fix pep-8 errors in gof

theano/gof/callcache.py

@@ -18,8 +18,8 @@ class CallCache(object):
 
     def persist(self, filename=None):
 	"""
-	Cache "filename" as a pickle file   
-	"""
+        Cache "filename" as a pickle file
+        """
         if filename is None:
             filename = self.filename
         with open(filename, 'w') as f:
@@ -27,16 +27,16 @@ class CallCache(object):
 
     def call(self, fn, args=(), key=None):
 	"""
-	Retrieve item from the cache(if available) 
-	based on a key
-	
-	Parameters
-	------------
-	key
-	    parameter to retrieve cache item
-	fn,args
-	    key to retrieve if "key" is None
-	"""
+        Retrieve item from the cache(if available)
+        based on a key
+
+        Parameters
+        ------------
+        key
+          parameter to retrieve cache item
+        fn,args
+          key to retrieve if "key" is None
+        """
         if key is None:
             key = (fn, tuple(args))
         if key not in self.cache:

theano/gof/cc.py

@@ -115,14 +115,12 @@ def failure_code(sub):
 def failure_code_init(sub):
     """
     Code for failure in the struct init.
-    
     Parameters:
     --------------
     sub
       Dictionary used to template the struct.
       * failure_var -> must contain a variable name to use for
       the failure code.
-    
     """
     return '''{
         if (!PyErr_Occurred()) {
@@ -137,8 +135,8 @@ def failure_code_init(sub):
 def code_gen(blocks):
     """
     From a list of L{CodeBlock} instances, returns a string
-    that executes them all in sequence. 
-    
+    that executes them all in sequence.
+
     Eg for C{(decl1, task1,
     cleanup1)} and C{(decl2, task2, cleanup2)} the returned string
     will be of the form:
@@ -156,7 +154,7 @@ def code_gen(blocks):
 
     Parameters:
     ----------------
-    blocks 
+    blocks
          List of CodeBlock instances such that
          * declarations, behavior and cleanup are in the run()
          method of the struct
@@ -895,7 +893,6 @@ class CLinker(link.Linker):
         """
         Returns a list of support code strings that are needed by
         one or more Variables or Ops.
-       
         The support code from Variables is added before the support code from Ops.This might contain duplicates.
         """
         ret = []
@@ -1172,10 +1169,8 @@ class CLinker(link.Linker):
             be allocated.
         storage_map: dict that map variables to storages.
             This is used when you need to customize the storage of
-            this thunk.
-	keep_lock
-            WRITEME
-        
+            this thunk.keep_lock
+        WRITEME
         Returns: thunk, input_storage, output_storage
 
         The return values can be used as follows:
@@ -1845,11 +1840,10 @@ def _default_checker(x, y):
     """
     Default checker for DualLinker. This checks that the
     variables contain the same data using ==.
-    
     Parameters
     -------------
-    x,y 
-	the variables to compare data
+    x,y
+    the variables to compare data
     """
     if x[0] != y[0]:
         raise Exception("Output mismatch.",

theano/gof/cmodule.py

@@ -1474,10 +1474,9 @@ class ModuleCache(object):
 
 def _rmtree(parent, ignore_nocleanup=False, msg='', level=logging.DEBUG,
             ignore_if_missing=False):
-    
     """
     On NFS filesystems, it is impossible to delete a directory with open
-    files in it.  
+    files in it.
 
     So instead, some commands in this file will respond to a
     failed rmtree() by touching a 'delete.me' file.  This file is a message
@@ -1485,13 +1484,13 @@ def _rmtree(parent, ignore_nocleanup=False, msg='', level=logging.DEBUG,
     Paramters
     ----------
     parent
-	Root node to start deleting from
+    Root node to start deleting from
     ignore_nocleanup
-	Delete the tree if flag is TRUE
+    Delete the tree if flag is TRUE
     level
-	Python Logging level. Set to "DEBUG" by default
+    Python Logging level. Set to "DEBUG" by default
     ignore_if_missing
-	If set to True, just return without any issue if parent is NULL 
+    If set to True, just return without any issue if parent is NULL
     """
     if ignore_if_missing and not os.path.exists(parent):
         return

theano/gof/graph.py

@@ -708,7 +708,7 @@ def variables_and_orphans(i, o):
     i : list
          Input L{Variable}s.
     o : list
-         Output L{Variable}s. 
+         Output L{Variable}s.
 
