[Biopython-dev] Moving from Numeric to NumPy

[Peter]

I've compiled a rough list of modules using Numeric with the aid of grep.

As far as I can tell, we have two big lumps of code (Michiel's 
Bio.Cluster module and Thomas' Bio.PDB and SVDSuperimposer modules) plus 
a selection of miscellaneous bits.

Thomas & Michiel - have you looked or made plans to moving your code?

Also, do we have any active developers familiar with the following modules:

Jeffrey Chang (no longer active?):
NaiveBayes.py
MaxEntropy.py

Harry Zuzan (no longer active?):
Affy/CelFile.py and Affy/celmodule.cc

Unnamed authors:
KDTree/KDTree.py (includes C++ code so tricky)
LogisticRegression.py
MarkovModel.py
Statistics/lowess.py
distance.py
kNN.py

Some of which could be converted "by hand" almost trivially (e.g. 
distance.py), but see also:

http://www.scipy.org/Porting_to_NumPy

Peter