[Biopython-dev] PEP8 lower case module names?

Michiel de Hoon mjldehoon at yahoo.com
Tue Sep 4 10:27:57 UTC 2012

Hi Peter,

--- On Tue, 9/4/12, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> One idea I was pondering is a new parallel namespace,
> ideally bio.* but we can't use that due to case
> insensitive file systems like Windows and (by default)
> Mac OS X. So perhaps biopy, or bp?

As you say, the ideal namespace is bio.*, so let's use that. We have been using Bio.* for more than 10 years. We should not get stuck with a non-ideal namespace for the next 10+ years because there may be some glitches switching from Bio.* to bio.*. Frankly I doubt that this will cause huge problems in practice.

> We could gradually move code over to the new namespace,
> using imports to preserve back compatibility - but support
> both namespaces during a (long) transition period.

Why do we need a transition period? It's just a matter of replacing upper case with lower case in the imports.

> What I like about this is it allows people to make a
> gradual
> conversion - and we don't have to burden of two main
> branches if we attempted a single jump to a Biopython v2.
> Does this seem worth considering?

Yes but by all means, let's keep this simple. In the past, changes to Biopython have very rarely caused any serious problems for users.


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