[Biopython-dev] Versions of numpy/Numeric

[Bruce Southey]

Peter wrote:
> 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
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>
>   
Actually the 'final' Python 2.6 was released yesterday (October 1st, 2008)!

Bruce