Update cython backend to match python backend

theano/scan_module/numpy_api_changes.diff

-diff --git a/theano/scan_module/scan_perform.c b/theano/scan_module/scan_perform.c
-index aaebb43..2d06b29 100644
---- a/theano/scan_module/scan_perform.c
-+++ b/theano/scan_module/scan_perform.c
-@@ -5595,7 +5595,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
+@@ -5597,7 +5597,7 @@
   *             cdef list stack
   *             cdef int offset
   */
@@ -11,29 +7,29 @@ index aaebb43..2d06b29 100644
    __Pyx_INCREF(__pyx_t_4);
    __pyx_v_descr = ((PyArray_Descr *)__pyx_t_4);
    __pyx_t_4 = 0;
-@@ -7147,7 +7147,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
+@@ -7126,7 +7126,7 @@
   *      arr.base = baseptr
   * 
   */
 -  Py_XDECREF(__pyx_v_arr->base);
 +  Py_XDECREF(PyArray_BASE(__pyx_v_arr));
  
-   /* "/home/anakha/.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":974
+   /* "numpy.pxd":973
   *          baseptr = <PyObject*>base
-@@ -7156,7 +7156,11 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
+@@ -7135,7 +7135,11 @@
   * 
   * cdef inline object get_array_base(ndarray arr):
   */
 -  __pyx_v_arr->base = __pyx_v_baseptr;
-+#if NPY_API_VERSION < 0x00000007
-+  PyArray_BASE(__pyx_v_arr) = __pyx_v_baseptr;
-+#else
-+  PyArray_SetBaseObject(__pyx_v_arr, __pyx_v_baseptr);
-+#endif
++  #if NPY_API_VERSION < 0x00000007
++      PyArray_BASE(__pyx_v_arr) = __pyx_v_baseptr;
++  #else
++      PyArray_SetBaseObject(__pyx_v_arr, __pyx_v_baseptr);
++  #endif
  
-   /* "/home/anakha/.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":966
-  * 
-@@ -7191,7 +7195,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
+   __Pyx_RefNannyFinishContext();
+ }
+@@ -7161,7 +7165,7 @@
   *         return None
   *     else:
   */
@@ -41,8 +37,8 @@ index aaebb43..2d06b29 100644
 +  __pyx_t_1 = ((PyArray_BASE(__pyx_v_arr) == NULL) != 0);
    if (__pyx_t_1) {
  
-     /* "/home/anakha/.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":978
-@@ -7214,8 +7218,8 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
+     /* "numpy.pxd":977
+@@ -7185,8 +7189,8 @@
   *         return <object>arr.base             # <<<<<<<<<<<<<<
   */
      __Pyx_XDECREF(__pyx_r);
@@ -52,4 +48,6 @@ index aaebb43..2d06b29 100644
 +    __pyx_r = ((PyObject *)PyArray_BASE(__pyx_v_arr));
      goto __pyx_L0;
    }
+   __pyx_L3:;
+
  

theano/scan_module/scan_perform.pyx

@@ -191,6 +191,10 @@ def perform(
     cdef unsigned int begin
     cdef unsigned int end
     cdef int cond
+    cdef unsigned int len_output_storage = (n_mit_mot_outs + n_mit_sot +
+                                            n_sit_sot + n_nit_sot +
+                                            n_shared_outs)
+    cdef int output_reused[500] # max 500 outputs
 
 
     if n_steps < 0:
@@ -304,11 +308,14 @@ def perform(
                 offset += 1
 
         # 4. collecting slices where the output should be stored
+
+        # 4.1. Collect slices for mitmots
         for idx in range(n_mit_mot_outs):
             output_storage[idx].storage[0] = None
 
+        # 4.2. Collect slices for mitsots, sitsots and nitsots
         offset = n_mit_mot_outs
-        if i !=0 and n_nit_sot >0:
+        if i != 0:
             for idx in range(n_outs + n_nit_sot - n_mit_mot):
                 if ( store_steps[<unsigned int>(idx+n_mit_mot)] == 1 or
                     vector_outs[<unsigned int>(idx+n_mit_mot)] == 1):
@@ -321,12 +328,21 @@ def perform(
             for idx in range(n_outs + n_nit_sot - n_mit_mot):
                 output_storage[<unsigned int>(idx+offset)].storage[0] = None
 
+        # 4.3. Collect slices for shared outputs
         offset += n_outs+n_nit_sot - n_mit_mot
         for idx in range(n_shared_outs):
             output_storage[<unsigned int>(idx+offset)].storage[0] = None
+
+        # 4.4. If there is a condition add it to the mix
         if as_while:
             pdx = offset + n_shared_outs
             output_storage[<unsigned int>pdx].storage[0] = None
+
+        # 4.5. Keep a reference to the variables currently in the
+        # output_storage to be able to compare them with the actual
+        # outputs of the inner function after its execution
+        old_output_storage = [o.storage[0] for o in output_storage]
+
         # 5. compute outputs
         t0_fn = time.time()
 
@@ -348,6 +364,11 @@ def perform(
             pdx = offset + n_shared_outs
             cond = output_storage[pdx].storage[0] == 0
 
+        # Check which of the pre-allocated outputs (if applicable) have
+        # been reused by the inner function
+        for j in range(len_output_storage):
+            output_reused[j] = (old_output_storage[j] is
+                                output_storage[j].storage[0])
 
         offset_out = 0
         # 5.1 Copy over the values for mit_mot outputs
@@ -363,8 +384,8 @@ def perform(
         offset_out -= n_mit_mot
 
         for j in range(begin, end):
-            if ( store_steps[j] == 1 or vector_outs[j] ==1 or
-                outs[j][0][pos[j]] is not output_storage[<unsigned int>(offset_out+j)].storage[0]):
+            if (store_steps[j] == 1 or vector_outs[j] == 1 or
+                not output_reused[<unsigned int>(offset_out+j)]):
 
                 outs[j][0][pos[j]] = output_storage[<unsigned int>(offset_out+j)].storage[0]
 
@@ -387,7 +408,7 @@ def perform(
                     outs[j][0] = outs[j][0][:store_steps[j]]
                 outs[j][0][pos[j]] = output_storage[jout].storage[0]
             elif (store_steps[j] == 1 or vector_outs[j] == 1 or
-                  outs[j][0][pos[j]] is not output_storage[j+offset_out].storage[0]):
+                  not output_reused[<unsigned int>(offset_out+j)]):
                 outs[j][0][pos[j]] = output_storage[j+offset_out].storage[0]