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

[Michiel de Hoon]

Hi everybody,

I now uploaded Bio/KDTree/KDTreemodule.c to CVS. Biopython should now compile with the new NumPy (and not any more with the old Numerical Python).

--Michiel.


--- On Sun, 9/14/08, Brad Chapman <chapmanb at 50mail.com> wrote:

> From: Brad Chapman <chapmanb at 50mail.com>
> Subject: Re: [Biopython-dev] NumPy conversion / Bio.KDTree / Bio.Cluster.
> To: biopython-dev at biopython.org
> Date: Sunday, September 14, 2008, 1:07 PM
> 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.
> > 
> > 
> >       
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at lists.open-bio.org
> >
> http://lists.open-bio.org/mailman/listinfo/biopython-dev
> -- 
>   Brad Chapman
>   chapmanb at 50mail.com
> 
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