implement reviews

src/reconstruction/CoreModel.jl

@@ -453,10 +453,8 @@ function change_objective!(
     rxn_idxs::Vector{Int};
     weights = ones(length(rxn_idxs)),
 )
-    nz_idxs, _ = findnz(objective(model))
-    model.c[nz_idxs] .= 0.0 # reset
-    dropzeros!(model.c) # cleanup
-    model.c[rxn_idxs] .= weights # set
+    model.c = spzeros(length(model.c))
+    model.c[rxn_idxs] .= weights
     nothing
 end
 

src/reconstruction/CoreModelCoupled.jl

@@ -428,31 +428,21 @@ end
 """
     change_objective!(
         model::CoreModelCoupled,
-        rxn_idxs::Vector{Int};
-        weights = ones(length(rxns)),
+        args...,
+        kwargs...,
     )
 
-Change the objective for `model` to reaction(s) with indices `rxn_ids`, optionally
-specifying their `weights`. By default, assume equal weights. If no objective exists in
-model, sets objective.
+Forwards arguments to [`change_objective!`](@ref).
 """
-function change_objective!(
-    model::CoreModelCoupled,
-    rxn_idxs::Vector{Int};
-    weights = ones(length(rxns)),
-)
-    change_objective!(model.lm, rxn_idxs; weights)
+function change_objective!(model::CoreModelCoupled, args...; kwargs...)
+    change_objective!(model.lm, args...; kwargs...)
 end
 
 change_objective!(model::CoreModelCoupled, rxn_xid::Int) =
     change_objective!(model.lm, [rxn_xid])
 
-function change_objective!(
-    model::CoreModelCoupled,
-    rxn_ids::Vector{String};
-    weights = ones(length(rxns)),
-)
-    change_objective!(model.lm, rxn_ids; weights)
+function change_objective!(model::CoreModelCoupled, args...; kwargs...)
+    change_objective!(model.lm, args...; kwargs...)
 end
 
 change_objective!(model::CoreModelCoupled, rxn_id::String) =

src/reconstruction/StandardModel.jl

@@ -248,14 +248,12 @@ function change_objective!(
 )
     all(!haskey(model.reactions, rid) for rid in rxn_ids) &&
         throw(DomainError(rxn_ids, "Some reaction ids were not found in model."))
-    k = 1 # counter
-    for rid in reactions(model)
-        if rid in rxn_ids
-            model.reactions[rid].objective_coefficient = weights[k]
-            k += 1
-        else # set others to zero
-            model.reactions[rid].objective_coefficient = 0.0
-        end
+
+    for rid in reactions(model) # reset to zero
+        model.reactions[rid].objective_coefficient = 0.0
+    end
+    for (k, rid) in enumerate(rxn_ids)
+        model.reactions[rid].objective_coefficient = weights[k]
     end
 end