eliminate the trailing spaces (and a case of mutability abuse)

src/analysis/gecko.jl

@@ -147,24 +147,15 @@ function make_gecko_model(
         push!(coupling_row_mass_group, _gecko_capacity(grp, idxs, mms, gmgb_(grp)))
     end
 
-    # create model with dummy objective
-    gm = GeckoModel(
-        spzeros(length(columns) + length(coupling_row_gene_product)),
+    GeckoModel(
+        [
+            _gecko_reaction_column_reactions(columns, model)' * objective(model)
+            spzeros(length(coupling_row_gene_product))
+        ],
         columns,
         coupling_row_reaction,
         collect(zip(coupling_row_gene_product, gpb_.(gids[coupling_row_gene_product]))),
         coupling_row_mass_group,
         model,
     )
-
-    #=
-    Set objective. This is a separate field because gene products can also be objectives. 
-    This way they can be set as objectives by the user.
-    =#
-    gm.objective .= [
-        _gecko_reaction_column_reactions(gm)' * objective(gm.inner)
-        spzeros(length(coupling_row_gene_product))
-    ]
-
-    return gm
 end

src/base/types/wrappers/GeckoModel.jl

@@ -16,7 +16,7 @@ end
 """
     struct _gecko_capacity
 
-A helper struct that contains the gene product capacity terms organized by 
+A helper struct that contains the gene product capacity terms organized by
 the grouping type, e.g. metabolic or membrane groups etc.
 """
 struct _gecko_capacity
@@ -217,7 +217,7 @@ end
 """
     balance(model::GeckoModel)
 
-Return the balance of the reactions in the inner model, concatenated with a vector of 
+Return the balance of the reactions in the inner model, concatenated with a vector of
 zeros representing the enzyme balance of a [`GeckoModel`](@ref).
 """
 balance(model::GeckoModel) =
@@ -233,7 +233,7 @@ n_genes(model::GeckoModel) = length(model.coupling_row_gene_product)
 """
     genes(model::GeckoModel)
 
-Return the gene ids of genes that have enzymatic constraints associated with them.  
+Return the gene ids of genes that have enzymatic constraints associated with them.
 """
 genes(model::GeckoModel) =
     genes(model.inner)[[idx for (idx, _) in model.coupling_row_gene_product]]

src/base/utils/gecko.jl

@@ -15,12 +15,20 @@ _gecko_reaction_name(original_name::String, direction::Int, isozyme_idx::Int) =
 Retrieve a utility mapping between reactions and split reactions; rows
 correspond to "original" reactions, columns correspond to "split" reactions.
 """
-_gecko_reaction_column_reactions(model::GeckoModel) = sparse(
-    [col.reaction_idx for col in model.columns],
-    1:length(model.columns),
-    [col.direction >= 0 ? 1 : -1 for col in model.columns],
-    n_reactions(model.inner),
-    length(model.columns),
+_gecko_reaction_column_reactions(model::GeckoModel) =
+    _gecko_reaction_column_reactions(model.columns, model.inner)
+
+"""
+    _gecko_reaction_column_reactions(columns, inner)
+
+Helper method that doesn't require the whole [`GeckoModel`](@ref).
+"""
+_gecko_reaction_column_reactions(columns, inner) = sparse(
+    [col.reaction_idx for col in columns],
+    1:length(columns),
+    [col.direction >= 0 ? 1 : -1 for col in columns],
+    n_reactions(inner),
+    length(columns),
 )
 
 """

test/analysis/gecko.jl

@@ -54,7 +54,7 @@ end
 
 @testset "GECKO small model" begin
     #=
-    Implement the small model found in the supplment of the 
+    Implement the small model found in the supplment of the
     original GECKO paper. This model is nice to troubleshoot with,
     because the stoich matrix is small.
     =#