From e7054358b51b988e87bca3bb1bf4b46d7be121ff Mon Sep 17 00:00:00 2001
From: Mirek Kratochvil <miroslav.kratochvil@uni.lu>
Date: Wed, 4 Aug 2021 10:30:40 +0200
Subject: [PATCH] remove unnecessary COBREXA and JuMP scope where possible
---
src/analysis/flux_balance_analysis.jl | 2 +-
src/analysis/modifications/optimizer.jl | 7 +++----
src/analysis/parsimonious_flux_balance_analysis.jl | 2 +-
src/base/constants.jl | 4 ++--
src/base/solver.jl | 7 +++----
5 files changed, 10 insertions(+), 12 deletions(-)
diff --git a/src/analysis/flux_balance_analysis.jl b/src/analysis/flux_balance_analysis.jl
index 0afd5b56c..82c4bdb72 100644
--- a/src/analysis/flux_balance_analysis.jl
+++ b/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
diff --git a/src/analysis/modifications/optimizer.jl b/src/analysis/modifications/optimizer.jl
index 556d5d5fd..287102cf9 100644
--- a/src/analysis/modifications/optimizer.jl
+++ b/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
"""
diff --git a/src/analysis/parsimonious_flux_balance_analysis.jl b/src/analysis/parsimonious_flux_balance_analysis.jl
index 6809949d6..01e7337f1 100644
--- a/src/analysis/parsimonious_flux_balance_analysis.jl
+++ b/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
diff --git a/src/base/constants.jl b/src/base/constants.jl
index 4334734e0..07fb78beb 100644
--- a/src/base/constants.jl
+++ b/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
diff --git a/src/base/solver.jl b/src/base/solver.jl
index 6bc725ac6..751396c04 100644
--- a/src/base/solver.jl
+++ b/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
"""
--
GitLab