[BioPython] plans for next release

[Jeffrey Chang]

Hello everybody,

We've been getting a lot of functionality into the core package.  Things
are starting to become useful!

Unfortunately, we've also started to pick up some "cruft", as Ewan Birney
likes to call it.  Most of it is my fault, though.  :(  Thus, the next
release will mainly be for refactoring and technology upgrades.  Here are
my thoughts:

- Since Martel is maturing and becoming useful (used in Clustalw code),
we'll integrate that with the release and installation process.  In
addition, we'll pull mxTextTools in as well, since its host (starship)
doesn't seem to be reliable and also for simplicity of installation.

- Deprecate Sequence.py.  The functionality is superceded by Seq.py.

- Move more code into __init__.py.  This is cosmetic and will prevent code
like:
from Prosite import Prosite

Unfortunately, this will break code.  Hopefully, the changes will be minor
and easy to fix.

Please send mail if you have any more structural changes, or if you
disagree with these plans.

Thanks,
Jeff