Merge pull request #4788 from slefrancois/flake8_new_api

doc/dev_start_guide.txt

@@ -11,13 +11,13 @@ You want to contribute to Theano? That is great! This page explain our
 workflow and some resource for doing so.
 
 Looking for an idea for a first contribution? Check `github issue
-<https://github.com/Theano/Theano/issues?q=is%3Aopen+is%3Aissue+label%3A%22Easy+fix%22>`
+<https://github.com/Theano/Theano/issues?q=is%3Aopen+is%3Aissue+label%3A%22Easy+fix%22>`_
 with a label ``easy fix``. They are good starter. It is recommanded
 that you write on the issue you want to work on it. This help make
 sure it is up to date and see if nobody else is working on it. Also,
 we can sometimes provides more information about it.  There is also
 the label `NeedSomeoneToFinish
-<https://github.com/Theano/Theano/labels/NeedSomeoneToFinish>` that is
+<https://github.com/Theano/Theano/labels/NeedSomeoneToFinish>`_ that is
 interresting to check. The difficulty level is variable.
 
 Resources
@@ -126,7 +126,11 @@ To setup VIM:
 
 #. Install flake8 (if not already installed) with::
 
-    pip install flake8
+    pip install "flake8<3"
+
+   .. warning:: Starting version 3.0.0, flake8 changed its dependancies and 
+      moved its Python API to a legacy module, breaking Theano's flake8 tests.
+      We recommend using a version prior to 3.  
 
    .. note:: You can use ``easy_install`` instead of ``pip``, and ``pep8``
       instead of ``flake8`` if you prefer. The important thing is that the

setup.py

@@ -166,7 +166,7 @@ def do_setup():
           install_requires=['numpy>=1.7.1', 'scipy>=0.11', 'six>=1.9.0'],
           # pygments is a dependency for Sphinx code highlight
           extras_require={
-              'test': ['nose>=1.3.0', 'nose-parameterized>=0.5.0'],
+              'test': ['nose>=1.3.0', 'nose-parameterized>=0.5.0', 'flake8<3'],
               'doc': ['Sphinx>=0.5.1', 'pygments']
           },
           package_data={

theano/gof/lazylinker_c.py

@@ -145,4 +145,4 @@ except ImportError:
         release_lock()
 
 from lazylinker_ext.lazylinker_ext import *  # noqa
-assert force_compile or (version == get_version())
+assert force_compile or (version == get_version())  # noqa

theano/gof/tests/test_destroyhandler.py

@@ -5,7 +5,8 @@ from theano.gof.type import Type
 from theano.gof import graph
 from theano.gof.graph import Variable, Apply
 from theano.gof.op import Op
-from theano.gof.opt import *  # noqa
+from theano.gof.opt import (OpKeyOptimizer, PatternSub, NavigatorOptimizer,
+                            TopoOptimizer, OpSub)
 
 from theano.gof import destroyhandler
 from theano.gof.fg import FunctionGraph, InconsistencyError

theano/gof/tests/test_link.py

@@ -11,7 +11,7 @@ from theano.gof.type import Type
 from theano.gof.op import Op
 from theano.gof import fg
 
-from theano.gof.link import *  # noqa
+from theano.gof.link import PerformLinker, WrapLinker, Container
 from theano.compat import cmp
 
 

theano/gof/tests/test_opt.py

@@ -3,9 +3,11 @@ from __future__ import absolute_import, print_function, division
 from theano.gof.type import Type
 from theano.gof.graph import Variable, Apply, Constant
 from theano.gof.op import Op
-from theano.gof.opt import *  # noqa
+from theano.gof.opt import (OpKeyOptimizer, PatternSub, TopoOptimizer, OpSub,
+                            MergeOptimizer, config, theano,
+                            EquilibriumOptimizer, logging, pre_constant_merge,
+                            pre_greedy_local_optimizer)
 from theano.gof.fg import FunctionGraph
-from theano.gof.toolbox import *  # noqa
 
 from theano import tensor as T
 

theano/gof/tests/test_toolbox.py

@@ -5,7 +5,7 @@ from theano.gof.type import Type
 from theano.gof.op import Op
 
 from theano.gof.fg import FunctionGraph
-from theano.gof.toolbox import *  # noqa
+from theano.gof.toolbox import NodeFinder
 
 
 def as_variable(x):

theano/tests/test_flake8.py

@@ -29,7 +29,8 @@ __contact__ = "Saizheng Zhang <saizhenglisa..at..gmail.com>"
 # - "'absolute_import' present"
 # - "'print_function' present"
 #   Redundant error code generated by flake8-future-import module
-ignore = ('E501', 'E123', 'E133', 'FI12', 'FI14', 'FI15', 'FI16', 'FI17', 'FI50', 'FI51', 'FI53')
+ignore = ('E501', 'E123', 'E133', 'FI12', 'FI14', 'FI15', 'FI16', 'FI17',
+          'FI50', 'FI51', 'FI53')
 
 whitelist_flake8 = [
     "compat/six.py",  # This is bundled code that will be deleted, don't fix it