Fixed more docgen errors

README.txt

@@ -4,12 +4,20 @@ To install the package, use:
     python setup.py test
     python setup.py install
 
+
 For the documentation, see the project website:
 
     http://pylearn.org/theano/
 
-This may be easier than building the documentation yourself, because we have
-custom ReST hooks that are used.
+We recommend you look at the documentation on the website, since it
+will be more current than the documentation included with the package.
+If you really wish to build the documentation yourself, you will need
+epydoc and sphinx. Issue the following command:
+
+    python ./doc/scripts/docgen.py
+
+Documentation is built into html/
+The PDF of the documentation is html/theano.pdf
 
 
 DIRECTORY LAYOUT

doc/advanced/function.txt

-
-.. _functioninterface:
-
-==================
-Function Interface
-==================
-
-This section details the various structures used to make ``function``
-work. You might want to read the sections about :ref:`compilation` and
-:ref:`optimization`.
-
-
-
-
-
-.. index::
-   single: Mode
-
-.. _mode:
-
-----
-Mode
-----
-
-WRITEME
-
-
-.. index::
-   single: function
-
-.. _function:
-
---------
-function
---------
-
-WRITEME
-
-
-.. index::
-   single: FunctionMaker
-
-.. _functionmaker:
-
--------------
-FunctionMaker
--------------
-
-WRITEME
-

doc/advanced/unittest.txt

@@ -183,7 +183,7 @@ might not be such a good idea.
 
 Here is a list of useful functions, as defined by TestCase: 
 
-* checking the state of boolean variables: assert_, failUnless, assertTrue, failIf, assertFalse
+* checking the state of boolean variables: assert, failUnless, assertTrue, failIf, assertFalse
 * checking for (in)equality constraints: assertEqual, failUnlessEqual, assertNotEqual, failIfEqual
 * checking for (in)equality constraints up to a given precision (very useful in theano): assertAlmostEqual, failUnlessAlmostEqual, assertNotAlmostEqual, failIfAlmostEqual
 

doc/advanced_tutorial/ex1/index.txt

-
-==================
-Example 1 - double
-==================
-
-WRITEME
-
-.. toctree::
-
-   type
-   op
-   ctype
-   cop

doc/advanced_tutorial/ex2/index.txt

-
-
-=====================
-Example 2 - cons_cell
-=====================
-
-.. toctree::
-
-   type
-

doc/advanced_tutorial/graphstructures.txt

@@ -137,7 +137,7 @@ Automatic wrapping
 
 All nodes in the graph must be instances of ``Apply`` or ``Result``, but
 ``<Op subclass>.make_node()`` typically wraps constants to satisfy those
-constraints. For example, the :ref:`tensor.add` op instance is written
+constraints. For example, the :api:`tensor.add` op instance is written
 so that:
 
 .. code-block:: python

doc/advanced_tutorial/index.txt

@@ -17,22 +17,20 @@ them using a Python implementation and then we will add a C
 implementation.
 
 This tutorial should be of most use to users who want to extend Theano
-with custom types and operations related to these types. Users who
-want to extend Theano with new operations on tensors should check
-:ref:`tensoroptutorial`, but it is a good idea to read this tutorial
-as well since it probably provides better grounding for the many
-concepts at work here.
+with custom types and operations related to these types.
+It is a good idea to read this tutorial as well since it provides
+grounding for fundamental Theano concepts.
 
 
 .. toctree::
 
    theano_vs_python
    graphstructures
-   ex1/type
-   ex1/op
+   type
+   op
    inplace
-   ex1/ctype
-   ex1/cop
+   ctype
+   cop
    optimization
    tips
 

doc/advanced_tutorial/ex1/op.txt → doc/advanced_tutorial/op.txt

@@ -79,7 +79,8 @@ An Op (:api:`gof.op.Op`) is any object which defines the following methods:
     A, are presented again, then outputs equal to B must be returned again.
   
   - You must be careful about aliasing outputs to inputs, and making
-    modifications to any of the inputs. See `Views and inplace operations`_
+    modifications to any of the inputs. See `Views and inplace operations
+    <views_and_inplace>`_
     before writing a ``perform`` implementation that does either of these
     things.
 

doc/basic_tutorial/function.txt

@@ -122,7 +122,7 @@ array(10.0)
 Advanced: Sharing Storage Between Functions
 -------------------------------------------
 
-``value`` can be a :api:`theano.gof.Container` as well as a literal.
+``value`` can be a :api:`theano.gof.link.Container` as well as a literal.
 This permits linking a value of a Variable in one function to the value of a Variable in another function.
 By using a ``Container`` as a value we can implement shared variables between functions.
 
@@ -164,7 +164,7 @@ The following restrictions apply to the inputs to ``theano.function``:
   exception?**]
 
 - Two ``In`` instances may not name the same Variable. I.e. you cannot
-give the same parameter multiple times.
+  give the same parameter multiple times.
 
 If no name is specified explicitly for an In instance, then its name
 will be taken from the Variable's name. Note that this feature can cause

doc/index.txt

@@ -8,9 +8,10 @@ efficiently evaluate mathematical expressions involving multi-dimensional
 arrays. Using Theano, it is not uncommon to see speed improvements of
 ten-fold over using pure NumPy.
 
-The latest release is version `0.1 <downloads/Theano-0.1.tar.gz>`.
-You can download the `PDF documentation <theano.pdf>`, rather than reading it
-online.
+The latest release is version `0.1
+<http://pylearn.org/theano/downloads/Theano-0.1.tar.gz>`.
+You can download the latest `PDF documentation
+<http://pylearn.org/theano/theano.pdf>`, rather than reading it online.
 
 Choose your own adventure:
 

doc/install.txt

@@ -148,12 +148,21 @@ territory and inform us of your progress!
 Generating the documentation
 ----------------------------
 
-Don't build the documentation, just find it on the web.
-You can read the HTML documentation `here
+You can read the latest HTML documentation `here
 <http://pylearn.org/theano/contents.html>`.
-You can download the PDF documentation `here
-<htt
 You can download the latest PDF documentation `here
 <http://pylearn.org/theano/theano.pdf`.
 
+We recommend you look at the documentation on the website, since it
+will be more current than the documentation included with the package.
+
+If you really wish to build the documentation yourself, you will need
+epydoc and sphinx, as described above. Issue the following command::
+
+    python ./doc/scripts/docgen.py
+
+Documentation is built into ``html/``.
+The PDF of the documentation is ``html/theano.pdf``.
+
+
 .. _theano-users: http://groups.google.com/group/theano-users?pli=1

doc/sandbox/performance.txt

@@ -13,6 +13,7 @@ speed improvements over basic numpy by using theano.
 
 With a little work, Theano could also implement more sophisticated
 optimizations:
+
  * automatic ordering of matrix multiplications 
  * profile-based memory layout decisions (e.g. row-major vs. col-major)
  * gcc intrinsics to use MMX, SSE2 parallelism for faster element-wise arithmetic

doc/sandbox/sandbox.txt

@@ -127,7 +127,8 @@ Guillaume can you make sure to hit these points:
 
         nosetests has ``failUnlessRaises``
 
-    * Convention is that all test files must start with test_, not _test_, so rename all that use the old convention?
+    * Convention is that all test files must start with ``test_``, not
+    ``_test_``, so rename all that use the old convention?
 
 =======================================================
 How to use the PrintOp