Merge pull request #505 from lamblin/pep8

bin/theano-cache

 #!/usr/bin/env python
-import logging, os, sys
+import logging
+import os
+import sys
+
 import theano
 from theano import config
 from theano.gof.cc import get_module_cache
@@ -41,4 +44,3 @@ else:
     print 'Type "theano-cache unlock" to unlock the cache directory'
     print 'Type "theano-cache cleanup" to delete keys in the old format'
     sys.exit(1)
-

bin/theano-nose

 #!/usr/bin/env python
 
-__authors__   = "Olivier Delalleau, Pascal Lamblin"
-__contact__   = "delallea@iro"
+__authors__ = "Olivier Delalleau, Pascal Lamblin"
+__contact__ = "delallea@iro"
 
 """
 This script should behave the same as the `nosetests` command.
@@ -68,6 +68,7 @@ def main():
 
     return nose.main(addplugins=addplugins)
 
+
 def help():
     help_msg = """
         This script behaves mostly the same as the `nosetests` command.

distribute_setup.py

@@ -144,7 +144,7 @@ def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
         except ImportError:
             return _do_download(version, download_base, to_dir, download_delay)
         try:
-            pkg_resources.require("distribute>="+version)
+            pkg_resources.require("distribute>=" + version)
             return
         except pkg_resources.VersionConflict:
             e = sys.exc_info()[1]
@@ -167,6 +167,7 @@ def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
         if not no_fake:
             _create_fake_setuptools_pkg_info(to_dir)
 
+
 def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
                         to_dir=os.curdir, delay=15):
     """Download distribute from a specified location and return its filename
@@ -203,6 +204,7 @@ def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
                 dst.close()
     return os.path.realpath(saveto)
 
+
 def _no_sandbox(function):
     def __no_sandbox(*args, **kw):
         try:
@@ -227,6 +229,7 @@ def _no_sandbox(function):
 
     return __no_sandbox
 
+
 def _patch_file(path, content):
     """Will backup the file then patch it"""
     existing_content = open(path).read()
@@ -245,15 +248,18 @@ def _patch_file(path, content):
 
 _patch_file = _no_sandbox(_patch_file)
 
+
 def _same_content(path, content):
     return open(path).read() == content
 
+
 def _rename_path(path):
     new_name = path + '.OLD.%s' % time.time()
     log.warn('Renaming %s into %s', path, new_name)
     os.rename(path, new_name)
     return new_name
 
+
 def _remove_flat_installation(placeholder):
     if not os.path.isdir(placeholder):
         log.warn('Unkown installation at %s', placeholder)
@@ -289,11 +295,13 @@ def _remove_flat_installation(placeholder):
 
 _remove_flat_installation = _no_sandbox(_remove_flat_installation)
 
+
 def _after_install(dist):
     log.warn('After install bootstrap.')
     placeholder = dist.get_command_obj('install').install_purelib
     _create_fake_setuptools_pkg_info(placeholder)
 
+
 def _create_fake_setuptools_pkg_info(placeholder):
     if not placeholder or not os.path.exists(placeholder):
         log.warn('Could not find the install location')
@@ -321,7 +329,9 @@ def _create_fake_setuptools_pkg_info(placeholder):
     finally:
         f.close()
 
-_create_fake_setuptools_pkg_info = _no_sandbox(_create_fake_setuptools_pkg_info)
+_create_fake_setuptools_pkg_info = _no_sandbox(
+        _create_fake_setuptools_pkg_info)
+
 
 def _patch_egg_dir(path):
     # let's check if it's already patched
@@ -343,6 +353,7 @@ def _patch_egg_dir(path):
 
 _patch_egg_dir = _no_sandbox(_patch_egg_dir)
 
