docs: correct some docstrings to remove warnings

* Some more docstrings cause warnings

cobra/core/dictlist.py

@@ -15,13 +15,17 @@ class DictList(list):
     This object behaves like a list, but has the O(1) speed
     benefits of a dict when looking up elements by their id.
 
-    Parameters
-    ----------
-    *args : iterable
-        iterable as single argument to create new DictList from
     """
 
     def __init__(self, *args):
+        """Instantiate a combined dict and list.
+
+        Parameters
+        ----------
+        args : iterable
+            iterable as single argument to create new DictList from
+
+        """
         if len(args) > 2:
             raise TypeError("takes at most 1 argument (%d given)" % len(args))
         super(DictList, self).__init__(self)
@@ -93,13 +97,12 @@ def query(self, search_function, attribute=None):
         Parameters
         ----------
         search_function : a string, regular expression or function
-            used to find the matching elements in the list.
-
+            Used to find the matching elements in the list.
             - a regular expression (possibly compiled), in which case the
             given attribute of the object should match the regular expression.
-
             - a function which takes one argument and returns True for
             desired values
+
         attribute : string or None
             the name attribute of the object to passed as argument to the
             `search_function`. If this is None, the object itself is used.

cobra/core/model.py

@@ -453,8 +453,8 @@ def add_boundary(self, metabolite, type="exchange", reaction_id=None,
 
         If you set the reaction `type` to something else, you must specify the
         desired identifier of the created reaction along with its upper and
-         lower bound. The name will be given by the metabolite name and the
-         given `type`.
+        lower bound. The name will be given by the metabolite name and the
+        given `type`.
 
         Parameters
         ----------

cobra/core/reaction.py

@@ -681,8 +681,8 @@ def get_coefficient(self, metabolite_id):
         return self._metabolites[_id_to_metabolites[metabolite_id]]
 
     def get_coefficients(self, metabolite_ids):
-        """Return the stoichiometric coefficients for a list of
-        metabolites in the reaction.
+        """
+        Return the stoichiometric coefficients for a list of metabolites.
 
         Parameters
         ----------
@@ -806,11 +806,16 @@ def add_metabolites(self, metabolites_to_add, combine=True,
                     combine=False, reversibly=False))
 
     def subtract_metabolites(self, metabolites, combine=True, reversibly=True):
-        """This function will 'subtract' metabolites from a reaction, which
-        means add the metabolites with -1*coefficient. If the final coefficient
-        for a metabolite is 0 then the metabolite is removed from the reaction.
+        """Subtract metabolites from a reaction.
 
-        The change is reverted upon exit when using the model as a context.
+        That means add the metabolites with -1*coefficient. If the final
+        coefficient for a metabolite is 0 then the metabolite is removed from
+        the reaction.
+
+        Notes
+        -----
+        * A final coefficient < 0 implies a reactant.
+        * The change is reverted upon exit when using the model as a context.
 
         Parameters
         ----------
@@ -828,8 +833,6 @@ def subtract_metabolites(self, metabolites, combine=True, reversibly=True):
             Whether to add the change to the context to make the change
             reversibly or not (primarily intended for internal use).
 
-        .. note:: A final coefficient < 0 implies a reactant.
-
         """
         self.add_metabolites({
             k: -v for k, v in iteritems(metabolites)},