Fix missing variable renames

theano/compile/debugmode.py

@@ -2102,17 +2102,14 @@ class _Maker(FunctionMaker):  # inheritance buys a few helper functions
         # Check if some input variables are unused
         self._check_unused_inputs(inputs, outputs, on_unused_input)
 
-#TODO: REMOVE THIS CRUFT - it's complicated for SymbolicInputKits
+        # Make a list of (SymbolicInput|SymblicInputKits, indices, [SymbolicInput,...]), one 
+        # tuple for each input. (See Function.indices for more details)
         indices = [[input] + self.expand_in(input, _inputs) for input in inputs]
-        expanded_inputs = reduce(list.__add__, [list(z)
-                                                for x, y, z in indices], [])
-
-        assert expanded_inputs == inputs  #JB - I added this to make sure we could delete above
 
         # make the fgraph
         for i in xrange(mode.stability_patience):
             fgraph, additional_outputs, equivalence_tracker = _optcheck_fgraph(
-                expanded_inputs, outputs, accept_inplace)
+                inputs, outputs, accept_inplace)
             fgraph.equivalence_tracker = equivalence_tracker
 
             # optimize the fgraph
@@ -2190,7 +2187,7 @@ class _Maker(FunctionMaker):  # inheritance buys a few helper functions
 
         self.indices = indices
         self.inputs = inputs
-        self.expanded_inputs = expanded_inputs
+        self.expanded_inputs = inputs
         self.outputs = outputs
         self.unpack_single = unpack_single
         self.return_none = return_none

theano/compile/function_module.py

@@ -1005,7 +1005,7 @@ class FunctionMaker(object):
         indices = [[input] + self.expand_in(input, _inputs) for input in inputs]
 
         # make the fgraph (copies the graph, creates NEW INPUT AND OUTPUT VARIABLES)
-        fgraph, additional_outputs = std_fgraph(expanded_inputs, outputs, accept_inplace)
+        fgraph, additional_outputs = std_fgraph(inputs, outputs, accept_inplace)
         fgraph.profile = profile
 
         self.fgraph = fgraph
@@ -1053,11 +1053,11 @@ class FunctionMaker(object):
         if hasattr(linker, 'accept_var_updates'):
             # hacky thing so VMLinker knows about updates
             self.linker.accept_var_updates(
-                    fgraph_updated_vars(fgraph, expanded_inputs))
+                    fgraph_updated_vars(fgraph, inputs))
 
         self.indices = indices
         self.inputs = inputs
-        self.expanded_inputs = expanded_inputs
+        self.expanded_inputs = inputs
         self.outputs = outputs
         self.unpack_single = unpack_single
         self.return_none = return_none