[Biopython-dev] BioPython Design
mcolosimo at mitre.org
Tue Jul 11 13:29:52 EDT 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/
> 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
More information about the Biopython-dev