[Biopython-dev] Versions of numpy/Numeric

[Peter]

On Wed, Sep 24, 2008, Peter wrote:
> 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 ...
>
> 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.

Testing on some other machines, with Biopython compiled from source
using CVS as of today:

Linux (Ubuntu Dapper Drake), python 2.4.3, Numeric 24.2 and numpy 1.0.1
Fine (including BioSQL).  I can't remove Numeric on this machine due
to other libraries still using it.

Windows XP, python 2.3.5, Numeric 23.1 and numpy 1.0
Fine (not testing BioSQL), except for a precision issue on
test_ProtParam.py (0.563 verus 0.562) which I have not fixed as this
is probably due to Numeric vs numpy.

Windows XP, python 2.3.5, numpy 1.0 [no Numeric]
Fine (not testing BioSQL).

Now that NumPy 1.2.0 has been released (announced on the numpy mailing
list on 26 Sept, but their website still needs updating), we should
make sure we test Biopython with that too.  Bruce tried with 1.2rc2
earlier so we should be fine.

Testing on a python 2.6 release candidate might be a good idea too...

Peter