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SciML · Mar 18, 2024 · 7dbb02c · 7dbb02c
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diff --git a/HISTORY.md b/HISTORY.md
@@ -22,7 +22,7 @@ rn = @reaction_network begin
     @parameters η
     k, 2X --> X2, [noise_scaling=η]
 end
-getnoisescaling(rn)
+get_noise_scaling(rn)
 ```
 - `SDEProblem` no longer takes the `noise_scaling` argument (she above for new approach to handle noise scaling).
 - Changed fields of internal `Reaction` structure. `ReactionSystems`s saved using `serialize` on previous Catalyst versions cannot be loaded using this (or later) versions.

diff --git a/src/reaction_network.jl b/src/reaction_network.jl
@@ -644,7 +644,7 @@ 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, [noisescaling=η]`.
+# 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; default_reaction_metadata::Expr)  
     # The rates, substrates, products, and metadata may be in a tupple form (e.g. `k, (X,Y) --> 0`).

diff --git a/src/reactionsystem.jl b/src/reactionsystem.jl
@@ -864,29 +864,49 @@ end
 ######################## Other accessors ##############################
 
 """
-    getnoisescaling(reaction::Reaction)
+has_noise_scaling(reaction::Reaction)
 
-Returns the noise scaling associated with a specific reaction. If the `:noise_scaling` metadata has
-set, returns that. Else, returns `1.0`.
+Checks whether a specific reaction has the metadata field `noise_scaing`. If so, returns `true`, else
+returns `false`.
+
+Arguments:
+- `reaction`: The reaction for which we wish to check.
+
+Example:
+```julia
+reaction = @reaction k, 0 --> X, [noise_scaling=0.0]
+has_noise_scaling(reaction)
+"""
+function has_noise_scaling(reaction::Reaction)
+    return hasmetadata(reaction, :noise_scaling)
+end
+
+"""
+get_noise_scaling(reaction::Reaction)
+
+Returns the noise_scaling metadata from a specific reaction.
 
 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)
+get_noise_scaling(reaction)
 """
-function getnoisescaling(reaction::Reaction)
-    has_metadata(reaction, :noise_scaling) && (return get_metadata(reaction, :noise_scaling))
-    return 1.0
+function get_noise_scaling(reaction::Reaction)
+    if has_noise_scaling(reaction)
+        return getmetadata(reaction, :noise_scaling)
+    else
+        error("Attempts to access noise_scaling metadata field for a reaction which does not have a value assigned for this metadata.")
+    end
 end
 
 
-# These are currently considered internal, but can be used by public accessor functions like getnoisescaling.
+# These are currently considered internal, but can be used by public accessor functions like get_noise_scaling.
 
 """
-    get_metadata_dict(reaction::Reaction)
+    getmetadata_dict(reaction::Reaction)
 
 Retrives the `ImmutableDict` containing all of the metadata associated with a specific reaction.
 
@@ -896,15 +916,15 @@ Arguments:
 Example:
 ```julia
 reaction = @reaction k, 0 --> X, [description="Production reaction"]
-get_metadata_dict(reaction)
+getmetadata_dict(reaction)
 ```
 """
-function get_metadata_dict(reaction::Reaction)
+function getmetadata_dict(reaction::Reaction)
     return reaction.metadata
 end
 
 """
-    has_metadata(reaction::Reaction, md_key::Symbol)
+    hasmetadata(reaction::Reaction, md_key::Symbol)
 
 Checks if a `Reaction` have a certain metadata field. If it does, returns `true` (else returns `false`).
