[Biopython-dev] questions for next release

[Jeffrey Chang]

> > - setup.py now accepts earlier versions (<0.8?) of distutils.  Should we
> > require the version that comes with Python 2.0?  This would simplify the
> > script, I think.
> 
> I think we should do this -- we can detect an old version and just
> tell people to upgrade. They need to ugrade if they are using such an
> old version :-).

OK.


> > - Any objections to moving more code into __init__.py?  For example, the
> > code in Prosite/Prosite.py would be moved to Prosite/__init__.py.  This
> > would definitely BREAK CODE, but the fix would be trivial. 
> 
> This is okay by me, although I don't really think it's necessary. I
> don't find it that annoying to import the double Prosites (or
> whatever) but that is just me. 

Yeah, it's mostly a cosmetic change.  Plus, it seems to match how things
are done in other packages, e.g. Martel, xml.


> > - Should we check in Brad's new GenBank code?
> > 
> > - ... and Brad's SeqFeature classes?
> 
> I hope to have a new version of these after this weekend, with
> suggestions from everyone included. Whether or not to include 'em is
> up to everyone else though. I do plan to do a GenBank specific record
> class, so if people don't like the SeqFeature classes, we can just
> include the GenBank specific stuff.

Alright.  Let's plan on including everything, unless anyone has strenuous
objectsion.  Let's see what happens...

Are you also including Andrew's location parser?


> > - Anyone good with Distutils and think they can get Martel and mxTextTools
> > to install with biopython?  :)
> 
> If we can get Martel and mxTextTools to install with distutils, then I 
> think I could try this. The last version of mxTextTools that I could
> find doesn't use distutils, but I might be missing a newer version
> that does. I thought I saw MAL asking lots of questions about
> distutils on the SIG mailing list...

Hmmm, if he's working on disutils-ing the package, then we shouldn't
duplicate that work.

Andrew, do you know anything about this?  Do you mind sending him a quick
email to see whether it's going to happen?


> I guess doing this would be a matter of:
> 
> o Doing a test import mxTextTools and Martel.
> 
> o If they can't be imported -- fetch them from an ftp site and unpack 
> them.

How to handle version differences?

Jeff