     """
     def expand(r):
@@ -775,7 +775,7 @@ def variables(i, o):
 def orphans(i, o):
     """
     Extracts list of variables within input and output nodes ( via dfs t     ravesal) and returns the "orphans" among them
-    
+
     Parameters
     ----------
     i : list
@@ -1225,7 +1225,7 @@ def op_as_string(i, op,
                  leaf_formatter=default_leaf_formatter,
                  node_formatter=default_node_formatter):
     """
-    Op to return a string representation of the subgraph 
+    Op to return a string representation of the subgraph
     between i and o
     """
     strs = as_string(i, op.inputs, leaf_formatter, node_formatter)

theano/gof/link.py

@@ -54,8 +54,7 @@ def thunk_hook(type, value, trace):
     """
     This function is meant to replace excepthook and do some
     special work if the exception value has a __thunk_trace__
-    field. 
-    
+    field.
     In that case, it retrieves the field, which should
     contain a trace as returned by L{traceback.extract_stack},
     and prints it out on L{stderr}.
@@ -64,7 +63,7 @@ def thunk_hook(type, value, trace):
     Parameters
     ------------
     type
-      Exception class  
+      Exception class
     value
       Exception instance
     trace
@@ -617,7 +616,7 @@ def map_storage(fgraph, order, input_storage, output_storage, storage_map=None):
 def streamline(fgraph, thunks, order, post_thunk_old_storage=None,
                no_recycling=None, nice_errors=True):
     """
-    WRITEME  
+    WRITEME
 
     Parameters
     ----------
@@ -714,7 +713,6 @@ class LocalLinker(Linker):
 def gc_helper(node_list):
     """
     Return the set of Variable instances which are computed by node_list.
-      
     Parameters
     ----------
     node_list
@@ -790,7 +788,7 @@ class PerformLinker(LocalLinker):
 
     def make_all(self, input_storage=None, output_storage=None, storage_map=None):
         """
-	Returns Function to run all nodes, list of input containers, list of outputs
+        Returns Function to run all nodes, list of input containers, list of outputs
 
         Parameters
         ----------

theano/gof/op.py

@@ -792,8 +792,8 @@ class Op(utils.object2, PureOp, CLinkerOp):
 
     def _props(self):
 	"""
-	Tuple of properties of all attributes
-	"""
+        Tuple of properties of all attributes
+        """
         return tuple(getattr(self, a) for a in self.__props__)
 
     def _props_dict(self):
@@ -927,7 +927,7 @@ class Op(utils.object2, PureOp, CLinkerOp):
 
     def make_thunk(self, node, storage_map, compute_map, no_recycling):
         """
-        This function must return a thunk, that is a zero-arguments 
+        This function must return a thunk, that is a zero-arguments
         function that encapsulates the computation to be performed
         by this op on the arguments of the node.
 
@@ -981,9 +981,8 @@ class Op(utils.object2, PureOp, CLinkerOp):
 
     def make_node(self, *inputs):
 	"""
-	Create a "apply" nodes for the inputs in that order.
-
-	"""
+        Create a "apply" nodes for the inputs in that order.
+        """
         if not hasattr(self, 'itypes'):
             raise NotImplementedError("You can either define itypes and otypes,\
              or implement make_node")
@@ -1068,7 +1067,7 @@ def debug_error_message(msg):
 
 def debug_assert(condition, msg=None):
     """
-    Customized assert with options to ignore the assert 
+    Customized assert with options to ignore the assert
     with just a warning
     """
     if msg is None:
@@ -1179,8 +1178,8 @@ class OpenMPOp(Op):
 
     def c_compile_args(self):
 	"""
-	Return the compilation arg "fopenmp" if openMP is supported
-	"""
+        Return the compilation arg "fopenmp" if openMP is supported
+        """
         self.update_self_openmp()
         if self.openmp:
             return ['-fopenmp']
@@ -1188,9 +1187,8 @@ class OpenMPOp(Op):
 
     def c_headers(self):
 	"""
-	Return the header file name "omp.h" if openMP is supported
-
-	"""
+        Return the header file name "omp.h" if openMP is supported
+        """
         self.update_self_openmp()
         if self.openmp:
             return ["omp.h"]
@@ -1199,8 +1197,8 @@ class OpenMPOp(Op):
     @staticmethod
     def test_gxx_support():
 	"""
-	Check if openMP is supported
-	"""
+        Check if openMP is supported
+        """
         code = """
         #include <omp.h>
 int main( int argc, const char* argv[] )
@@ -1418,7 +1416,7 @@ class COp(Op):
 
     def c_init_code(self):
 	"""
-	Get the code section for init_code
+        Get the code section for init_code
         """
         if 'init_code' in self.code_sections:
             return [self.code_sections['init_code']]
@@ -1588,8 +1586,8 @@ class COp(Op):
 
