Update flake8 settings

doc/dev_start_guide.txt

@@ -126,7 +126,7 @@ To setup VIM:
 
 #. Install flake8 (if not already installed) with::
 
-    pip install "flake8<3"
+    pip install flake8
 
    .. warning:: Starting version 3.0.0, flake8 changed its dependencies and
       moved its Python API to a legacy module, breaking Theano's flake8 tests.

setup.cfg

 [flake8]
-ignore=E501,E123,E133,FI12,FI14,FI15,FI50,FI51,FI53,W503,W504,E203,C901,E231,E741
+select = C,E,F,W
+ignore = E203,E231,E501,E741,W503,W504,C901
+max-line-length = 88
 per-file-ignores =
     theano/sparse/sandbox/sp2.py:F401
     tests/sparse/test_basic.py:E402