[Biopython-dev] Biopython 1.49 beta released

[Bruce Southey]

Hi,
In connection with Peter's email on forthcoming release, I was wondering 
what to do about certain modules that do not seem to be used. I started 
to look at the examples that lack test coverage in case one could do 
something for the Biopython 1.49 release. But this should not provide 
any reason for delay the release and may stretch beyond it.

Given the potential long term impact and spirit of people who donated 
the code, I was thinking that the release notes could denote which 
modules are unsupported and need some usage feedback.  In future 
releases the use of these modules would raise a warning about being 
unsupported or obsolete. Please note that I am not against any of these 
modules except for the requirement to maintain them and developing 
suitable tests.

The possible modules are those that Peter previously mentioned that had 
no tests:

Bio.Affy
Bio.AlignAce
Bio.EZRetrieve
Bio.Emboss (everything except the primer parsers)
Bio.Encodings (obsolete?)
Bio.FilteredReader (obsolete?)
Bio.MaxEntropy
Bio.NMR
Bio.NaiveBayes
Bio.NetCatch (obsolete?)

I think that Bio.MaxEntropy and Bio.NaiveBayes are useful and I did 
provide an example that is included in the code. However I am not 
confident in these methods to maintain these mainly due to my lack of 
knowledge.

Similarly for Bio.Affy, I currently work a lot with two-dye systems but 
not Affy. I find that Bio.Affy provides insufficient functionality 
because it does really only reads the intensities and misses other 
important information in version 3 of Affy format. I do recognize that 
it could be a base for Affy stuff that may be useful for users such as 
the PopGen users that use Affy SNP arrays.

Bruce


Peter wrote:
> OK,
>
> Progress since Biopython 1.49 beta was released:
>
>   
>> We've had a few Numeric -> NumPy bugs reported,
>>
>> http://bugzilla.open-bio.org/show_bug.cgi?id=2658
>> Bug 2658 - Bio.PDB.Neighborsearch
>>     
>
> Fixed.
>
>   
>> http://bugzilla.open-bio.org/show_bug.cgi?id=2649
>> Bug 2649 - Bio.KDTree (probably fixed)
>>     
>
> No confirmation from the original reporter, but looks OK.
>
>   
>> 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.
>>     
>
> No-one seems to want a second beta, which saves me some time :)
>
> There have been a few other bugs reported and fixed in the meantime,
> right now the only thing I think holding up the release of Biopython
> 1.49 is:
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=2677
> Bug 2677 - BioSQL seqfeature enhancements
>
> Is there anything else?
>
> Peter
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