clean up reaction_stoichiometry comments

src/base/types/CoreModel.jl

@@ -84,8 +84,7 @@ objective(a::CoreModel)::SparseVec = a.c
 """
     reaction_stoichiometry(model::CoreModel, rid::String)::Dict{String, Float64}
 
-Return the reaction equation of reaction with ID `rid` in model. The reaction
-equation maps metabolite ids to their stoichiometric coefficients.
+Return the stoichiometry of reaction with ID `rid`.
 """
 reaction_stoichiometry(m::CoreModel, rid::String)::Dict{String,Float64} =
     Dict(m.mets[k] => v for (k, v) in zip(findnz(m.S[:, first(indexin([rid], m.rxns))])...))
@@ -93,8 +92,7 @@ reaction_stoichiometry(m::CoreModel, rid::String)::Dict{String,Float64} =
 """
     reaction_stoichiometry(model::CoreModel, ridx::Integer)::Dict{String, Float64}
 
-Return the reaction equation of reaction with index `ridx` in model. The reaction
-equation maps metabolite ids to their stoichiometric coefficients.
+Return the stoichiometry of reaction at index `ridx`.
 """
 reaction_stoichiometry(m::CoreModel, ridx::Integer)::Dict{String,Float64} =
     Dict(m.mets[k] => v for (k, v) in zip(findnz(m.S[:, ridx])...))

src/base/types/CoreModelCoupled.jl

@@ -101,16 +101,14 @@ coupling_bounds(a::CoreModelCoupled)::Tuple{SparseVec,SparseVec} = (a.cl, a.cu)
 """
     reaction_stoichiometry(model::CoreModelCoupled, rid::String)::Dict{String, Float64}
 
-Return the reaction equation of reaction with id `rid` in model. The reaction
-equation maps metabolite ids to their stoichiometric coefficients.
+Return the stoichiometry of reaction with ID `rid`.
 """
 reaction_stoichiometry(m::CoreModelCoupled, rid::String) = reaction_stoichiometry(m.lm, rid)
 
 """
     reaction_stoichiometry(model::CoreModelCoupled, ridx::Integer)::Dict{String, Float64}
 
-Return the reaction equation of reaction with index `ridx` in model. The reaction
-equation maps metabolite ids to their stoichiometric coefficients.
+Return the stoichiometry of reaction at index `ridx`.
 """
 function reaction_stoichiometry(m::CoreModelCoupled, ridx::Integer)::Dict{String,Float64}
     reaction_stoichiometry(m.lm, ridx)

src/base/types/JSONModel.jl

@@ -259,8 +259,7 @@ metabolite_notes(model::JSONModel, mid::String)::Notes =
 """
     reaction_stoichiometry(model::JSONModel, rid::String)::Dict{String, Float64}
 
-Return the reaction equation of reaction with ID `rid` in model. The reaction
-equation maps metabolite ids to their stoichiometric coefficients.
+Return the stoichiometry of reaction with ID `rid`.
 """
 reaction_stoichiometry(model::JSONModel, rid::String)::Dict{String,Float64} =
     model.rxns[model.rxn_index[rid]]["metabolites"]

src/base/types/MATModel.jl

@@ -171,8 +171,7 @@ metabolite_compartment(m::MATModel, mid::String) = _maybemap(
 """
     reaction_stoichiometry(model::MATModel, rid::String)::Dict{String, Float64}
 
-Return the reaction equation of reaction with ID `rid` in model. The reaction
-equation maps metabolite ids to their stoichiometric coefficients.
+Return the stoichiometry of reaction with ID `rid`.
 """
 function reaction_stoichiometry(m::MATModel, rid::String)::Dict{String,Float64}
     ridx = first(indexin([rid], m.mat["rxns"]))
@@ -182,8 +181,7 @@ end
 """
     reaction_stoichiometry(model::MATModel, ridx::Integer)::Dict{String, Float64}
 
-Return the reaction equation of reaction with index `ridx` in model. The reaction
-equation maps metabolite ids to their stoichiometric coefficients.
+Return the stoichiometry of reaction at index `ridx`.
 """
 function reaction_stoichiometry(m::MATModel, ridx::Integer)::Dict{String,Float64}
     met_inds = findall(m.mat["S"][:, ridx] .!= 0.0)

src/base/types/SBMLModel.jl

@@ -139,8 +139,7 @@ const _sbml_export_notes = _sbml_export_annotation
 """
     reaction_stoichiometry(model::SBMLModel, rid::String)::Dict{String, Float64}
 
-Return the reaction equation of reaction with ID `rid` in model. The reaction
-equation maps metabolite ids to their stoichiometric coefficients.
+Return the stoichiometry of reaction with ID `rid`.
 """
 reaction_stoichiometry(m::SBMLModel, rid::String)::Dict{String,Float64} =
     m.sbml.reactions[rid].stoichiometry

src/base/types/StandardModel.jl

@@ -270,8 +270,7 @@ reaction_annotations(model::StandardModel, id::String)::Maybe{Annotations} =
 """
     reaction_stoichiometry(model::StandardModel, rid::String)::Dict{String, Float64}
 
-Return the reaction equation of reaction with id `rid` in model. The reaction
-equation maps metabolite ids to their stoichiometric coefficients.
+Return the stoichiometry of reaction with ID `rid`.
 """
 reaction_stoichiometry(m::StandardModel, rid::String)::Dict{String,Float64} =
     m.reactions[rid].metabolites

src/base/types/abstract/MetabolicModel.jl

@@ -307,16 +307,16 @@ function reaction_subsystem(model::MetabolicModel, reaction_id::String)::Maybe{S
 end
 
 """
-    reaction_stoichiometry(model::MetaboliteModel, rxn_id::String)::Dict{String, Float64}
+    reaction_stoichiometry(model::MetaboliteModel, rid::String)::Dict{String, Float64}
 
-Return the reaction equation of reaction with id `rxn_id` in model. The reaction
-equation maps metabolite ids to their stoichiometric coefficients.
+Return the stoichiometry of reaction with ID `rid` in the model. The dictionary
+maps the metabolite IDs to their stoichiometric coefficients.
 """
-function reaction_stoichiometry(m::MetabolicModel, rxn_id::String)::Dict{String,Float64}
+function reaction_stoichiometry(m::MetabolicModel, rid::String)::Dict{String,Float64}
     mets = metabolites(m)
     Dict(
         mets[k] => v for (k, v) in
-        zip(findnz(stoichiometry(m)[:, first(indexin([rxn_id], reactions(m)))])...)
+        zip(findnz(stoichiometry(m)[:, first(indexin([rid], reactions(m)))])...)
     )
 end