Lint fixes

[ayan-b]

No description provided.

[ayan-b]

@yunhailuo This PR is ready. Please review. 😊

[yunhailuo]

Sorry. Just re-organized travis code. Please rebase.

[ayan-b]

Rebased. :)

[ayan-b]

Please take a look @yunhailuo.

[yunhailuo]

I have some hesitation on how we would ignore rules. Like W503 should be ignored as they said so. But others, overall ignores in config or inline ignore, I'd prefer to be careful and specific. By being specific, I mean

• Overall ignore should be restricted unless there is clear reason to do so;
• Inline ignore should be specific to certain rule(s).

This is my general thinking. We will need some discussions like:

• Which rule(s) should definitely be ignored for all? Only W503?
• Is it overwhelming if for some rules, which are not really ignore for all, are too many for inline?
• ...

[yunhailuo]

Looks good. Let me know your thoughts on global ignore when you are ready.

[ayan-b]

Global Ignores:

• W605 (invalid escape sequence '*'): Quite a few docstrings use \*\*, so its ignored.
• E722 (do not use bare 'except'): Some except is bare, so its ignored. I think we can use local ignore here. No longer ignoring globally.
• E121 (continuation line under-indented for hanging indent) No longer ignoring globally.
• E126 (continuation line over-indented for hanging indent) No longer ignoring globally.

Local Ignores:

• E203 (whitespace before ':'): Not PEP8 compliant for slicing.

[yunhailuo]

• Quite a few docstrings use */*/

An example?

[ayan-b]

• Quite a few docstrings use */*/

An example?

https://github.com/yunhailuo/xena-GDC-ETL/blob/76b792ca984be32874687a3d682b3e06bdd95a36/xena_gdc_etl/xena_dataset.py#L430

[ayan-b]

02b9ead uses black to format code: black -l 79 -S xena_gdc_etl tests.

[yunhailuo]

Thanks for the example. Looked into W605 a little bit. In the long run, it may become SyntaxError. We should not ignore it. It seems make docstring a raw string will fix it. I haven't try though. I saw only four in xena_dataset.py.

[yunhailuo]

02b9ead uses black to format code: black -l 79 -S xena_gdc_etl tests.

What is black? A link for intro or doc?

[ayan-b]

@yunhailuo black: https://black.readthedocs.io/

[ayan-b]

No longer ignoring W605.

[yunhailuo]

I actually like quite some changes made by black here. But some are confusing to me. I guess the question is what it is and if they are really official. We can follow it since it's kind of official/good. But I don't think we have to following it 100%. I'd say we could have a few small tweaks.

I went through most but it's a lot and I probably didn't cover all details. The good part though is you help us with tests so that we could be confident about it working.

My suggestion is make changes by black (both auto and manual tweaks after) a single independent commit. That way we might, though less likely, be able to revert it later if needed.

[yunhailuo]

Should we just delete these three lines? I'd like to but need a second opinion.

[yunhailuo]

@yunhailuo black: https://black.readthedocs.io/

Thanks. Seems like a good tool to have and use.

[ayan-b]

I guess the question is what it is and if they are really official.

black claims their styles are subset to PEP8. In fact, the code is actually hosted in the Python org. https://github.com/python/black

[ayan-b]

Now all the black lint fixes are in 866d14b.

[yunhailuo]

Looks good. Really a lot of changes. Great job!