renamed Env to FunctionGraph. closes 719

doc/extending/pipeline.txt

@@ -36,32 +36,32 @@ Here is an overview of the various steps that are done with the
 computation graph in the compilation phase:
 
 
-Step 1 - Create an Env
+Step 1 - Create a FunctionGraph
 ^^^^^^^^^^^^^^^^^^^^^^
 
 The subgraph given by the end user is wrapped in a structure called
-*Env*. That structure defines several hooks on adding and
+*FunctionGraph*. That structure defines several hooks on adding and
 removing (pruning) nodes as well as on modifying links between nodes
 (for example, modifying an input of an :ref:`apply` node) (see the
 article about :ref:`libdoc_gof_env` for more information).
 
-Env provides a method to change the input of an Apply node from one
+FunctionGraph provides a method to change the input of an Apply node from one
 Variable to another and a more high-level method to replace a Variable
 with another. This is the structure that :ref:`Optimizers
 <optimization>` work on.
 
 Some relevant :ref:`Features <libdoc_gof_envfeature>` are typically added to the
-Env, namely to prevent any optimization from operating inplace on
+FunctionGraph, namely to prevent any optimization from operating inplace on
 inputs declared as immutable.
 
 
 Step 2 - Execute main Optimizer
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Once the Env is made, an :term:`optimizer` is produced
+Once the FunctionGraph is made, an :term:`optimizer` is produced
 by the :term:`mode` passed to ``function`` or to the Method/Module's
 ``make`` (the Mode basically has two important fields, ``linker`` and
-``optimizer``). That optimizer is applied on the Env using its
+``optimizer``). That optimizer is applied on the FunctionGraph using its
 optimize() method.
 
 The optimizer is typically obtained through :attr:`optdb`.
@@ -71,7 +71,8 @@ Step 3 - Execute linker to obtain a thunk
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Once the computation graph is optimized, the :term:`linker` is
-extracted from the Mode. It is then called with the Env as argument to
+extracted from the Mode. It is then called with the FunctionGraph as
+argument to
 produce a ``thunk``, which is a function with no arguments that
 returns nothing. Along with the thunk, one list of input containers (a
 theano.gof.Container is a sort of object that wraps another and does

theano/compile/debugmode.py

@@ -13,7 +13,7 @@ import numpy
 
 import theano
 from theano import gof
-from theano.gof import Env, graph, utils, link, ops_with_inner_function
+from theano.gof import FunctionGraph as Env, graph, utils, link, ops_with_inner_function
 from theano.gof.link import raise_with_op
 from theano.gof.cc import CLinker
 from theano.gof.python25 import all, any, product as itertools_product
@@ -667,7 +667,7 @@ def _optcheck_env(input_specs, output_specs, accept_inplace=False):
 
     inputs, outputs = gof.graph.clone(orig_inputs, orig_outputs)
     equivalence_tracker = _VariableEquivalenceTracker()
-    env = gof.env.Env(inputs, outputs,
+    env = gof.fg.FunctionGraph(inputs, outputs,
             #DestroyHandler is not needed because it is actually installed by an optimization
             # after canonicalization.  This variables in a big speed gain.
             #features=[equivalence_tracker, gof.DestroyHandler(do_imports_on_attach=False)])

theano/compile/function_module.py

@@ -129,7 +129,7 @@ def std_env(input_specs, output_specs, accept_inplace = False):
     orig_outputs = [spec.variable for spec in output_specs] + updates
 
     inputs, outputs = gof.graph.clone(orig_inputs, orig_outputs)
-    env = gof.env.Env(inputs, outputs)
+    env = gof.fg.FunctionGraph(inputs, outputs)
 
     for node in env.nodes:
         if getattr(node.op, 'destroy_map', None):

theano/gof/__init__.py

@@ -5,8 +5,10 @@ from cc import \
 
 import compiledir # adds config vars
 
-from env import \
-    InconsistencyError, MissingInputError, Env
+from fg import \
+    InconsistencyError, MissingInputError, FunctionGraph
+#deprecated alias to support code written with old name
+Env = FunctionGraph
 
 from destroyhandler import \
     DestroyHandler

theano/gof/destroyhandler.py

@@ -10,7 +10,7 @@ import toolbox
 import graph
 from theano.gof.python25 import deque
 