+
 def _before_install():
     log.warn('Before install bootstrap.')
     _fake_setuptools()
@@ -351,7 +362,7 @@ def _before_install():
 def _under_prefix(location):
     if 'install' not in sys.argv:
         return True
-    args = sys.argv[sys.argv.index('install')+1:]
+    args = sys.argv[(sys.argv.index('install') + 1):]
     for index, arg in enumerate(args):
         for option in ('--root', '--prefix'):
             if arg.startswith('%s=' % option):
@@ -359,7 +370,7 @@ def _under_prefix(location):
                 return location.startswith(top_dir)
             elif arg == option:
                 if len(args) > index:
-                    top_dir = args[index+1]
+                    top_dir = args[index + 1]
                     return location.startswith(top_dir)
         if arg == '--user' and USER_SITE is not None:
             return location.startswith(USER_SITE)
@@ -380,7 +391,8 @@ def _fake_setuptools():
                                   replacement=False))
     except TypeError:
         # old distribute API
-        setuptools_dist = ws.find(pkg_resources.Requirement.parse('setuptools'))
+        setuptools_dist = ws.find(
+                pkg_resources.Requirement.parse('setuptools'))
 
     if setuptools_dist is None:
         log.warn('No setuptools distribution found')
@@ -422,7 +434,8 @@ def _relaunch():
     log.warn('Relaunching...')
     # we have to relaunch the process
     # pip marker to avoid a relaunch bug
-    if sys.argv[:3] == ['-c', 'install', '--single-version-externally-managed']:
+    if (sys.argv[:3] ==
+            ['-c', 'install', '--single-version-externally-managed']):
         sys.argv[0] = 'setup.py'
     args = [sys.executable] + sys.argv
     sys.exit(subprocess.call(args))
@@ -448,7 +461,7 @@ def _extractall(self, path=".", members=None):
             # Extract directories with a safe mode.
             directories.append(tarinfo)
             tarinfo = copy.copy(tarinfo)
-            tarinfo.mode = 448 # decimal for oct 0700
+            tarinfo.mode = 448  # decimal for oct 0700
         self.extract(tarinfo, path)
 
     # Reverse sort directories.

doc/conf.py

@@ -3,16 +3,16 @@
 # theano documentation build configuration file, created by
 # sphinx-quickstart on Tue Oct  7 16:34:06 2008.
 #
-# This file is execfile()d with the current directory set to its containing dir.
+# This file is execfile()d with the current directory set to its containing
+# directory.
 #
 # The contents of this file are pickled, so don't put values in the namespace
-# that aren't pickleable (module imports are okay, they're removed automatically).
+# that aren't pickleable (module imports are okay, they're removed
+# automatically).
 #
 # All configuration values have a default value; values that are commented out
 # serve to show the default value.
 
-import sys, os
-
 # If your extensions are in another directory, add it here. If the directory
 # is relative to the documentation root, use os.path.abspath to make it
 # absolute, like shown here.
@@ -21,8 +21,8 @@ import sys, os
 # General configuration
 # ---------------------
 
-# Add any Sphinx extension module names here, as strings. They can be extensions
-# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo']
 
 todo_include_todos = True
@@ -64,11 +64,12 @@ today_fmt = '%B %d, %Y'
 # List of documents that shouldn't be included in the build.
 #unused_docs = []
 
-# List of directories, relative to source directories, that shouldn't be searched
-# for source files.
+# List of directories, relative to source directories, that shouldn't be
+# searched for source files.
 exclude_dirs = ['images', 'scripts', 'sandbox']
 
-# The reST default role (used for this markup: `text`) to use for all documents.
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
 #default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
@@ -166,7 +167,8 @@ htmlhelp_basename = 'theanodoc'
 latex_font_size = '11pt'
 
 # Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, document class [howto/manual]).
+# (source start file, target name, title, author, document class
+# [howto/manual]).
 latex_documents = [
   ('index', 'theano.tex', 'theano Documentation',
    'LISA lab, University of Montreal', 'manual'),

doc/scripts/docgen.py

@@ -4,16 +4,14 @@ import os
 import shutil
 import inspect
 
-from epydoc import docintrospecter 
+from epydoc import docintrospecter
 from epydoc.apidoc import RoutineDoc
 
