Fix warnings and errors during documentation generation.

doc/extending/type.txt

@@ -32,10 +32,11 @@ default values.
       reference to ``value`` (i.e. casting prohibited).
       If ``strict`` is False, then casting may happen, but downcasting should
       only be used in two situations:
-          * if ``allow_downcast`` is True
-          * if ``allow_downcast`` is ``None`` and the default behavior for this
-            type allows downcasting for the given ``value`` (this behavior is
-            type-dependent, you may decide what your own type does by default)
+
+      * if ``allow_downcast`` is True
+      * if ``allow_downcast`` is ``None`` and the default behavior for this
+        type allows downcasting for the given ``value`` (this behavior is
+        type-dependent, you may decide what your own type does by default)
 
       We need to define ``filter`` with three arguments. The second argument
       must be called ``strict`` (Theano often calls it by keyword) and must

doc/index.txt

@@ -88,7 +88,7 @@ You can download the latest `PDF documentation <http://deeplearning.net/software
 
 Check out how Theano can be used for Machine Learning: `Deep Learning Tutorials <http://www.deeplearning.net/tutorial>`_.
 
-Theano was featured at `SciPy 2010 <http://www.iro.umontreal.ca/~lisa/publications2/index.php/publications/show/461>`_.
+Theano was featured at `SciPy 2010 <http://www.iro.umontreal.ca/~lisa/publications2/index.php/publications/show/461>`__.
 
 Community
 =========

doc/internal/how_to_release.txt

@@ -42,9 +42,8 @@ Tag the release
 ===============
 
 You will need to commit the previous changes, tag the resulting version, and
-push that into the original repository::
-
-Tag the release. The syntax is something like the following::
+push that into the original repository. The syntax is something like the
+following::
 
     hg commit -m"modifications for 0.X release" setup.py doc/conf.py NEWS.txt
     hg tag 0.X
@@ -89,9 +88,11 @@ Account jaberg is listed as submitter.
 1. log in as jaberg to mloss
 2. search for theano and click the logo
 3. press 'update this project' on the left and change
+
   - the version number
   - the download link
-  - the description of what has changed 
+  - the description of what has changed
+
 4. press save
 
 Make sure the "what's changed" text isn't too long because it will show up on

doc/internal/python.txt

-.. _python:
+.. _python_booster:
 
 ================
 Python booster

doc/library/scan.txt

@@ -350,12 +350,11 @@ will always be ``12``.
 Reference
 =========
 
-.. automodule:: theano.scan
+.. automodule:: theano.scan_module
 
 .. autofunction:: theano.map
 .. autofunction:: theano.reduce
 .. autofunction:: theano.foldl
 .. autofunction:: theano.foldr
 .. autofunction:: theano.scan
-    :noindex:
 

doc/tutorial/shape_info.txt

@@ -19,17 +19,18 @@ Currently shape informations are used for 2 things in Theano:
   method.
 
   ex:
-.. code-block:: python
 
-   import theano
-   x = theano.tensor.matrix('x')
-   f = theano.function([x], (x**2).shape)
-   theano.printing.debugprint(f)
-   #MakeVector [@43860304] ''   2
-   # |Shape_i{0} [@43424912] ''   1
-   # | |x [@43423568]
-   # |Shape_i{1} [@43797968] ''   0
-   # | |x [@43423568]
+  .. code-block:: python
+
+     import theano
+     x = theano.tensor.matrix('x')
+     f = theano.function([x], (x**2).shape)
+     theano.printing.debugprint(f)
+     #MakeVector [@43860304] ''   2
+     # |Shape_i{0} [@43424912] ''   1
+     # | |x [@43423568]
+     # |Shape_i{1} [@43797968] ''   0
+     # | |x [@43423568]
 
 The output of this compiled function do not contain any multiplication
 or power. Theano has removed them to compute directly the shape of the