Fixes some RST errors.

doc/core_development_guide.txt

@@ -21,7 +21,7 @@ some of them might be outdated though:
 * :ref:`pipeline` -- Describes the steps of compiling a Theano Function.
 
 * :ref:`graphstructure` -- Describes the symbolic graphs generated by
-  :func:`theano.scan`.
+  :mod:`theano.scan`.
 
 * :ref:`unittest` -- Tutorial on how to use unittest in testing Theano.
 

doc/extending/op.txt

@@ -257,6 +257,7 @@ Trying out our new Op
 
 .. If you modify this code, also change :
 .. theano/tests/test_tutorial.py:T_extending.test_extending_1
+
 In the following code, we use our new Op:
 
 >>> x, y = double('x'), double('y')

doc/library/scan.txt

@@ -216,4 +216,5 @@ Reference
 .. autofunction:: theano.foldl
 .. autofunction:: theano.foldr
 .. autofunction:: theano.scan
+    :noindex:
 

doc/nice_quotes.txt

@@ -24,4 +24,3 @@ deserves broad recognition among the scientific python community.
 -- Olivier Grisel
 
 
--------------------------

doc/proposals/conditional.txt

@@ -70,7 +70,7 @@ There are two interface items I propose to add.  The first is a Thunk object
 (which we have never had before), and the second is a new function (make_thunk)
 in the PureOp class (a superclass of Op) that will return a Thunk.
 
-..code-block:: python
+.. code-block:: python
 
   class Thunk (object):
     """Abstract class / interface
@@ -98,7 +98,7 @@ in the PureOp class (a superclass of Op) that will return a Thunk.
        None.
        """
 
-..code-block:: python
+.. code-block:: python
 
     class PureOp(object):                       # recall:
                                                 # Op inherits from PureOp

doc/release.txt

@@ -18,17 +18,19 @@ welcome on the mailing list.
 1) We will perform a monthly release of Theano. These will be "lightweight"
    releases and will include everything that was done in the last month. All
    outstanding feature requests are pushed back to the following month, so as
-   not to delay the current release.  
+   not to delay the current release.
 
 2) Asynchronous releases will only be made when a bug generating incorrect
    output is discovered and fixed.
 
 3) Each release must satisfy the following criteria. Non-compliance will
    result in us delaying or skipping the release in question.
+
     1) No regression errors.
     2) No known, silent errors.
     3) No errors giving incorrect results.
     4) No test errors/failures, except for known errors.
+
         1) Known errors should not be used to encode "feature wish lists", as
            is currently the case.
         2) Incorrect results should raise errors and not known errors (this
@@ -37,10 +39,11 @@ welcome on the mailing list.
            ticket in the error message.
 
 4) The release numbers will follow the X.Y.Z scheme:
+
    1) We update Z by 1 for each lightweight release.
    2) We update Y for bug fixes, interface changes and/or significant features
       we wish to publicize.
-   4) The Theano v1.0.0 release will be made when the interface is deemed
+   3) The Theano v1.0.0 release will be made when the interface is deemed
       stable enough and covers most of numpy's interface.
 
 5) The trunk will be tagged on each release.
@@ -53,14 +56,15 @@ Optional:
 
 8) A 1-week scrum might take place before a release, in order to fix bugs
    which would otherwise prevent a release.
+
     1) Occasional deadlines might cause us to skip a release.
-    1) Everybody can (and should) participate, even people on the mailing
+    2) Everybody can (and should) participate, even people on the mailing
        list.
-    2) The scrum should encourage people to finish what they have already
+    3) The scrum should encourage people to finish what they have already
        started (missing documentation, missing test, ...). This should help
        push out new features and keep the documentation up to date.
-    3) If possible, aim for the inclusion of one new interesting feature.
-    4) Participating in the scrum should benefit all those involved, as you
+    4) If possible, aim for the inclusion of one new interesting feature.
+    5) Participating in the scrum should benefit all those involved, as you
        will learn more about our tools and help develop them in the process. A
        good indication that you should participate is if you have a need for a
        feature which is not yet implemented.

doc/sandbox/index2.txt

@@ -7,10 +7,8 @@ Advanced Topics (under construction)
 
 .. toctree::
     :maxdepth: 2
-   
+
     env
-    features
-    optimization
     compilation
     ccodegen
     function

doc/sandbox/module.txt

@@ -42,6 +42,7 @@ Components.  Wheras Components are represent symbolic things (ie. Variables), Co
    single: component; Component
 
 .. _component:
+
 ---------
 Component
 ---------
@@ -81,6 +82,7 @@ allocated in phase 1 with sensible values.
    single: component; External
 
 .. _external:
+
 --------
 External
 --------
@@ -94,6 +96,7 @@ WRITEME
    single: component; Member
 
 .. _member:
+
 ------
 Member
 ------
@@ -106,6 +109,7 @@ WRITEME
    single: component; Method
 
 .. _method:
+
 ------
 Method
 ------
@@ -118,6 +122,7 @@ WRITEME
    single: component; Module
 
