update

Author: TorkelE

HISTORY.md

@@ -22,7 +22,7 @@ rn = @reaction_network begin
     @parameters η
     k, 2X --> X2, [noise_scaling=η]
 end
-get_metadata(rn, :noise_scaling)
+getnoisescaling(rn)
 ```
 - Changed fields of internal `Reaction` structure. `ReactionSystems`s saved using `serialize` on previous Catalyst versions cannot be loaded using this (or later) versions.
 - Simulation of spatial ODEs now supported. For full details, please see https://github.com/SciML/Catalyst.jl/pull/644 and upcoming documentation. Note that these methods are currently considered alpha, with the interface and approach changing even in non-breaking Catalyst releases.

docs/src/api/catalyst_api.md

@@ -178,9 +178,6 @@ substoichmat
 prodstoichmat
 netstoichmat
 reactionrates
-get_metadata_dict
-has_metadata
-get_metadata
 ```
 
 ## [Functions to extend or modify a network](@id api_network_extension_and_modification)

src/Catalyst.jl

@@ -80,7 +80,6 @@ export mm, mmr, hill, hillr, hillar
 include("networkapi.jl")
 export species, nonspecies, reactionparams, reactions, speciesmap, paramsmap
 export numspecies, numreactions, numreactionparams, setdefaults!, symmap_to_varmap
-export get_metadata_dict, has_metadata, get_metadata
 export make_empty_network, addspecies!, addparam!, addreaction!, reactionparamsmap
 export dependants, dependents, substoichmat, prodstoichmat, netstoichmat
 export conservationlaws, conservedquantities, conservedequations, conservationlaw_constants

src/reactionsystem.jl

@@ -98,7 +98,7 @@ Notes:
 - The three-argument form assumes all reactant and product stoichiometric coefficients
   are one.
 """
-struct Reaction{R, S, T}
+struct Reaction{S, T}
     """The rate function (excluding mass action terms)."""
     rate::Any
     """Reaction substrates."""
@@ -120,7 +120,7 @@ struct Reaction{R, S, T}
     Contain additional data, such whenever the reaction have a specific noise-scaling expression for
     the chemical Langevin equation.
     """
-    metadata::Vector{Pair{Symbol, R}}
+    metadata::Vector{Pair{Symbol, Any}}
 end
 
 """
@@ -187,7 +187,7 @@ function Reaction(rate, subs, prods, substoich, prodstoich;
     end
 
     # Check that all metadata entries are unique.
-    if length(unique(entry[1] for entry in metadata)) < length(metadata)
+    if any(metadata[i] in metadata[i+1:end] for i in eachindex(metadata))
         error("Repeated entries for the same metadata encountered in the following metadata set: $([entry[1] for entry in metadata]).")
     end
 
@@ -853,6 +853,28 @@ end
 
 ######################## Other accessors ##############################
 
+"""
+    getnoisescaling(reaction::Reaction)
+
+Returns the noise scaling associated with a specific reaction. If the `:noise_scaling` metadata has
+set, returns that. Else, returns `1.0`.
+
+Arguments:
+- `reaction`: The reaction for which we wish to retrive all metadata.
+
+Example:
+```julia
+reaction = @reaction k, 0 --> X, [noise_scaling=0.0]
+getnoisescaling(reaction)
+"""
+function getnoisescaling(reaction::Reaction)
+    has_metadata(reaction, :noise_scaling) && (return get_metadata(reaction, :noise_scaling))
+    return 1.0
+end
+
+
+# These are currently considered internal, but can be used by public accessor functions like getnoisescaling.
+
 """
     get_metadata_dict(reaction::Reaction)
 
@@ -909,7 +931,8 @@ function get_metadata(reaction::Reaction, md_key::Symbol)
     if !has_metadata(reaction, md_key) 
         error("The reaction does not have a metadata field $md_key. It does have the following metadata fields: $(keys(get_metadata_dict(reaction))).")
     end
-    return get_metadata_dict(reaction)[findfirst(isequal(md_key, entry[1]) for entry in get_metadata_dict(reaction))][2]
+    metadata = get_metadata_dict(reaction)
+    return metadata[findfirst(isequal(md_key, entry[1]) for entry in get_metadata_dict(reaction))][2]
 end
 
 ######################## Conversion to ODEs/SDEs/jump, etc ##############################