remove warning when generating the documentation.

doc/index.txt

@@ -135,7 +135,7 @@ Community
 
 * We use `Github tickets <http://github.com/Theano/Theano/issues>`__ to keep track of issues
   (however, some old tickets can still be found on
-  ``Assembla <http://www.assembla.com/spaces/theano/tickets>`__).
+  `Assembla <http://www.assembla.com/spaces/theano/tickets>`__).
 
 * Come visit us in Montreal! Most developers are students in the LISA_ group at the `University of Montreal`_.
 

doc/library/tensor/basic.txt

@@ -1220,6 +1220,7 @@ Linear Algebra
 
     :param x: A Tensor with sizes e.g.: for  3D (dim1, dim3, dim2)
     :param y: A Tensor with sizes e.g.: for 3D (dim1, dim2, dim4)
+
     This function computes the dot product between the two tensors, by iterating
     over the first dimension using scan.
     Returns a tensor of size e.g. if it is 3D: (dim1, dim3, dim4)

doc/tutorial/examples.txt

@@ -433,12 +433,12 @@ to another is shown below.
 
 This gives the following output:
 
-.. code-block:: shell
+.. code-block:: bash
 
-    By default, the two functions are out of sync.
+    # By default, the two functions are out of sync.
     f1() returns  [ 0.72803009]
     f2() returns  [ 0.55056769]
-    We now copy the state of the theano random number generators.
+    # We now copy the state of the theano random number generators.
     f1() returns  [ 0.59044123]
     f2() returns  [ 0.59044123]
 

theano/gradient.py

@@ -384,11 +384,11 @@ def grad(cost, wrt, consider_constant=None,
 
     :type return_disconnected: string
     :param return_disconnected:
-        'zero' : If wrt[i] is disconnected, return value i will be
+        - 'zero' : If wrt[i] is disconnected, return value i will be
                    wrt[i].zeros_like()
-        'None' : If wrt[i] is disconnected, return value i will be
+        - 'None' : If wrt[i] is disconnected, return value i will be
                    None
-        'Disconnected' : returns variables of type DisconnectedType
+        - 'Disconnected' : returns variables of type DisconnectedType
 
     :rtype: Variable or list/tuple of Variables (depending upon `wrt`)
 

theano/sandbox/cuda/basic_ops.py

@@ -2443,9 +2443,10 @@ class GpuIncSubtensor(tensor.IncSubtensor, GpuOp):
 
     def copy_of_x(self, x):
         """
-            x: a string giving the name of a C variable pointing to an array
+            :param x: a string giving the name of a C variable
+                pointing to an array
 
-            Returns C code expression to make a copy of x.
+            :return: C code expression to make a copy of x
 
             Base class uses PyArrayObject *, subclasses may override for
             different types of arrays.
@@ -2454,8 +2455,8 @@ class GpuIncSubtensor(tensor.IncSubtensor, GpuOp):
 
     def make_view_array(self, x, view_ndim):
         """
-            x: a string identifying an array to be viewed
-            view_ndim: a string specifying the number of dimensions
+            :param x: a string identifying an array to be viewed
+            :param view_ndim: a string specifying the number of dimensions
                 to have in the view
 
             This doesn't need to actually set up the view with the

theano/tensor/basic.py

@@ -4971,9 +4971,10 @@ class IncSubtensor(Op):
 
     def copy_of_x(self, x):
         """
-            x: a string giving the name of a C variable pointing to an array
+            :param x: a string giving the name of a C variable
+                pointing to an array
 
-            Returns C code expression to make a copy of x.
+            :return: C code expression to make a copy of x
 
             Base class uses PyArrayObject *, subclasses may override for
             different types of arrays.
@@ -4991,8 +4992,8 @@ class IncSubtensor(Op):
 
     def make_view_array(self, x, view_ndim):
         """
-            x: a string identifying an array to be viewed
-            view_ndim: a string specifying the number of dimensions
+            :param x: a string identifying an array to be viewed
+            :param view_ndim: a string specifying the number of dimensions
                 to have in the view
 
             This doesn't need to actually set up the view with the