fix: allow multiple exchanges in summary (#718)

* fix: allow multiple exchanges in summary

* Correct a problem with multiple exchanges for one metabolite.
* Enhance printing by giving an option to display names.
* Allow passing in of an FVA solution.
* Many internal changes related to data frame handling.

cobra/core/metabolite.py

@@ -207,38 +207,40 @@ def remove_from_model(self, destructive=False):
         """
         self._model.remove_metabolites(self, destructive)
 
-    def summary(self, solution=None, threshold=0.01, fva=False,
+    def summary(self, solution=None, threshold=0.01, fva=None, names=False,
                 floatfmt='.3g'):
-        """Print a summary of the reactions which produce and consume this
-        metabolite.
+        """
+        Print a summary of the production and consumption fluxes.
 
         This method requires the model for which this metabolite is a part
         to be solved.
 
         Parameters
         ----------
-        solution : cobra.core.Solution
+        solution : cobra.Solution, optional
             A previously solved model solution to use for generating the
             summary. If none provided (default), the summary method will
             resolve the model. Note that the solution object must match the
             model, i.e., changes to the model such as changed bounds,
             added or removed reactions are not taken into account by this
             method.
-
-        threshold : float
-            a value below which to ignore reaction fluxes
-
-        fva : float (0->1), or None
+        threshold : float, optional
+            Threshold below which fluxes are not reported.
+        fva : pandas.DataFrame, float or None, optional
             Whether or not to include flux variability analysis in the output.
-            If given, fva should be a float between 0 and 1, representing the
+            If given, fva should either be a previous FVA solution matching
+            the model or a float between 0 and 1 representing the
             fraction of the optimum objective to be searched.
+        names : bool, optional
+            Emit reaction and metabolite names rather than identifiers (default
+            False).
+        floatfmt : string, optional
+            Format string for floats (default '.3g').
 
-        floatfmt : string
-            format method for floats, passed to tabulate. Default is '.3g'.
         """
         from cobra.flux_analysis.summary import metabolite_summary
         return metabolite_summary(self, solution=solution, threshold=threshold,
-                                  fva=fva, floatfmt=floatfmt)
+                                  fva=fva, names=names, floatfmt=floatfmt)
 
     def _repr_html_(self):
         return """

cobra/core/model.py

@@ -934,34 +934,37 @@ def objective_direction(self, value):
         else:
             raise ValueError("Unknown objective direction '{}'.".format(value))
 
-    def summary(self, solution=None, threshold=1E-8, fva=None, floatfmt='.3g'):
-        """Print a summary of the input and output fluxes of the model. This
-        method requires the model to have been previously solved.
+    def summary(self, solution=None, threshold=1E-06, fva=None, names=False,
+                floatfmt='.3g'):
+        """
+        Print a summary of the input and output fluxes of the model.
 
         Parameters
         ----------
-        solution: cobra.core.Solution
+        solution: cobra.Solution, optional
             A previously solved model solution to use for generating the
             summary. If none provided (default), the summary method will
             resolve the model. Note that the solution object must match the
             model, i.e., changes to the model such as changed bounds,
             added or removed reactions are not taken into account by this
             method.
-
-        threshold : float
-            tolerance for determining if a flux is zero (not printed)
-
-        fva : int or None
-            Whether or not to calculate and report flux variability in the
-            output summary
-
-        floatfmt : string
-            format method for floats, passed to tabulate. Default is '.3g'.
+        threshold : float, optional
+            Threshold below which fluxes are not reported.
+        fva : pandas.DataFrame, float or None, optional
+            Whether or not to include flux variability analysis in the output.
+            If given, fva should either be a previous FVA solution matching
+            the model or a float between 0 and 1 representing the
+            fraction of the optimum objective to be searched.
+        names : bool, optional
+            Emit reaction and metabolite names rather than identifiers (default
+            False).
+        floatfmt : string, optional
+            Format string for floats (default '.3g').
 
         """
         from cobra.flux_analysis.summary import model_summary
         return model_summary(self, solution=solution, threshold=threshold,
-                             fva=fva, floatfmt=floatfmt)
+                             fva=fva, names=names, floatfmt=floatfmt)
 
     def __enter__(self):
         """Record all future changes to the model, undoing them when a call to