Merge pull request #3130 from harlouci/flake8_gof

theano/configparser.py

@@ -177,7 +177,7 @@ def get_config_md5():
     """
     all_opts = sorted([c for c in _config_var_list if c.in_c_key],
                       key=lambda cv: cv.fullname)
-    return theano.gof.cc.hash_from_code('\n'.join(
+    return theano.gof.utils.hash_from_code('\n'.join(
         ['%s = %s' % (cv.fullname, cv.__get__()) for cv in all_opts]))
 
 

theano/gof/cc.py

 """
 Defines Linkers that deal with C implementations.
 """
+
 from __future__ import print_function
 
 # Python imports
 from copy import copy
 import os
 import sys
-from theano.compat import izip
+import logging
 
 import numpy
 
+import theano
+from theano import config
 from theano.compat import PY3
+from theano.compat import izip
 from six import string_types, reraise
 from six.moves import StringIO, xrange
-from theano.gof.utils import MethodNotDefined
-
-import theano
-from theano import config
-
-if PY3:
-    import hashlib
-
-    def hash_from_code(msg):
-        # hashlib.md5() requires an object that supports buffer interface,
-        # but Python 3 (unicode) strings don't.
-        if isinstance(msg, str):
-            msg = msg.encode()
-        # Python 3 does not like module names that start with
-        # a digit.
-        return 'm' + hashlib.md5(msg).hexdigest()
-
-else:
-    import hashlib
-
-    def hash_from_code(msg):
-        try:
-            return hashlib.md5(msg).hexdigest()
-        except TypeError:
-            assert isinstance(msg, numpy.ndarray)
-            return hashlib.md5(numpy.getbuffer(msg)).hexdigest()
-
-
-def hash_from_file(file_path):
-    """Return the MD5 hash of a file."""
-    return hash_from_code(open(file_path, 'rb').read())
-
 
 # Note that we need to do this before importing cutils, since when there is
 # no theano cache dir initialized yet, importing cutils may require compilation
 # of cutils_ext.
 from theano.configparser import AddConfigVar, StrParam
-AddConfigVar('gcc.cxxflags',
-             "Extra compiler flags for gcc",
-             StrParam(""))
 
 # gof imports
 from theano.gof import graph
 from theano.gof import link
 from theano.gof import utils
-
+from theano.gof import cmodule
 from theano.gof.compilelock import get_lock, release_lock
+from theano.gof.callcache import CallCache
 
-from theano.gof import cmodule
+AddConfigVar('gcc.cxxflags',
+             "Extra compiler flags for gcc",
+             StrParam(""))
 
 
-import logging
 _logger = logging.getLogger("theano.gof.cc")
 
-from theano.gof.callcache import CallCache
 
 run_cthunk = None  # Will be imported only when needed.
 
@@ -314,9 +284,8 @@ def get_c_declare(r, name, sub):
     """Wrapper around c_declare that declares py_name"""
 
     if any([c != "output" and getattr(c.op, 'check_input',
-        config.check_input) for (c, _) in r.clients]) or (r.owner
-        and getattr(r.owner.op, 'check_input', True)):
-
+           config.check_input) for (c, _) in r.clients]) or (
+            r.owner and getattr(r.owner.op, 'check_input', True)):
         c_declare = r.type.c_declare(name, sub, True)
     else:
         c_declare = r.type.c_declare(name, sub, False)
@@ -532,7 +501,7 @@ class CLinker(link.Linker):
                             if isinstance(r, graph.Constant) and
                             r not in self.inputs)
         self.temps = list(set(self.variables).difference(
-                self.inputs).difference(self.outputs).difference(self.orphans))
+            self.inputs).difference(self.outputs).difference(self.orphans))
         self.consts = []
 
     def code_gen(self):
@@ -821,7 +790,7 @@ class CLinker(link.Linker):
         ret = []
         # generic support code
         for x in [y.type for y in self.variables] + [
-            y.op for y in self.node_order]:
+                y.op for y in self.node_order]:
             try:
                 ret.append(x.c_support_code())
             except utils.MethodNotDefined:
@@ -840,11 +809,11 @@ class CLinker(link.Linker):
 # FillMissing must disable some of them. Putting -ffast-math would
 # make it disable all other parameter at the same time.
         ret += ["-fno-math-errno",
-                #"-funsafe-math-optimizations",
-                #"-fno-signaling-nans",
-                #"-fcx-limited-range",
-                #"-fno-rounding-math",
-                #"-ffinite-math-only",
+                # "-funsafe-math-optimizations",
+                # "-fno-signaling-nans",
+                # "-fcx-limited-range",
+                # "-fno-rounding-math",
+                # "-ffinite-math-only",
 
                 # the current code generate label event if they are not used.
                 # Could use gcc attribute for those label only
@@ -853,7 +822,7 @@ class CLinker(link.Linker):
                 "-Wno-write-strings",  # generated by our code generator...
                 ]
         for x in [y.type for y in self.variables] + [
-            y.op for y in self.node_order]:
+                y.op for y in self.node_order]:
             try:
                 ret += x.c_compile_args()
             except utils.MethodNotDefined:
@@ -866,7 +835,7 @@ class CLinker(link.Linker):
         # to reorder them
         ret += c_compiler.compile_args()
         for x in [y.type for y in self.variables] + [
-            y.op for y in self.node_order]:
+                y.op for y in self.node_order]:
             try:
                 for i in x.c_no_compile_args():
                     try:
@@ -886,7 +855,7 @@ class CLinker(link.Linker):
         """
         ret = []
         for x in [y.type for y in self.variables] + [
-            y.op for y in self.node_order]:
+                y.op for y in self.node_order]:
             try:
                 ret += x.c_headers()
             except utils.MethodNotDefined:
@@ -901,7 +870,7 @@ class CLinker(link.Linker):
         """
         ret = []
         for x in [y.type for y in self.variables] + [
-            y.op for y in self.node_order]:
+                y.op for y in self.node_order]:
             try:
                 ret += x.c_init_code()
             except utils.MethodNotDefined:
@@ -911,7 +880,7 @@ class CLinker(link.Linker):
     def c_compiler(self):
         c_compiler = None
         for x in [y.type for y in self.variables] + [
-            y.op for y in self.node_order]:
+                y.op for y in self.node_order]:
             if hasattr(x, 'c_compiler'):
                 x_compiler = x.c_compiler()
             else:
@@ -938,7 +907,7 @@ class CLinker(link.Linker):
         """
         ret = []
         for x in [y.type for y in self.variables] + [
-            y.op for y in self.node_order]:
+                y.op for y in self.node_order]:
             try:
                 ret += x.c_header_dirs()
             except utils.MethodNotDefined:
@@ -954,7 +923,7 @@ class CLinker(link.Linker):
         """
         ret = []
         for x in [y.type for y in self.variables] + [
-            y.op for y in self.node_order]:
+                y.op for y in self.node_order]:
             try:
                 ret += x.c_libraries()
             except utils.MethodNotDefined:
@@ -970,7 +939,7 @@ class CLinker(link.Linker):
         """
         ret = []
         for x in [y.type for y in self.variables] + [
-            y.op for y in self.node_order]:
+                y.op for y in self.node_order]:
             try:
                 ret += x.c_lib_dirs()
             except utils.MethodNotDefined:
@@ -1150,7 +1119,7 @@ class CLinker(link.Linker):
                                  libraries=self.libraries(),
                                  header_dirs=self.header_dirs(),
                                  c_compiler=self.c_compiler(),
-                             )
+                                 )
 
     def cmodule_key_(self, fgraph, no_recycling, compile_args=None,
                      libraries=None, header_dirs=None, insert_config_md5=True,
@@ -1335,7 +1304,6 @@ class CLinker(link.Linker):
                 preargs.remove('-DREPLACE_WITH_AMDLIBM')
             if 'amdlibm' in libs:
                 libs.remove('amdlibm')
-        src_code = mod.code()
         get_lock()
         try:
             _logger.debug("LOCATION %s", str(location))
@@ -1371,9 +1339,9 @@ class CLinker(link.Linker):
             code = self.instantiate_code(1 + len(self.args))
             instantiate = cmodule.ExtFunction('instantiate', code,
                                               method=cmodule.METH_VARARGS)
-                #['error_storage'] + argnames,
-                #local_dict = d,
-                # global_dict = {})
+            # ['error_storage'] + argnames,
+            # local_dict = d,
+            # global_dict = {})
 
