up

Author: TorkelE

docs/src/api/catalyst_api.md

@@ -178,7 +178,7 @@ substoichmat
 prodstoichmat
 netstoichmat
 reactionrates
-get_metadata_vec
+get_metadata_dict
 has_metadata
 get_metadata
 ```

src/Catalyst.jl

@@ -80,7 +80,7 @@ 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_vec, has_metadata, get_metadata
+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

@@ -854,7 +854,7 @@ end
 ######################## Other accessors ##############################
 
 """
-    get_metadata_vec(reaction::Reaction)
+    get_metadata_dict(reaction::Reaction)
 
 Retrives the `ImmutableDict` containing all of the metadata associated with a specific reaction.
 
@@ -864,10 +864,10 @@ Arguments:
 Example:
 ```julia
 reaction = @reaction k, 0 --> X, [noise_scaling=0.0]
-get_metadata_vec(reaction)
+get_metadata_dict(reaction)
 ```
 """
-function get_metadata_vec(reaction::Reaction)
+function get_metadata_dict(reaction::Reaction)
     return reaction.metadata
 end
 
@@ -887,7 +887,7 @@ has_metadata(reaction, :noise_scaling)
 ```
 """
 function has_metadata(reaction::Reaction, md_key::Symbol)
-    return any(isequal(md_key, entry[1]) for entry in get_metadata_vec(reaction))
+    return any(isequal(md_key, entry[1]) for entry in get_metadata_dict(reaction))
 end
 
 """
@@ -907,9 +907,9 @@ get_metadata(reaction, :noise_scaling)
 """
 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_vec(reaction))).")
+        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_vec(reaction)[findfirst(isequal(md_key, entry[1]) for entry in get_metadata_vec(reaction))][2]
+    return get_metadata_dict(reaction)[findfirst(isequal(md_key, entry[1]) for entry in get_metadata_dict(reaction))][2]
 end
 
 ######################## Conversion to ODEs/SDEs/jump, etc ##############################

test/dsl/dsl_basics.jl

@@ -169,9 +169,9 @@ let
     # Checks DSL reactions are correct.
     rxs = reactions(rs)
     @test isequal([r1, r2, r3], rxs)
-    @test isequal(get_metadata_vec(r1), get_metadata_vec(rxs[1]))
-    @test isequal(get_metadata_vec(r2), get_metadata_vec(rxs[2]))
-    @test isequal(get_metadata_vec(r3), get_metadata_vec(rxs[3]))
+    @test isequal(get_metadata_dict(r1), get_metadata_dict(rxs[1]))
+    @test isequal(get_metadata_dict(r2), get_metadata_dict(rxs[2]))
+    @test isequal(get_metadata_dict(r3), get_metadata_dict(rxs[3]))
 
     # Checks that accessor functions works on the DSL.
     @test has_metadata(rxs[1], :noise_scaling)
@@ -190,9 +190,9 @@ let
     rx3 = @reaction k, 2X --> X2
 
     @test isequal([rx1, rx2, rx3], rxs)
-    @test isequal(get_metadata_vec(rx1), get_metadata_vec(rxs[1]))
-    @test isequal(get_metadata_vec(rx2), get_metadata_vec(rxs[2]))
-    @test isequal(get_metadata_vec(rx3), get_metadata_vec(rxs[3]))
+    @test isequal(get_metadata_dict(rx1), get_metadata_dict(rxs[1]))
+    @test isequal(get_metadata_dict(rx2), get_metadata_dict(rxs[2]))
+    @test isequal(get_metadata_dict(rx3), get_metadata_dict(rxs[3]))
 end
 
 # Checks that repeated metadata throws errors.

test/reactionsystem_structure/reactions.jl

@@ -16,7 +16,7 @@ let
     metadata = [:noise_scaling => 0.0]
     r = Reaction(k, [X], [X2], [2], [1]; metadata=metadata)
 
-    @test get_metadata_vec(r) == [:noise_scaling => 0.0]
+    @test get_metadata_dict(r) == [:noise_scaling => 0.0]
     @test has_metadata(r, :noise_scaling)
     @test !has_metadata(r, :nonexisting_metadata)
     @test get_metadata(r, :noise_scaling) == 0.0
@@ -36,7 +36,7 @@ let
     r2 = Reaction(k, [X], [X2], [2], [1]; metadata=metadata)
 
     @test isequal(r1, r2)
-    @test get_metadata_vec(r1) == Pair{Symbol,Any}[]
+    @test get_metadata_dict(r1) == Pair{Symbol,Any}[]
     @test !has_metadata(r1, :md)
 end
 
@@ -57,7 +57,7 @@ let
     push!(metadata, :md_6 => (0.1, 2.0))
     r = Reaction(k, [X], [X2], [2], [1]; metadata=metadata)
 
-    @test get_metadata_vec(r) isa Vector{Pair{Symbol,Any}}
+    @test get_metadata_dict(r) isa Vector{Pair{Symbol,Any}}
     @test has_metadata(r, :md_1)
     @test has_metadata(r, :md_2)
     @test has_metadata(r, :md_3)