automatic formatting changes

src/reconstruction/community.jl

@@ -24,7 +24,7 @@ function Base.push!(
     species_name,
     has_biomass_objective;
     biomass_id = "",
-    ) where {M<:MetabolicModel}
+) where {M<:MetabolicModel}
 
     if has_biomass_objective && biomass_id == ""
         throw(

test/reconstruction/community.jl

@@ -12,16 +12,25 @@
     exchange_rxn_ids = filter(startswith("EX_"), boundary_rxn_ids)
     exchange_met_ids = filter(endswith("_e"), boundary_met_ids)
 
-    biomass_ids = ["BIOMASS_Ecoli_core_w_GAM","BIOMASS_Ecoli_core_w_GAM"]
-
-    community = COBREXA.join([m1, m2], exchange_rxn_ids, exchange_met_ids; add_biomass_objective=true, biomass_ids=biomass_ids)
+    biomass_ids = ["BIOMASS_Ecoli_core_w_GAM", "BIOMASS_Ecoli_core_w_GAM"]
+
+    community = COBREXA.join(
+        [m1, m2],
+        exchange_rxn_ids,
+        exchange_met_ids;
+        add_biomass_objective = true,
+        biomass_ids = biomass_ids,
+    )
 
     env_ex_inds = indexin(exchange_rxn_ids, reactions(community))
     m2_ex_inds = indexin(exchange_rxn_ids, reactions(m2))
     community.xl[env_ex_inds] .= m2.xl[m2_ex_inds]
     community.xu[env_ex_inds] .= m2.xu[m2_ex_inds]
 
-    biomass_metabolite_inds = indexin(["species_1_BIOMASS_Ecoli_core_w_GAM", "species_2_BIOMASS_Ecoli_core_w_GAM"], metabolites(community))
+    biomass_metabolite_inds = indexin(
+        ["species_1_BIOMASS_Ecoli_core_w_GAM", "species_2_BIOMASS_Ecoli_core_w_GAM"],
+        metabolites(community),
+    )
 
     community.S[biomass_metabolite_inds, end] .= -1.0
     community.c[end] = 1.0
@@ -30,7 +39,7 @@
 
     d = flux_balance_analysis_dict(community, Tulip.Optimizer)
     @test size(stoichiometry(community)) == (166, 211)
-    @test isapprox(d["community_biomass"], 0.41559777495618294, atol = TEST_TOLERANCE,)
+    @test isapprox(d["community_biomass"], 0.41559777495618294, atol = TEST_TOLERANCE)
 end
 
 @testset "Heterogenous model join" begin
@@ -54,7 +63,13 @@ end
 
     biomass_ids = ["BIOMASS_Ecoli_core_w_GAM", "BIOMASS_Ec_iJO1366_core_53p95M"]
 
-    community = COBREXA.join([m1, m2], exchange_rxn_ids, exchange_met_ids; add_biomass_objective=true, biomass_ids=biomass_ids)
+    community = COBREXA.join(
+        [m1, m2],
+        exchange_rxn_ids,
+        exchange_met_ids;
+        add_biomass_objective = true,
+        biomass_ids = biomass_ids,
+    )
 
     env_ex_inds = indexin(exchange_rxn_ids, reactions(community))
     m2_ex_inds = indexin(exchange_rxn_ids, reactions(m2))
@@ -63,21 +78,24 @@ end
     for (env_ex, m2_ex, m1_ex) in zip(env_ex_inds, m2_ex_inds, m1_ex_inds)
         m2lb = isnothing(m2_ex) ? 0.0 : m2.xl[m2_ex]
         m2ub = isnothing(m2_ex) ? 0.0 : m2.xu[m2_ex]
-        
+
         m1lb = isnothing(m1_ex) ? 0.0 : m1.xl[m1_ex]
         m1ub = isnothing(m1_ex) ? 0.0 : m1.xu[m1_ex]
-         
-        community.xl[env_ex] = m1lb + m2lb 
-        community.xu[env_ex] = m1ub + m2ub 
+
+        community.xl[env_ex] = m1lb + m2lb
+        community.xu[env_ex] = m1ub + m2ub
     end
 
-    biomass_metabolite_inds = indexin(["species_1_BIOMASS_Ecoli_core_w_GAM", "species_2_BIOMASS_Ec_iJO1366_core_53p95M"], metabolites(community))
-    
+    biomass_metabolite_inds = indexin(
+        ["species_1_BIOMASS_Ecoli_core_w_GAM", "species_2_BIOMASS_Ec_iJO1366_core_53p95M"],
+        metabolites(community),
+    )
+
     community.S[biomass_metabolite_inds, end] .= -1.0
     community.c[end] = 1.0
     community.xl[end] = 0.0
     community.xu[end] = 1000.0
 
     @test size(stoichiometry(community)) == (2203, 3003)
-    @test isapprox(d["community_biomass"], 0.8, atol = TEST_TOLERANCE,)
+    @test isapprox(d["community_biomass"], 0.8, atol = TEST_TOLERANCE)
 end