             # Static methods that can run and destroy the struct built by
             # instantiate.
@@ -1498,7 +1466,7 @@ class _CThunk(object):
         global run_cthunk
         if run_cthunk is None:
             # Lazy import to avoid compilation when importing theano.
-            from theano.gof.cutils import run_cthunk
+            from theano.gof.cutils import run_cthunk  # noqa
         self.cthunk = cthunk
         self.init_tasks = init_tasks
         self.tasks = tasks
@@ -1534,7 +1502,8 @@ class _CThunk(object):
                 exc_value.__thunk_trace__ = trace
             except Exception:
                 print(('ERROR retrieving error_storage.'
-                                      ' Was the error set in the c code?'), end=' ', file=sys.stderr)
+                       'Was the error set in the c code?'),
+                      end=' ', file=sys.stderr)
                 print(self.error_storage, file=sys.stderr)
                 raise
             reraise(exc_type, exc_value, exc_trace)
@@ -1641,11 +1610,11 @@ class OpWiseCLinker(link.LocalLinker):
 
             for node in order:
                 if self.allow_gc:
-                    post_thunk_old_storage.append([storage_map[input]
-                        for input in node.inputs
-                        if ((input in computed) and
-                            (input not in fgraph.outputs) and
-                            node == last_user[input])])
+                    post_thunk_old_storage.append(
+                        [storage_map[input] for input in node.inputs
+                         if ((input in computed) and
+                             (input not in fgraph.outputs) and
+                             node == last_user[input])])
 
             if no_recycling is True:
                 no_recycling = list(storage_map.values())
@@ -1741,12 +1710,12 @@ class DualLinker(link.Linker):
         no_recycling = self.no_recycling
 
         _f, i1, o1, thunks1, order1 = (
-                link.PerformLinker(schedule=self.schedule).accept(fgraph,
-                                no_recycling=no_recycling).make_all(**kwargs))
+            link.PerformLinker(schedule=self.schedule).accept(
+                fgraph, no_recycling=no_recycling).make_all(**kwargs))
         kwargs.pop('input_storage', None)
         _f, i2, o2, thunks2, order2 = (
-                OpWiseCLinker(schedule=self.schedule).accept(fgraph,
-                                no_recycling=no_recycling).make_all(**kwargs))
+            OpWiseCLinker(schedule=self.schedule).accept(
+                fgraph, no_recycling=no_recycling).make_all(**kwargs))
 
         def f():
             for input1, input2 in izip(i1, i2):

theano/gof/cmodule.py

 """Generate and compile C modules for Python,
 """
+
 from __future__ import print_function
+
 import atexit
 import six.moves.cPickle as pickle
 import logging
@@ -15,12 +17,6 @@ import time
 import platform
 import distutils.sysconfig
 
-importlib = None
-try:
-    import importlib
-except ImportError:
-    pass
-
 import numpy.distutils  # TODO: TensorType should handle this
 
 import theano
@@ -28,7 +24,7 @@ from theano.compat import PY3, decode, decode_iter
 from six import b, BytesIO, StringIO, string_types, iteritems
 from theano.gof.utils import flatten
 from theano.configparser import config
-from theano.gof.cc import hash_from_code
+from theano.gof.utils import hash_from_code
 from theano.misc.windows import (subprocess_Popen,
                                  output_subprocess_Popen)
 
@@ -38,10 +34,17 @@ from theano.gof.compiledir import gcc_version_str, local_bitwidth
 
 from theano.configparser import AddConfigVar, BoolParam
 
-AddConfigVar('cmodule.mac_framework_link',
-        "If set to True, breaks certain MacOS installations with the infamous "
-        "Bus Error",
-        BoolParam(False))
+importlib = None
+try:
+    import importlib
+except ImportError:
+    pass
+
+AddConfigVar(
+    'cmodule.mac_framework_link',
+    "If set to True, breaks certain MacOS installations with the infamous "
+    "Bus Error",
+    BoolParam(False))
 
 AddConfigVar('cmodule.warn_no_version',
              "If True, will print a warning when compiling one or more Op "
@@ -131,15 +134,16 @@ class ExtFunction(object):
         It goes into the DynamicModule's method table.
         """
         return '\t{"%s", %s, %s, "%s"}' % (
-                self.name, self.name, self.method, self.doc)
+            self.name, self.name, self.method, self.doc)
 
 
 class DynamicModule(object):
     def __init__(self, name=None):
-        assert name is None, ("The 'name' parameter of DynamicModule"
-                " cannot be specified anymore. Instead, 'code_hash'"
-                " will be automatically computed and can be used as"
-                " the module's name.")
+        assert name is None, (
+            "The 'name' parameter of DynamicModule"
+            " cannot be specified anymore. Instead, 'code_hash'"
+            " will be automatically computed and can be used as"
+            " the module's name.")
         # While the module is not finalized, we can call add_...
         # when it is finalized, a hash is computed and used instead of
         # the placeholder, and as module name.
@@ -171,18 +175,18 @@ static struct PyModuleDef moduledef = {{
 }};
 """.format(name=self.hash_placeholder), file=stream)
             print(("PyMODINIT_FUNC PyInit_%s(void) {" %
-                              self.hash_placeholder), file=stream)
+                  self.hash_placeholder), file=stream)
             for block in self.init_blocks:
                 print('  ', block, file=stream)
             print("    PyObject *m = PyModule_Create(&moduledef);", file=stream)
             print("    return m;", file=stream)
         else:
             print(("PyMODINIT_FUNC init%s(void){" %
-                              self.hash_placeholder), file=stream)
+                  self.hash_placeholder), file=stream)
             for block in self.init_blocks:
                 print('  ', block, file=stream)
             print('  ', ('(void) Py_InitModule("%s", MyMethods);'
-                                    % self.hash_placeholder), file=stream)
+                  % self.hash_placeholder), file=stream)
         print("}", file=stream)
 
     def add_include(self, str):
@@ -351,9 +355,9 @@ def is_same_entry(entry_1, entry_2):
     if os.path.realpath(entry_1) == os.path.realpath(entry_2):
         return True
     if (os.path.basename(entry_1) == os.path.basename(entry_2) and
-        (os.path.basename(os.path.dirname(entry_1)) ==
-         os.path.basename(os.path.dirname(entry_2))) and
-        os.path.basename(os.path.dirname(entry_1)).startswith('tmp')):
+            (os.path.basename(os.path.dirname(entry_1)) ==
+             os.path.basename(os.path.dirname(entry_2))) and
+            os.path.basename(os.path.dirname(entry_1)).startswith('tmp')):
         return True
     return False
 
