[Biopython-dev] [Bug 1733] compiler recognition in setup.py

[Michiel Jan Laurens de Hoon]

Thanks, Thomas. Then unless somebody objects, I will switch off compilation of 
KDTree by default in setup.py, but still have it included with the Biopython 
source distribution.

--Michiel.

thamelry at binf.ku.dk wrote:

>>From the KDTree source code, it seems
>>that KDTree is implemented in C++ for the benefit of speed
> 
> 
> Correct.
> 
> 
>>Can these routines be implemented in C or (better yet) using
>>Numerical Python?
> 
> 
> An implementation in C is of course possible. A Numpy implementation is
> too slow (the KDTree prototype made use of Python/Numpy). But the problem
> really lies with Distutils: it does not deal well with C++ code.
> 
> I don't think KDTree will be missed by many Biopython people, so it can be
> left out as far as I am concerned. It probably makes sense to make it
> available as an independent package (I know some astronomers are using it
> to study star maps for example :-).
> 
> Best regards,
> 
> -Thomas
> 
> 
> 
> 
> 
> 
> 
> 

-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon