Only ignore some flake8 errors in __init__.py files

setup.cfg

@@ -3,6 +3,7 @@ select = C,E,F,W
 ignore = E203,E231,E501,E741,W503,W504,C901
 max-line-length = 88
 per-file-ignores =
+    **/__init__.py:F401,E402,F403
     theano/sparse/sandbox/sp2.py:F401
     tests/sparse/test_basic.py:E402
     tests/sparse/test_opt.py:E402
@@ -19,7 +20,6 @@ per-file-ignores =
 exclude =
     versioneer.py
     doc/
-    __init__.py
     theano/_version.py
 
 [versioneer]

tests/tensor/nnet/__init__.py

-