Fix d3viz doc errors.

doc/library/d3viz/index.txt

 .. _libdoc_d3viz:
 
-============================================================================
+=========================================================================
 :mod:`d3viz` -- d3viz: Interactive visualization of Theano compute graphs
-============================================================================
+=========================================================================
 
-.. module:: d3viz
+.. module:: theano.d3viz
    :platform: Unix, Windows
    :synopsis: Allows to interactively visualize Theano compute graphs
 .. moduleauthor:: Christof Angermueller
@@ -109,7 +109,7 @@ the the :py:mod:`theano.d3viz.d3viz` module, which can be called as before:
     import theano.d3viz as d3v
     d3v.d3viz(predict, 'examples/mlp.html')
 
-`Open visualization! <../../_static/mlp.html>`_
+`Open visualization! <../../_static/mlp.html>`__
 
 When you open the output file ``mlp.html`` in your web-browser, you will
 see an interactive visualization of the compute graph. You can move the
@@ -150,7 +150,7 @@ random data:
 
     d3v.d3viz(predict_profiled, 'examples/mlp2.html')
 
-`Open visualization! <../../_static/mlp2.html>`_
+`Open visualization! <../../_static/mlp2.html>`__
 
 When you open the HTML file in your browser, you will find an additional
 ``Toggle profile colors`` button in the menu bar. By clicking on it,
@@ -213,7 +213,7 @@ defines a nested graph, which will be visualized accordingly by
 
     d3v.d3viz(f, 'examples/ofg.html')
 
-`Open visualization! <../../_static/ofg.html>`_
+`Open visualization! <../../_static/ofg.html>`__
 
 In this example, an operation with three inputs is defined, which is
 used to build a function that calls this operations twice, each time
@@ -243,7 +243,7 @@ the following example.
 
     d3v.d3viz(f, 'examples/ofg2.html')
 
-`Open visualization! <../../_static/ofg2.html>`_
+`Open visualization! <../../_static/ofg2.html>`__
 
 Feedback
 --------

theano/compile/builders.py

@@ -14,7 +14,7 @@ class OpFromGraph(gof.Op):
     This creates an `Op` from inputs and outputs lists of variables.
 
     The signature is similar to theano.function() and the resulting
-    `Op`'s perform will do the same operation as:
+    `Op`'s perform will do the same operation as::
 
         orig_function(inputs, outputs, **kwargs)
 

theano/compile/function_module.py

@@ -242,7 +242,7 @@ class Function(object):
 
     A Function instance may be serialized using the `pickle` or
     `cPickle` modules.  This will save all default inputs, the graph,
-    and *** to the pickle file (WRITEME).
+    and WRITEME to the pickle file.
 
     A Function instance have a ``trust_input`` field that default to
     False. When True, we don't do extra check of the input to give

theano/d3viz/d3viz.py

@@ -18,9 +18,9 @@ def replace_patterns(x, replace):
 
     Parameters
     ----------
-    s: str
+    s : str
         String on which function is applied
-    replace: dict
+    replace : dict
         `key`, `value` pairs where key is a regular expression and `value` a
         string by which `key` is replaced
     """
@@ -34,7 +34,7 @@ def escape_quotes(s):
 
     Parameters
     ----------
-    s: str
+    s : str
         String on which function is applied
     """
     s = re.sub(r'''(['"])''', r'\\\1', s)
@@ -66,10 +66,12 @@ def d3viz(fct, outfile, copy_deps=True, *args, **kwargs):
         Path to output HTML file.
     copy_deps : bool, optional
         Copy javascript and CSS dependencies to output directory.
-    *args : tuple, optional
-        Arguments passed to PyDotFormatter.
-    *kwargs : dict, optional
-        Arguments passed to PyDotFormatter.
+
+    Notes
+    -----
+    This function accepts extra parameters which will be forwarded to
+    :class:`theano.d3viz.formatting.PyDotFormatter`.
+
     """
 
     # Create DOT graph
@@ -121,10 +123,12 @@ def d3write(fct, path, *args, **kwargs):
         A compiled Theano function, variable, apply or a list of variables.
     path: str
         Path to output file
-    *args : tuple, optional
-        Arguments passed to PyDotFormatter.
-    *kwargs : dict, optional
-        Arguments passed to PyDotFormatter.
+
+    Notes
+    -----
+    This function accepts extra parameters which will be forwarded to
+    :class:`theano.d3viz.formatting.PyDotFormatter`.
+
     """
 
     formatter = PyDotFormatter(*args, **kwargs)

theano/gof/utils.py

@@ -192,13 +192,13 @@ def deprecated(filename, msg=''):
     """
     Decorator which will print a warning message on the first call.
 
-    Use it like this:
+    Use it like this::
 
       @deprecated('myfile', 'do something different...')
       def fn_name(...)
           ...
 
-    And it will print:
+    And it will print::
 
       WARNING myfile.fn_name deprecated. do something different...