fixing add reactions

cameo/flux_analysis/simulation.py

@@ -202,7 +202,7 @@ def lmoma(model, reference=None, cache={}, volatile=True, *args, **kwargs):
             solution = model.solve()
             return solution
         except SolveError as e:
-            print "lmoma could not determine an optimal solution for objective %s" % model.objective
+            #print "lmoma could not determine an optimal solution for objective %s" % model.objective
             raise e
 
     finally:

cameo/solver_based_model.py

@@ -509,11 +509,11 @@ def add_reactions(self, reaction_list):
             if reaction.reversibility and self._reversible_encoding == "split":
                 reaction_variable = self.solver.interface.Variable(reaction.id, lb=0, ub=reaction._upper_bound)
                 aux_var = self.solver.interface.Variable(reaction._get_reverse_id(), lb=0, ub=-reaction._lower_bound)
-                self.solver.add(aux_var)
+                self.solver._add_variable(aux_var)
             else:
                 reaction_variable = self.solver.interface.Variable(reaction.id, lb=reaction._lower_bound,
                                                                    ub=reaction._upper_bound)
-            self.solver.add(reaction_variable)
+            self.solver._add_variable(reaction_variable)
 
             for metabolite, coeff in reaction.metabolites.iteritems():
                 if metabolite.id in constr_terms:
@@ -528,8 +528,7 @@ def add_reactions(self, reaction_list):
             try:
                 self.solver.constraints[met_id] += expr
             except KeyError:
-                super(SolverBasedModel, self).add_metabolites([metabolites[met_id]])
-                self.solver.add(self.solver.interface.Constraint(expr, name=met_id, lb=0, ub=0))
+                self.solver._add_constraint(self.solver.interface.Constraint(expr, name=met_id, lb=0, ub=0))
 
     def remove_reactions(self, the_reactions):
         for reaction in the_reactions:

cameo/strain_design/heuristic/__init__.py

@@ -163,11 +163,11 @@ def heuristic_method(self, heuristic_method):
     def _evaluator(self):
         raise NotImplementedError
 
-    def run(self, view=config.default_view, **kwargs):
+    def run(self, view=config.default_view, maximize=True, **kwargs):
         t = time.time()
         print time.strftime("Starting optimization at %a, %d %b %Y %H:%M:%S", time.localtime(t))
         res = self.heuristic_method.evolve(generator=self._generator,
-                                           maximize=True,
+                                           maximize=maximize,
                                            view=view,
                                            evaluator=self._evaluator,
                                            **kwargs)

tests/test_solver_based_model.py

@@ -5,6 +5,7 @@
 import unittest
 
 import os
+from cobra import Metabolite
 from optlang import Objective
 from cameo import load_model
 from cameo.exceptions import UndefinedSolution
@@ -182,7 +183,6 @@ def test_all_objects_point_to_all_other_correct_objects_after_copy(self):
                     self.assertEqual(reaction2.get_model(), model)
                     self.assertEqual(reaction2, model.reactions.get_by_id(reaction2.id))
 
-
     def test_remove_reactions(self):
         reactions_to_remove = self.model.reactions[10:30]
         self.assertTrue(all([reaction.get_model() is self.model for reaction in reactions_to_remove]))
@@ -203,6 +203,12 @@ def test_add_demand(self):
                 self.model.solver.variables["DemandReaction_" + metabolite.id] in self.model.solver.constraints[
                     metabolite.id].expression)
 
+    def test_add_demand_for_non_existing_metabolite(self):
+        metabolite = Metabolite(id="a_metabolite")
+        self.model.add_demand(metabolite)
+        self.assertTrue(self.model.solver.variables["DM_" + metabolite.id]
+                        in self.model.solver.constraints[metabolite.id].expression)
+
     def test_objective(self):
         obj = self.model.objective
         self.assertEqual(