Reorganized docs

doc/contents.txt

@@ -6,9 +6,10 @@ Contents
 ========
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 3
 
    index
+   LICENSE
    install
    tutorials/index
    advanced/index
@@ -16,6 +17,6 @@ Contents
    examples/index
    glossary
    links
-   LICENSE
-
+   internal/index
+   doc/index
 

doc/doc/concepts.txt

-.. _concepts:
-
-================
-Concepts
-================
-
-This page introduces some important terminology for describing how theano
-works.
-
-Lets start by looking at what happens in a simple theano program.
-
-.. code-block:: python
-
-    x = tensor.matrix('x')
-    y = tensor.matrix('y')
-    z = x + y
-    f = theano.function(input=[x,y], output=z, mode='FAST_RUN')
-    print f(numpy.ones(2,3), numpy.ones(2,3))
-
-The first three lines build a :term:`graph` whose nodes correspond to variables (``x,y,z``) and expressions (just the '+' here).
-The variables in such a graph are :term:`Result` instances of some
-:term:`Type`, and the expressions are :term:`Apply` instances of some
-:term:`Op`.
-
-The line ``f = theano.function([x,y], [z], mode='FAST_RUN')`` :term:`compiles
-<Compilation>`.
-the graph we built and returns a :term:`function` whose ``__call__`` method
-takes as arguments the values to use for ``x`` and ``y``.
-The :term:`mode` controls which :term:`transformations <Graph Transformation>` are applied to the graph as we compile it.
-
-The line ``print f(numpy.ones(2,3), numpy.ones(2,3))`` creates two
-matrices, and then uses f's ``__call__`` method to run the compiled
-function on those inputs.
-The compiled function is executed by a :term:`linker`, which was also specified by the :term:`mode` argument to ``function``.
-The instance f's ``__call__`` method returns a value for ``z`` (given ``x,y``) which we print.

doc/doc/extending.txt

-.. _extending:
-
-================
-Extending theano
-================
-
-When you're comfortable with the material in :ref:`concepts`, move on to:
-
-* HowtoCreateType create a new data type,
-* HowtoCreateOp create a new type of Op,
-* HowtoAddTransformation add a transformation to an existing transformation mode,
-* Create a new mode by HowtoCreateLinker creating a new linker, or HowtoCreateTransformationMode create a new transformation mode.
-

doc/doc/graph.txt

-.. _graph:
-
-================================================
-Graph: interconnected Apply and Result instances
-================================================
-
-<MOVED TO advanced/graphstructures.txt>
-
-.. _README: ../README.html
-.. _Download: ../README.html#downloading-theano
-.. _Documentation: index.html
-.. _Wiki: http://pylearn.org/theano
-.. _task list: http://lgcm.iro.umontreal.ca/theano/query?status=accepted&status=assigned&status=new&status=reopened&group=milestone&max=200&col=id&col=summary&col=status&col=owner&col=type&col=priority&col=component&col=time&report=9&order=priority
-
-

doc/doc/index.txt

-=====================================
-Theano Project Documentation Overview
-=====================================
+=========================================================
+Sandbox, this documentation may or may not be out-of-date
+=========================================================
 
 .. toctree::
    :glob:

doc/doc/dev_start_guide.txt → doc/internal/dev_start_guide.txt

+
+.. _dev_start_guide:
+
 =====================
 Developer Start Guide
 =====================
@@ -38,7 +41,7 @@ As a developer, you should clone this repository like this:
 - `hg clone 'http://username:password@pylearn.org/hg/theano' theano`
 
 
-Nighlty test
+Nightly test
 ============
 
 Their is nightly build done. The output is at: http://lgcm/nightly_build/do_nightly_build.txt

doc/internal/extending.txt

+.. _extending:
+
+================
+Extending theano
+================
+
+
+How to Add Transformations
+==========================
+
+WRITEME
+
+How to Create a Linker
+======================
+
+WRITEME
+
+How to Create a Transformation Mode
+===================================
+
+WRITEME

doc/internal/index.txt

+
+.. _internal:
+
+======================
+Internal documentation
+======================
+
+Structure
+=========
+
+.. toctree::
+   :maxdepth: 2
+
+   dev_start_guide
+   extending

doc/tutorials/basic/module.txt

@@ -6,14 +6,14 @@ Using Module
 Now that we're familiar with the basics, we introduce Theano's more
 advanced interface, Module. This interface allows you to define Theano
 "objects" which can have many state variables and many methods sharing
-these states. This is what you should use to define complex systems such
-as a neural network.
+these states. The Module system simplifies the way to define complex
+systems such as a neural network.
 
 
 Remake of the "state" example
 =============================
 
-Let's use Module to re-implement :ref:`this example
+Let's use Module to re-implement :ref:`the example using state
 <functionstateexample>`.
 
 >>> m = Module()
@@ -44,21 +44,21 @@ Here we instantiate an empty Module.
 
 >>> m.state = Member(T.dscalar())
 
-Then we declare a variable for use with our Module. That variable will
-be a :ref:`member` of the module, which means that it will be
+Then we declare a Result for use with our Module. That Result will
+be a :ref:`member` of the Module, which means that it will be
 accessible as a field of the object we will create later (for reading
 and writing). It will also be accessible from any :ref:`method`
 defined in our Module.
 
 .. note::
 
-   There is no need to name the variable explicitly here. m.state will
+   There is no need to name the Result explicitly here. ``m.state`` will
    be given the name 'state' automatically.
 
 
 >>> m.inc = External(T.dscalar('inc'))
 
-The inc variable doesn't need to be declared as a Member because it
+The ``inc`` variable doesn't need to be declared as a Member because it
 will only serve as an input to the method we will define. This is why
 it is defined as an :ref:`external` variable. Do note that it is
 inconsequential if you do declare it as a Member - it is unlikely