@@ -429,8 +433,8 @@ def get_safe_part(key):
     # Find the md5 hash part.
     c_link_key = key[1]
     for key_element in c_link_key[1:]:
-        if (isinstance(key_element, string_types)
-                and key_element.startswith('md5:')):
+        if (isinstance(key_element, string_types) and
+                key_element.startswith('md5:')):
             md5 = key_element[4:]
             break
 
@@ -761,9 +765,9 @@ class ModuleCache(object):
                         # simpler to implement).
                         rmtree(root, ignore_nocleanup=True,
                                msg=(
-                                'invalid cache entry format -- this '
-                                'should not happen unless your cache '
-                                'was really old'),
+                                   'invalid cache entry format -- this '
+                                   'should not happen unless your cache '
+                                   'was really old'),
                                level=logging.WARN)
                         continue
 
@@ -964,7 +968,7 @@ class ModuleCache(object):
                 # process that could be changing the file at the same
                 # time.
                 if (key[0] and not key_broken and
-                    self.check_for_broken_eq):
+                        self.check_for_broken_eq):
                     self.check_key(key, key_data.key_pkl)
             self._update_mappings(key, key_data, module.__file__, check_in_keys=not key_broken)
             return module
@@ -1149,15 +1153,14 @@ class ModuleCache(object):
                 # This is to make debugging in pdb easier, by providing
                 # the offending keys in the local context.
                 # key_data_keys = list(key_data.keys)
-                ## import pdb; pdb.set_trace()
+                # import pdb; pdb.set_trace()
                 pass
         elif found > 1:
             msg = 'Multiple equal keys found in unpickled KeyData file'
         if msg:
             raise AssertionError(
-                    "%s. Verify the __eq__ and __hash__ functions of your "
-                    "Ops. The file is: %s. The key is: %s" %
-                    (msg, key_pkl, key))
+                "%s. Verify the __eq__ and __hash__ functions of your "
+                "Ops. The file is: %s. The key is: %s" % (msg, key_pkl, key))
         # Also verify that there exists no other loaded key that would be equal
         # to this key. In order to speed things up, we only compare to keys
         # with the same version part and config md5, since we can assume this
@@ -1195,10 +1198,10 @@ class ModuleCache(object):
         if age_thresh_del < self.age_thresh_use:
             if age_thresh_del > 0:
                 _logger.warning("Clearing modules that were not deemed "
-                        "too old to use: age_thresh_del=%d, "
-                        "self.age_thresh_use=%d",
-                        age_thresh_del,
-                        self.age_thresh_use)
+                                "too old to use: age_thresh_del=%d, "
+                                "self.age_thresh_use=%d",
+                                age_thresh_del,
+                                self.age_thresh_use)
             else:
                 _logger.info("Clearing all modules.")
             age_thresh_use = age_thresh_del
@@ -1210,8 +1213,8 @@ class ModuleCache(object):
             # processes and get all module that are too old to use
             # (not loaded in self.entry_from_key).
             too_old_to_use = self.refresh(
-                    age_thresh_use=age_thresh_use,
-                    delete_if_problem=delete_if_problem)
+                age_thresh_use=age_thresh_use,
+                delete_if_problem=delete_if_problem)
 
             for entry in too_old_to_use:
                 # TODO: we are assuming that modules that haven't been
@@ -1242,8 +1245,8 @@ class ModuleCache(object):
         """
         with compilelock.lock_ctx():
             self.clear_old(
-                    age_thresh_del=-1.0,
-                    delete_if_problem=delete_if_problem)
+                age_thresh_del=-1.0,
+                delete_if_problem=delete_if_problem)
             self.clear_unversioned(min_age=unversioned_min_age)
             if clear_base_files:
                 self.clear_base_files()
@@ -1333,7 +1336,7 @@ class ModuleCache(object):
                 if filename.startswith('tmp'):
                     try:
                         open(os.path.join(self.dirname, filename, 'key.pkl')
-                                ).close()
+                             ).close()
                         has_key = True
                     except IOError:
                         has_key = False
@@ -1420,8 +1423,8 @@ def get_module_cache(dirname, init_args=None):
                         'was created prior to this call')
     if _module_cache.dirname != dirname:
         _logger.warning("Returning module cache instance with different "
-                "dirname (%s) than you requested (%s)",
-                _module_cache.dirname, dirname)
+                        "dirname (%s) than you requested (%s)",
+                        _module_cache.dirname, dirname)
     return _module_cache
 
 
@@ -1685,7 +1688,7 @@ class GCC_compiler(Compiler):
                     break
 
         if ('g++' not in theano.config.cxx and
-            'clang++' not in theano.config.cxx):
+                'clang++' not in theano.config.cxx):
             _logger.warn(
                 "OPTIMIZATION WARNING: your Theano flag `cxx` seems not to be"
                 " the g++ compiler. So we disable the compiler optimization"
@@ -1719,9 +1722,9 @@ class GCC_compiler(Compiler):
                     selected_lines = []
                     for line in lines:
                         if ("COLLECT_GCC_OPTIONS=" in line or
-                            "CFLAGS=" in line or
-                            "CXXFLAGS=" in line or
-                            "-march=native" in line):
+                                "CFLAGS=" in line or
+                                "CXXFLAGS=" in line or
+                                "-march=native" in line):
                             continue
                         elif "-march=" in line:
                             selected_lines.append(line.strip())
@@ -1805,9 +1808,9 @@ class GCC_compiler(Compiler):
                     for line in default_lines:
                         if line.startswith(part[0]):
                             part2 = [p for p in join_options(line.split())
-                                     if (not 'march' in p and
-                                         not 'mtune' in p and
-                                         not 'target-cpu' in p)]
+                                     if ('march' not in p and
+                                         'mtune' not in p and
+                                         'target-cpu' not in p)]
                             new_flags = [p for p in part if p not in part2]
                             # Replace '-target-cpu value', which is an option
                             # of clang, with '-march=value', for g++
@@ -2021,14 +2024,13 @@ class GCC_compiler(Compiler):
         cmd.append(cppfilename)
         cmd.extend(['-L%s' % ldir for ldir in lib_dirs])
         cmd.extend(['-l%s' % l for l in libs])
-        #print >> sys.stderr, 'COMPILING W CMD', cmd
+        # print >> sys.stderr, 'COMPILING W CMD', cmd
         _logger.debug('Running cmd: %s', ' '.join(cmd))
 
         def print_command_line_error():
             # Print command line when a problem occurred.
-            print((
-                    "Problem occurred during compilation with the "
-                    "command line below:"), file=sys.stderr)
+            print(("Problem occurred during compilation with the "
+                   "command line below:"), file=sys.stderr)
             print(' '.join(cmd), file=sys.stderr)
 
         try:

theano/gof/destroyhandler.py

@@ -46,7 +46,6 @@ def _contains_cycle(fgraph, orderings):
     """
 
     # These are lists of Variable instances
-    inputs = fgraph.inputs
     outputs = fgraph.outputs
 
     # this is hard-coded reimplementation of functions from graph.py
@@ -65,8 +64,6 @@ def _contains_cycle(fgraph, orderings):
     # (defaultdict runs faster than dict in the case where the key
     # is not in the dictionary, at least in CPython)
 
-    iset = set(inputs)
-
     # IG: I tried converting parent_counts to use an id for the key,
     # so that the dict would do reference counting on its keys.
     # This caused a slowdown.
@@ -236,9 +233,9 @@ def fast_inplace_check(inputs):
     protected_inputs.extend(fgraph.outputs)
 
     inputs = [i for i in inputs if
-              not isinstance(i, graph.Constant)
-              and not fgraph.destroyers(i)
-              and i not in protected_inputs]
+              not isinstance(i, graph.Constant) and
+              not fgraph.destroyers(i) and
+              i not in protected_inputs]
     return inputs
 
 if 0:
@@ -293,7 +290,7 @@ if 0:
             TODO: WRITEME: what does this do besides the checks?
             """
 
-            ####### Do the checking ###########
+            # Do the checking #
             already_there = False
             if self.fgraph not in [None, fgraph]:
                 raise Exception("A DestroyHandler instance can only serve"
@@ -309,7 +306,7 @@ if 0:
                     "DestroyHandler feature is already present or in"
                     " conflict with another plugin.")
 
