[Biopython-dev] [Bug 2251] [PATCH] NumPy support for BioPython

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri Aug 24 14:18:19 UTC 2007


------- Comment #12 from biopython-bugzilla at maubp.freeserve.co.uk  2007-08-24 10:18 EST -------
Looking at Ed's patch, from the point of view of the pure python modules in
Biopython, if we currently have something this trivial example:

import Numeric
m = Numeric.zeros([3,3], "f")

This becomes:

import Bio.numpy_wrapper
m = numpy_wrapper.zeros([3,3], "f")

where the Bio.numpy_wrapper and other similar classes act as proxies for the
real Numeric, or numpy's backwards compatible numpy.oldnumeric, depending on
what was used when numpy_selector.c was compiled.


If Biopython was compiled with Numeric, then numpy_selector.c will tell the
wrapper classes to import Numeric etc.

If Biopython was compiled with NumPy support, then numpy_selector.c will tell
the wrapper classes to import numpy.oldnumeric etc.

This shouldn't matter for anyone compiling from source, but for Windows users I
guess we'll have to provide two versions of the installer during the transition
period from Numeric to NumPy.  I imagine that Linux distributions will also
have to handle the switch at some point too...

Are the two C interfaces not binary compatible? Is is really not possible to
make the choice at run time?

Any progress on that 64bit problem?

Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.

More information about the Biopython-dev mailing list