[BioPython] PDBParser looking for Numeric module

Yasushi Masuda ymasuda at ethercube.com
Thu Feb 9 22:34:26 EST 2006


I agree it's not the time to move numpy (yet!), but I'd like to
note that now numpy has fft and linalg, corresponding to FFT and
LinearAlgebra, respectively.

Michiel De Hoon wrote:
> Use this link:
>> http://sourceforge.net/projects/numpy/
> Don't use this one:
>> http://numeric.scipy.org/
>> The numeric libraries have been around for a long time (reaching version
>> 24.2) and are well tested.
>> However, its developers are moving to numpy instead - at some point
>> BioPython will eventually need to convert its code to the replacement
>> library.
> Note that currently the Numerical Python maintainers are the same people as
> the SciPy developers -- the new numpy module was originally called
> scipy-core; one of its goals was to force people to start using SciPy by
> removing parts of Numerical Python, such as LinearAlgebra and FFT. Note also
> that the documentation for numpy is not free. Given the success of good old
> Numerical Python, I doubt that numpy will replace Numerical Python any time
> soon, if ever. Therefore, I don't think that Biopython should convert to
> numpy unless most other Python packages relevant to computational biology do
> so.

Yasushi Masuda
ymasuda at ethercube.com

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