-            ####### end of checking ############
+            # end of checking #
 
             def get_destroyers_of(r):
                 droot, impact, root_destroyer = self.refresh_droot_impact()
@@ -362,8 +359,8 @@ if 0:
                             "Multiple destroyers of %s" % input_root)
                     droot[input_root] = input_root
                     root_destroyer[input_root] = app
-                    #input_impact = set([input_root])
-                    #add_impact(input_root, self.view_o, input_impact)
+                    # input_impact = set([input_root])
+                    # add_impact(input_root, self.view_o, input_impact)
                     input_impact = get_impact(input_root, self.view_o)
                     for v in input_impact:
                         assert v not in droot
@@ -390,7 +387,7 @@ if 0:
         def on_import(self, fgraph, app, reason):
             """Add Apply instance to set which must be computed"""
 
-            #if app in self.debug_all_apps: raise ProtocolError("double import")
+            # if app in self.debug_all_apps: raise ProtocolError("double import")
             # self.debug_all_apps.add(app)
             # print 'DH IMPORT', app, id(app), id(self), len(self.debug_all_apps)
 
@@ -421,7 +418,7 @@ if 0:
 
         def on_prune(self, fgraph, app, reason):
             """Remove Apply instance from set which must be computed"""
-            #if app not in self.debug_all_apps: raise ProtocolError("prune without import")
+            # if app not in self.debug_all_apps: raise ProtocolError("prune without import")
             # self.debug_all_apps.remove(app)
 
             # UPDATE self.clients
@@ -458,7 +455,7 @@ if 0:
                 # considered 'outputs' of the graph.
                 pass
             else:
-                #if app not in self.debug_all_apps: raise ProtocolError("change without import")
+                # if app not in self.debug_all_apps: raise ProtocolError("change without import")
 
                 # UPDATE self.clients
                 self.clients[old_r][app] -= 1
@@ -529,9 +526,10 @@ if 0:
                 droot, impact, __ignore = self.refresh_droot_impact()
 
                 # check for destruction of constants
-                illegal_destroy = [r for r in droot if
-                        getattr(r.tag, 'indestructible', False) or
-                        isinstance(r, graph.Constant)]
+                illegal_destroy = [
+                    r for r in droot if
+                    getattr(r.tag, 'indestructible', False) or
+                    isinstance(r, graph.Constant)]
                 if illegal_destroy:
                     # print 'destroying illegally'
                     raise InconsistencyError(
@@ -603,7 +601,7 @@ if 0:
                             if input in root_impact \
                                     and (i not in tolerated or input is not destroyed_variable):
                                 raise InconsistencyError("Input aliasing: %s (%i, %i)"
-                                        % (app, destroyed_idx, i))
+                                                         % (app, destroyed_idx, i))
 
                         # add the rule: app must be preceded by all other Apply instances that
                         # depend on destroyed_input
@@ -621,7 +619,7 @@ if 0:
             return rval
 
 
-class DestroyHandler(toolbox.Bookkeeper):
+class DestroyHandler(toolbox.Bookkeeper):  # noqa
     """
     The DestroyHandler class detects when a graph is impossible to evaluate
     because of aliasing and destructive operations.
@@ -702,7 +700,7 @@ class DestroyHandler(toolbox.Bookkeeper):
         TODO: WRITEME: what does this do besides the checks?
         """
 
-        ####### Do the checking ###########
+        # Do the checking #
         already_there = False
         if self.fgraph is fgraph:
             already_there = True
@@ -720,7 +718,7 @@ class DestroyHandler(toolbox.Bookkeeper):
                 "DestroyHandler feature is already present"
                 " or in conflict with another plugin.")
 
-        ####### Annotate the FunctionGraph ############
+        # Annotate the FunctionGraph #
         self.unpickle(fgraph)
         fgraph.destroy_handler = self
 
@@ -945,12 +943,13 @@ class DestroyHandler(toolbox.Bookkeeper):
             droot, impact, __ignore = self.refresh_droot_impact()
 
             # check for destruction of constants
-            illegal_destroy = [r for r in droot if \
-                    getattr(r.tag, 'indestructible', False) or \
-                    isinstance(r, graph.Constant)]
+            illegal_destroy = [r for r in droot if
+                               getattr(r.tag, 'indestructible', False) or
+                               isinstance(r, graph.Constant)]
             if illegal_destroy:
-                raise InconsistencyError("Attempting to destroy indestructible variables: %s" %
-                        illegal_destroy)
+                raise InconsistencyError(
+                    "Attempting to destroy indestructible variables: %s" %
+                    illegal_destroy)
 
             # add destroyed variable clients as computational dependencies
             for app in self.destroyers:
@@ -995,24 +994,27 @@ class DestroyHandler(toolbox.Bookkeeper):
 
                     # CHECK FOR INPUT ALIASING
                     # OPT: pre-compute this on import
-                    tolerate_same = getattr(app.op, 'destroyhandler_tolerate_same', [])
+                    tolerate_same = getattr(app.op,
+                                            'destroyhandler_tolerate_same', [])
                     assert isinstance(tolerate_same, list)
                     tolerated = OrderedSet(idx1 for idx0, idx1 in tolerate_same
-                            if idx0 == destroyed_idx)
+                                           if idx0 == destroyed_idx)
                     tolerated.add(destroyed_idx)
-                    tolerate_aliased = getattr(app.op, 'destroyhandler_tolerate_aliased', [])
+                    tolerate_aliased = getattr(
+                        app.op, 'destroyhandler_tolerate_aliased', [])
                     assert isinstance(tolerate_aliased, list)
                     ignored = OrderedSet(idx1 for idx0, idx1 in tolerate_aliased
-                            if idx0 == destroyed_idx)
+                                         if idx0 == destroyed_idx)
                     # print 'tolerated', tolerated
                     # print 'ignored', ignored
                     for i, input in enumerate(app.inputs):
                         if i in ignored:
                             continue
                         if input in root_impact \
-                                and (i not in tolerated or input is not destroyed_variable):
+                                and (i not in tolerated or
+                                     input is not destroyed_variable):
                             raise InconsistencyError("Input aliasing: %s (%i, %i)"
-                                    % (app, destroyed_idx, i))
+                                                     % (app, destroyed_idx, i))
 
                     # add the rule: app must be preceded by all other Apply instances that
                     # depend on destroyed_input

theano/gof/fg.py

@@ -13,7 +13,6 @@ from theano.gof import graph
 from theano.gof import utils
 from theano.gof import toolbox
 from theano import config
-import warnings
 
 from theano.compat import OrderedDict
 from six import iteritems, itervalues
@@ -22,6 +21,7 @@ from theano.misc.ordered_set import OrderedSet
 
 NullType = None
 
+
 class CachedConstantError(Exception):
     """An exception thrown when we put in a FunctionGraph a Constant
     that is cached.  This should not happen as the user can reuse this
@@ -143,7 +143,7 @@ class FunctionGraph(utils.object2):
         self.variable_locks = {}
         self.profile = None
 
