remove unnecessary COBREXA and JuMP scope where possible

src/analysis/flux_balance_analysis.jl

@@ -80,6 +80,6 @@ function flux_balance_analysis(
         mod(model, opt_model)
     end
 
-    COBREXA.JuMP.optimize!(opt_model)
+    optimize!(opt_model)
     return opt_model
 end

src/analysis/modifications/optimizer.jl

@@ -9,7 +9,7 @@ If you want to change the objective and sense at the same time, use
 [`change_objective`](@ref) instead to do both at once.
 """
 function change_sense(objective_sense)
-    (model, opt_model) -> COBREXA.JuMP.set_objective_sense(opt_model, objective_sense)
+    (model, opt_model) -> set_objective_sense(opt_model, objective_sense)
 end
 
 """
@@ -22,7 +22,7 @@ problems that may require different optimizers for different parts, such as the
 [`parsimonious_flux_balance_analysis`](@ref).
 """
 function change_optimizer(optimizer)
-    (model, opt_model) -> COBREXA.JuMP.set_optimizer(opt_model, optimizer)
+    (model, opt_model) -> set_optimizer(opt_model, optimizer)
 end
 
 """
@@ -33,8 +33,7 @@ to the JuMP documentation and the documentation of the specific optimizer for
 usable keys and values.
 """
 function change_optimizer_attribute(attribute_key, value)
-    (model, opt_model) ->
-        COBREXA.JuMP.set_optimizer_attribute(opt_model, attribute_key, value)
+    (model, opt_model) -> set_optimizer_attribute(opt_model, attribute_key, value)
 end
 
 """

src/analysis/parsimonious_flux_balance_analysis.jl

@@ -65,7 +65,7 @@ function parsimonious_flux_balance_analysis(
 
     # get the objective
     Z = objective_value(opt_model)
-    original_objective = COBREXA.JuMP.objective_function(opt_model)
+    original_objective = objective_function(opt_model)
 
     # prepare the model for pFBA
     for mod in qp_modifications

src/base/constants.jl

@@ -56,5 +56,5 @@ const _constants = (
     ),
 )
 
-const MAX_SENSE = COBREXA.MOI.MAX_SENSE
-const MIN_SENSE = COBREXA.MOI.MIN_SENSE
+const MAX_SENSE = MOI.MAX_SENSE
+const MIN_SENSE = MOI.MIN_SENSE

src/base/solver.jl

@@ -16,7 +16,7 @@ function make_optimization_model(model::MetabolicModel, optimizer; sense = MOI.M
     m, n = size(stoichiometry(model))
     xl, xu = bounds(model)
 
-    optimization_model = COBREXA.JuMP.Model(optimizer)
+    optimization_model = Model(optimizer)
     @variable(optimization_model, x[i = 1:n])
     @objective(optimization_model, sense, objective(model)' * x)
     @constraint(optimization_model, mb, stoichiometry(model) * x .== balance(model)) # mass balance
@@ -42,7 +42,7 @@ Use JuMP to solve an instance of CoreModel
 """
 function optimize_model(model::MetabolicModel, optimizer; sense = MOI.MIN_SENSE)
     optimization_model = make_optimization_model(model, optimizer; sense = sense)
-    COBREXA.JuMP.optimize!(optimization_model)
+    optimize!(optimization_model)
     return optimization_model
 end
 
@@ -55,8 +55,7 @@ optimal).  Return `false` if any other termination status is reached.
 Termination status is defined in the documentation of `JuMP`.
 """
 function is_solved(optmodel)
-    COBREXA.JuMP.termination_status(optmodel) in [MOI.OPTIMAL, MOI.LOCALLY_SOLVED] ? true :
-    false
+    termination_status(optmodel) in [MOI.OPTIMAL, MOI.LOCALLY_SOLVED] ? true : false
 end
 
 """