[Biopython-dev] NumPy conversion / Bio.KDTree / Bio.Cluster.

[Brad Chapman]

Hi Michiel;
Great stuff. One quick note, it doesn't look like KDTreemodule.c got
checked into CVS:

gcc: Bio/KDTree/KDTreemodule.c: No such file or directory

> ls -l Bio/KDTree/
total 64
-rw-rw-r-- 1 chapmanb chapmanb  2641 2007-04-23 05:45 CKDTree.py
drwxrwxr-x 2 chapmanb chapmanb  4096 2008-09-14 12:39 CVS
-rw-rw-r-- 1 chapmanb chapmanb   166 2007-04-23 05:45 HISTORY
-rw-rw-r-- 1 chapmanb chapmanb   432 2007-04-23 05:45 __init__.py
-rw-rw-r-- 1 chapmanb synbio   29504 2008-09-14 09:15 KDTree.c
-rw-rw-r-- 1 chapmanb synbio     689 2008-09-14 12:39 KDTree.h
-rw-rw-r-- 1 chapmanb synbio    8165 2008-09-14 12:39 KDTree.py
-rw-rw-r-- 1 chapmanb synbio     151 2008-09-14 09:15 Neighbor.h

Brad

On Sun, 14 Sep 2008 06:23:53 -0700 (PDT), "Michiel de Hoon"
<mjldehoon at yahoo.com> said:
> Hi everybody,
> 
> I just committed a bunch of changes to Bio.Cluster, Bio.KDTree, and
> setup.py that deal with the old Numerical Python to new NumPy conversion.
> With these changes, Biopython should compile with NumPy; any remaining
> references to the old Numerical Python are at the Python-level only.
> Since these are rather big changes, please try with the current version
> of CVS to see if everything compiles cleanly and all tests pass.
> Comments, questions, suggestions are welcome.
> 
> I also uploaded a plain C (instead of C++) version of Bio.KDTree, and
> adjusted setup.py accordingly.
> 
> --Michiel.
> 
> 
>       
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-- 
  Brad Chapman
  chapmanb at 50mail.com