Switch numerical scaling to relative

corda/corda.py

@@ -16,8 +16,10 @@
 from collections import Counter
 import re
 from optlang.symbolics import Zero
+from optlang.interface import OPTIMAL
 
-UPPER = 1e6    # default upper bound
+UPPER = 1e6    # default internal bound for metabolic requirements
+SCALE = 1e3    # default bound scaling
 CI = 1.01      # cost increase for redundancy detection
 
 
@@ -115,9 +117,13 @@ def __init__(self, model, confidence, met_prod=None, n=np.inf,
         self.redundancies = {}
         for r in self.model.reactions:
             if r.lower_bound < -self.tol:
-                r.lower_bound = -UPPER
+                r.lower_bound *= SCALE
+            else:
+                r.lower_bound = 0
             if r.upper_bound > self.tol:
-                r.upper_bound = UPPER
+                r.upper_bound *= SCALE
+            else:
+                r.upper_bound = 0
             if r.id in confidence:
                 if confidence[r.id] not in [-1, 0, 1, 2, 3]:
                     raise ValueError("Not a valid confidence value!")
@@ -197,7 +203,6 @@ def associated(self, targets, conf=None, penalize_medium=True,
                 continue
             else:
                 va.lb = max(self.tflux, va.lb)
-                va.ub = UPPER
             has_new = True
             pen = penalties.copy()
             iteration = 0
@@ -269,8 +274,8 @@ def build(self):
             if self.conf[v.name] == 1 or self.conf[v.name] == 2:
                 self.model.objective.set_linear_coefficients({v: 1})
                 sol = self.model.solver.optimize()
-                if (sol == "optimal" and
-                        self.model.objective.value > self.tflux):
+                if (sol == OPTIMAL and
+                        self.model.solver.objective.value > self.tflux):
                         self.conf[v.name] = 3
             self.model.objective.set_linear_coefficients({v: 0})
 

tests/test_large.py

@@ -62,7 +62,7 @@ def test_build_works(self, large):
         assert len(include) > 3
         rec = opt.cobra_model("reconstruction")
         sol = rec.optimize()
-        assert sol.f > 1
+        assert sol.objective_value > 1
 
     @pytest.mark.parametrize("solver", solvers)
     def test_benchmark_large(self, large, benchmark, solver):

tests/test_util.py

@@ -31,19 +31,6 @@ def test_none(self):
 
 class TestMisc:
 
-    def test_remove_breaks(self):
-        model = Model("test model")
-        A = Metabolite("A")
-        r = Reaction("r")
-        r.add_metabolites({A: -1})
-        r.lower_bound = -1000
-        r.upper_bound = 1000
-        model.add_reaction(r)
-        convert_to_irreversible(model)
-        model.remove_reactions(["r"])
-        with pytest.raises(KeyError):
-            revert_to_reversible(model)
-
     def test_cemet(self):
         model = test_model()
         assert len(model.reactions) == 60