+
 def Op_to_RoutineDoc(op, routine_doc, module_name=None):
     routine_doc.specialize_to(RoutineDoc)
 
-    #NB: this code is lifted from
-    # /u/bergstrj/pub/prefix/x86_64-unknown-linux-gnu-Fedora_release_7__Moonshine_/lib/python2.5/site-packages/epydoc
-    # /u/bergstrj/pub/prefix/x86_64-unknown-linux-gnu-Fedora_release_7__Moonshine_/lib/python2.5/site-packages/epydoc/docintrospecter.py
-
+    #NB: this code is lifted from epydoc/docintrospecter.py
 
     # op should be an op instance
     assert hasattr(op, 'perform')
@@ -32,7 +30,7 @@ def Op_to_RoutineDoc(op, routine_doc, module_name=None):
         routine_doc.kwarg = kwarg
 
         # Set default values for positional arguments.
-        routine_doc.posarg_defaults = [None]*len(args)
+        routine_doc.posarg_defaults = [None] * len(args)
 
         # Set the routine's line number.
         if hasattr(func, 'func_code'):
@@ -50,8 +48,8 @@ def Op_to_RoutineDoc(op, routine_doc, module_name=None):
     return routine_doc
 
 docintrospecter.register_introspecter(
-    lambda value: getattr(value, '__epydoc_asRoutine', False), 
-    Op_to_RoutineDoc, 
+    lambda value: getattr(value, '__epydoc_asRoutine', False),
+    Op_to_RoutineDoc,
     priority=-1)
 
 
@@ -63,13 +61,17 @@ if __name__ == '__main__':
     throot = "/".join(sys.path[0].split("/")[:-2])
 
     options = defaultdict(bool)
-    options.update(dict([x, y or True] for x, y in getopt.getopt(sys.argv[1:], 'o:', ['epydoc', 'rst', 'help', 'nopdf'])[0]))
+    options.update(dict([x, y or True] for x, y in
+        getopt.getopt(sys.argv[1:],
+                      'o:',
+                      ['epydoc', 'rst', 'help', 'nopdf'])[0]))
     if options['--help']:
         print 'Usage: %s [OPTIONS]' % sys.argv[0]
         print '  -o <dir>: output the html files in the specified dir'
         print '  --rst: only compile the doc (requires sphinx)'
         print '  --nopdf: do not produce a PDF file from the doc, only HTML'
-        print '  --epydoc: only compile the api documentation (requires epydoc)'
+        print '  --epydoc: only compile the api documentation',
+        print '(requires epydoc)'
         print '  --help: this help'
         sys.exit(0)
 
@@ -94,13 +96,14 @@ if __name__ == '__main__':
 
     if options['--all'] or options['--epydoc']:
         mkdir("api")
-        from epydoc.cli import cli
         sys.path[0:0] = [throot]
 
         #Generate HTML doc
 
         ## This causes problems with the subsequent generation of sphinx doc
-        #sys.argv[:] = ['', '--config', '%s/doc/api/epydoc.conf' % throot, '-o', 'api']
+        #from epydoc.cli import cli
+        #sys.argv[:] = ['', '--config', '%s/doc/api/epydoc.conf' % throot,
+        #               '-o', 'api']
         #cli()
         ## So we use this instead
         os.system("epydoc --config %s/doc/api/epydoc.conf -o api" % throot)
@@ -131,6 +134,3 @@ if __name__ == '__main__':
                 print 'OSError:', e
             except IOError, e:
                 print 'IOError:', e
-
-
-

setup.py

@@ -53,6 +53,7 @@ ISRELEASED          = False
 
 VERSION             = '%d.%d.%d%s' % (MAJOR, MINOR, MICRO, SUFFIX)
 
+
 def git_version():
     """
     Return the sha1 of local git HEAD as a string.
@@ -86,13 +87,15 @@ def git_version():
         git_revision = "unknown-git"
     return git_revision
 