-    ### Setup a Variable ###
+    # Setup a Variable #
     def __setup_r__(self, r):
         # sets up r so it belongs to this fgraph
         if getattr(r, 'cached', False):
@@ -152,12 +152,12 @@ class FunctionGraph(utils.object2):
                 " graph that has a cached constant. This should not happen."
                 " Clone the graph before building the FunctionGraph.")
         if (hasattr(r, 'fgraph') and
-            r.fgraph is not None and
-            r.fgraph is not self):
+                r.fgraph is not None and
+                r.fgraph is not self):
             raise Exception("%s is already owned by another fgraph" % r)
         r.fgraph = self
         r.clients = []
-        #self.execute_callbacks('on_setup_variable', r)
+        # self.execute_callbacks('on_setup_variable', r)
 
     def __setup_node__(self, node):
         # sets up node so it belongs to this fgraph
@@ -177,7 +177,7 @@ class FunctionGraph(utils.object2):
                                 str(node.op), str(node.op.destroy_map)))
         node.fgraph = self
         node.deps = {}
-        #self.execute_callbacks('on_setup_node', node)
+        # self.execute_callbacks('on_setup_node', node)
 
     def disown(self):
         """ WRITEME
@@ -201,7 +201,7 @@ class FunctionGraph(utils.object2):
         self.inputs = None
         self.outputs = None
 
-    ### clients ###
+    # clients #
     def clients(self, r):
         """
         Set of all the (node, i) pairs such that node.inputs[i] is r.
@@ -221,9 +221,9 @@ class FunctionGraph(utils.object2):
         if set(r.clients).intersection(set(new_clients)):
             print('ERROR: clients intersect!', file=sys.stderr)
             print('  RCLIENTS of', r, [(n, i, type(n), id(n))
-                                                      for n, i in r.clients], file=sys.stderr)
+                                       for n, i in r.clients], file=sys.stderr)
             print('  NCLIENTS of', r, [(n, i, type(n), id(n))
-                                                      for n, i in new_clients], file=sys.stderr)
+                                       for n, i in new_clients], file=sys.stderr)
         assert not set(r.clients).intersection(set(new_clients))
         r.clients += new_clients
 
@@ -245,7 +245,7 @@ class FunctionGraph(utils.object2):
             return True
         return False
 
-    ### import ###
+    # import #
     def __import_r__(self, variable, reason):
         global NullType
         if NullType is None:
@@ -279,9 +279,8 @@ class FunctionGraph(utils.object2):
                     if hasattr(r, 'fgraph') and r.fgraph is not self:
                         raise Exception("%s is already owned by another fgraph" % r)
                     if (r.owner is None and
-                        not isinstance(r, graph.Constant) and
-                        r not in self.inputs):
-
+                            not isinstance(r, graph.Constant) and
+                            r not in self.inputs):
                         # Verbose error message
                         # Show a complete chain of variables from the missing input to an output
                         if config.exception_verbosity == 'high':
@@ -373,7 +372,7 @@ class FunctionGraph(utils.object2):
             assert node.fgraph is self
             self.execute_callbacks('on_import', node, reason)
 
-    ### prune ###
+    # prune #
     def __prune_r__(self, variable, reason=None):
         """Should be called for variable that aren't used anymore:
         len(var.clients) == 0
@@ -430,7 +429,7 @@ class FunctionGraph(utils.object2):
             self.__remove_clients__(input, [(apply_node, i)], reason=reason)
         # self.__prune_r__(apply_node.inputs)
 
-    ### change input ###
+    # change input #
     def change_input(self, node, i, new_r, reason=None):
         """WRITEME
         Changes node.inputs[i] to new_r.
@@ -475,7 +474,7 @@ class FunctionGraph(utils.object2):
         if prune:
             self.__prune_r__(r, reason=reason)
 
-    ### replace ###
+    # replace #
     def replace(self, r, new_r, reason=None, verbose=None):
         """ WRITEME
         This is the main interface to manipulate the subgraph in FunctionGraph.
@@ -582,7 +581,7 @@ class FunctionGraph(utils.object2):
         if detach is not None:
             detach(self)
 
-    ### callback utils ###
+    # callback utils #
     def execute_callbacks(self, name, *args, **kwargs):
         """WRITEME
         Calls
@@ -618,7 +617,7 @@ class FunctionGraph(utils.object2):
             d[feature] = fn(*args)
         return d
 
-    ### misc ###
+    # misc #
     def toposort(self):
         """WRITEME
         Returns an ordering of the graph's Apply nodes such that:
@@ -712,8 +711,8 @@ class FunctionGraph(utils.object2):
                 missing, excess)
         for variable in variables:
             if (variable.owner is None and
-                variable not in self.inputs and
-                not isinstance(variable, graph.Constant)):
+                    variable not in self.inputs and
+                    not isinstance(variable, graph.Constant)):
                 raise Exception("Undeclared input.", variable)
             if variable.fgraph is not self:
                 raise Exception("Variable should belong to the FunctionGraph.",
@@ -737,7 +736,7 @@ class FunctionGraph(utils.object2):
     def __repr__(self):
         return self.__str__()
 
-    ### clone ###
+    # clone #
     def clone(self, check_integrity=True):
         """WRITEME"""
         return self.clone_get_equiv(check_integrity)[0]

theano/gof/link.py

@@ -7,14 +7,14 @@ import traceback
 import numpy
 
 import theano
-from theano.compat import PY3, izip
+from theano.compat import izip
 from six import reraise
 from six.moves import StringIO
 from theano.gof import utils
 from theano.gof import graph
 from theano.gof.type import Type
 
-from .utils import MethodNotDefined, undef
+from .utils import undef
 
 __excepthook = sys.excepthook
 
@@ -281,9 +281,9 @@ def raise_with_op(node, thunk=None, exc_info=None, storage_map=None):
             else:
                 detailed_err_msg += "\n"
         detailed_err_msg += " TotalSize: %s Byte(s) %.3f GB\n" % (
-            total_size, total_size/1024./1024/1024)
+            total_size, total_size / 1024. / 1024 / 1024)
         detailed_err_msg += " TotalSize inputs: %s Byte(s) %.3f BG\n" % (
-            total_size_inputs, total_size_inputs/1024./1024/1024)
+            total_size_inputs, total_size_inputs / 1024. / 1024 / 1024)
 
     else:
         hints.append(
@@ -326,7 +326,7 @@ class Linker(object):
         raise utils.MethodNotDefined("make_thunk", type(self),
                                      self.__class__.__name__)
 
