sync between cython implementation of scan and cython one.

theano/scan_module/scan_perform.pyx

@@ -56,7 +56,7 @@ import cython
 
 import numpy
 cimport numpy
-
+from theano import gof
 import time
 import copy
 from theano.sandbox import cuda
@@ -331,7 +331,19 @@ def perform(
             output_storage[<unsigned int>pdx].storage[0] = None
         # 5. compute outputs
         t0_fn = time.time()
-        fn()
+
+        try:
+            fn()
+        except Exception:
+            if hasattr(fn, 'position_of_error'):
+                # this is a new vm-provided function
+                # the C VM needs this because the exception manipulation
+                # done by raise_with_op is not implemented in C.
+                gof.vm.raise_with_op(fn.nodes[fn.position_of_error])
+            else:
+                # old-style linkers raise their own exceptions
+                raise
+
         dt_fn = time.time() - t0_fn
         t_fn += dt_fn
         if self.as_while:
@@ -435,6 +447,16 @@ def perform(
         elif store_steps[idx] > i - self.mintaps[idx]:
             outs[idx][0][i-self.mintaps[idx]:] = 0
 
+            # This is a fix for a bug introduced by while. If you say
+            # you want to loop up to a condition, you expect the output
+            # to have that length ( and not the maximal length possible)
+            #
+            # Without this the behaviour of a scan op is not consistent
+            # if optimization gets applied compared to when optimization
+            # do not get applied
+            if i < n_steps:
+                outs[idx][0] = outs[idx][0][:-(n_steps - i)]
+
     t_call = time.time() - t0_call
 
     if hasattr(fnct.maker, 'profile'):