cleanup start

src/COBREXA.jl

@@ -48,24 +48,25 @@ include("io.jl")
 include("solver.jl")
 
 # these functions build or extend constrainttrees of metabolic models
-include("builders/core.jl")
-include("builders/genes.jl")
-include("builders/objectives.jl")
+include("builders/communities.jl")
 include("builders/enzymes.jl")
-include("builders/thermodynamic.jl")
+include("builders/fbc.jl")
+include("builders/knockouts.jl")
 include("builders/loopless.jl")
-include("builders/communities.jl")
+include("builders/objectives.jl")
+include("builders/thermodynamic.jl")
+include("builders/unsigned.jl")
 
 # these are the one shot analysis functions
-include("frontend/flux_balance_analysis.jl")
-include("frontend/parsimonious_flux_balance.jl")
-include("frontend/minimization_of_metabolic_adjustment_analysis.jl")
 include("frontend/enzyme_constrained_flux_balance_analysis.jl")
+include("frontend/flux_balance_analysis.jl")
 include("frontend/loopless_flux_balance_analysis.jl")
 include("frontend/max_min_driving_force_analysis.jl")
+include("frontend/minimization_of_metabolic_adjustment_analysis.jl")
+include("frontend/parsimonious_flux_balance.jl")
 
-include("misc/modifications.jl")
 include("misc/bounds.jl")
+include("misc/modifications.jl")
 include("misc/utils.jl")
 
 end # module COBREXA

src/builders/fbc.jl

@@ -0,0 +1,47 @@
+
+# Copyright (c) 2021-2024, University of Luxembourg
+# Copyright (c) 2021-2024, Heinrich-Heine University Duesseldorf
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""
+$(TYPEDSIGNATURES)
+
+A constraint tree that models the content of the given instance of
+`AbstractFBCModel`.
+
+The constructed tree contains subtrees `fluxes` (with the reaction-defining
+"variables") and `flux_stoichiometry` (with the metabolite-balance-defining
+constraints), and a single constraint `objective` thad describes the objective
+function of the model.
+"""
+function fbc_model_constraints(model::A.AbstractFBCModel)
+    rxns = Symbol.(A.reactions(model))
+    mets = Symbol.(A.metabolites(model))
+    lbs, ubs = A.bounds(model)
+    stoi = A.stoichiometry(model)
+    bal = A.balance(model)
+    obj = A.objective(model)
+
+    #TODO: is sparse() required below?
+    return C.ConstraintTree(
+        :fluxes^C.variables(keys = rxns, bounds = zip(lbs, ubs)) *
+        :flux_stoichiometry^C.ConstraintTree(
+            met => C.Constraint(value = C.LinearValue(sparse(row)), bound = C.EqualTo(b))
+            for (met, row, b) in zip(mets, eachrow(stoi), bal)
+        ) *
+        :objective^C.Constraint(C.LinearValue(sparse(obj))),
+    )
+end
+
+export fbc_model_constraints

src/builders/core.jl → src/builders/unsigned.jl

@@ -17,38 +17,6 @@
 """
 $(TYPEDSIGNATURES)
 
-A constraint tree that models the content of the given instance of
-`AbstractFBCModel`.
-
-The constructed tree contains subtrees `fluxes` (with the reaction-defining
-"variables") and `flux_stoichiometry` (with the metabolite-balance-defining
-constraints), and a single constraint `objective` thad describes the objective
-function of the model.
-"""
-function fbc_model_constraints(model::A.AbstractFBCModel)
-    rxns = Symbol.(A.reactions(model))
-    mets = Symbol.(A.metabolites(model))
-    lbs, ubs = A.bounds(model)
-    stoi = A.stoichiometry(model)
-    bal = A.balance(model)
-    obj = A.objective(model)
-
-    #TODO: is sparse() required below?
-    return C.ConstraintTree(
-        :fluxes^C.variables(keys = rxns, bounds = zip(lbs, ubs)) *
-        :flux_stoichiometry^C.ConstraintTree(
-            met => C.Constraint(value = C.LinearValue(sparse(row)), bound = C.EqualTo(b))
-            for (met, row, b) in zip(mets, eachrow(stoi), bal)
-        ) *
-        :objective^C.Constraint(C.LinearValue(sparse(obj))),
-    )
-end
-
-export fbc_model_constraints
-
-"""
-$(TYPEDSIGNATURES)
-
 Shortcut for allocation non-negative ("unsigned") variables. The argument
 `keys` is forwarded to `ConstraintTrees.variables` as `keys`.
 """
@@ -97,6 +65,7 @@ sign_split_constraints(;
 
 export sign_split_constraints
 
+# TODO: docs, doesn't apply to fluxes only
 function fluxes_in_direction(fluxes::C.ConstraintTree, direction = :forward)
     keys = Symbol[]
     for (id, flux) in fluxes