Fix broken source links

doc/library/compile/debugmode.txt

@@ -5,7 +5,7 @@
 :mod:`debugmode`
 =================
 
-.. module:: debugmode
+.. module:: theano.compile.debugmode
    :platform: Unix, Windows
    :synopsis: defines DebugMode
 .. moduleauthor:: LISA

doc/library/compile/function.txt

@@ -5,7 +5,7 @@
 :mod:`function` - defines theano.function
 ===========================================
 
-.. module:: function
+.. module:: theano.compile.function
    :platform: Unix, Windows
    :synopsis: defines theano.function and related classes
 .. moduleauthor:: LISA

doc/library/compile/io.txt

@@ -10,7 +10,7 @@
 :mod:`io` - defines theano.function [TODO]
 ===========================================
 
-.. module:: io
+.. module:: theano.compile.io
    :platform: Unix, Windows
    :synopsis: defines In and Out
 .. moduleauthor:: LISA

doc/library/compile/mode.txt

@@ -5,7 +5,7 @@
 :mod:`mode` -- controlling compilation
 ======================================
 
-.. module:: mode
+.. module:: theano.compile.mode
    :platform: Unix, Windows
    :synopsis: controlling compilation
 .. moduleauthor:: LISA

doc/library/compile/nanguardmode.txt

@@ -5,7 +5,7 @@
 :mod:`nanguardmode`
 ===================
 
-.. module:: nanguardmode
+.. module:: theano.compile.nanguardmode
    :platform: Unix, Windows
    :synopsis: defines NanGuardMode
 .. moduleauthor:: LISA

doc/library/compile/profilemode.txt

@@ -6,7 +6,7 @@
 ================================================
 
 
-.. module:: profilemode
+.. module:: theano.compile.profilemode
    :platform: Unix, Windows
    :synopsis: profiling Theano functions with ProfileMode
 .. moduleauthor:: LISA

doc/library/gof/fgraph.txt

@@ -2,26 +2,40 @@
 .. _libdoc_gof_fgraph:
 
 ================================================
-:mod:`fgraph` -- Graph Container [doc TODO]
+:mod:`fg` -- Graph Container [doc TODO]
 ================================================
 
-.. module:: fgraph
+.. module:: theano.gof.fg
    :platform: Unix, Windows
    :synopsis: Theano Internals
 .. moduleauthor:: LISA
 
 
-Guide
-=====
+.. _fgraph:
 
 FunctionGraph
 -------------
 
+.. autoclass:: theano.gof.FunctionGraph
+    :members: 
+
+    ***TODO***
+
+    .. note:: FunctionGraph(inputs, outputs) clones the inputs by
+        default. To avoid this behavior, add the parameter
+        clone=False. This is needed as we do not want cached constants
+        in fgraph.
+
 .. _libdoc_gof_fgraphfeature:
 
+.. _fgraphfeature:
+
 FunctionGraph Features
 ----------------------
 
+.. autoclass:: theano.gof.toolbox.Feature 
+    :members: 
+
 .. _libdoc_gof_fgraphfeaturelist:
 
 FunctionGraph Feature List
@@ -29,14 +43,3 @@ FunctionGraph Feature List
 * ReplaceValidate
 * DestroyHandler
 
-Reference
-=========
-
-.. class:: FunctionGraph
-
-    ***TODO***
-
-    .. note:: FunctionGraph(inputs, outputs) clones the inputs by
-        default. To avoid this behavior, add the parameter
-        clone=False. This is needed as we do not want cached constants
-        in fgraph.

doc/library/gof/graph.txt

@@ -4,14 +4,12 @@
 :mod:`graph` -- Interface for the Theano graph
 ==============================================
 
-.. module:: graph
-   :platform: Unix, Windows
-   :synopsis: Interface for types of symbolic variables
-.. moduleauthor:: LISA
-
 ---------
 Reference
 ---------
 
 .. automodule:: theano.gof.graph
+   :platform: Unix, Windows
+   :synopsis: Interface for types of symbolic variables
    :members:
+.. moduleauthor:: LISA

doc/library/gof/type.txt

@@ -4,14 +4,12 @@
 :mod:`type` -- Interface for types of variables
 ================================================
 
-.. module:: type
-   :platform: Unix, Windows
-   :synopsis: Interface for types of symbolic variables
-.. moduleauthor:: LISA
-
 ---------
 Reference
 ---------
 
 .. automodule:: theano.gof.type
+   :platform: Unix, Windows
+   :synopsis: Interface for types of symbolic variables
    :members:
+.. moduleauthor:: LISA

doc/library/gof/utils.txt

@@ -8,14 +8,12 @@
 
    from theano.gof.utils import *
 
-.. module:: utils
-   :platform: Unix, Windows
-   :synopsis: Utilities functions operating on the graph
-.. moduleauthor:: LISA
-
 ---------
 Reference
 ---------
 
 .. automodule:: theano.gof.utils
+   :platform: Unix, Windows
+   :synopsis: Utilities functions operating on the graph
    :members:
+.. moduleauthor:: LISA

doc/library/printing.txt

@@ -4,7 +4,7 @@
 :mod:`printing` -- Graph Printing and Symbolic Print Statement
 ===============================================================
 
-.. module:: printing
+.. module:: theano.printing
    :platform: Unix, Windows
    :synopsis: Provides the Print Op and graph-printing routines.
 .. moduleauthor:: LISA

doc/library/tensor/nnet/index.txt

@@ -4,7 +4,7 @@
 :mod:`nnet`  -- Ops related to neural networks
 ==================================================
 
