[Biopython-dev] questions for next release

[Brad Chapman]

Hey Jeff;

> The plan was to try and get out a relatively quick release with Martel &
> mxTextTools bundled in.  

Release early, release often -- sounds good!

> - 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 :-).

> - 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. 

The only sort of objection is that sometimes people don't look for
actual code in __init__.py files (I know I didn't at first when I was
using python), so it could make it more confusing to browse the code
if you are new to python.

But you know lots more about python coding and style than I, so if you 
prefer it, I'm not going to stop ya :-)

>  If this does
> happen, does anyone know how to move code between files without losing the
> CVS logs of the changes?

I'm not enough of a CVS expert to know this -- maybe Ewan, the master
o' CVS (and everything else :-), would be a good person to ask?

> - 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.

> - 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...

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.

o Run setup.py on these modules and install them, then go back 
to the regular installation.

I think the newly formed catalog-sig
(http://python.org/sigs/catalog-sig/) is interested in getting
something like this going generally, but I'm not sure at all about the 
status of any kind of implementation.

Brad