[Biopython-dev] Testing Biopython with NumPy 1.3

[Brad Chapman]

Hi Peter;
Things work on FreeBSD 7.1 with python2.5 and the numpy release
candidate:

> python2.5
Python 2.5.4 (r254:67916, Feb 18 2009, 08:20:57) [GCC 4.2.1 20070719  [FreeBSD]] on freebsd7
>>> import numpy
>>> numpy.__version__
'1.3.0rc1'

> python2.5 test_Cluster.py
test_clusterdistance (__main__.TestCluster) ... ok
test_distancematrix_kmedoids (__main__.TestCluster) ... ok
test_kcluster (__main__.TestCluster) ... ok
test_matrix_parse (__main__.TestCluster) ... ok
test_median_mean (__main__.TestCluster) ... ok
test_somcluster (__main__.TestCluster) ... ok
test_treecluster (__main__.TestCluster) ... ok

----------------------------------------------------------------------
Ran 7 tests in 0.009s

OK

The whole test suite passes as well. Maybe this is a windows issue?
Brad


> On Mon, Mar 30, 2009 at 11:29 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> > David Cournapeau has just updated sourceforge - so I will try again with
> > the actual release candidate instead of just the beta...
> 
> Nope - using numpy-1.3.0rc1-win32-superpack-python2.6.exe on Windows
> XP, Python 2.6 using the python.org installer, with Biopython compiled
> with cygwin mingw32 as normal, same error - test_Cluster.py is failing
> on the second line of Bio/Cluster/__init__.py, "from cluster import
> *".
> 
> So the question stands - has anyone else tried Biopython (from CVS)
> with NumPy 1.3 (beta or release candidate) on any platform?  I should
> be able to check it tonight on a Linux machine myself without too much
> trouble... but a few more data points wouldn't hurt ;)
> 
> Peter
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