[BioPython] Problems with Win Release for Python 2.5: Numeric, KDTree

[Hendrik Weisser]

Hi,

I'm new to BioPython and although I can already see how greatly helpful the 
package could be for me, I have some problems using it on Windows, with 
Python 2.5 (specifically, the Bio.PDB module, which is what I need at the 
moment).

1. issue:
BioPython requires the package Numeric, which is no longer supported and - 
what's worse - *not available* for Python 2.5.
I could fix this by manually changing the code to import numpy instead, so 
that "from Bio.PDB import *" would work. But I don't think it's a good idea 
to put an installer for use with Python 2.5 on the website, if the 
requirements cannot be met directly...

2. issue:
I want to use the NeighborSearch class in Bio.PDB, but the required KDTree 
module doesn't get made during install.
I already found out that the corresponding section in setup.py in the 
sources is commented out ("Disabled by default to avoid C++ compilation 
errors"), but uncommenting this and trying to build from the source doesn't 
work for me. Therefore, a new Windows installer that includes KDTree would 
be very much appreciated (according to the mailing list archives, this 
solved the same problem when it occurred with Python 2.4).

3. issue (bug?):
In the Entity class in Bio.PDB, the method "get_full_id()" fails because 
(typically) at the structure level, get_parent() throws an exception (which 
is not handled later) instead of returning "None".


The main question for me is whether these issues (the 2nd, mostly) can be 
adressed quickly, or whether it is recommended to use the "old" Python 2.4 
and corresponding packages for the time being. Can anyone help me with that?


Thanks in advance


Hendrik Weisser