Small documentation corrections.

doc/basic_tutorial/adding.txt

@@ -85,7 +85,7 @@ The second step is to combine ``x`` and ``y`` into their sum ``z``:
 function to pretty-print out the computation associated to ``z``.
 
 >>> print pp(z)
-x + y
+(x + y)
 
 -------------------------------------------
 

doc/basic_tutorial/examples.txt

@@ -97,17 +97,17 @@ Here is code to compute this gradient:
 >>> y = x**2
 >>> gy = T.grad(y, x)
 >>> pp(gy)
-'fill(x ** 2, 1.0) * 2 * x ** (2 - 1)'
+'((fill((x ** 2), 1.0) * 2) * (x ** (2 - 1)))'
 >>> f = function([x], gy)
 >>> f(4)
 array(8.0)
 >>> f(94.2)
 array(188.40000000000001)
 
-In the example above, we can see from ``pp(gw)`` that we are computing
+In the example above, we can see from ``pp(gy)`` that we are computing
 the correct symbolic gradient.
-``fill(x ** 2, 1.0)`` means to make a matrix of the same shape as ``x **
-2`` and fill it with 1.0.
+``fill((x ** 2), 1.0)`` means to make a matrix of the same shape as
+``x ** 2`` and fill it with 1.0.
 
 .. note::
     The optimizer will simplify the symbolic gradient expression.
@@ -252,7 +252,7 @@ array(5.9000000000000004)
 Mode
 ====
 
-The ``mode`` parameter to ``theano.function`` controls how the
+The ``mode`` parameter to :api:`theano.function` controls how the
 inputs-to-outputs graph is transformed into a callable object.
 
 Theano defines the following modes by name:
@@ -263,11 +263,11 @@ Theano defines the following modes by name:
     implementations. This mode can take much longer than the other modes, 
     but can identify many kinds of problems.
 
-The default mode is typically 'FAST_RUN', but it can be controlled via
-the environment variable 'THEANO_DEFAULT_MODE', which can in turn be
-overridden by setting ``theano.compile.mode.default_mode`` directly,
+The default mode is typically ``FAST_RUN``, but it can be controlled via
+the environment variable ``THEANO_DEFAULT_MODE``, which can in turn be
+overridden by setting :api:`theano.compile.mode.default_mode` directly,
 which can in turn be overridden by passing the keyword argument to
-``theano.function``.
+:api:`theano.function`.
 
 For a finer level of control over which optimizations are applied, and
 whether C or python implementations are used, read

doc/basic_tutorial/module.txt

@@ -49,7 +49,7 @@ Here we instantiate an empty Module.
 >>> m.state = T.dscalar()
 >>> m.inc = T.dscalar('inc')
 
-Then we declares for use with our Module.
+Then we declare Variables for use with our Module.
 Since we assign these input Variables as attributes of the Module,
 they will be *member Variables* of the Module.
 Member Variables are special in a few ways, which we will see shortly.
@@ -57,7 +57,7 @@ Member Variables are special in a few ways, which we will see shortly.
 .. note::
 
    There is no need to name the Variable explicitly here. ``m.state`` will
-   be given the name 'state' automatically.
+   be given the name ``'state'`` automatically.
 
 
 .. note::
@@ -70,9 +70,9 @@ Member Variables are special in a few ways, which we will see shortly.
 >>> m.new_state = m.state + m.inc
 
 This line creates a Variable corresponding to some symbolic computation.
-Although this line also assigns a Variable to a Module attribute, it does not
-become a member Variable like state and inc because it represents an expression
-result.
+Although this line also assigns a Variable to a Module attribute, it
+does not become a member Variable like ``state`` and ``inc`` because it
+represents an expression *result*.
 
 
 >>> m.add = Method(m.inc, m.new_state, {m.state: m.new_state})
@@ -94,17 +94,19 @@ computation and whose attributes contain values such as numbers and numpy
 ndarrays.
 
 At this point something special happens for our member Variables too.
-In the 'acc' object, make allocates room to store numbers for m's member
-Variables.  By using the string 'state' as a keyword argument, we tell Theano to
-store the number 0 for the member Variable called 'state'.  By not mentioning
-the 'inc' variable, we associate None to the 'inc' Variable.
+In the ``acc`` object, make allocates room to store numbers for ``m``'s
+member Variables.  By using the string ``'state'`` as a keyword
+argument, we tell Theano to store the number ``0`` for the member
+Variable called ``state``.  By not mentioning the ``inc`` variable, we
+associate ``None`` to the ``inc`` Variable.
 
 
 >>> acc.state, acc.inc
 array(0.0), None
 
-Since 'state' was declared as a member Variable of 'm', we can access it's value
-in the 'acc' object by the same attribute.  Ditto for 'inc'.
+Since ``state`` was declared as a member Variable of ``m``, we can
+access it's value in the ``acc`` object by the same attribute.
+Ditto for ``inc``.
 
 .. note::
 
@@ -119,16 +121,19 @@ array(2.0)
 >>> acc.state, acc.inc
 array(2.0), None
 
-When we call the ``acc.add`` method, the value 2 is used for the symbolic 'm.inc'
-The first line evaluates the output and all the updates given to the
-'acc' Method's ``updates`` field. We only had
-one update which mapped ``state`` to ``new_state`` and you can see
-that it works as intended, adding the argument to the internal state.
-
-Note also that 'acc.inc' is still None after our call.  Since 'm.inc' was listed
-as an input the Method, the method got it's own private storage container for
-'m.inc'.  If we had left 'm.inc' out of the Method input list,  then it the
-method would have used the module's storage for ``m.inc`` instead.
+When we call the ``acc.add`` method, the value ``2`` is used for the
+symbolic ``m.inc``.  The first line evaluates the output and all the
+updates given in the ``updates`` argument of the call to Method that
+declared ``acc``. We only had one update which mapped ``state`` to
+``new_state`` and you can see that it works as intended, adding the
+argument to the internal state.
+
+Note also that ``acc.inc`` is still ``None`` after our call.  Since
+``m.inc`` was listed as an input in the call to Method that created
+``m.add``, when ``acc.add`` was created by the call to ``m.make``, a
+private storage container was allocated to hold the first parameter.
+If we had left ``m.inc`` out of the Method input list, then ``acc.add``
+would have used ``acc.inc`` instead.
 
 
 >>> acc.state = 39.99