From 21a2d7c27194c4025e364802a0b525010a403d49 Mon Sep 17 00:00:00 2001
From: Mirek Kratochvil <exa.exa@gmail.com>
Date: Thu, 17 Jun 2021 15:29:27 +0200
Subject: [PATCH] format 341 + add a tiny simplification
---
src/analysis/modifications/optimizer.jl | 6 +++--
src/reconstruction/community.jl | 3 +--
test/analysis/flux_balance_analysis.jl | 32 ++++++++++---------------
3 files changed, 17 insertions(+), 24 deletions(-)
diff --git a/src/analysis/modifications/optimizer.jl b/src/analysis/modifications/optimizer.jl
index 06ef5895e..7c27b4aa0 100644
--- a/src/analysis/modifications/optimizer.jl
+++ b/src/analysis/modifications/optimizer.jl
@@ -83,13 +83,15 @@ function change_objective(
# Construct objective_indices array
if typeof(new_objective) == String
- objective_indices = [first(indexin([new_objective], reactions(model)))]
+ objective_indices = indexin([new_objective], reactions(model))
else
objective_indices =
[first(indexin([rxnid], reactions(model))) for rxnid in new_objective]
end
- any(isnothing.(objective_indices)) && throw(DomainError(new_objective, "No matching reaction found for one or more ids."))
+ any(isnothing.(objective_indices)) && throw(
+ DomainError(new_objective, "No matching reaction found for one or more ids."),
+ )
# Initialize weights
opt_weights = spzeros(n_reactions(model))
diff --git a/src/reconstruction/community.jl b/src/reconstruction/community.jl
index 8e17abbf8..48830fb11 100644
--- a/src/reconstruction/community.jl
+++ b/src/reconstruction/community.jl
@@ -283,8 +283,7 @@ function join_with_exchanges(
nnz_total =
sum(length(first(nnz)) for nnz in nnzs) +
length(models) * length(exchange_rxn_ids) +
- length(exchange_met_ids) +
- nnz_add
+ length(exchange_met_ids) + nnz_add
n_reactions_metabolic = sum(reaction_lengths)
n_reactions_total = n_reactions_metabolic + length(exchange_rxn_ids) + column_add
n_metabolites_metabolic = sum(metabolite_lengths)
diff --git a/test/analysis/flux_balance_analysis.jl b/test/analysis/flux_balance_analysis.jl
index 33a494ca8..3ae86d196 100644
--- a/test/analysis/flux_balance_analysis.jl
+++ b/test/analysis/flux_balance_analysis.jl
@@ -69,28 +69,20 @@ end
)
@test_throws DomainError flux_balance_analysis_dict(
- model,
- Tulip.Optimizer;
- modifications = [
- change_constraint("gbbrsh", -12, -12)
- ],
- )
+ model,
+ Tulip.Optimizer;
+ modifications = [change_constraint("gbbrsh", -12, -12)],
+ )
@test_throws DomainError flux_balance_analysis_dict(
- model,
- Tulip.Optimizer;
- modifications = [
- change_objective("gbbrsh")
- ],
- )
+ model,
+ Tulip.Optimizer;
+ modifications = [change_objective("gbbrsh")],
+ )
@test_throws DomainError flux_balance_analysis_dict(
- model,
- Tulip.Optimizer;
- modifications = [
- change_objective(
- ["BIOMASS_Ecoli_core_w_GAM"; "gbbrsh"]
- )
- ],
- )
+ model,
+ Tulip.Optimizer;
+ modifications = [change_objective(["BIOMASS_Ecoli_core_w_GAM"; "gbbrsh"])],
+ )
end
@testset "Flux balance analysis with CoreModelCoupled" begin
--
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