 
@@ -915,15 +935,15 @@ Arguments:
 Example:
 ```julia
 reaction = @reaction k, 0 --> X, [description="Production reaction"]
-has_metadata(reaction, :description)
+hasmetadata(reaction, :description)
 ```
 """
-function has_metadata(reaction::Reaction, md_key::Symbol)
-    return any(isequal(md_key, entry[1]) for entry in get_metadata_dict(reaction))
+function hasmetadata(reaction::Reaction, md_key::Symbol)
+    return any(isequal(md_key, entry[1]) for entry in getmetadata_dict(reaction))
 end
 
 """
-    get_metadata(reaction::Reaction, md_key::Symbol)
+getmetadata(reaction::Reaction, md_key::Symbol)
 
 Retrives a certain metadata value from a `Reaction`. If the metadata does not exists, throws an error.
 
@@ -934,15 +954,15 @@ Arguments:
 Example:
 ```julia
 reaction = @reaction k, 0 --> X, [description="Production reaction"]
-get_metadata(reaction, :description)
+getmetadata(reaction, :description)
 ```
 """
-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))).")
+function getmetadata(reaction::Reaction, md_key::Symbol)
+    if !hasmetadata(reaction, md_key) 
+        error("The reaction does not have a metadata field $md_key. It does have the following metadata fields: $(keys(getmetadata_dict(reaction))).")
     end
-    metadata = get_metadata_dict(reaction)
-    return metadata[findfirst(isequal(md_key, entry[1]) for entry in get_metadata_dict(reaction))][2]
+    metadata = getmetadata_dict(reaction)
+    return metadata[findfirst(isequal(md_key, entry[1]) for entry in getmetadata_dict(reaction))][2]
 end
 
 
@@ -1065,7 +1085,7 @@ function assemble_diffusion(rs, sts, ispcs; combinatoric_ratelaws = true,
 
     for (j, rx) in enumerate(get_rxs(rs))
         rlsqrt = sqrt(abs(oderatelaw(rx; combinatoric_ratelaw = combinatoric_ratelaws)))
-        rlsqrt *= getnoisescaling(rx)
+        has_noise_scaling(rx) && (rlsqrt *= get_noise_scaling(rx))
         remove_conserved && (rlsqrt = substitute(rlsqrt, depspec_submap))
 
         for (spec, stoich) in rx.netstoich
@@ -1485,7 +1505,6 @@ function Base.convert(::Type{<:SDESystem}, rs::ReactionSystem;
                       name = nameof(rs), combinatoric_ratelaws = get_combinatoric_ratelaws(rs),
                       include_zero_odes = true, checks = false, remove_conserved = false,
                       default_u0 = Dict(), default_p = Dict(), defaults = _merge(Dict(default_u0), Dict(default_p)),
-                      noise_scaling = nothing, # To be removed (used for deprication message only).
                       kwargs...)
     spatial_convert_err(rs::ReactionSystem, SDESystem)
 
@@ -1535,7 +1554,6 @@ function Base.convert(::Type{<:JumpSystem}, rs::ReactionSystem; name = nameof(rs
                       combinatoric_ratelaws = get_combinatoric_ratelaws(rs),
                       remove_conserved = nothing, checks = false,
                       default_u0 = Dict(), default_p = Dict(), defaults = _merge(Dict(default_u0), Dict(default_p)),
-                      noise_scaling = nothing, # To be removed (used for deprication message only).
                       kwargs...)
     spatial_convert_err(rs::ReactionSystem, JumpSystem)
 

diff --git a/test/dsl/dsl_basics.jl b/test/dsl/dsl_basics.jl
@@ -169,30 +169,30 @@ let
     # Checks DSL reactions are correct.
     rxs = reactions(rs)
     @test isequal([r1, r2, r3], rxs)
-    @test isequal(Catalyst.get_metadata_dict(r1), Catalyst.get_metadata_dict(rxs[1]))
-    @test isequal(Catalyst.get_metadata_dict(r2), Catalyst.get_metadata_dict(rxs[2]))
-    @test isequal(Catalyst.get_metadata_dict(r3), Catalyst.get_metadata_dict(rxs[3]))
+    @test isequal(Catalyst.getmetadata_dict(r1), Catalyst.getmetadata_dict(rxs[1]))
+    @test isequal(Catalyst.getmetadata_dict(r2), Catalyst.getmetadata_dict(rxs[2]))
+    @test isequal(Catalyst.getmetadata_dict(r3), Catalyst.getmetadata_dict(rxs[3]))
 