-from env import InconsistencyError
+from fg import InconsistencyError
 
 class ProtocolError(Exception):
     """WRITEME"""

theano/gof/env.py → theano/gof/fg.py

 
-"""WRITEME"""
+"""
+fg.py: fg stands for FunctionGraph
+Contains the FunctionGraph class and exception
+types that it can raise
+"""
 import sys
-from copy import copy
 import graph
 import utils
 import toolbox
@@ -11,7 +14,7 @@ from theano import config
 
 class InconsistencyError(Exception):
     """
-    This exception should be thrown by listeners to Env when the
+    This exception should be thrown by listeners to FunctionGraph when the
     graph's state is invalid.
     """
     pass
@@ -24,14 +27,18 @@ class MissingInputError(Exception):
 
 
 
-class Env(utils.object2):
+class FunctionGraph(utils.object2):
     """ WRITEME
-    An Env represents a subgraph bound by a set of input variables and a
-    set of output variables. The inputs list should contain all the inputs
+    A FunctionGraph represents a subgraph bound by a set of input variables and a
+    set of output variables, ie a subgraph that specifies a theano function.
+    The inputs list should contain all the inputs
     on which the outputs depend. Variables of type Constant are
     not counted as inputs.
 
-    The Env supports the replace operation which allows to replace a
+    Historically, the FunctionGraph was called an Env. Many other objects refer
+    to the FunctionGraph they belong to as their "env".
+
+    The FunctionGraph supports the replace operation which allows to replace a
     variable in the subgraph by another, e.g. replace (x + x).out by (2
     * x).out. This is the basis for optimization in theano.
 
@@ -42,34 +49,34 @@ class Env(utils.object2):
     The .clients field combined with the .owner field and the Apply nodes'
     .inputs field allows the graph to be traversed in both directions.
 
-    It can also be "extended" using env.extend(some_object). See the
+    It can also be "extended" using function_graph.extend(some_object). See the
     toolbox and ext modules for common extensions.
 
     Features added with the`extend` function can handle the following events:
 
-    - feature.on_attach(env)
+    - feature.on_attach(function_graph)
         Called by extend. The feature has great freedom in what
-        it can do with the env: it may, for example, add methods
+        it can do with the function_graph: it may, for example, add methods
         to it dynamically.
 
-    - feature.on_detach(env)
+    - feature.on_detach(function_graph)
         Called by remove_feature(feature).  Should remove any dynamically-added
-        functionality that it installed into the env.
+        functionality that it installed into the function_graph.
 
-    - feature.on_import(env, node)*
-        Called whenever a node is imported into env, which is
+    - feature.on_import(function_graph, node)*
+        Called whenever a node is imported into function_graph, which is
         just before the node is actually connected to the graph.
 
-    - feature.on_prune(env, node)*
-        Called whenever a node is pruned (removed) from the env,
+    - feature.on_prune(function_graph, node)*
+        Called whenever a node is pruned (removed) from the function_graph,
         after it is disconnected from the graph.
 
-    - feature.on_change_input(env, node, i, r, new_r, [reason=None])*
+    - feature.on_change_input(function_graph, node, i, r, new_r, [reason=None])*
         Called whenever node.inputs[i] is changed from r to new_r.
         At the moment the callback is done, the change has already
         taken place.
 
-    - feature.orderings(env)
+    - feature.orderings(function_graph)
         Called by toposort. It should return a dictionary of
         {node: predecessors} where predecessors is a list of
         nodes that should be computed before the key node.
@@ -77,10 +84,10 @@ class Env(utils.object2):
         * If you raise an exception in the functions marked with an
           asterisk, the state of the graph might be inconsistent.
 
-    - feature.on_setup_node(env, node):
+    - feature.on_setup_node(function_graph, node):
         WRITEME
 
-    - feature.on_setup_variable(env, variable):
+    - feature.on_setup_variable(function_graph, variable):
         WRITEME
 
     """
@@ -90,14 +97,14 @@ class Env(utils.object2):
 
     def __init__(self, inputs, outputs, features=None):
         """
-        Create an Env which operates on the subgraph bound by the inputs and
+        Create an FunctionGraph which operates on the subgraph bound by the inputs and
         outputs sets.
 
         This class keeps a pointer to the inputs and outputs, and also modifies
         them.
 
-        #TODO: document what variables are[not] set in the env when a feature
-        is added via the constructor.  How constructed is the env?
+        #TODO: document what variables are[not] set in the FunctionGraph when a feature
+        is added via the constructor.  How constructed is the FunctionGraph?
 