+
 def write_version_py(filename=os.path.join('theano', 'generated_version.py')):
     cnt = """
 # THIS FILE IS GENERATED FROM THEANO SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
 git_revision = '%(git_revision)s'
-full_version = '%(version)s.dev-%%(git_revision)s' %% {'git_revision': git_revision}
+full_version = '%(version)s.dev-%%(git_revision)s' %% {
+        'git_revision': git_revision}
 release = %(isrelease)s
 
 if not release:

theano/__init__.py

@@ -95,7 +95,6 @@ import scalar
 #import sparse
 import gradient
 from gradient import Rop, Lop, grad
-import gof
 
 if config.device.startswith('gpu') or config.init_gpu_device.startswith('gpu'):
     import theano.sandbox.cuda

theano/configdefaults.py

 import os
 import logging
 import subprocess
-import sys
 
 from theano.configparser import (
-        AddConfigVar, BoolParam, ConfigParam, EnumStr, IntParam, FloatParam,
-        StrParam, TheanoConfigParser)
+        AddConfigVar, BoolParam, ConfigParam, EnumStr, IntParam,
+        TheanoConfigParser)
 
 
 _logger = logging.getLogger('theano.configdefaults')
@@ -41,10 +40,13 @@ AddConfigVar('int_division',
         EnumStr('int', 'raise', 'floatX'),
         in_c_key=False)
 
-#gpu mean let the driver select the gpu. Needed in case of gpu in exclusive mode.
-#gpuX mean use the gpu number X.
+# gpu means let the driver select the gpu. Needed in case of gpu in
+# exclusive mode.
+# gpuX mean use the gpu number X.
 AddConfigVar('device',
-        "Default device for computations. If gpu*, change the default to try to move computation to it and to put shared variable of float32 on it.",
+        ("Default device for computations. If gpu*, change the default to try "
+         "to move computation to it and to put shared variable of float32 "
+         "on it."),
         EnumStr('cpu', 'gpu',
             'gpu0', 'gpu1', 'gpu2', 'gpu3',
             'gpu4', 'gpu5', 'gpu6', 'gpu7',
@@ -93,14 +95,16 @@ try:
                      stdin=dummy_stdin.fileno())
     # Keep the default linker the same as the one for the mode FAST_RUN
     AddConfigVar('linker',
-                 "Default linker used if the theano flags mode is Mode or ProfileMode",
+                 ("Default linker used if the theano flags mode is Mode "
+                  "or ProfileMode"),
                  EnumStr('c|py', 'py', 'c', 'c|py_nogc', 'c&py',
                      'vm', 'cvm', 'vm_nogc', 'cvm_nogc'),
                  in_c_key=False)
 except OSError:
     # g++ is not present, linker should default to python only
     AddConfigVar('linker',
-                 "Default linker used if the theano flags mode is Mode or ProfileMode",
+                 ("Default linker used if the theano flags mode is Mode "
+                  "or ProfileMode"),
                  EnumStr('py', 'c|py', 'c', 'c|py_nogc', 'c&py',
                      'vm', 'cvm', 'vm_nogc', 'cvm_nogc'),
                  in_c_key=False)
@@ -113,12 +117,14 @@ del dummy_stdin
 
 #Keep the default optimizer the same as the one for the mode FAST_RUN
 AddConfigVar('optimizer',
-        "Default optimizer. If not None, will use this linker with the Mode object(not ProfileMode or DebugMode)",
+        ("Default optimizer. If not None, will use this linker with the Mode "
+         "object (not ProfileMode or DebugMode)"),
         EnumStr('fast_run', 'merge', 'fast_compile', 'None'),
         in_c_key=False)
 
 AddConfigVar('on_opt_error',
-        "What to do when an optimization crashes: warn and skip it, or raise the exception",
+        ("What to do when an optimization crashes: warn and skip it, or raise "
+         "the exception"),
         EnumStr('warn', 'raise'),
         in_c_key=False)
 
