Fix format mistakes in the docs.

a994cf7c · Arnaud Bergeron · 15c90dd3 · a994cf7c · a994cf7c · a994cf7c
--- a/doc/citation.txt
+++ b/doc/citation.txt
@@ -13,7 +13,7 @@ required) to cite the following two papers:
  `"Theano: new features and speed improvements"
  <http://arxiv.org/pdf/1211.5590.pdf>`_.
  NIPS 2012 deep learning workshop. (`BibTex
-  <http://www.iro.umontreal.ca/~lisa/publications2/index.php/export/publication/551/bibtex>`_)
+  <http://www.iro.umontreal.ca/~lisa/publications2/index.php/export/publication/551/bibtex>`__)
 * J. Bergstra, O. Breuleux, F. Bastien, P. Lamblin, R.
  Pascanu, G. Desjardins, J. Turian, D. Warde-Farley and Y.
@@ -21,7 +21,7 @@ required) to cite the following two papers:
  <http://www.iro.umontreal.ca/~lisa/pointeurs/theano_scipy2010.pdf>`_.
  *Proceedings of the Python for Scientific Computing Conference (SciPy)
  2010. June 30 - July 3, Austin, TX* (`BibTeX
-  <http://www.iro.umontreal.ca/~lisa/publications2/index.php/export/publication/461/bibtex>`_)
+  <http://www.iro.umontreal.ca/~lisa/publications2/index.php/export/publication/461/bibtex>`__)
 Theano is primarily developed by academics, and so citations matter a lot to
 us. As an added benefit, you increase Theano's exposure and potential user

--- a/doc/extending/optimization.txt
+++ b/doc/extending/optimization.txt
@@ -886,7 +886,7 @@ To understand this profile here is some explanation of how optimizations work:
  * 0.028s means it spent that time calls to ``fgraph.validate()``
  * 0.131s means it spent that time for callbacks. This is a mechanism that can trigger other execution when there is a change to the FunctionGraph.
  * ``time      - (name, class, index) - validate time`` tells how the information for each sub-optimizer get printed.
-  * All other instances of ``SeqOptimizer`` are described like this. In particular, some sub-optimizer from OPT_FAST_RUN that are also ``SeqOptimizer``s.
+  * All other instances of ``SeqOptimizer`` are described like this. In particular, some sub-optimizer from OPT_FAST_RUN that are also ``SeqOptimizer``.
 * The ``SeqOptimizer`` will print some stats at the start:
@@ -965,7 +965,7 @@ To understand this profile here is some explanation of how optimizations work:
    a total of .7s. Its name is ``'canonicalize'``. It is an
    ``EquilibriumOptimizer``. It was executed at index 4 by the
    ``SeqOptimizer``. It spent 0.004s in the *validate* phase.
-  * All other lines are from the profiler of the ``EquilibriumOptimizer`.
+  * All other lines are from the profiler of the ``EquilibriumOptimizer``.
  * An ``EquilibriumOptimizer`` does multiple passes on the Apply nodes from
    the graph, trying to apply local and global optimizations.

--- a/doc/index.txt
+++ b/doc/index.txt
@@ -178,8 +178,8 @@ Community
 Help!
 =====
-How to seek help
+How to Seek Help
---------------
+----------------
 The appropriate venue for seeking help depends on the kind of question you have.

--- a/doc/install.txt
+++ b/doc/install.txt
@@ -199,10 +199,13 @@ the Theano cache like this:
 Bleeding-edge install instructions
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Master Tests Status:
+.. only:: html
-.. image:: https://secure.travis-ci.org/Theano/Theano.png?branch=master
+   Master Tests Status:
-    :target: http://travis-ci.org/Theano/Theano/builds
+   .. raw:: html
+      <a href="http://travis-ci.org/Theano/Theano/builds"><img src="https://secure.travis-ci.org/Theano/Theano.png?branch=master" /></a>&nbsp;
 If you are a developer of Theano, then check out the :ref:`dev_start_guide`.