 .. _module:
+
 ------
 Module
 ------
@@ -140,7 +145,7 @@ In the Module system, the analog of the file is the `Module`, the analog of the
 `Method`, and the analog of the variable is the `Member`.  Module, Member, and Method all work
 at the symbolic level.  Once a graph of Modules, Members, and Methods is ready for use, it must
 be compiled with a call to `make` which will return an isomorphic structure in which Modules
-have become `ModuleInstances`, Members have become `Container`s, and Methods have become
-`Function`s.
+have become `ModuleInstances`, Members have become `Containers`, and Methods have become
+`Functions`.
 This structure contains numbers and functions, and is ready for computation.
 

doc/sandbox/module2.txt

@@ -209,7 +209,7 @@ Here, we make a new ``Module`` and we give it two inner ``Modules`` like
 the one defined in the basic example. Each inner module has methods inc
 and dec as well as a state c and their state is directly accessible from
 the outer module, which means that it can define methods using them. The
-instance(inst) we make from the ``Module``(m) reflects the hierarchy
+instance (inst) we make from the ``Module`` (m) reflects the hierarchy
 that we created. Unlike the method using function, there is no need to
 manipulate any containers directly.
 
@@ -219,7 +219,7 @@ Advanced example
 
 Complex models can be implemented by subclassing ``Module`` (though that is not mandatory). Here is a complete, extensible (and working) regression model implemented using this system:
 
-.. literalinclude:: ../code/regression.py
+.. literalinclude:: ../../benchmark/regression/regression.py
 
 Here is how we use the model:
 

doc/sandbox/sandbox.txt

@@ -129,7 +129,7 @@ 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?
+        ``_test_``, so rename all that use the old convention?
 
 
 =======================================================

doc/sandbox/software.txt

 Other software to look at and maybe recommend to users:
 
- * [http://www.pytables.org/moin PyTables] - This is looking really
- promising for dataset storage and experiment logging... This might
- actually be useful for large data sets.
- * [http://matplotlib.sourceforge.net/ MatPlotLib] - visualization tools
- (plot curves interactively, like matlab's figure window)
- * [http://www.pythonware.com/products/pil/ PIL] - Python Image Library:
- write your matrices out in png! (Kinda a weird recommendation, I think)
- * [http://www.logilab.org/857 pylint] - Syntax checker for python to
- help beautify your code. (We'd be hypocrites to recommend this :)
- * [http://www.winpdb.org/ Winpdb] - A Platform Independent Python
- Debugger. (Except it doesn't really help you debug Theano graphs)
- * [http://wiki.python.org/moin/IntegratedDevelopmentEnvironments Python Integrated Development Environments] - for all your coding needs
+* [http://www.pytables.org/moin PyTables] - This is looking really
+    promising for dataset storage and experiment logging... This might
+    actually be useful for large data sets.
+* [http://matplotlib.sourceforge.net/ MatPlotLib] - visualization tools
+    (plot curves interactively, like matlab's figure window)
+* [http://www.pythonware.com/products/pil/ PIL] - Python Image Library:
+    write your matrices out in png! (Kinda a weird recommendation, I think)
+* [http://www.logilab.org/857 pylint] - Syntax checker for python to
+    help beautify your code. (We'd be hypocrites to recommend this :)
+* [http://www.winpdb.org/ Winpdb] - A Platform Independent Python
+    Debugger. (Except it doesn't really help you debug Theano graphs)
+* [http://wiki.python.org/moin/IntegratedDevelopmentEnvironments Python
+    Integrated Development Environments] - for all your coding needs
 

doc/sandbox/sparse.txt

@@ -34,9 +34,9 @@ Their seam new format planed for scipy 0.7.x:
     ``bsr_matrix``
         Block Compressed Row (BSR). From their doc: The Block Compressed Row (BSR) format is very similar to the Compressed Sparse Row (CSR) format. BSR is appropriate for sparse matrices with dense sub matrices like the last example below. Block matrices often arise in vector-valued finite element discretizations. In such cases, BSR is considerably more efficient than CSR and CSC for many sparse arithmetic operations.
     ``dia_matrix``
-	Sparse matrix with DIAgonal storage
+    Sparse matrix with DIAgonal storage
 
-There are four member variables that comprise a compressed matrix ``sp``(for at least csc, csr and bsr):
+There are four member variables that comprise a compressed matrix ``sp`` (for at least csc, csr and bsr):
 
     ``sp.shape``
         gives the shape of the matrix.

doc/tutorial/examples.txt

@@ -53,6 +53,7 @@ We can verify that this alternate form produces the same values:
 
 .. If you modify this code, also change :
 .. theano/tests/test_tutorial.py:T_examples.test_examples_2
+
 >>> s2 = (1 + T.tanh(x / 2)) / 2
 >>> logistic2 = function([x], s2)
 >>> logistic2([[0, 1], [-1, -2]])
@@ -69,6 +70,7 @@ squared difference between two matrices ``a`` and ``b`` at the same time:
 
 .. If you modify this code, also change :
 .. theano/tests/test_tutorial.py:T_examples.test_examples_3
+
 >>> a, b = T.dmatrices('a', 'b')
 >>> diff = a - b
 >>> abs_diff = abs(diff)

doc/tutorial/modes.txt

@@ -56,6 +56,7 @@ cluster!).
 
 .. If you modify this code, also change :
 .. theano/tests/test_tutorial.py:T_modes.test_modes_1
+
 DebugMode is used as follows:
 
 .. code-block:: python