[BioPython] NumPy

[Bruce Southey]

On Fri, Aug 29, 2008 at 9:47 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Hi everybody,
>
> Previously we discussed on the developer's mailing list whether Biopython should adopt the "new" Numerical Python (aka NumPy, currently at version 1.1.1) instead of the "old" Numerical Python (version 24.2). My objections against NumPy were that its documentation is not freely available, it doesn't compile cleanly on all platforms, and some other scientific and computational biology libraries use the old Numerical Python.

Actually NumPy is doing a 1.2 release and may be one to watch. Also
NumPy will be using Nose for testing so if not installed you can not
run the tests. I did not find Travis book that much different from
existing documentation. In anay case, you can get it at:
http://svn.scipy.org/svn/numpy/trunk/doc/numpybook/
http://www.tramy.us/numpybook.pdf

I would also point out the huge NumPy 'Marathon':
http://scipy.org/Developer_Zone/DocMarathon2008
http://sd-2116.dedibox.fr/pydocweb/wiki/Front%20Page/


>
> Last week, the NumPy documentation did become freely available. Compilation of NumPy is still not perfect on all platforms (e.g. on Cygwin it may fail), however recently I have also noticed that compilation of the "old" Numerical Python may fail on modern systems. As far as I can tell, MMTK and PyMOL are (still?) based on the "old" Numerical Python, but Matplotlib now relies on the "new" Numerical Python.

The Cygwin has a major bug that is not due to NumPy. But I am sure the
NumPy developers would like to know any compilation problems.

>
> In my opinion, the balance is now tilting in favor of the new NumPy, and we should consider transitioning Biopython to the new NumPy. Does anybody have a strong preference for the "old" Numerical Python?
>

Actually, how critical is having Numerical Python in BioPython in the
first place?
Is there a case to remove functionality or have special sub-modules?

One rather critical aspect is that both NumPy and Matplotlib also
require Python 2.4.

Regards
Bruce