--- a/doc/install_ubuntu.txt
+++ b/doc/install_ubuntu.txt
@@ -174,11 +174,6 @@ Change to the Theano directory and run:
 Manual Openblas instruction
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.. comment::
-    I believe this is outdated, my machine seems to be using 8 threads 
-    happily with the binary openblas...
 The openblas included in some older Ubuntu version is limited to 2
 threads. Ubuntu 14.04 do not have this limit. If you want to use more
 cores at the same time, you will need to compile it yourself. Here is

--- a/doc/install_windows.txt
+++ b/doc/install_windows.txt
@@ -120,7 +120,7 @@ dependencies is to install `Enthought Python Distribution (EPD) <http://enthough
 If you are affiliated with a university (as student or employee), you can
 download the installation for free.
 EPD installation includes, in particular, Python (and the development headers),
-NumPy, SciPy, nose, sphinx, easy_install, pydot (but *not* `Graphviz`_, which is
+NumPy, SciPy, nose, sphinx, easy_install, pydot (but *not* Graphviz, which is
 necessary for it to work), g++, and the MKL
 implementation of blas.
@@ -299,7 +299,7 @@ By default neither Python, GCC, nor Visual Studio was added to the
 PATH. Save the following shell script as ``c:\scisoft\env.bat`` to
 configure the system path:
-.. code-block:: cmd
+.. code-block:: none
   REM configuration of paths
   set VSFORPYTHON="C:\Program Files (x86)\Common Files\Microsoft\Visual C++ for Python\9.0"
@@ -335,7 +335,7 @@ programs are found:
 Finally we need to create a link library for GCC. Open up the Python
 shell and ``cd`` to ``c:\SciSoft``. Then execute:
-.. code-block:: cmd
+.. code-block:: none
   gendef WinPython-64bit-2.7.9.4\python-2.7.9.amd64\python27.dll

--- a/doc/library/sandbox/cuda/dnn.txt
+++ b/doc/library/sandbox/cuda/dnn.txt
@@ -129,12 +129,14 @@ Functions
 =========
 .. automodule:: theano.sandbox.cuda.dnn
+   :noindex:
   :members: dnn_conv, dnn_pool
 Convolution Ops
 ===============
 .. automodule:: theano.sandbox.cuda.dnn
+   :noindex:
   :members: GpuDnnConvDesc, GpuDnnConv, GpuDnnConv3d, GpuDnnConvGradW,
             GpuDnnConv3dGradW, GpuDnnConvGradI, GpuDnnConv3dGradI
@@ -142,10 +144,12 @@ Pooling Ops
 ===========
 .. automodule:: theano.sandbox.cuda.dnn
+   :noindex:
   :members: GpuDnnPoolDesc, GpuDnnPool, GpuDnnPoolGrad
 Softmax Ops
 ===========
 .. automodule:: theano.sandbox.cuda.dnn
+   :noindex:
   :members: GpuDnnSoftmax, GpuDnnSoftmaxGrad
--- a/doc/library/tensor/basic.txt
+++ b/doc/library/tensor/basic.txt
@@ -1652,6 +1652,7 @@ Linear Algebra
 	      number, then the stop is not inclusive.
    Example:
    >>> a = T.mgrid[0:5, 0:3]
    >>> a[0].eval()
    array([[0, 0, 0],
@@ -1675,6 +1676,7 @@ Linear Algebra
              not a complex number, then the stop is not inclusive.
    Example:
    >>> b = T.ogrid[0:5, 0:3]
    >>> b[0].eval()
    array([[0],

--- a/doc/tutorial/examples.txt
+++ b/doc/tutorial/examples.txt
@@ -465,9 +465,9 @@ There are :ref:`other distributions implemented <libdoc_tensor_raw_random>`.
 Other Implementations
 ---------------------
-There is 2 other implementations based on :ref:`MRG31k3p
+There are 2 other implementations based on :ref:`MRG31k3p
 <libdoc_rng_mrg>` and :class:`CURAND <theano.sandbox.cuda.rng_curand>`.
- The RandomStream only work on the CPU, MRG31k3p
+The RandomStream only work on the CPU, MRG31k3p
 work on the CPU and GPU. CURAND only work on the GPU.
 .. note::