-    ## DELETEME ##
+    # DELETEME #
     def make_function(self, unpack_single=True, **kwargs):
         """
         Returns a function that takes values corresponding to the inputs of the
@@ -350,8 +350,8 @@ class Linker(object):
 
         def execute(*args):
             def e_arity(takes, got):
-                return 'Function call takes exactly %i %s (%i given)' \
-                        % (takes, ['argument', 'arguments'][takes > 1], got)
+                return 'Function call takes exactly %i %s (%i given)' % (
+                    takes, ['argument', 'arguments'][takes > 1], got)
             if (len(args) != len(inputs)):
                 raise TypeError(e_arity(len(inputs), len(args)))
             for arg, variable in izip(args, inputs):
@@ -394,7 +394,7 @@ class Container(object):
         """
         if not isinstance(storage, list) or not len(storage) >= 1:
             raise TypeError("storage must be a list of length at least one")
-        #self.r = r
+        # self.r = r
         if isinstance(r, Type):
             self.type = r
         else:
@@ -454,12 +454,11 @@ class Container(object):
             deepcopy(self.strict, memo=memo),
             deepcopy(self.allow_downcast, memo=memo),
             deepcopy(self.name, memo=memo),
-            )
+        )
         # Work around NumPy deepcopy of ndarray with 0 dimention that
         # don't return an ndarray.
         if (r.storage[0] is not None and
-            not self.type.is_valid_value(r.storage[0])):
-
+                not self.type.is_valid_value(r.storage[0])):
             assert not data_was_in_memo
             assert self.type.is_valid_value(self.storage[0])
             # This should also work for read only container.
@@ -672,7 +671,7 @@ class PerformLinker(LocalLinker):
             no_recycling = []
         if self.fgraph is not None and self.fgraph is not fgraph:
             return type(self)(allow_gc=self.allow_gc).accept(fgraph, no_recycling)
-            #raise Exception("Cannot accept from a Linker that is already tied to another FunctionGraph.")
+            # raise Exception("Cannot accept from a Linker that is already tied to another FunctionGraph.")
         self.fgraph = fgraph
         self.no_recycling = no_recycling
         return self
@@ -721,9 +720,12 @@ class PerformLinker(LocalLinker):
 
         for node in order:
             if self.allow_gc:
-                post_thunk_old_storage.append([storage_map[input]
-                    for input in node.inputs
-                    if (input in computed) and (input not in fgraph.outputs) and node == last_user[input]])
+                post_thunk_old_storage.append(
+                    [storage_map[input]
+                     for input in node.inputs
+                     if (input in computed) and (
+                        input not in fgraph.outputs) and (
+                        node == last_user[input])])
 
         if no_recycling is True:
             # True seems like some special code for *everything*?? -JB
@@ -855,7 +857,7 @@ class WrapLinker(Linker):
         make_all += [l.make_all(**kwargs) for l in self.linkers[1:]]
 
         fns, input_lists, output_lists, thunk_lists, order_lists \
-                = zip(*make_all)
+            = zip(*make_all)
 
         order_list0 = order_lists[0]
         for order_list in order_lists[1:]:

theano/gof/opt.py

@@ -29,6 +29,7 @@ from . import destroyhandler as dh
 _logger = logging.getLogger('theano.gof.opt')
 _optimizer_idx = [0]
 
+
 def _list_of_nodes(fgraph):
     return list(graph.io_toposort(fgraph.inputs, fgraph.outputs))
 
@@ -99,7 +100,7 @@ class Optimizer(object):
     def print_summary(self, stream=sys.stdout, level=0, depth=-1):
         name = getattr(self, 'name', None)
         print("%s%s %s id=%i" % (
-                (' ' * level), self.__class__.__name__, name, id(self)), file=stream)
+            (' ' * level), self.__class__.__name__, name, id(self)), file=stream)
 
     @staticmethod
     def print_profile(stream, prof, level=0):
@@ -121,9 +122,9 @@ class FromFunctionOptimizer(Optimizer):
 
     def print_summary(self, stream=sys.stdout, level=0, depth=-1):
         print("%s%s id=%i" % (
-                ' ' * level,
-                str(self.apply),
-                id(self)), file=stream)
+            ' ' * level,
+            str(self.apply),
+            id(self)), file=stream)
 
     def __call__(self, *args, **kwargs):
         return self.fn(*args, **kwargs)
@@ -222,7 +223,7 @@ class SeqOptimizer(Optimizer, list):
     def print_summary(self, stream=sys.stdout, level=0, depth=-1):
         name = getattr(self, 'name', None)
         print("%s%s %s id=%i" % (
-                (' ' * level), self.__class__.__name__, name, id(self)), file=stream)
+            (' ' * level), self.__class__.__name__, name, id(self)), file=stream)
         # This way, -1 will do all depth
         if depth != 0:
             depth -= 1
@@ -241,8 +242,8 @@ class SeqOptimizer(Optimizer, list):
         elif hasattr(opts, "__name__"):
             print(blanc, opts.__name__, end=' ', file=stream)
         print((" time %.3fs for %d/%d nodes"
-                          " before/after optimization" % (
-                              sum(prof), nb_node_before, nb_node_after)), file=stream)
+               " before/after optimization" % (
+                   sum(prof), nb_node_before, nb_node_after)), file=stream)
         print(blanc, "  %.3fs for fgraph.validate()" % (validate_time), file=stream)
         print(blanc, "  %.3fs for callback" % (callback_time), file=stream)
         if level == 0:
@@ -324,7 +325,7 @@ class SeqOptimizer(Optimizer, list):
                     new_t[idx] += p[1][p[0].index(l)]
                     if hasattr(l, 'merge_profile'):
                         assert len(p[6][p[0].index(l)]) == \
-                                len(new_sub_profile[idx])
+                            len(new_sub_profile[idx])
                         new_sub_profile[idx] = l.merge_profile(
                             new_sub_profile[idx], p[6][p[0].index(l)])
                     else:
@@ -729,6 +730,7 @@ def pre_constant_merge(vars):
     const_sig_inv = {}
     if isinstance(vars, graph.Variable):
         vars = [vars]
+
     def recursive_merge(var):
         if var in seen_var:
             return var
@@ -761,7 +763,7 @@ def pre_constant_merge(vars):
 
 
 ########################
-### Local Optimizers ###
+#   Local Optimizers   #
 ########################
 
 class LocalOptimizer(object):
@@ -817,12 +819,14 @@ class LocalOptimizer(object):
 
     def print_summary(self, stream=sys.stdout, level=0, depth=-1):
         print("%s%s id=%i" % (
-                (' ' * level), self.__class__.__name__, id(self)), file=stream)
+            (' ' * level), self.__class__.__name__, id(self)), file=stream)
 
 
-theano.configparser.AddConfigVar('metaopt.verbose',
-        "Enable verbose output for meta optimizers",
-        theano.configparser.BoolParam(False), in_c_key=False)
+theano.configparser.AddConfigVar(
+    'metaopt.verbose',
+    "Enable verbose output for meta optimizers",
+    theano.configparser.BoolParam(False),
+    in_c_key=False)
 
 
 class LocalMetaOptimizer(LocalOptimizer):
@@ -933,9 +937,9 @@ class FromFunctionLocalOptimizer(LocalOptimizer):
 
     def print_summary(self, stream=sys.stdout, level=0, depth=-1):
         print("%s%s id=%i" % (
-                ' ' * level,
-                str(self.transform),
-                id(self)), file=stream)
+            ' ' * level,
+            str(self.transform),
+            id(self)), file=stream)
 
 
 def local_optimizer(tracks, inplace=False):
@@ -992,7 +996,7 @@ class LocalOptGroup(LocalOptimizer):
 
     def print_summary(self, stream=sys.stdout, level=0, depth=-1):
         print("%s%s id=%i" % (
-                (' ' * level), self.__class__.__name__, id(self)), file=stream)
+            (' ' * level), self.__class__.__name__, id(self)), file=stream)
         if depth != 0:
             depth -= 1
             for lopt in self.opts:
@@ -1003,19 +1007,6 @@ class LocalOptGroup(LocalOptimizer):
             opt.add_requirements(fgraph)
 