@@ -160,16 +166,18 @@ AddConfigVar('nocleanup',
 # changed at runtime.
 AddConfigVar('tensor.cmp_sloppy',
         "Relax tensor._allclose (0) not at all, (1) a bit, (2) more",
-        IntParam(0, lambda i: i in (0,1,2), allow_override=False),
+        IntParam(0, lambda i: i in (0, 1, 2), allow_override=False),
         in_c_key=False)
 
 AddConfigVar('tensor.local_elemwise_fusion',
-        "Enable or not in fast_run mode(fast_run optimization) the elemwise fusion optimization",
+        ("Enable or not in fast_run mode(fast_run optimization) the elemwise "
+         "fusion optimization"),
         BoolParam(True),
         in_c_key=False)
 
 AddConfigVar('gpu.local_elemwise_fusion',
-        "Enable or not in fast_run mode(fast_run optimization) the gpu elemwise fusion optimization",
+        ("Enable or not in fast_run mode(fast_run optimization) the gpu "
+         "elemwise fusion optimization"),
         BoolParam(True),
         in_c_key=False)
 
@@ -179,7 +187,8 @@ AddConfigVar('lib.amdlibm',
         BoolParam(False))
 
 AddConfigVar('op.set_flops',
-        "currently used only in ConvOp. The profile mode will print the flops/s for the op.",
+        ("currently used only in ConvOp. The profile mode will print the "
+         "flops/s for the op."),
         BoolParam(False),
         in_c_key=False)
 
@@ -244,8 +253,14 @@ AddConfigVar('numpy.seterr_invalid',
 ### To disable some warning about old bug that are fixed now.
 ###
 AddConfigVar('warn.ignore_bug_before',
-             "If 'None', we warn about all Theano bugs found by default. If 'all', we don't warn about Theano bugs found by default. If a version, we print only the warnings relative to Theano bugs found after that version. Warning for specific bugs can be configured with specific [warn] flags.",
-             EnumStr('None', 'all', '0.3','0.4', '0.4.1', '0.5', allow_override=False),
+             ("If 'None', we warn about all Theano bugs found by default. "
+              "If 'all', we don't warn about Theano bugs found by default. "
+              "If a version, we print only the warnings relative to Theano "
+              "bugs found after that version. "
+              "Warning for specific bugs can be configured with specific "
+              "[warn] flags."),
+             EnumStr('None', 'all', '0.3', '0.4', '0.4.1', '0.5',
+                     allow_override=False),
              in_c_key=False)
 
 
@@ -263,34 +278,48 @@ def warn_default(version):
 
 
 AddConfigVar('warn.argmax_pushdown_bug',
-             "Warn if in past version of Theano we generated a bug with the theano.tensor.nnet.nnet.local_argmax_pushdown optimization. Was fixed 27 may 2010",
+             ("Warn if in past version of Theano we generated a bug with the "
+              "theano.tensor.nnet.nnet.local_argmax_pushdown optimization. "
+              "Was fixed 27 may 2010"),
              BoolParam(warn_default('0.3')),
              in_c_key=False)
 
 AddConfigVar('warn.gpusum_01_011_0111_bug',
-             "Warn if we are in a case where old version of Theano had a silent bug with GpuSum pattern 01,011 and 0111 when the first dimensions was bigger then 4096. Was fixed 31 may 2010",
+             ("Warn if we are in a case where old version of Theano had a "
+              "silent bug with GpuSum pattern 01,011 and 0111 when the first "
+              "dimensions was bigger then 4096. Was fixed 31 may 2010"),
              BoolParam(warn_default('0.3')),
              in_c_key=False)
 
