From 8001a5fcfed44ce65d43984e0bb7b35160d0dfaa Mon Sep 17 00:00:00 2001
From: Mirek Kratochvil <miroslav.kratochvil@uni.lu>
Date: Tue, 30 Jan 2024 13:59:35 +0100
Subject: [PATCH] convert FBA to frontend

---
 docs/src/examples/02-flux-balance-analysis.jl |  2 +-
 docs/src/examples/02a-optimizer-parameters.jl |  4 ++--
 docs/src/examples/02b-model-modifications.jl  |  4 ++--
 src/analysis/frontend.jl                      |  6 +++---
 src/frontend/balance.jl                       | 15 ++++++---------
 5 files changed, 14 insertions(+), 17 deletions(-)

diff --git a/docs/src/examples/02-flux-balance-analysis.jl b/docs/src/examples/02-flux-balance-analysis.jl
index 7527c869..a30a51fb 100644
--- a/docs/src/examples/02-flux-balance-analysis.jl
+++ b/docs/src/examples/02-flux-balance-analysis.jl
@@ -43,7 +43,7 @@ model = load_model("e_coli_core.json")
 # is captured in the default behavior of function
 # [`flux_balance_analysis`](@ref):
 
-solution = flux_balance_analysis(model, GLPK.Optimizer)
+solution = flux_balance_analysis(model, optimizer = GLPK.Optimizer)
 
 @test isapprox(solution.objective, 0.8739, atol = TEST_TOLERANCE) #src
 
diff --git a/docs/src/examples/02a-optimizer-parameters.jl b/docs/src/examples/02a-optimizer-parameters.jl
index 0bc355c9..f5d27f56 100644
--- a/docs/src/examples/02a-optimizer-parameters.jl
+++ b/docs/src/examples/02a-optimizer-parameters.jl
@@ -46,7 +46,7 @@ model = load_model("e_coli_core.json")
 # limit for IPM algorithm may now look as follows:
 solution = flux_balance_analysis(
     model,
-    Tulip.Optimizer;
+    optimizer = Tulip.Optimizer,
     settings = [silence, set_optimizer_attribute("IPM_IterationsLimit", 1000)],
 )
 
@@ -59,7 +59,7 @@ solution = flux_balance_analysis(
 
 solution = flux_balance_analysis(
     model,
-    Tulip.Optimizer;
+    optimizer = Tulip.Optimizer,
     settings = [set_optimizer_attribute("IPM_IterationsLimit", 2)],
 )
 
diff --git a/docs/src/examples/02b-model-modifications.jl b/docs/src/examples/02b-model-modifications.jl
index cb281a9b..0ff693cc 100644
--- a/docs/src/examples/02b-model-modifications.jl
+++ b/docs/src/examples/02b-model-modifications.jl
@@ -78,7 +78,7 @@ model.reactions["CS"].stoichiometry
 
 import GLPK
 
-base_solution = flux_balance_analysis(model, GLPK.Optimizer)
+base_solution = flux_balance_analysis(model, optimizer = GLPK.Optimizer)
 base_solution.objective
 
 # Now, for example, we can limit the intake of glucose by the model:
@@ -91,7 +91,7 @@ model.reactions["EX_glc__D_e"].lower_bound = -5.0
 
 # ...and solve the modified model:
 #
-low_glucose_solution = flux_balance_analysis(model, GLPK.Optimizer)
+low_glucose_solution = flux_balance_analysis(model, optimizer = GLPK.Optimizer)
 low_glucose_solution.objective
 
 @test isapprox(low_glucose_solution.objective, 0.41559777, atol = TEST_TOLERANCE) #src
diff --git a/src/analysis/frontend.jl b/src/analysis/frontend.jl
index 6e051cdc..ff99e41c 100644
--- a/src/analysis/frontend.jl
+++ b/src/analysis/frontend.jl
@@ -24,9 +24,9 @@ front-end analysis function.
 function frontend_optimized_values(
     builder,
     args...;
-    objective = identity,
+    objective,
     output = identity,
-    sense,
+    sense = Maximal,
     optimizer,
     settings = [],
     kwargs...,
@@ -39,8 +39,8 @@ function frontend_optimized_values(
         objective = objective(constraints),
         output = output(constraints),
         sense,
-        settings,
         optimizer,
+        settings,
     )
 end
 
diff --git a/src/frontend/balance.jl b/src/frontend/balance.jl
index 0f52bff6..1c43ecee 100644
--- a/src/frontend/balance.jl
+++ b/src/frontend/balance.jl
@@ -24,14 +24,11 @@ Most arguments are forwarded to [`optimized_values`](@ref).
 Returns a tree with the optimization solution of the same shape as
 given by [`flux_balance_constraints`](@ref).
 """
-function flux_balance_analysis(model::A.AbstractFBCModel, optimizer; kwargs...)
-    constraints = flux_balance_constraints(model)
-    optimized_values(
-        constraints;
-        objective = constraints.objective.value,
-        optimizer,
-        kwargs...,
-    )
-end
+flux_balance_analysis(model::A.AbstractFBCModel; kwargs...) = frontend_optimized_values(
+    flux_balance_constraints,
+    model;
+    objective = x -> x.objective.value,
+    kwargs...,
+)
 
 export flux_balance_analysis