modifications depend
-on which arguments are provided.
+Takes a `ReactionSystem` and remakes it, returning a modified `ReactionSystem`. Modifications depend
+on which additional arguments are provided. The input `ReactionSystem` is not mutated.
 
 Arguments:
-- `rs::ReactionSystem`: The `ReactionSystem` which you wish to make a remade version of.
+- `rs::ReactionSystem`: The `ReactionSystem` which you wish to remake.
 - `default_reaction_metadata::Vector{Pair{Symbol, T}}`: A vector with default `Reaction` metadata values.
-    Each metadata in each `Reaction` of the updated `ReactionSystem` will have teh value desiganted in
+    Each metadata in each `Reaction` of the updated `ReactionSystem` will have the value desiganted in
     `default_reaction_metadata` (however, `Reaction`s that already have that metadata designated will not
     have their value updated).
 """
-#function remake_ReactionSystem_internal(rs::ReactionSystem;  default_reaction_metadata::Vector{Pair{Symbol, T}} = Vector{Pair{Symbol, Any}}()) where {T}
-function remake_ReactionSystem_internal(rs; default_reaction_metadata = default_reaction_metadata)
-    # Updates the metadata for all reactions (reactions are ignored).
+function remake_ReactionSystem_internal(rs::ReactionSystem;  default_reaction_metadata = [])
+    # Updates the metadata for all reactions (equation are ignored).
+    updated_equations = [set_default_metadata(rx, default_reaction_metadata) for rx in reactions(rs)]
     updated_reactions = [set_default_metadata(rx, default_reaction_metadata) for rx in reactions(rs)]
-    rs = @set rs.rxs = updated_reactions  
+    @set! rs.eqs = updated_equations
+    @set! rs.rxs = updated_reactions
     return rs
 end
 
 # For a `Reaction`, adds missing default metadata values. Equations are passed back unmodified.
-function set_default_metadata(rx, default_metadata)
+function set_default_metadata(rx::Reaction, default_metadata)
     missing_metadata = filter(md -> !in(md[1], entry[1] for entry in rx.metadata), default_metadata)
     updated_metadata = vcat(rx.metadata, missing_metadata)
     updated_metadata = convert(Vector{Pair{Symbol, Any}}, updated_metadata)
     return @set rx.metadata = updated_metadata
 end
+set_default_metadata(eq::Equation, default_metadata) = eq
 
+"""
+    remake_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.
+
+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)
+    return remake_ReactionSystem_internal(rs, default_reaction_metadata = [:noise_scaling => noise_scaling])
+end
 
 
 """

test/model_simulation/simulate_SDEs.jl

@@ -234,6 +234,22 @@ let
     @test var(sol[:X1]) > var(sol[:X2]) > var(sol[:X3]) > var(sol[:X4]) > var(sol[:X5])  
 end
 
+# Tests the `remake_noise_scaling` function.
+let
+    # Creates noise scaling networks.
+    noise_scaling_network1 = @reaction_network begin
+        p, 0 --> X, [noise_scaling=2.0]
+        d, X --> 0
+    end
+    noise_scaling_network2 = remake_noise_scaling(noise_scaling_network1, 0.5)
+
+    # Checks that the two networks' reactions have the correct metadata.
+    @test reactions(noise_scaling_network1)[1].metadata == [:noise_scaling => 2.0]
+    @test reactions(noise_scaling_network1)[2].metadata == []
+    @test reactions(noise_scaling_network2)[1].metadata == [:noise_scaling => 2.0]
+    @test reactions(noise_scaling_network2)[2].metadata == [:noise_scaling => 0.5]
+end
+
 
 ### Checks Simulations Don't Error ###