Fix docstrings and simplify function arguments

docs/src/notebooks/7_community_model.jl

@@ -49,7 +49,6 @@ model_names = ["cytbd_ko", "atps4r_ko"]
 community_model = join_with_exchanges(
     [cytbd_knockout_model, atps4r_knockout_model],
     ex_rxn_mets;
-    add_biomass_objective = true,
     biomass_ids = ["BIOMASS_Ecoli_core_w_GAM", "BIOMASS_Ecoli_core_w_GAM"],
     model_names = model_names,
 )

src/reconstruction/community.jl

@@ -175,7 +175,6 @@ end
 """
     join_with_exchanges(models::Vector{M},
         exchange_rxn_mets::Dict{String, String};
-        add_biomass_objective=false,
         biomass_ids::Vector{String},
         model_names=String[]
     )
@@ -190,12 +189,12 @@ bounds of the environmental variables are all set to zero. Thus, to run a simula
 need to constrain them appropriately. All the other bounds are inherited from the models
 used to construct the community model.
 
-If `add_biomass_objective` is true then `biomass_ids` needs to be supplied as well. This
-creates a model with an extra reaction added to the end of the stoichiometric matrix (last
-column) that can be assigned as the objective reaction. It also creates biomass
-"metabolites" that can be used in this objective reaction. Note, this reaction is
-unspecified, further action needs to be taken to specify it, e.g. assign weights to the last
-column of the stoichiometric matrix in the rows corresponding to the biomass metabolites.
+If `biomass_ids` is supplied, then a community model is returned that has an extra reaction
+added to the end of the stoichiometric matrix (last column) that can be assigned as the
+objective reaction. It also creates biomass "metabolites" that can be used in this objective
+reaction. Note, this reaction is unspecified, further action needs to be taken to specify
+it, e.g. assign weights to the last column of the stoichiometric matrix in the rows
+corresponding to the biomass metabolites.
 
 To further clarify how this `join` works. Suppose you have 2 organisms with stoichiometric
 matrices S₁ and S₂ and you want to link them with `exchange_rxn_mets = Dict(er₁ => em₁, er₂
@@ -215,7 +214,7 @@ S   =   em₂|                             |
 ```
 The exchange reactions in each model get linked to environmental metabolites, `emᵢ`, and
 these get linked to environmental exchanges, `erᵢ`. These `erᵢ` behave like normal single
-organism exchange reactions. When `add_biomass_objective` is true each model's biomass
+organism exchange reactions. When `biomass_ids` are supplied, each model's biomass
 becomes a pseudo-metabolite (`bmᵢ`). These can be weighted in column `b`, called the
 `community_biomass` reaction in the community model, if desired. Refer to the tutorial if
 this is unclear.
@@ -234,7 +233,6 @@ biomass_ids = ["BIOMASS_Ecoli_core_w_GAM", "BIOMASS_Ecoli_core_w_GAM"]
 community = join_with_exchanges(
     [m1, m2],
     exchange_rxn_mets;
-    add_biomass_objective = true,
     biomass_ids = biomass_ids,
 )
 ```
@@ -242,23 +240,13 @@ community = join_with_exchanges(
 function join_with_exchanges(
     models::Vector{M},
     exchange_rxn_mets::Dict{String,String};
-    add_biomass_objective = true,
     biomass_ids = String[],
     model_names = String[],
 )::CoreModel where {M<:MetabolicModel}
 
     exchange_rxn_ids = keys(exchange_rxn_mets)
     exchange_met_ids = values(exchange_rxn_mets)
-    if add_biomass_objective && isempty(biomass_ids)
-        throw(
-            DomainError(
-                "biomass_ids",
-                "Please add supply the string ids of the biomass functions when
-                `add_biomass_objective` is true.",
-            ),
-        )
-    end
-
+    add_biomass_objective = isempty(biomass_ids) ? false : true
     if length(exchange_met_ids) != length(exchange_rxn_ids)
         throw(
             DomainError(

test/reconstruction/community.jl

@@ -3,7 +3,7 @@
     m2 = test_toyModel()
     ex_rxn_mets = Dict("EX_m1(e)" => "m1[e]", "EX_m3(e)" => "m3[e]")
 
-    c1 = join_with_exchanges([m1, m2], ex_rxn_mets; add_biomass_objective = false)
+    c1 = join_with_exchanges([m1, m2], ex_rxn_mets)
 
     # test of stoichs are the same
     @test all(c1.S[1:6, 1:7] .== c1.S[7:12, 8:14])
@@ -24,12 +24,7 @@
     @test all(lb[1:14] .== -ub[1:14] .== -1000)
     @test all(lb[15:16] .== -ub[15:16] .== 0.0)
 
-    c2 = join_with_exchanges(
-        [m1, m2],
-        ex_rxn_mets;
-        add_biomass_objective = true,
-        biomass_ids = ["biomass1", "biomass1"],
-    )
+    c2 = join_with_exchanges([m1, m2], ex_rxn_mets; biomass_ids = ["biomass1", "biomass1"])
     # test if same base stoich matrix
     @test all(c2.S[1:14, 1:16] .== c1.S)
     # test if biomass reaction and metabolites are added correctly
@@ -58,12 +53,7 @@ end
 
     biomass_ids = ["BIOMASS_Ecoli_core_w_GAM", "BIOMASS_Ecoli_core_w_GAM"]
 
-    community = join_with_exchanges(
-        [m1, m2],
-        exchange_rxn_mets;
-        add_biomass_objective = true,
-        biomass_ids = biomass_ids,
-    )
+    community = join_with_exchanges([m1, m2], exchange_rxn_mets; biomass_ids = biomass_ids)
 
     env_ex_inds = indexin(keys(exchange_rxn_mets), reactions(community))
     m2_ex_inds = indexin(keys(exchange_rxn_mets), reactions(m2))
@@ -96,12 +86,7 @@ end
 
     biomass_ids = ["BIOMASS_Ecoli_core_w_GAM", "BIOMASS_Ec_iJO1366_core_53p95M"]
 
-    community = join_with_exchanges(
-        [m1, m2],
-        exchange_rxn_mets;
-        add_biomass_objective = true,
-        biomass_ids = biomass_ids,
-    )
+    community = join_with_exchanges([m1, m2], exchange_rxn_mets; biomass_ids = biomass_ids)
 
     env_ex_inds = indexin(keys(exchange_rxn_mets), reactions(community))
     m2_ex_inds = indexin(keys(exchange_rxn_mets), reactions(m2))
@@ -148,12 +133,7 @@ end
 
     biomass_ids = ["BIOMASS_Ecoli_core_w_GAM"]
 
-    community = join_with_exchanges(
-        [m1],
-        exchange_rxn_mets;
-        add_biomass_objective = true,
-        biomass_ids = biomass_ids,
-    )
+    community = join_with_exchanges([m1], exchange_rxn_mets; biomass_ids = biomass_ids)
 
     env_ex_inds = indexin(keys(exchange_rxn_mets), reactions(community))
     m1_ex_inds = indexin(keys(exchange_rxn_mets), reactions(m1))