     # Checks that accessor functions works on the DSL.
-    @test Catalyst.has_metadata(rxs[1], :noise_scaling)
-    @test !Catalyst.has_metadata(rxs[1], :md_1)
-    @test !Catalyst.has_metadata(rxs[2], :noise_scaling)
-    @test Catalyst.has_metadata(rxs[2], :md_1)
-    @test !Catalyst.has_metadata(rxs[3], :noise_scaling)
-    @test !Catalyst.has_metadata(rxs[3], :md_1)
+    @test Catalyst.hasmetadata(rxs[1], :noise_scaling)
+    @test !Catalyst.hasmetadata(rxs[1], :md_1)
+    @test !Catalyst.hasmetadata(rxs[2], :noise_scaling)
+    @test Catalyst.hasmetadata(rxs[2], :md_1)
+    @test !Catalyst.hasmetadata(rxs[3], :noise_scaling)
+    @test !Catalyst.hasmetadata(rxs[3], :md_1)
 
-    @test isequal(Catalyst.get_metadata(rxs[1], :noise_scaling), η)
-    @test isequal(Catalyst.get_metadata(rxs[2], :md_1), 1.0)
+    @test isequal(Catalyst.getmetadata(rxs[1], :noise_scaling), η)
+    @test isequal(Catalyst.getmetadata(rxs[2], :md_1), 1.0)
 
     # Test that metadata works for @reaction macro.
     rx1 = @reaction k, 2X --> X2, [noise_scaling=$η]
     rx2 = @reaction k, 2X --> X2, [md_1=1.0, md_2=false, md_3="Hello world", md_4=:sym, md_5=X+X2^k-1, md_6=(0.1,2.0)]
     rx3 = @reaction k, 2X --> X2
 
     @test isequal([rx1, rx2, rx3], rxs)
-    @test isequal(Catalyst.get_metadata_dict(rx1), Catalyst.get_metadata_dict(rxs[1]))
-    @test isequal(Catalyst.get_metadata_dict(rx2), Catalyst.get_metadata_dict(rxs[2]))
-    @test isequal(Catalyst.get_metadata_dict(rx3), Catalyst.get_metadata_dict(rxs[3]))
+    @test isequal(Catalyst.getmetadata_dict(rx1), Catalyst.getmetadata_dict(rxs[1]))
+    @test isequal(Catalyst.getmetadata_dict(rx2), Catalyst.getmetadata_dict(rxs[2]))
+    @test isequal(Catalyst.getmetadata_dict(rx3), Catalyst.getmetadata_dict(rxs[3]))
 end
 
 # Checks that repeated metadata throws errors.

diff --git a/test/reactionsystem_structure/reactions.jl b/test/reactionsystem_structure/reactions.jl
@@ -16,10 +16,10 @@ let
     metadata = [:noise_scaling => 0.0]
     r = Reaction(k, [X], [X2], [2], [1]; metadata=metadata)
 
-    @test Catalyst.get_metadata_dict(r) == [:noise_scaling => 0.0]
-    @test Catalyst.has_metadata(r, :noise_scaling)
-    @test !Catalyst.has_metadata(r, :nonexisting_metadata)
-    @test Catalyst.get_metadata(r, :noise_scaling) == 0.0
+    @test Catalyst.getmetadata_dict(r) == [:noise_scaling => 0.0]
+    @test Catalyst.hasmetadata(r, :noise_scaling)
+    @test !Catalyst.hasmetadata(r, :nonexisting_metadata)
+    @test Catalyst.getmetadata(r, :noise_scaling) == 0.0
 
     metadata_repeated = [:noise_scaling => 0.0, :noise_scaling => 1.0, :metadata_entry => "unused"]
     @test_throws Exception Reaction(k, [X], [X2], [2], [1]; metadata=metadata_repeated)
@@ -36,8 +36,8 @@ let
     r2 = Reaction(k, [X], [X2], [2], [1]; metadata=metadata)
 
     @test isequal(r1, r2)
-    @test Catalyst.get_metadata_dict(r1) == Pair{Symbol,Any}[]
-    @test !Catalyst.has_metadata(r1, :md)
+    @test Catalyst.getmetadata_dict(r1) == Pair{Symbol,Any}[]
+    @test !Catalyst.hasmetadata(r1, :md)
 end
 