         """
 
@@ -171,12 +178,12 @@ class Env(utils.object2):
 
     def disown(self):
         """ WRITEME
-        Cleans up all of this Env's nodes and variables so they are not
-        associated with this Env anymore.
+        Cleans up all of this FunctionGraph's nodes and variables so they are not
+        associated with this FunctionGraph anymore.
 
-        The Env should not be used anymore after disown is called.
+        The FunctionGraph should not be used anymore after disown is called.
 
-        This may not clean everything this Env's features set in the
+        This may not clean everything this FunctionGraph's features set in the
         nodes and variables. If there are no features, this should set
         them back to what they were originally.
         """
@@ -362,7 +369,7 @@ class Env(utils.object2):
 
     def __prune__(self, node):
         if node not in self.nodes:
-            raise Exception("%s does not belong to this Env and cannot be pruned." % node)
+            raise Exception("%s does not belong to this FunctionGraph and cannot be pruned." % node)
         assert node.env is self
         # If node's outputs have no clients, removes it from the graph
         # and recursively tries to prune its inputs. If at least one
@@ -392,7 +399,7 @@ class Env(utils.object2):
         current value of node.inputs[i] which we want to replace.
 
         For each feature that has a 'on_change_input' method, calls:
-          feature.on_change_input(env, node, i, old_r, new_r, [reason])
+          feature.on_change_input(function_graph, node, i, old_r, new_r, [reason])
         """
         # TODO: ERROR HANDLING FOR LISTENERS (should it complete the change or revert it?)
         if node == 'output':
@@ -405,7 +412,7 @@ class Env(utils.object2):
         else:
             if node.env is not self:
                 raise Exception("Cannot operate on %s because it does not"
-                        " belong to this Env" % node)
+                        " belong to this FunctionGraph" % node)
             r = node.inputs[i]
             if not r.type == new_r.type:
                 raise TypeError("The type of the replacement must be the"
@@ -432,11 +439,11 @@ class Env(utils.object2):
 
     def replace(self, r, new_r, reason=None):
         """ WRITEME
-        This is the main interface to manipulate the subgraph in Env.
+        This is the main interface to manipulate the subgraph in FunctionGraph.
         For every node that uses r as input, makes it use new_r instead.
         """
         if r.env is not self:
-            raise Exception("Cannot replace %s because it does not belong to this Env" % r, str(reason))
+            raise Exception("Cannot replace %s because it does not belong to this FunctionGraph" % r, str(reason))
         if not r.type == new_r.type:
             raise TypeError("The type of the replacement must be the same as the type of the original Variable.", r, new_r, r.type, new_r.type, str(reason))
         if r not in self.variables:
@@ -466,7 +473,7 @@ class Env(utils.object2):
     # would expect it to do similarly.
     def extend(self, feature):
         """WRITEME
-        Adds a feature to this env. The feature may define one
+        Adds a feature to this function_graph. The feature may define one
         or more of the following methods:
 
         """
@@ -484,7 +491,7 @@ class Env(utils.object2):
         """WRITEME
         Removes the feature from the graph.
 
-        Calls feature.on_detach(env) if an on_detach method is defined.
+        Calls feature.on_detach(function_graph) if an on_detach method is defined.
         """
         try:
             self._features.remove(feature)
@@ -545,7 +552,7 @@ class Env(utils.object2):
             an 'orderings' method.
 
         If a feature has an 'orderings' method, it will be called with
-        this env as sole argument. It should return a dictionary of
+        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.
         """
@@ -555,9 +562,9 @@ class Env(utils.object2):
             # This special case happens a lot because the OpWiseCLinker produces
             # 1-element graphs.
             return list(self.nodes)
-        env = self
+        fg = self
         ords = self.orderings()
-        order = graph.io_toposort(env.inputs, env.outputs, ords)
+        order = graph.io_toposort(fg.inputs, fg.outputs, ords)
         return order
 