 AddConfigVar('warn.sum_sum_bug',
-             "Warn if we are in a case where Theano version between version 9923a40c7b7a and the 2 august 2010(fixed date), generated an error in that case. This happen when their is 2 consecutive sum in the graph, bad code was generated. Was fixed 2 August 2010",
+             ("Warn if we are in a case where Theano version between version "
+              "9923a40c7b7a and the 2 august 2010 (fixed date), generated an "
+              "error in that case. This happens when there are 2 consecutive "
+              "sums in the graph, bad code was generated. "
+              "Was fixed 2 August 2010"),
              BoolParam(warn_default('0.3')),
              in_c_key=False)
 
 AddConfigVar('warn.sum_div_dimshuffle_bug',
-             "Warn if previous versions of Theano (between rev. 3bd9b789f5e8, 2010-06-16, and cfc6322e5ad4, 2010-08-03) would have given incorrect result. This bug was triggered by sum of division of dimshuffled tensors.",
+             ("Warn if previous versions of Theano (between rev. "
+              "3bd9b789f5e8, 2010-06-16, and cfc6322e5ad4, 2010-08-03) "
+              "would have given incorrect result. This bug was triggered by "
+              "sum of division of dimshuffled tensors."),
              BoolParam(warn_default('0.3')),
              in_c_key=False)
 
 AddConfigVar('warn.subtensor_merge_bug',
         "Warn if previous versions of Theano (before 0.5rc2) could have given "
-        "incorrect results when indexing into a subtensor with negative stride "
-        "(for instance, for instance, x[a:b:-1][c]).",
+        "incorrect results when indexing into a subtensor with negative "
+        "stride (for instance, for instance, x[a:b:-1][c]).",
         BoolParam(warn_default('0.5')),
         in_c_key=False)
 
 AddConfigVar('compute_test_value',
-        "If 'True', Theano will run each op at graph build time, using Constants, SharedVariables and the tag 'test_value' as inputs to the function. This helps the user track down problems in the graph before it gets optimized.",
+        ("If 'True', Theano will run each op at graph build time, using "
+         "Constants, SharedVariables and the tag 'test_value' as inputs "
+         "to the function. This helps the user track down problems in the "
+         "graph before it gets optimized."),
         EnumStr('off', 'ignore', 'warn', 'raise'),
         in_c_key=False)
 
@@ -310,5 +339,5 @@ AddConfigVar('exception_verbosity',
         A. Elemwise{add_no_inplace}
                 B. log_likelihood_v_given_h
                 C. log_likelihood_h""",
-        EnumStr('low','high'),
+        EnumStr('low', 'high'),
         in_c_key=False)

theano/updates.py

 """Defines Updates object for storing a (SharedVariable, new_value) mapping.
 
 """
-__authors__   = "theano-dev"
+__authors__ = "theano-dev"
 __copyright__ = "(c) 2010, Universite de Montreal"
-__license__   = "3-clause BSD License"
-__contact__   = "theano-dev <theano-dev@googlegroups.com>"
+__license__ = "3-clause BSD License"
+__contact__ = "theano-dev <theano-dev@googlegroups.com>"
 
 __docformat__ = "restructuredtext en"
 
-from theano.compile.sharedvalue  import SharedVariable
+from theano.compile.sharedvalue import SharedVariable
 import logging
 logger = logging.getLogger('theano.updates')
 
+
 class Updates(dict):
     """
     Dict-like mapping from SharedVariable keys to their new values.
@@ -30,14 +31,16 @@ class Updates(dict):
 
             return super(Updates, self).__setitem__(key, value)
         else:
-            raise TypeError('Updates keys must inherit from SharedVariable', key)
+            raise TypeError('Updates keys must inherit from SharedVariable',
+                    key)
+
     def update(self, other):
         for key, val in dict(other).iteritems():
             if key in self:
                 if self[key] == val:
                     continue
                 raise KeyError('Collision', key)
-            self[key] = val # __setitem__ does type-checking
+            self[key] = val  # __setitem__ does type-checking
 
     def __add__(self, other):
         rval = Updates()
@@ -50,4 +53,3 @@ class Updates(dict):
         rval.update(other)
         rval.update(self)
         return rval
-