[Biopython-dev] Biopython 1.49 beta released

[Bruce Southey]

Peter wrote:
> On Sun, Nov 9, 2008 at 3:16 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>   
>> Dear Biopythoneers,
>>
>> We are pleased to announce a beta release of Biopython 1.49. There are
>> been some significant changes since Biopython 1.48 was released two
>> months ago, which is why we are initially releasing a beta for wider
>> testing.
>>
>> As previously announced, the big news is that Biopython now uses NumPy
>> rather than its precursor Numeric (the original Numerical Python
>> library).
>>     
>
> We've had a few Numeric -> NumPy bugs reported,
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=2658
> Bug 2658 - Bio.PDB.Neighborsearch
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=2649
> Bug 2649 - Bio.KDTree (probably fixed)
>
> I don't think we should release Biopython 1.49 final until these are
> resolved - but if there was interest I could put out a second beta.
>
> Peter
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>
>   
I noticed that Bio.PDB.Neighborsearch is not being tested.

Is there someway to identify which functions are not getting tested?
I know it is considerable effort but it would allow the development of 
tests that at the very least exercise all the Biopython code. (Hopefully 
this is not as bad as the Numpy documentation marathon.)

Bruce