 
-class _LocalOpKeyOptGroup(LocalOptGroup):
-    """WRITEME"""
-
-    def __init__(self, optimizers):
-        if any(not hasattr(opt, 'op_key'), optimizers):
-            raise TypeError(
-                "All LocalOptimizers passed here must have an op_key method.")
-        CompositeLocalOptimizer.__init__(self, optimizers)
-
-    def op_key(self):
-        return [opt.op_key() for opt in self.opts]
-
-
 class OpSub(LocalOptimizer):
     """WRITEME
     Replaces the application of a certain op by the application of
@@ -1086,10 +1077,10 @@ class OpRemove(LocalOptimizer):
 
     def print_summary(self, stream=sys.stdout, level=0, depth=-1):
         print("%s%s(%s) id=%i" % (
-                ' ' * level,
-                self.__class__.__name__,
-                str(self.op),
-                id(self)), file=stream)
+            ' ' * level,
+            self.__class__.__name__,
+            str(self.op),
+            id(self)), file=stream)
 
 
 class PatternSub(LocalOptimizer):
@@ -1217,6 +1208,7 @@ class PatternSub(LocalOptimizer):
         if node.op != self.op:
             return False
         # TODO: if we remove pdb, do this speed things up?
+
         def match(pattern, expr, u, allow_multiple_clients=False, pdb=False):
             # TODO move outside match
             def retry_with_equiv():
@@ -1233,9 +1225,8 @@ class PatternSub(LocalOptimizer):
             if isinstance(pattern, (list, tuple)):
                 if expr.owner is None:
                     return False
-                if (not (expr.owner.op == pattern[0])
-                        or (not allow_multiple_clients
-                            and len(expr.clients) > 1)):
+                if (not (expr.owner.op == pattern[0]) or
+                        (not allow_multiple_clients and len(expr.clients) > 1)):
                     return retry_with_equiv()
                 if len(pattern) - 1 != len(expr.owner.inputs):
                     return retry_with_equiv()
@@ -1263,16 +1254,16 @@ class PatternSub(LocalOptimizer):
                     return retry_with_equiv()
                 else:
                     u = u.merge(expr, v)
-            elif (isinstance(pattern, (int, float))
-                    and isinstance(expr, graph.Constant)):
+            elif (isinstance(pattern, (int, float)) and
+                    isinstance(expr, graph.Constant)):
                 if numpy.all(
                         theano.tensor.constant(pattern).value == expr.value):
                     return u
                 else:
                     return retry_with_equiv()
-            elif (isinstance(pattern, graph.Constant)
-                    and isinstance(expr, graph.Constant)
-                    and pattern.equals(expr)):
+            elif (isinstance(pattern, graph.Constant) and
+                    isinstance(expr, graph.Constant) and
+                    pattern.equals(expr)):
                 return u
             else:
                 return retry_with_equiv()
@@ -1308,17 +1299,17 @@ class PatternSub(LocalOptimizer):
         def pattern_to_str(pattern):
             if isinstance(pattern, (list, tuple)):
                 return "%s(%s)" % (
-                        str(pattern[0]),
-                        ", ".join([pattern_to_str(p) for p in pattern[1:]]))
+                    str(pattern[0]),
+                    ", ".join([pattern_to_str(p) for p in pattern[1:]]))
             elif isinstance(pattern, dict):
                 return "%s subject to %s" % (
-                        pattern_to_str(pattern['pattern']),
-                        str(pattern.get('constraint', 'no conditions')))
+                    pattern_to_str(pattern['pattern']),
+                    str(pattern.get('constraint', 'no conditions')))
             else:
                 return str(pattern)
         return "%s -> %s" % (
-                pattern_to_str(self.in_pattern),
-                pattern_to_str(self.out_pattern))
+            pattern_to_str(self.in_pattern),
+            pattern_to_str(self.out_pattern))
 
     def __repr__(self):
         return str(self)
@@ -1326,16 +1317,16 @@ class PatternSub(LocalOptimizer):
     def print_summary(self, stream=sys.stdout, level=0, depth=-1):
         name = getattr(self, '__name__', getattr(self, 'name', None))
         print("%s%s %s(%s, %s) id=%i" % (
-                ' ' * level,
-                self.__class__.__name__,
-                name,
-                str(self.in_pattern),
-                str(self.out_pattern),
-                id(self)), file=stream)
+            ' ' * level,
+            self.__class__.__name__,
+            name,
+            str(self.in_pattern),
+            str(self.out_pattern),
+            id(self)), file=stream)
 
 
 ##################
-### Navigators ###
+#   Navigators   #
 ##################
 
 # Use the following classes to apply LocalOptimizers
@@ -1545,7 +1536,7 @@ class NavigatorOptimizer(Optimizer):
 
     def print_summary(self, stream=sys.stdout, level=0, depth=-1):
         print("%s%s (%i)" % (
-                (' ' * level), self.__class__.__name__, id(self)), file=stream)
+            (' ' * level), self.__class__.__name__, id(self)), file=stream)
         if depth != 0:
             self.local_opt.print_summary(stream, level=(level + 2),
                                          depth=(depth - 1))
@@ -1734,7 +1725,7 @@ class EquilibriumOptimizer(NavigatorOptimizer):
             self.final_optimizers = final_optimizers
         self.max_use_ratio = max_use_ratio
         assert self.max_use_ratio is not None, (
-                'max_use_ratio has to be a number')
+            'max_use_ratio has to be a number')
 
     def get_local_optimizers(self):
         for opt in self.local_optimizers_all:
@@ -1811,8 +1802,8 @@ class EquilibriumOptimizer(NavigatorOptimizer):
                     node_created[gopt] += change_tracker.nb_imported - nb
                     if global_process_count[gopt] > max_use:
                         max_use_abort = True
-                        opt_name = (getattr(gopt, "name", None)
-                                    or getattr(gopt, "__name__", ""))
+                        opt_name = (getattr(gopt, "name", None) or
+                                    getattr(gopt, "__name__", ""))
             global_sub_profs.append(sub_profs)
 
             global_opt_timing.append(float(time.time() - t0))
@@ -1858,8 +1849,8 @@ class EquilibriumOptimizer(NavigatorOptimizer):
                             node_created[lopt] += change_tracker.nb_imported - nb
                             if global_process_count[lopt] > max_use:
                                 max_use_abort = True
-                                opt_name = (getattr(lopt, "name", None)
-                                            or getattr(lopt, "__name__", ""))
+                                opt_name = (getattr(lopt, "name", None) or
+                                            getattr(lopt, "__name__", ""))
                             if node not in fgraph.apply_nodes:
                                 # go to next node
                                 break
@@ -1884,8 +1875,8 @@ class EquilibriumOptimizer(NavigatorOptimizer):
                     node_created[gopt] += change_tracker.nb_imported - nb
                     if global_process_count[gopt] > max_use:
                         max_use_abort = True
-                        opt_name = (getattr(gopt, "name", None)
-                                    or getattr(gopt, "__name__", ""))
+                        opt_name = (getattr(gopt, "name", None) or
+                                    getattr(gopt, "__name__", ""))
             final_sub_profs.append(sub_profs)
 
             global_opt_timing[-1] += time.time() - t_before_final_opt
@@ -1896,9 +1887,9 @@ class EquilibriumOptimizer(NavigatorOptimizer):
         end_nb_nodes = len(fgraph.apply_nodes)
 
