[BioPython] KDTree optional compilation

[Michiel Jan Laurens de Hoon]

Anton wrote:
> K. Arun <karbak <at> gmail.com> writes:
>> I just updated to version 1.42 (thanks !), and noticed I had to
>> uncomment the KDTree entry in setup.py in the NUMPY_PACKAGES section
>> to use Bio.PDB.NeighborSearch.  Since KDTree is essential to this
>> module, would it possible to add a note about this in the README, or
>> print a message during compilation to the effect that setup.py needs
>> to be modified ?
Yes. Can you write a patch for setup.py?

> I installed my BioPython using the Windows installer. Therefore the
> NeighborSearch module is not working (requires KDTree). In fact there was no way
> during the installation to add this module. 
I thought I had included KDTree with the Windows installer, but it 
turned out that setup.py automatically skips KDTree on Windows. This is 
to avoid compilation problems with the C++ code in KDTree. It works on 
some platforms, but not on others.
Luckily, MinGW can compile C++ code for Python 2.4 (but not for Python 
2.3). I put a new Windows installer for Python 2.4 on the website (same 
file name, but file size is now 1,074 Kb).

--Michiel.

-- 
Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1130 St Nicholas Avenue
New York, NY 10032