[Biopython-dev] BioPython Design

Michiel de Hoon mdehoon at c2b2.columbia.edu
Sun Jul 2 21:19:46 UTC 2006

Colosimo, Marc E. wrote:
> When will this next release be made ...
I'm planning for the weekend of 15/16 July.

> ... and what is going into it?
Whatever is in CVS at that time. So essentially today's CVS plus as many 
  bug fixes as possible. I'd hold off on any major changes until after 
the  release.

> <rant>
> </rant>

I pretty much agree with Marc here.

 > My suggestion is if enough people are going to ISMB this year
 > (which I am not), that time should be made to think about a
 > road map for BioPython.

Unfortunately, I won't be going either. A Biopython road map seems like 
a good idea though.

 > My suggestions are:
 > 1) split off a branch for ver 2.0 that supports Python 2.4 only
 > (this would suck for Mac people, like me, but its time to move on)

Is there something essential in 2.4 that's missing in 2.3? Not that I 
object against supporting 2.4 only, I'm just wondering. Though I'd be 
hesitant to split off a separate branch, since Biopython is confusing 
enough already as it is.

Btw, I am running Python 2.4 on Mac OS X, and AFAICT there is no problem 
   for Mac users to support 2.4 only.

 > 2) clean house - remove depreciated items, restructure IO, etc...

I totally agree.

 > 3) move to SciPy/NumPy verse Numeric (could try 

Here, I'm a bit hesitant. SciPy does not have a good track record in 
terms of portability. The latest version of numpy looks better though 
(it compiled without problems on all platforms I tried). But I don't 
really want to pay $40 for the documentation.

 > 4) use Cheese Shop for missing modules
 > 5) documentation

My guess is that maintaining the documentation will be easier once we 
cleaned up Biopython.


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