Merge pull request #54 from COBREXA/mk-remove-bounds

implement bounds removal (helpful for sign splitting)

Project.toml

@@ -1,7 +1,7 @@
 name = "COBREXA"
 uuid = "babc4406-5200-4a30-9033-bf5ae714c842"
 authors = ["The developers of COBREXA.jl"]
-version = "2.0.2"
+version = "2.1.0"
 
 [deps]
 AbstractFBCModels = "5a4f3dfa-1789-40f8-8221-69268c29937c"

docs/src/examples/04-community-models.jl

@@ -121,15 +121,17 @@ flux_balance_constraints(ecoli, interface = :boundary).interface
 # (such as `EX_` for exchanges).
 
 # Even if all of these methods fail, a suitable interface yourself can be
-# produced manually:
+# produced manually. (Additionally, we can do useful stuff, such as removing
+# the unnecessary bounds from the exchange descriptions.)
 custom_model = flux_balance_constraints(ecoli)
-custom_model *=
+custom_model *= remove_bounds(
     :interface^C.ConstraintTree(
         :biomass => custom_model.fluxes.BIOMASS_Ecoli_core_w_GAM,
         :exchanges => C.ConstraintTree(
             k => v for (k, v) in custom_model.fluxes if startswith(string(k), "EX_")
         ),
-    )
+    ),
+)
 custom_model.interface.exchanges
 
 # ## Connecting the community constraints manually

src/misc/bounds.jl

@@ -39,3 +39,18 @@ relative_tolerance_bound(tolerance) = x -> begin
 end
 
 export relative_tolerance_bound
+
+"""
+$(TYPEDSIGNATURES)
+
+Make a copy of a constraint tree with all bounds removed. This is helpful when
+creating large trees only for for value representation purposes, which should
+not directly constraint anything (and thus should not put additional stress on
+the constraint solver).
+"""
+remove_bounds(cs::C.ConstraintTree) =
+    C.map(cs) do c
+        C.Constraint(c.value, nothing)
+    end
+
+export remove_bounds