[Biopython-dev] Versions of numpy/Numeric

[Peter]

Hi again,

I was wondering what versions of numpy and Numeric have been tested
with Biopython CVS?  For anyone who didn't know, you can check at the
python prompt with:

import numpy
print numpy.version.version

and,

import Numeric
print Numeric.__version__

Using CVS Biopython compiled from source, the unit tests all seem fine
on the following three setups:

Mac OS X, python 2.5.2, Numeric 24.2 and numpy 1.1.1
Test suite looks fine

Linux, python 2.5, Numeric 24.2 and numpy 1.0
Fine, ignoring the Numeric eigenvalue problem in
test_SVDSuperimposer.py previously discussed

Linux, python 2.3, numpy 1.1.1 [no Numeric]
Fine, after fixing some broken imports which were using recent python
syntax, and reducing the number of decimal places used in
test_SVDSuperimposer.py (numpy and Numeric give very slightly
different answers).

Note that testing where there is NO version of Numeric is important
(as in this third example), as if both numpy and Numeric are installed
currently most of the pure python modules will use Numeric by choice.

Also note that running the test suite via run_tests.py will hide any
deprecation warnings from numpy - I tried running
test_SVDSuperimposer.py on its own and got:
/home/xxx/lib/python2.3/site-packages/numpy/lib/utils.py:114:
DeprecationWarning: ('matrixmultiply is deprecated, use dot',)
I've now updated Bio/SVDSuperimposer/SVDSuperimposer.py to use dot
instead of matrixmultiply (this works on both numpy and Numeric).

Peter