[Biopython-dev] Offer to convert BioPython to NumPy

Ed Schofield edschofield at gmail.com
Fri Mar 2 17:52:44 UTC 2007

Hi everyone,

Last month there was some interest expressed on this list (and the general
discussion list) about conversion of the codebase from Numeric to NumPy. I'd
like to volunteer to lead this effort.

I'm a (minor) NumPy developer and a (less minor) SciPy developer. My main
contributions to SciPy have been the maximum entropy module and parts of the
sparse matrix module. I've recently moved into the field of computational
biology, and I'm happy to see that BioPython exists; I am sure it will save
me time. But I don't want to go back to using Numeric, since NumPy is so
much better (and is now the only array package supported by SciPy).

I think trying to retain compatibility with Numeric would be unrealistic.
But I would hope that a transition to a NumPy-only codebase would be quick
(a week or so). If there are any technical problems we are sure to get a
quick response on the numpy-discussion list.

Bruce, if you're still interested in helping with the porting, we could
split up the work. I suggest that we make our changes in a new CVS branch.
That way our changes would be unintrusive until the patch-set is ready and

-- Ed

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