[Biopython-dev] PEP8 lower case module names?

[Kai Blin]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

On 2012-10-26 14:42, Peter Cock wrote:

> My personal preference is for a new lowercase namespace like 
> biopy.* or biopython.* which can co-exist with Bio.* during a 
> transition period. However, this did not seem popular.

That'd still mean older scripts would break after the transition
period, and we'll end up encoding the language name in the module,
which seems a bit silly.

Having said that, I see the least amount of pain for BioPython users
going that route, with the possibly larger maintenance headache for
BioPython developers.

I think this is one of these "what color do we paint the bikeshed"
discussions, where there really isn't any objectively superior solution.

> That was my thinking - but it does go against the general advice to
> library authors in that API changes from Python 2.x to 3.x are 
> discouraged.

Right, but from dealing with the python folks on Freenode IRC, I
gather that many of them assume the switch from Python 2.x to 3.x is a
very low-impact change for code authors. I tend to disagree there. :)

> We can of course stick with Bio.* as it is (which I believe is
> Brad's favoured option). And I'm OK with this - it is the simplest
> option (and doesn't prevent us doing some more minor changes if we 
> want to, such as reorganising all the Bio.SeqXXXX modules under one
> directory).

As I said, strong feeling of a bikeshed discussion here. :)

> Perhaps a blog post & email to the announcement mailing list 
> soliciting feedback on this proposal is the best way forward, 
> perhaps with a web-survey form? e.g.

To be honest, I don't care that much about which solution is decided
on, as long as the decision is made soon. I've got some programs that
need the HMMer2 parser that I've added to Bow's SearchIO code, and I'm
hoping to get that into BioPython soon instead of having to ship with
a custom BioPython for publication.

Cheers,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universität Tübingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 Tübingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://www.enigmail.net/

iQEcBAEBAgAGBQJQipFTAAoJEKM5lwBiwTTP4nkIAI5TegXeWy6b8FoPmq46XPzz
iVh6g0t37xAJ9Aat3aE5vDklF7yqEwcVPKxFkj2Nd2MLaDqhfnuldE9pEqbPmZfl
eQptF5JXTAlw/YKAPFzTyFSIlKv3wiuTiGeTxKJtXewOkgEu6VwzNgjPnCYhamaT
Nda7NQEA6mlmaH7ABwO1mLLObk7i90oqVNDIuhnOAAA1ZrVnnQ4QHRupbiLZVd3d
3od3JVM4h+ZT5AL12Lts9lAdrc94MVri5i0P1VSQEnAQV/LJ5uoT2a4l2DRFM35R
NR501X7ubTQPrK8ATveTWaCYYcn/XMnS7dEpvSWsxFR8oM+69LxF3UVtH2ShfDs=
=Teym
-----END PGP SIGNATURE-----