[Biopython-dev] Offer to convert BioPython to NumPy

[Bruce Southey]

Hi,
That would be great because I have not had any time to look into this!
Also, I realized that I need to understand more about BioPython first.

However, most files appear to only need very small changes but
virtually all the uses (except Bio/KDTree/KDTree.py)  use the 'from
Numeric import *'.

Bruce

Bio/LogisticRegression.py
Bio/MarkovModel.py
Bio/MaxEntropy.py
Bio/NaiveBayes.py
Bio/distance.py
Bio/kNN.py
Bio/Affy/CelFile.py
Bio/Cluster/__init__.py
Bio/KDTree/KDTree.py
Bio/PDB/Atom.py
Bio/PDB/Entity.py
Bio/PDB/FragmentMapper.py
Bio/PDB/MMCIFParser.py
Bio/PDB/Model.py
Bio/PDB/NeighborSearch.py
Bio/PDB/PDBParser.py
Bio/PDB/Polypeptide.py
Bio/PDB/ResidueDepth.py
Bio/PDB/Superimposer.py
Bio/PDB/Superimposer.py
Bio/PDB/Vector.py
Bio/PDB/Vector.py
Bio/SVDSuperimposer/SVDSuperimposer.py
Bio/SVDSuperimposer/SVDSuperimposer.py
Bio/Statistics/lowess.py



On 3/2/07, Michiel Jan Laurens de Hoon <mdehoon at c2b2.columbia.edu> wrote:
> Ed Schofield wrote:
> > 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.
> Thanks! I'd be happy to see Biopython to get to work with numpy.
> >
> > I think trying to retain compatibility with Numeric would be unrealistic.
> Why is that so? For example, matplotlib happily supports Numeric, NumPy,
> and numarray.
>
> Given that the latest version of NumPy does not compile out of the box
> on Cygwin, I'd be very hesitant to drop Numeric support for Biopython.
>
> --Michiel.
>
>
> --
> Michiel de Hoon
> Center for Computational Biology and Bioinformatics
> Columbia University
> 1130 St Nicholas Avenue
> New York, NY 10032
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