     def orderings(self):
@@ -605,10 +612,10 @@ class Env(utils.object2):
             raise Exception("The nodes are inappropriately cached. missing, in excess: ", missing, excess)
         for node in nodes:
             if node.env is not self:
-                raise Exception("Node should belong to the env.", node)
+                raise Exception("Node should belong to the FunctionGraph.", node)
             for i, variable in enumerate(node.inputs):
                 if variable.env is not self:
-                    raise Exception("Input of node should belong to the env.", variable, (node, i))
+                    raise Exception("Input of node should belong to the FunctionGraph.", variable, (node, i))
                 if (node, i) not in variable.clients:
                     raise Exception("Inconsistent clients list.", (node, i), variable.clients)
         variables = set(graph.variables(self.inputs, self.outputs))
@@ -620,14 +627,14 @@ class Env(utils.object2):
             if variable.owner is None and variable not in self.inputs and not isinstance(variable, graph.Constant):
                 raise Exception("Undeclared input.", variable)
             if variable.env is not self:
-                raise Exception("Variable should belong to the env.", variable)
+                raise Exception("Variable should belong to the FunctionGraph.", variable)
             for node, i in variable.clients:
                 if node == 'output':
                     if self.outputs[i] is not variable:
                         raise Exception("Inconsistent clients list.", variable, self.outputs[i])
                     continue
                 if node not in nodes:
-                    raise Exception("Client not in env.", variable, (node, i))
+                    raise Exception("Client not in FunctionGraph.", variable, (node, i))
                 if node.inputs[i] is not variable:
                     raise Exception("Inconsistent clients list.", variable, node.inputs[i])
 
@@ -648,7 +655,7 @@ class Env(utils.object2):
         """WRITEME"""
         equiv = graph.clone_get_equiv(self.inputs, self.outputs)
         self.check_integrity()
-        e = Env([equiv[i] for i in self.inputs],
+        e = FunctionGraph([equiv[i] for i in self.inputs],
                 [equiv[o] for o in self.outputs])
         e.check_integrity()
         for feature in self._features:

theano/gof/op.py

@@ -21,7 +21,7 @@ from theano import config
 import cc
 import graph
 import utils
-from env import Env
+from fg import FunctionGraph as Env
 
 
 class CLinkerObject(object):

theano/gof/opt.py

@@ -11,7 +11,7 @@ import time
 import numpy
 
 import graph
-from env import InconsistencyError
+from fg import InconsistencyError
 import op
 import utils
 import unify
@@ -598,7 +598,7 @@ def is_same_graph_with_merge(var1, var2, givens=None):
     givens = copied[2]
     # Create Env.
     inputs = theano.gof.graph.inputs(vars)
-    env = theano.gof.env.Env(inputs, vars)
+    env = theano.gof.fg.FunctionGraph(inputs, vars)
     # Perform Variable substitution.
     for to_replace, replace_by in givens.iteritems():
         env.replace(to_replace, replace_by)

theano/gof/tests/test_cc.py

@@ -6,7 +6,8 @@ from theano.gof.cc import *
 from theano.gof.type import Type
 from theano.gof.graph import Variable, Apply, Constant
 from theano.gof.op import Op
-from theano.gof import env
+from theano.gof import fg
+env = fg
 from theano.gof import toolbox
 
 
@@ -171,7 +172,7 @@ def inputs():
 
 
 def Env(inputs, outputs):
-    e = env.Env(inputs, outputs)
+    e = fg.FunctionGraph(inputs, outputs)
     return e
 
 

theano/gof/tests/test_destroyhandler.py

@@ -8,7 +8,7 @@ from theano.gof.op import Op
 from theano.gof.opt import *
 
 from theano.gof import destroyhandler
-from theano.gof.env import Env, InconsistencyError
+from theano.gof.fg import FunctionGraph as Env, InconsistencyError
 from theano.gof.toolbox import ReplaceValidate
 
 from copy import copy

theano/gof/tests/test_opt.py

@@ -3,7 +3,7 @@ from theano.gof.type import Type
 from theano.gof.graph import Variable, Apply, Constant
 from theano.gof.op import Op
 from theano.gof.opt import *
-from theano.gof.env import Env
+from theano.gof.fg import FunctionGraph as Env
 from theano.gof.toolbox import *
 
 

theano/gof/tests/test_toolbox.py

@@ -3,7 +3,7 @@ from theano.gof.graph import Variable, Apply
 from theano.gof.type import Type
 from theano.gof.op import Op
 
-from theano.gof.env import Env, InconsistencyError
+from theano.gof.fg import FunctionGraph as Env, InconsistencyError
 from theano.gof.toolbox import *
 
 
@@ -85,4 +85,4 @@ class TestNodeFinder:
                 raise Exception("Expected: %i times %s" % (num, type))
 
 
-    
+

theano/tensor/tests/test_merge.py

@@ -3,7 +3,7 @@ from theano.gof.type import Type
 from theano.gof.graph import Variable, Apply, Constant
 from theano.gof.op import Op
 from theano.gof.opt import *
-from theano.gof.env import Env
+from theano.gof.fg import FunctionGraph as Env
 from theano.gof.toolbox import *
 import theano.tensor.basic as T