         if max_use_abort:
-            _logger.error("EquilibriumOptimizer max'ed out by '%s'" % opt_name
-                          + ". You can safely raise the current threshold of "
-                          + "%f with the theano flag 'optdb.max_use_ratio'." %
+            _logger.error("EquilibriumOptimizer max'ed out by '%s'" % opt_name +
+                          ". You can safely raise the current threshold of " +
+                          "%f with the theano flag 'optdb.max_use_ratio'." %
                           config.optdb.max_use_ratio)
         fgraph.remove_feature(change_tracker)
         return (self, loop_timing, loop_process_count,
@@ -1909,7 +1900,7 @@ class EquilibriumOptimizer(NavigatorOptimizer):
     def print_summary(self, stream=sys.stdout, level=0, depth=-1):
         name = getattr(self, 'name', None)
         print("%s%s %s id=%i" % (
-                (' ' * level), self.__class__.__name__, name, id(self)), file=stream)
+            (' ' * level), self.__class__.__name__, name, id(self)), file=stream)
         if depth != 0:
             for lopt in self.get_local_optimizers():
                 lopt.print_summary(stream, level=(level + 2),
@@ -1925,11 +1916,11 @@ class EquilibriumOptimizer(NavigatorOptimizer):
         blanc = ('    ' * level)
         print(blanc, "EquilibriumOptimizer", end=' ', file=stream)
         print(blanc, getattr(opt, "name",
-                                        getattr(opt, "__name__", "")), file=stream)
+                             getattr(opt, "__name__", "")), file=stream)
         print(blanc, "  time %.3fs for %d passes" % (
-                sum(loop_timing), len(loop_timing)), file=stream)
+            sum(loop_timing), len(loop_timing)), file=stream)
         print(blanc, "  nb nodes (start, end,  max) %d %d %d" % (
-                start_nb_nodes, end_nb_nodes, max_nb_nodes), file=stream)
+            start_nb_nodes, end_nb_nodes, max_nb_nodes), file=stream)
         print(blanc, "  time io_toposort %.3fs" % sum(
             io_toposort_timing), file=stream)
         s = sum([time_opts[o] for o in opt.get_local_optimizers()])
@@ -1948,12 +1939,12 @@ class EquilibriumOptimizer(NavigatorOptimizer):
                 if len(d) > 5:
                     lopt += " ..."
             print(blanc, ('  %2d - %.3fs %d (%.3fs in global opts, '
-                                     '%.3fs io_toposort) - %d nodes - %s' % (
-                                         i, loop_timing[i],
-                                         sum(loop_process_count[i].values()),
-                                         global_opt_timing[i],
-                                         io_toposort_timing[i], nb_nodes[i],
-                                         lopt)), file=stream)
+                          '%.3fs io_toposort) - %d nodes - %s' % (
+                              i, loop_timing[i],
+                              sum(loop_process_count[i].values()),
+                              global_opt_timing[i],
+                              io_toposort_timing[i], nb_nodes[i],
+                              lopt)), file=stream)
 
         count_opt = []
         not_used = []
@@ -1975,8 +1966,9 @@ class EquilibriumOptimizer(NavigatorOptimizer):
                 not_used_time += time_opts[o]
 
         if count_opt:
-            print(blanc, \
-                    '  times - times applied - nb node created - name:', file=stream)
+            print(blanc,
+                  '  times - times applied - nb node created - name:',
+                  file=stream)
             count_opt.sort()
             for (t, count, n_created, o) in count_opt[::-1]:
                 print(blanc, '  %.3fs - %d - %d - %s' % (
@@ -2010,7 +2002,7 @@ class EquilibriumOptimizer(NavigatorOptimizer):
 
     @staticmethod
     def merge_profile(prof1, prof2):
-        #(opt, loop_timing, loop_process_count, max_nb_nodes,
+        # (opt, loop_timing, loop_process_count, max_nb_nodes,
         # global_opt_timing, nb_nodes, time_opts, io_toposort_timing) = prof1
         local_optimizers = OrderedSet(prof1[0].get_local_optimizers()).union(
             prof2[0].get_local_optimizers())
@@ -2085,7 +2077,7 @@ class EquilibriumOptimizer(NavigatorOptimizer):
                 final_sub_profs)
 
 #################
-### Utilities ###
+#   Utilities   #
 #################
 
 
@@ -2096,7 +2088,7 @@ def _check_chain(r, chain):
     while chain:
         elem = chain.pop()
         if elem is None:
-            if not r.owner is None:
+            if r.owner is not None:
                 return False
         elif r.owner is None:
             return False
@@ -2105,20 +2097,20 @@ def _check_chain(r, chain):
                 return False
         else:
             try:
-                if (issubclass(elem, op.Op)
-                        and not isinstance(r.owner.op, elem)):
+                if (issubclass(elem, op.Op) and
+                        not isinstance(r.owner.op, elem)):
                     return False
             except TypeError:
                 return False
         if chain:
             r = r.owner.inputs[chain.pop()]
     # print 'check_chain', _check_chain.n_calls
-    #_check_chain.n_calls += 1
+    # _check_chain.n_calls += 1
 
     # The return value will be used as a Boolean, but some Variables cannot
     # be used as Booleans (the results of comparisons, for instance)
     return (r is not None)
-#_check_chain.n_calls = 0
+# _check_chain.n_calls = 0
 
 
 def check_chain(r, *chain):

theano/gof/utils.py

@@ -3,9 +3,11 @@ import linecache
 import traceback
 import sys
 
+import numpy
 from six import iteritems
 
 from theano import config
+from theano.compat import PY3
 
 
 def simple_extract_stack(f=None, limit=None):
@@ -435,3 +437,31 @@ def remove(predicate, coll):
     [1, 3]
     """
     return [x for x in coll if not predicate(x)]
+
+
+if PY3:
+    import hashlib
+
+    def hash_from_code(msg):
+        # hashlib.md5() requires an object that supports buffer interface,
+        # but Python 3 (unicode) strings don't.
+        if isinstance(msg, str):
+            msg = msg.encode()
+        # Python 3 does not like module names that start with
+        # a digit.
+        return 'm' + hashlib.md5(msg).hexdigest()
+
+else:
+    import hashlib
+
+    def hash_from_code(msg):
+        try:
+            return hashlib.md5(msg).hexdigest()
+        except TypeError:
+            assert isinstance(msg, numpy.ndarray)
+            return hashlib.md5(numpy.getbuffer(msg)).hexdigest()
+
+
+def hash_from_file(file_path):
+    """Return the MD5 hash of a file."""
+    return hash_from_code(open(file_path, 'rb').read())

theano/sandbox/cuda/nvcc_compiler.py

@@ -10,7 +10,7 @@ import numpy
 
 from theano.compat import decode, decode_iter
 from theano.gof import local_bitwidth
-from theano.gof.cc import hash_from_file
+from theano.gof.utils import hash_from_file
 from theano.gof.cmodule import (std_libs, std_lib_dirs,
                                 std_include_dirs, dlimport,
                                 Compiler,

theano/sparse/utils.py

-from theano.gof.cc import hash_from_code
+from theano.gof.utils import hash_from_code
 
 
 def hash_from_sparse(data):

theano/tensor/utils.py

@@ -2,7 +2,7 @@ import numpy
 
 import theano
 from theano.compat import izip
-from theano.gof.cc import hash_from_code
+from theano.gof.utils import hash_from_code
 
 
 def hash_from_ndarray(data):

theano/tests/test_flake8.py

@@ -233,16 +233,10 @@ whitelist_flake8 = [
     "sparse/sandbox/sp2.py",
     "sparse/sandbox/truedot.py",
     "sparse/sandbox/sp.py",
-    "gof/destroyhandler.py",
     "gof/unify.py",
     "gof/graph.py",
     "gof/__init__.py",
-    "gof/cc.py",
-    "gof/opt.py",
-    "gof/link.py",
-    "gof/fg.py",
     "gof/op.py",
-    "gof/cmodule.py",
     "gof/tests/test_cmodule.py",
     "gof/tests/test_destroyhandler.py",
     "gof/tests/test_opt.py",