Update comment and add doc about the new warning in the infer_shape tester.

doc/tutorial/extending_theano.txt

@@ -228,13 +228,23 @@ output.
 ``self._compile_and_check`` compiles a Theano function. It takes as
 parameters the lists of input and output Theano variables, as would be
 provided to ``theano.function``, and a list of real values to pass to the
-compiled function (do not use symmetric shapes, e.g. (3, 3),
-as they can easily hide errors). It also takes the op class as a parameter
+compiled function. It also takes the op class as a parameter
 in order to verify that no instance of it appears in the shape-optimized graph.
 
 If there is an error, the function raises an exception. If you want to
 see it fail, you can implement an incorrect ``infer_shape``.
 
+When testing with input values with shapes that take the same value
+over different dimensions (for instance, a square matrix, or a tensor3
+with shape (n, n, n), or (m, n, m)), it is not possible to detect if
+the output shape was computed correctly, or if some shapes with the
+same value have been mixed up. For instance, if the infer_shape uses
+the width of a matrix instead of its height, then testing with only
+square matrices will not detect the problem. This is why the
+``self._compile_and_check`` method print a warning in such a case. If
+your op work only in such case, you can diable the warning with the
+warn=True parameter.
+
 .. code-block:: python
 
     from theano.tests import unittest_tools as utt

theano/tests/unittest_tools.py

@@ -176,7 +176,19 @@ class InferShapeTester(unittest.TestCase):
 
     def _compile_and_check(self, inputs, outputs, numeric_inputs, cls,
                            excluding=None, warn=True):
-        """This tests the infer_shape method only"""
+        """This tests the infer_shape method only
+
+        When testing with input values with shapes that take the same
+        value over different dimensions (for instance, a square
+        matrix, or a tensor3 with shape (n, n, n), or (m, n, m)), it
+        is not possible to detect if the output shape was computed
+        correctly, or if some shapes with the same value have been
+        mixed up. For instance, if the infer_shape uses the width of a
+        matrix instead of its height, then testing with only square
+        matrices will not detect the problem. If warn=True, we emit a
+        warning when testing with such values.
+
+        """
         mode = self.mode
         if excluding:
             mode = mode.excluding(*excluding)
@@ -194,9 +206,12 @@ class InferShapeTester(unittest.TestCase):
                 else:
                     shp = inp.shape
                 if len(set(shp)) != len(shp):
-                    _logger.warn("While testing the shape, we received input"
-                                 " with dimensions of the same shape %s! This"
-                                 " lower the quality of the verification.",
+                    _logger.warn(
+                        "While testing the shape inference, we received an"
+                        " input with a shape that has some repeated values: %s"
+                        ", like a square matrix. This makes it impossible to"
+                        " check if the values for these dimensions have been"
+                        " correctly used, or if they have been mixed up.",
                         str(inp.shape))
                     break