[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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>
>   
Hi,
Please note numpy 1.2 does require Python 2.4+ so if BioPython will 
still support Python 2.3+ then we need someone to test with numpy 1.1.

Download numpy 1.2 from the links at:
http://sourceforge.net/projects/numpy/

There are two Windows installation files for Python 2.4 and 2.5  
attempts to install the appropriate binary for the processor type and 
instruction set (such as i.e. SSE). This avoids people installing the 
wrong version and associated 'bugs' and 'crashes' that may result.

Also, it was noted by David on the numpy list "that updated packages for 
various linux distributions (Fedora,
Centos/RHEL, OpenSuse) are available":
http://download.opensuse.org/repositories/home:/ashigabou/

Regards
Bruce