Update Cython-generated Scan code

theano/scan/numpy_api_changes.diff

-@@ -6667,7 +6667,7 @@
-  *             cdef list stack
-  *             cdef int offset
-  */
--  __pyx_t_3 = ((PyObject *)__pyx_v_self->descr);
-+  __pyx_t_3 = ((PyObject *)PyArray_DESCR(__pyx_v_self));
-   __Pyx_INCREF(__pyx_t_3);
-   __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3);
-   __pyx_t_3 = 0;
-@@ -8237,7 +8237,7 @@
-  *      arr.base = baseptr
-  *
-  */
--  Py_XDECREF(__pyx_v_arr->base);
-+  Py_XDECREF(PyArray_BASE(__pyx_v_arr));
-
-   /* "numpy.pxd":973
-  *          baseptr = <PyObject*>base
-@@ -8246,7 +8246,11 @@
-  *
-  * 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
-
-   __Pyx_RefNannyFinishContext();
- }
-@@ -8285,7 +8285,7 @@
-  *         return None
-  *     else:
-  */
--  __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0);
-+  __pyx_t_1 = ((PyArray_BASE(__pyx_v_arr) == NULL) != 0);
-   if (__pyx_t_1) {
-
-     /* "numpy.pxd":977
-@@ -8307,8 +8311,8 @@
-  *         return <object>arr.base             # <<<<<<<<<<<<<<
-  */
-     __Pyx_XDECREF(__pyx_r);
--    __Pyx_INCREF(((PyObject *)__pyx_v_arr->base));
--    __pyx_r = ((PyObject *)__pyx_v_arr->base);
-+    __Pyx_INCREF(((PyObject *)PyArray_BASE(__pyx_v_arr)));
-+    __pyx_r = ((PyObject *)PyArray_BASE(__pyx_v_arr));
-     goto __pyx_L0;
-   }
-   __pyx_L3:;

theano/scan/scan_perform.pyx

+# cython: language_level=3
 """
  This code implements the operations that scan has to carry on when called
  as a stand alone function.
@@ -64,7 +65,7 @@ from theano import gof
 
 
 def get_version():
-    return 0.296
+    return 0.297
 
 @cython.boundscheck(False)
 def perform(
@@ -404,14 +405,15 @@ def perform(
                 # done by raise_with_op is not implemented in C.
                 if hasattr(fn, 'thunks'):
                     # For the CVM
-                    gof.link.raise_with_op(fn.nodes[fn.position_of_error],
+                    gof.link.raise_with_op(fn.maker.fgraph,
+                                           fn.nodes[fn.position_of_error],
                                            fn.thunks[fn.position_of_error])
                 else:
                     # For the c linker
                     # We don't have access from python to all the
                     # temps values So for now, we just don't print
                     # the extra shapes/strides info
-                    gof.vm.raise_with_op(fn.nodes[fn.position_of_error])
+                    gof.link.raise_with_op(fn.maker.fgraph, fn.nodes[fn.position_of_error])
             else:
                 # old-style linkers raise their own exceptions
                 raise

theano/scan/scan_perform_ext.py

 """
-To update the scan Cython code in Theano you must
-- update the version in this file and scan_perform.py
-- call "cd theano/scan/; cython scan_perform.pyx; patch scan_perform.c numpy_api_changes.diff"
+
+To update the `Scan` Cython code you must
+- update the version value in this file and `scan_perform.py`, and
+- run `cython scan_perform.pyx; mv scan_perform.c c_code`
 
 """
 
@@ -24,7 +25,7 @@ from theano.gof.compilelock import get_lock, release_lock
 _logger = logging.getLogger("theano.scan.scan_perform")
 
 
-version = 0.296  # must match constant returned in function get_version()
+version = 0.297  # must match constant returned in function get_version()
 
 need_reload = False
 
@@ -143,7 +144,7 @@ except ImportError:
         release_lock()
 
 # This is caused as cython use the old NumPy C-API but we use the new one.
-# To fix it completly, we would need to modify Cython to use the new API.
+# To fix it completely, we would need to modify Cython to use the new API.
 with warnings.catch_warnings():
     warnings.filterwarnings("ignore", message="numpy.ndarray size changed")
     from scan_perform.scan_perform import get_version, perform  # noqa: F401