start cleaning the variables

Project.toml

@@ -20,7 +20,7 @@ StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 AbstractFBCModels = "0.2.2"
 Aqua = "0.7"
 Clarabel = "0.6"
-ConstraintTrees = "0.8"
+ConstraintTrees = "0.9"
 DistributedData = "0.2"
 DocStringExtensions = "0.8, 0.9"
 Downloads = "1"

docs/src/examples/03-parsimonious-flux-balance.jl

@@ -39,8 +39,7 @@ model = load_model("e_coli_core.json") # load the model
 
 # Use the convenience function to run standard pFBA on
 
-vt =
-    parsimonious_flux_balance_analysis(model, Clarabel.Optimizer; settings = [silence])
+vt = parsimonious_flux_balance_analysis(model, Clarabel.Optimizer; settings = [silence])
 
 # Or use the piping functionality
 

src/COBREXA.jl

@@ -58,6 +58,7 @@ include("builders/loopless.jl")
 include("builders/objectives.jl")
 include("builders/thermodynamic.jl")
 include("builders/unsigned.jl")
+include("builders/variables.jl")
 
 # simplified front-ends for the above
 include("frontend/balance.jl")

src/builders/unsigned.jl

@@ -22,8 +22,7 @@ Shortcut for allocation non-negative ("unsigned") variables. The argument
 """
 unsigned_variables(; keys) = C.variables(; keys, bounds = C.Between(0.0, Inf))
 
-export unsigned_variables
-
+export unsigned_variables # TODO kill
 
 """
 $(TYPEDSIGNATURES)
@@ -62,11 +61,26 @@ sign_split_constraints(;
         bound = C.EqualTo(0.0),
     ) for (k, s) in signed
 )
-#TODO the example above might as well go to docs
+#TODO the example above needs to go to docs
+# TODO this is a prime treezip candidate
 
 export sign_split_constraints
 
+positive_bound_contribution(b::C.EqualTo) = b.equal_to >= 0 ? b : C.EqualTo(0.0)
+positive_bound_contribution(b::C.Between) =
+    b.lower >= 0 && b.upper >= 0 ? b :
+    b.lower <= 0 && b.upper <= 0 ? C.EqualTo(0) :
+    C.Between(max(0, b.lower), max(0, b.upper))
+# TODO binary doesn't really fit here but it would be great if it could.
+
+unsigned_positive_contribution_variables(cs::C.ConstraintTree) =
+    variables_for(c -> positive_bound_contribution(c.bound), cs)
+
+unsigned_negative_contribution_variables(cs::C.ConstraintTree) =
+    variables_for(c -> positive_bound_contribution(c.bound), cs)
+
 # TODO: docs, doesn't apply to fluxes only
+# TODO replace by the above
 function fluxes_in_direction(fluxes::C.ConstraintTree, direction = :forward)
     keys = Symbol[]
     for (id, flux) in fluxes

src/builders/variables.jl

@@ -0,0 +1,8 @@
+
+variables_for(makebound, cs::C.ConstraintTree) =
+    let var_idx = 0
+        C.tree_map(cs, C.Constraint) do c
+            var_idx += 1
+            C.variable(idx = var_idx, bound = makebound(c))
+        end
+    end

src/frontend/mmdf.jl

@@ -109,12 +109,7 @@ function max_min_driving_force_analysis(
         )
 
 
-    optimized_constraints(
-        m;
-        objective = m.max_min_driving_force.value,
-        optimizer,
-        settings,
-    )
+    optimized_constraints(m; objective = m.max_min_driving_force.value, optimizer, settings)
 end
 
 export max_min_driving_force_analysis