merged

__init__.py

 """
-WRITEME: Some module-level documentation.
+Theano is an optimizing compiler in Python, built to evaluate complicated expressions
+(especially matrix-valued ones) as quickly as possible. 
+Theano compiles expression graphs (see :doc:`graph` ) that are built by Python code.
+The expressions in these graphs are called `Apply` nodes and the variables in these graphs are called `Result` nodes.
 
-Here is how to make a link into the wiki: check out the :wiki:`DefineGraph()`.
+You compile a graph by calling `function`, which takes a graph, and returns a callable object.
+One of theano's most important features is that `function` can transform your graph before
+compiling it.
+It can replace simple expressions with faster or more numerically stable implementations.
+
+To learn more, check out:
+
+- Joseph Turian's n00b walk through ( :wiki:`UserBasic` )
+
+- an introduction to extending theano ( :wiki:`UserAdvanced` )
+
+- Terminology Glossary (:wiki:`glossary`)
+
+- Index of Howto documents (:wiki:`IndexHowto`)
 
 """
 

doc/doc.idx

-graph	/graph.html
-tensor	/graph.html
-result	/graph.html
-howto	/graph.html
+graph	graph.html
+tensor	graph.html
+result	graph.html
+howto	graph.html

gof/op.py

-""" Defines base clases `Op` and `Op_clinker`.
+"""Defines base classes `Op`, `PureOp`, and `CLinkerOp`
 
 The `Op` class is the base interface for all operations
 compatible with `gof`'s :doc:`graph` routines.
 
+
 """
 
 __docformat__ = "restructuredtext en"
@@ -11,20 +12,20 @@ import utils
 import traceback
 
 
-class Op_clinker(utils.object2):
+class CLinkerOp(object):
     """
     Interface definition for `Op` subclasses compiled by `CLinker`.
 
-    A subclass should implement
+    A subclass should implement WRITEME.
 
-    WRITEME: structure of automatically generated C code.
+    WRITEME: structure of automatically generated C code.  Put this in doc/code_structure.txt
 
     """
 
     def c_code(self, node, name, inputs, outputs, sub):
         """Required: Return the C implementation of an Op.
 
-        Returns C code that does the computation associated to this L{Op},
+        Returns C code that does the computation associated to this `Op`,
         given names for the inputs and outputs.
         
         :Parameters:
@@ -137,15 +138,7 @@ class Op_clinker(utils.object2):
         """
         raise utils.AbstractFunctionError()
 
-
-#TODO: 
-# This is a somewhat ugly use of inheritance because Op is an abstract interface that has
-# nothing to do with code generation.
-# 
-# Better would be for Op subclasses wanting to work with the CLinker to have a second
-# inheritance from Op_clinker.
-
-class Op(Op_clinker):
+class PureOp(object):
     """
     An :term:`Op` is a type of operation.
 
@@ -161,9 +154,6 @@ class Op(Op_clinker):
 
     - performing the calculation of outputs from given inputs (via the `perform`),
 
-    - producing c code to perform calculation of outputs from inputs (via `c_code`, 
-      `c_code_cleanup`, `c_support_code`, `c_headers`, `c_libraries`, `c_compile_args`)
-
     - [optionally] building gradient-calculating graphs (via `grad`).
 
 
@@ -186,7 +176,7 @@ class Op(Op_clinker):
 
     def make_node(self, *inputs):
         """
-        Contract: return an Apply instance representing the
+        Required: return an Apply instance representing the
         application of this Op to the provided inputs.
 
         All subclasses should over-ride this function.
@@ -198,8 +188,7 @@ class Op(Op_clinker):
         raise utils.AbstractFunctionError(self)
 
     def __call__(self, *inputs):
-        """
-        Return some or all output[s] of `make_node`.  
+        """Optional: Return some or all output[s] of `make_node`.  
 
         It is called by code such as:
 
@@ -232,7 +221,7 @@ class Op(Op_clinker):
 
     def perform(self, node, inputs, output_storage):
         """
-        Contract:  Calculate the function on the inputs and put the results in the
+        Required:  Calculate the function on the inputs and put the results in the
         output storage.  Return None.
 
         :Parameters:
@@ -254,4 +243,6 @@ class Op(Op_clinker):
         """
         raise utils.AbstractFunctionError(self)
 
-
+class Op(utils.object2, PureOp, CLinkerOp): 
+    """Convenience class to bundle `PureOp` and `CLinkerOp`"""
+    pass

local.epydoc

@@ -120,13 +120,9 @@ separate-classes: no
 
 # Use this URL prefix to configure the string returned for external API.
 #external-api-root: epydoc:http://epydoc.sourceforge.net/api
-external-api: wiki
-external-api-root: wiki:http://lgcm.iro.umontreal.ca/theano/wiki/
-external-api-file: wiki:wiki.idx
-
-external-api: doc
-external-api-root: doc:http://lgcm.iro.umontreal.ca/doc/
-external-api-file: doc:doc/doc.idx
+external-api: wiki doc
+external-api-root: wiki:http://lgcm.iro.umontreal.ca/theano/wiki/ doc:http://lgcm.iro.umontreal.ca/auto_theano/doc/
+external-api-file: wiki:wiki.idx doc:doc/doc.idx
 
 ### Graph options
 

wiki.idx

-DefineGraph	DefineGraph
-DefineTensorResult	DefineTensor#TensorResult
-Connection.cursor()	NothingInvalid.html
+wiki.DefineGraph	DefineGraph
+wiki.DefineTensorResult	DefineTensor#TensorResult
+wiki.HowtoList	HowtoList
+wiki.UserBasic	UserBasic
+wiki.UserAdvanced	UserAdvanced
+wiki.TerminologyGlossary	TerminologyGlossary
+wiki.glossary	TerminologyGlossary
+wiki.IndexHowto	IndexHowto