[Biopython-dev] BioPython Design

Marc Colosimo mcolosimo at mitre.org
Tue Jul 11 17:29:52 UTC 2006

On Jul 2, 2006, at 5:19 PM, Michiel de Hoon wrote:

> > 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.

There are two off the top of my head:

Generator expressions (PEP 289, <http://www.python.org/doc/peps/ 
pep-0289>) This could be very useful in cleaning up the old code
Decorators for Functions (PEP 318,  <http://www.python.org/dev/peps/ 
pep-0318>)  I like the idea of using staticmethod and classmethod.  
The accepts and returns decorators are also interesting. I wish I  
could find a list of all possible decorators.

In any case, some clean up of the code is needed because people have  
used the string "Decorator" (Alphabet.__init__.py and NeCatch.py)

> > 2) clean house - remove depreciated items, restructure IO, etc...
> I totally agree.
> > 3) move to SciPy/NumPy verse Numeric (could try "numpy/lib/ 
> convertcode.py")
> 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.

I saw this, but didn't know it was the only documentation. However,  
as far as I can tell Numeric is dead <http://numeric.scipy.org/> is  


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