STY: PEP8 style correction for all warnings, and almost all errors. Except E402, E501 and E731

[miykael]

This PR covers the rest of PEP8 violations mentioned in #597, that were not already covered by #1255. Only exceptions are:

• E402 module level import not at top of file (N=402)
• E501 line too long (80 > 79 characters) (N=8631)
• E731 do not assign a lambda expression, use a def (N=40)

In my opinion, E402 cannot be corrected and E731 would be a mess to correct.
E501 can be corrected, but just needs a lot of manual correction. Therefore, I think it makes sense to correct them with another PR.

Also, there are the following PEP8 violations that I haven't corrected and I would be happy to have a feedback if they should or shouldn't be changed:

E712 comparison to False should be 'if cond is False:' or 'if not cond:'
The four errors are all in file nipype/pipeline/plugins/base.py, on line 235 + 236, 331 and 341. Because they compare the values of a numpy array to a boolean, we cannot replace '==' with is.

W191 indentation contains tabs and E101 indentation contains mixed spaces and tabs
The six W191 and two E101 violations exist because of nipype/utils/tests/test_cmd.py on line 84-89, because of the tab character in file nipype/utils/nipype_cmd.py on line 17.

E116 unexpected indentation (comment)
The 5 E116 violations are caused by nipype/interfaces/fsl/preprocess.py on line 243-247 and I don't dare to delete this.

E265 block comment should start with '# '
The 28 E265 violations are caused by multiple lines in file doc/conf.py, for example line 53, 73, 77, etc. I didn't add the space after # so that it's still clear what is a comment and what is commented code.

[satra]

this change is affecting a test. the test should be updated.

[satra]

@miykael - can you merge this with master now?

[miykael]

Yes, but how do I do this? Do I merge my pep8StyleCorrections branch with master and than just correct any given conflict with a new commit?

[satra]

yes