Set correct flux bounds

cobra/core/reaction.py

@@ -25,7 +25,7 @@
 from cobra.util.util import format_long_string
 
 
-CONFIGURATION = Configuration()
+config = Configuration()
 
 # precompiled regular expressions
 # Matches and/or in a gene reaction rule
@@ -88,9 +88,9 @@ def __init__(self, id=None, name='', subsystem='', lower_bound=0.0,
 
         # from cameo ...
         self._lower_bound = lower_bound if lower_bound is not None else \
-            CONFIGURATION.lower_bound
+            config.lower_bound
         self._upper_bound = upper_bound if upper_bound is not None else \
-            CONFIGURATION.upper_bound
+            config.upper_bound
 
     def _set_id_with_model(self, value):
         if value in self.model.reactions:
@@ -1050,23 +1050,20 @@ def build_reaction_from_string(self, reaction_str, verbose=True,
         # reversible case
         arrow_match = reversible_arrow_finder.search(reaction_str)
         if arrow_match is not None:
-            self.lower_bound = -1000
-            self.upper_bound = 1000
+            self.bounds = config.lower_bound, config.upper_bound
         else:  # irreversible
             # try forward
             arrow_match = forward_arrow_finder.search(reaction_str)
             if arrow_match is not None:
-                self.upper_bound = 1000
-                self.lower_bound = 0
+                self.bounds = 0, config.upper_bound
             else:
                 # must be reverse
                 arrow_match = reverse_arrow_finder.search(reaction_str)
                 if arrow_match is None:
                     raise ValueError("no suitable arrow found in '%s'" %
                                      reaction_str)
                 else:
-                    self.upper_bound = 0
-                    self.lower_bound = -1000
+                    self.bounds = config.lower_bound, 0
         reactant_str = reaction_str[:arrow_match.start()].strip()
         product_str = reaction_str[arrow_match.end():].strip()
 

cobra/test/test_core/test_core_reaction.py

@@ -10,9 +10,10 @@
 import pytest
 import six
 
-from cobra.core import Metabolite, Model, Reaction
+from cobra.core import Configuration, Metabolite, Model, Reaction
 
 
+config = Configuration()
 stable_optlang = ["glpk", "cplex", "gurobi"]
 
 
@@ -269,6 +270,18 @@ def test_build_from_string(model):
         assert model.metabolites.foo
         assert len(model.metabolites) == m
 
+    with model:
+        old_bounds = config.bounds
+        assert old_bounds == (-1000, 1000)
+        config.bounds = (-5, 5)
+        pgi.build_reaction_from_string("g6p_c <--> f6p_c + new",
+                                       verbose=False)
+        assert pgi.bounds == (-5, 5)
+        config.bounds = old_bounds
+        pgi.build_reaction_from_string("g6p_c --> f6p_c + new",
+                                       verbose=False)
+        assert pgi.bounds == (0, 1000)
+
 
 def test_bounds_setter(model):
     rxn = model.reactions.get_by_id("PGI")