biopython-dev at maubp.freeserve.co.uk
Wed Mar 7 10:35:05 UTC 2007
Chris Lasher wrote:
> On 3/6/07, Peter <biopython-dev at maubp.freeserve.co.uk> wrote:
>> Only Michiel has replied, so I assume there are no other strong views on
>> the dev mailing list.
> If you're still soliciting opinions, here's mine: I am really fond of
> the SeqIO.parse function, rather than SeqIO.read, since read is a
> builtin function. Different namespaces, but parse is unambiguous.
We have gone for Bio.SeqIO.parse and Bio.SeqIO.write
Is read really a built in function? Its not on this list:
> For remaining function/method names, I would really prefer to stick to
> the PEP 8 style guide, which specifies:
>> Function Names
>> Function names should be lowercase, with words separated by underscores
>> as necessary to improve readability.
>> mixedCase is allowed only in contexts where that's already the
>> prevailing style (e.g. threading.py), to retain backwards compatibility.
> e.g., to_dict() instead of toDict().
Any views on to_dict versus as_dict, to_alignment versus as_alignment?
As an aside, we should really have a "coding styles" page on the wiki
somewhere, and by default I would also reference PEP 8:
(And I should probably go through the new SeqIO code and make sure it
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