 # Tests creation.
@@ -57,21 +57,21 @@ let
     push!(metadata, :md_6 => (0.1, 2.0))
     r = Reaction(k, [X], [X2], [2], [1]; metadata=metadata)
 
-    @test Catalyst.get_metadata_dict(r) isa Vector{Pair{Symbol,Any}}
-    @test Catalyst.has_metadata(r, :md_1)
-    @test Catalyst.has_metadata(r, :md_2)
-    @test Catalyst.has_metadata(r, :md_3)
-    @test Catalyst.has_metadata(r, :md_4)
-    @test Catalyst.has_metadata(r, :md_5)
-    @test Catalyst.has_metadata(r, :md_6)
-    @test !Catalyst.has_metadata(r, :md_8)
+    @test Catalyst.getmetadata_dict(r) isa Vector{Pair{Symbol,Any}}
+    @test Catalyst.hasmetadata(r, :md_1)
+    @test Catalyst.hasmetadata(r, :md_2)
+    @test Catalyst.hasmetadata(r, :md_3)
+    @test Catalyst.hasmetadata(r, :md_4)
+    @test Catalyst.hasmetadata(r, :md_5)
+    @test Catalyst.hasmetadata(r, :md_6)
+    @test !Catalyst.hasmetadata(r, :md_8)
 
-    @test isequal(Catalyst.get_metadata(r, :md_1), 1.0)
-    @test isequal(Catalyst.get_metadata(r, :md_2), false)
-    @test isequal(Catalyst.get_metadata(r, :md_3), "Hello world")
-    @test isequal(Catalyst.get_metadata(r, :md_4), :sym)
-    @test isequal(Catalyst.get_metadata(r, :md_5), X + X2^k -1)
-    @test isequal(Catalyst.get_metadata(r, :md_6), (0.1, 2.0))
+    @test isequal(Catalyst.getmetadata(r, :md_1), 1.0)
+    @test isequal(Catalyst.getmetadata(r, :md_2), false)
+    @test isequal(Catalyst.getmetadata(r, :md_3), "Hello world")
+    @test isequal(Catalyst.getmetadata(r, :md_4), :sym)
+    @test isequal(Catalyst.getmetadata(r, :md_5), X + X2^k -1)
+    @test isequal(Catalyst.getmetadata(r, :md_6), (0.1, 2.0))
 end
 
 # Noise scaling metadata.
@@ -85,6 +85,6 @@ let
     r1 = Reaction(k, [X], [X2], [2], [1])
     r2 = Reaction(k, [X], [X2], [2], [1]; metadata=metadata)
 
-    @test isequal(Catalyst.getnoisescaling(r1), 1.0)
-    @test isequal(Catalyst.getnoisescaling(r2), η)
+    @test isequal(Catalyst.get_noise_scaling(r1), 1.0)
+    @test isequal(Catalyst.get_noise_scaling(r2), η)
 end
diff --git a/test/reactionsystem_structure/reactionsystem.jl b/test/reactionsystem_structure/reactionsystem.jl
@@ -707,6 +707,6 @@ end
 
 # Tests metadata.
 let
-    @test isnothing(ModelingToolkit.get_metadata(rs))
+    @test isnothing(ModelingToolkit.getmetadata(rs))
 end