Fixing and adding test for combine kwarg in reaction.add_metabolites

cobra/core/reaction.py

@@ -10,7 +10,7 @@
 from operator import attrgetter
 from warnings import warn
 
-from six import iteritems, string_types
+from six import iteritems, iterkeys, string_types
 from future.utils import raise_from, raise_with_traceback
 
 from cobra.exceptions import OptimizationError
@@ -799,10 +799,20 @@ def add_metabolites(self, metabolites_to_add, combine=True,
 
         context = get_context(self)
         if context and reversibly:
-            # Just subtract the metabolites that were added
-            context(partial(
-                self.subtract_metabolites, metabolites_to_add, combine=True,
-                reversibly=False))
+            if combine:
+                # Just subtract the metabolites that were added
+                context(partial(
+                    self.subtract_metabolites, metabolites_to_add,
+                    combine=True, reversibly=False))
+            else:
+                # Reset them with add_metabolites
+                mets_to_reset = {
+                    key: old_coefficients[model.metabolites.get_by_any(key)[0]]
+                    for key in iterkeys(metabolites_to_add)}
+
+                context(partial(
+                    self.add_metabolites, mets_to_reset,
+                    combine=False, reversibly=False))
 
     def subtract_metabolites(self, metabolites, combine=True, reversibly=True):
         """This function will 'subtract' metabolites from a reaction, which

cobra/test/test_model.py

@@ -142,6 +142,18 @@ def test_add_metabolite(self, model):
                    model.metabolites.get_by_id("g6p_c")] == -1
         assert model.metabolites.h_c not in reaction._metabolites
 
+        # Test combine=False
+        reaction = model.reactions.get_by_id("ATPM")
+        old_stoich = reaction._metabolites[
+            model.metabolites.get_by_id("h2o_c")]
+        with model:
+            reaction.add_metabolites({'h2o_c': 2.5}, combine=False)
+            assert reaction._metabolites[
+                model.metabolites.get_by_id("h2o_c")] == 2.5
+
+        assert reaction._metabolites[
+            model.metabolites.get_by_id("h2o_c")] == old_stoich
+
         # test adding to a new Reaction
         reaction = Reaction("test")
         assert len(reaction._metabolites) == 0