     def c_code_cleanup(self, node, name, inputs, outputs, sub):
 	"""
-	Stitches all the macros and "code_cleanup" together
- 	"""
+        Stitches all the macros and "code_cleanup" together
+        """
         if 'code_cleanup' in self.code_sections:
             op_code = self.code_sections['code_cleanup']
 

theano/gof/toolbox.py

@@ -115,19 +115,19 @@ class Bookkeeper(Feature):
 
     def on_attach(self, fgraph):
 	"""
-	Called by FunctionGraph.attach_feature, the method that attaches
+        Called by FunctionGraph.attach_feature, the method that attaches
         the feature to the FunctionGraph. Since this is called after the
         FunctionGraph is initially populated, this is where you should
         run checks on the initial contents of the FunctionGraph.
-	"""
+        """
         for node in graph.io_toposort(fgraph.inputs, fgraph.outputs):
             self.on_import(fgraph, node, "on_attach")
 
     def on_detach(self, fgraph):
 	"""
-	Should remove any dynamically added functionality 
+        Should remove any dynamically added functionality
         that it installed into the function_graph
-	"""
+        """
         for node in graph.io_toposort(fgraph.inputs, fgraph.outputs):
             self.on_prune(fgraph, node, 'Bookkeeper.detach')
 
@@ -189,9 +189,9 @@ class History(Feature):
 
     def on_detach(self, fgraph):
 	"""
-        Should remove any dynamically added functionality 
+        Should remove any dynamically added functionality
         that it installed into the function_graph
-	"""
+        """
         del fgraph.checkpoint
         del fgraph.revert
         del self.history[fgraph]
@@ -238,18 +238,18 @@ class Validator(Feature):
 
     def on_detach(self, fgraph):
         """
-	Should remove any dynamically added functionality 
+        Should remove any dynamically added functionality
         that it installed into the function_graph
-	"""
-	del fgraph.validate
+        """
+        del fgraph.validate
         del fgraph.consistent
 
     def validate_(self, fgraph):
 	"""
-	If the caller is replace_all_validate, just raise the
+        If the caller is replace_all_validate, just raise the
         exception. replace_all_validate will print out the
         verbose output. Or it has to be done here before raise.
-	"""
+        """
         t0 = time.time()
         try:
             ret = fgraph.execute_callbacks('validate')
@@ -313,9 +313,9 @@ class ReplaceValidate(History, Validator):
 
     def on_detach(self, fgraph):
 	"""
-	Should remove any dynamically added functionality 
+        Should remove any dynamically added functionality
         that it installed into the function_graph
-	"""
+        """
         History.on_detach(self, fgraph)
         Validator.on_detach(self, fgraph)
         del self._nodes_removed
@@ -440,9 +440,9 @@ class NodeFinder(Bookkeeper):
 
     def on_detach(self, fgraph):
 	"""
-	Should remove any dynamically added functionality 
+        Should remove any dynamically added functionality
         that it installed into the function_graph
-	"""
+        """
         if self.fgraph is not fgraph:
             raise Exception("This NodeFinder instance was not attached to the"
                             " provided fgraph.")
@@ -493,9 +493,9 @@ class PrintListener(Feature):
 
     def on_detach(self, fgraph):
 	"""
-	Should remove any dynamically added functionality 
-	that it installed into the function_graph
-	"""
+        Should remove any dynamically added functionality
+        that it installed into the function_graph
+        """
         if self.active:
             print("-- detaching from: ", fgraph)
 

theano/gof/unify.py

@@ -4,7 +4,7 @@ can be "unified" if there exists an assignment to all unification variables
 such that the two expressions are equal.
 
 For instance, [5, A, B] and [A, C, 9] can be unified if A=C=5 and B=9,
-yielding [5, 5, 9]. 
+yielding [5, 5, 9].
 [5, [A, B]] and [A, [1, 2]] cannot be unified because there is no value for A
 that satisfies the constraints. That's useful for pattern matching.
 
@@ -135,8 +135,6 @@ class Unification:
     """
     This class represents a possible unification of a group of variables
     with each other or with tangible values.
-
-    
     Parameters
     ----------
     inplace : bool

theano/gof/vm.py

@@ -728,8 +728,8 @@ class VM_Linker(link.LocalLinker):
 
     def accept(self, fgraph, no_recycling=None):
         """
-        Check if fgraph is the first FunctionGraph that has ever been 
-        associated to self, else, create a new VM_Linker 
+        Check if fgraph is the first FunctionGraph that has ever been
+        associated to self, else, create a new VM_Linker
         associated to fgraph
 
         Parameters