[BioPython] Updates to the source tree

[Brad Chapman]

> There have been a lot of work done on the CVS tree over the last 
week.  
> I've integrated Andrew's Seq package as well as Cayte's UnitTests.  

Cool! Thanks for doing this, Jeff.

> Because of the overlap in functionality, Bio/Sequence.py is being
> deprecated in favor of Bio/Seq.py.  Code that uses Sequence.py 
(including
> Brad's biopython-corba stuff) will need to migrate over to the new
> module.  Sequence.py will be removed from the tree before we do an 
alpha
> release, which will probably be in a few months.

The current biopython-corba actually already uses Seq.py (Andrew's 
sequence class). Unfortunately, it also uses Andrew's SeqIO/FASTA.py 
class, but I'll work to switch it over as soon as we can get all of 
the parsers feeding into Seq.py. At the same time I'll also switch 
the "biopython-lookalike" biopython-corba interface so it resembles 
what is in cvs (right now it resembles what was in Andrew's module).

> I've added in support for distutils.  It is now possible to create 
source
> and binary distributions for people without access to CVS.  Expect 
that to
> happen soon, after all authors get their code in a somewhat runnable
> state.  I imagine we will probably use distutils to distribute the
> biopython package once it's ready for release, unless someone wants 
to
> muck around with configure and Makefiles!

I was also going to try and get biopython-corba ready so it was 
distutils friendly, but I'm not positive how we want biopython-corba 
to be related to biopython. The way it is set up right now, the 
biopython-corba stuff would go in a separate directory in 
site-packages (Biocorba) from the main biopython package (which goes 
in Bio). The reason I thought this was a good idea is that then you 
can call the "biopython-lookalike" interface with code like:

from Biocorba.Bio.Seq import Seq

So to change Biocorba code to Biopython code, you would just have to 
drop the Biocorba part of the import. I guess we could also make it:

from Bio.Biocorba.Seq import Seq

and have Biocorba install inside of the Bio module, but this would 
make looking at the biopython-corba code confusing. I think it is easy 
to understand now because the biopython-lookalike interface is in a 
totally separate Bio module from the Server and Script code.
    So what to people think? Should biocorba go inside of Bio, or be 
a separately installed module?

    Also I noticed that you had some SVM extension stuff listed in 
setup.py (neat!). Are we planning on having a separate extensions 
package for this stuff (like Bioperl). Just curious :-)

Brad