[Biopython-dev] Fwd: git pre-commit hook for PEP8 style checking

Travis Wrightsman twrig002 at ucr.edu
Mon Oct 20 20:51:42 UTC 2014

I agree with Chris on this one, especially on complex formulas. The amount of white space can actually detract from my ability to follow the logic. However, in most cases I'd say white space helps readability :)

Can we also ignore the docstring PEP rules for now until we get the actual code looking nice and clean?


> On Oct 20, 2014, at 11:32 AM, Christian Brueffer <christian at brueffer.de> wrote:
> I agree, that's why it's in the ignore_list in the hook :-)  The length
> is configurable through "pep8 --max-line-length=n" though, in case we
> agree something should be done about that sometime down the line.
> The current ignored codes are these:
> E121-E129, E131, and E501 (indentation and long lines)
> Maybe we should also ignore the following for now:
> E261    at least two spaces before inline comment
> E225    missing whitespace around operator
> E226      missing whitespace around arithmetic operator
> E227    missing whitespace around bitwise or shift operator
> E228    missing whitespace around modulo operator
> Especially whitespace around operators is controversial, I think.  I
> like it most of the time, but in some cases (e.g., array slicing,
> complex formulas), I find no whitespace to be more readable.
> Thoughts?
> Chris
>> On 10/20/14 7:54 PM, Peter Cock wrote:
>> That sounds like a good approach Christian - start gently with only a
>> small set of PEP8 tests on the commit hook :)
>> What about PEP8 E501 (line too long) with its default of 78 characters,
>> this is really a human judgement call - and indeed PEP8 was actually
>> revised here:
>> - https://hg.python.org/peps/rev/fb24c80e9afb
>> - http://legacy.python.org/dev/peps/pep-0008/#maximum-line-length
>> So unless the pep8 tool E501 line length is configurable, I would not
>> favour including it in a standard git commit hook.
>> Peter
>> On Mon, Oct 20, 2014 at 6:32 PM, Christian Brueffer
>> <christian at brueffer.de> wrote:
>>> I also see PEP8 and docstrings as mostly seperate issues, especially since
>>> I'm basically done fixing the few issues that concerned them.
>>> It's true that some error classes have a high occurrence, i.e., various
>>> kinds of indentation issues (which are the biggest bunch currently excluded
>>> from the commit hook), whitespace around operators etc.
>>> What I'd like to see is do is take measures to prevent easy stuff from
>>> creeping back in (e.g., EOL and EOF whitespace, bad indentation ...), while
>>> slowly chugging away at the bigger issues.
>>> That's also why I'd like input on which rules to in/exclude in the commit
>>> hook.  I think it's better catch the worst offenders with buy-in from
>>> everyone, than to enforce everything at once and have make the
>>> commit process so annoying that people just add a git alias including
>>> --no-verify :-)
>>> Chris
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