[Biopython-dev] PEP8 lower case module names?

Michiel de Hoon mjldehoon at yahoo.com
Thu Sep 6 10:13:38 UTC 2012

--- On Thu, 9/6/12, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> For any shared server, [...] you
> would be forced into a mass change at one go.

OK, for multiple users on a shared server I see your point.

> Here's a further (and slightly more radical) idea: We
> stick with using 'Bio' and the current mixed case
> names on Python 2, but adopt 'bio' and other PEP8
> compatible names for Python 3 (as a uniform
> strict automatic rule: mixed case -> lower case)?
> i.e. Do this as part of our 2to3 process.

The Python developers argue against combining a switch to Python 3 with other major changes, since then if bugs arise it is unclear if it is due to the switch to Python 3 or due to the other changes. But perhaps it's OK if we have one Bio.* version for Python 2 and one bio.* version for Python 3 that are otherwise completely identical to each other.

> How about over the next year we gradually consolidate
> modules under the existing mixed case names? e.g.
> move Bio.AlignIO functionality and Bio.Align, 

I guess you meant "merge Bio.AlignIO functionality into Bio.Align".

> and Bio.Seq* under Bio.Seq (leaving backwards compatible
> imports supported but deprecated).

Sounds good to me. AFAIAC, we don't need to do this gradually over the next year. May as well do it for the next release.


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