-.. module:: nnet
+.. module:: theano.tensor.nnet
    :platform: Unix, Windows
    :synopsis: various ops relating to neural networks
 .. moduleauthor:: LISA

doc/library/tensor/nnet/nnet.txt

@@ -4,7 +4,7 @@
 :mod:`nnet` -- Ops for neural networks
 ======================================================
 
-.. module:: tensor.nnet
+.. module:: theano.tensor.nnet.nnet
    :platform: Unix, Windows
    :synopsis: Ops for neural networks
 .. moduleauthor:: LISA

doc/library/tensor/raw_random.txt

@@ -5,7 +5,7 @@
 :mod:`raw_random` -- Low-level random numbers
 =============================================
 
-.. module:: raw_random
+.. module:: theano.tensor.raw_random
    :synopsis: symbolic random variables
 .. moduleauthor:: LISA
 

doc/library/tensor/shared_randomstreams.txt

@@ -4,7 +4,7 @@
 :mod:`shared_randomstreams` -- Friendly random numbers
 ======================================================
 
-.. module:: shared_randomstreams
+.. module:: theano.tensor.shared_randomstreams
    :platform: Unix, Windows
    :synopsis: symbolic random variables
 .. moduleauthor:: LISA

doc/sandbox/fg.txt

-
-.. _fgraph:
-
-=============
-FunctionGraph
-=============
-
-TODO: clean up/update the doc/check if complete
-WRITEME
-
-.. autoclass:: theano.gof.fg.FunctionGraph
-
-.. _fgraphfeature:
-
-Feature
-=======
-
-.. autoclass:: theano.gof.toolbox.Feature
-    :members:

doc/sandbox/index2.txt

@@ -8,7 +8,6 @@ Advanced Topics (under construction)
 .. toctree::
     :maxdepth: 2
 
-    fg
     compilation
     ccodegen
     function

theano/gof/fg.py

@@ -593,10 +593,10 @@ class FunctionGraph(utils.object2):
 
     # callback utils #
     def execute_callbacks(self, name, *args, **kwargs):
-        """
-        Calls
-          getattr(feature, name)(*args)
-        for each feature which has a method called after name.
+        """Execute callbacks
+
+        Calls `getattr(feature, name)(*args)` for each feature which has
+        a method called after name.
 
         """
         t0 = time.time()
@@ -614,11 +614,11 @@ class FunctionGraph(utils.object2):
         self.execute_callbacks_time += time.time() - t0
 
     def collect_callbacks(self, name, *args):
-        """
-        Returns a dictionary d such that:
-          d[feature] == getattr(feature, name)(*args)
-        For each feature which has a method called after name.
+        """Collects callbacks
 
+        Returns a dictionary d such that
+        `d[feature] == getattr(feature, name)(*args)`
+        For each feature which has a method called after name.
         """
         d = {}
         for feature in self._features:
@@ -631,17 +631,18 @@ class FunctionGraph(utils.object2):
 
     # misc #
     def toposort(self):
-        """
-        Return an ordering of the graph's Apply nodes such that:
-        - All the nodes of the inputs of a node are before that node.
-        - Satisfies the orderings provided by each feature that has
+        """Toposort
+
+        Return an ordering of the graph's Apply nodes such that
+
+        * All the nodes of the inputs of a node are before that node.
+        * Satisfies the orderings provided by each feature that has
           an 'orderings' method.
 
         If a feature has an 'orderings' method, it will be called with
         this FunctionGraph as sole argument. It should return a dictionary of
-        {node: predecessors} where predecessors is a list of nodes
-        that should be computed before the key node.
-
+        `{node: predecessors}` where predecessors is a list of nodes that
+        should be computed before the key node.
         """
         if len(self.apply_nodes) < 2:
             # optimization
@@ -760,17 +761,20 @@ class FunctionGraph(utils.object2):
         return self.clone_get_equiv(check_integrity)[0]
 
     def clone_get_equiv(self, check_integrity=True, attach_feature=True):
-        """Clone the graph and get a memo( a dict )that map old node to new node
-        ----------------------------
+        """Clone the graph and get a dict that maps old nodes to new ones
+
         Parameters:
-            check_integrity - { bool } Whether to check integrity.
+            check_integrity: bool
+                Whether to check integrity. Default is True.
+            attach_feature: bool
+                Whether to attach feature of origin graph to cloned graph.
                 Default is True.
-            attach_feature - { bool } Whether to attach feature of origin graph to
-                                cloned graph. Default is True.
-        ----------------------------
+
         Returns:
-            e - { FunctionGraph } Cloned fgraph. Every node in cloned graph is cloned.
-            equiv - { dict } A dict that map old node to new node.
+            e: FunctionGraph
+                Cloned fgraph. Every node in cloned graph is cloned.
+            equiv: dict
+                A dict that map old node to new node.
         """
         equiv = graph.clone_get_equiv(self.inputs, self.outputs)
 

theano/gof/graph.py

 """
 Node classes (`Apply`, `Variable`) and expression graph algorithms.
-
-To read about what theano graphs are from a user perspective, have a look at
-`graph.html <../doc/graph.html>`__.
-
 """
 from __future__ import absolute_import, print_function, division
 
@@ -1246,9 +1242,9 @@ def as_string(i, o,
         Input `Variable` s.
     o : list
         Output `Variable` s.
-    leaf_formatter : function
+    leaf_formatter : theano.function
         Takes a `Variable`  and returns a string to describe it.
-    node_formatter : function
+    node_formatter : callable
         Takes an `Op`  and the list of strings corresponding to its arguments
         and returns a string to describe it.