[Bioperl-l] Splitting Bioperl and Test related Suggestions

Chris Fields cjfields at uiuc.edu
Thu Jul 5 12:57:28 EDT 2007

On Jul 5, 2007, at 11:44 AM, David Messina wrote:

>> [Chris]
>> The 1.5 releases I believe break some aspects of 1.4 API
> Yes, this is true.
> I question, though, whether it's relevant given that virtually no  
> one uses 1.4 anymore. In any case, I would venture that the number  
> of people who would be bitten by the 1.4->1.5 API change is much  
> smaller than the number of people who download 1.4 and then ask us  
> why it doesn't work.
> I think that, rather than continuing to call 1.5.x the developer  
> release in order to adhere to the API guarantee, it would be much  
> clearer to users if we state clearly that everyone should download  
> 1.5.x, and that if you're upgrading from 1.4 to 1.5 there are API  
> changes.

You'd be surprised how many are still using bioperl 1.2.3 (Ensembl)  
and 1.4 (any admin too scared to go with a 'dev' release).  The real  
answer is to get out a stable 1.6 ASAP.  The problem we currently  
have is (horrible Texas pun) 'too many pokers in the fire.'  We have  
svn migration, major changes in the test suite, talk about splitting  
bioperl, a lot of bugs to sort through, new code to add or work on,  
etc.  Not to mention our $jobs!

I think we should just bite the bullet and proceed with pulling out  
the controversial operator overloading in Bio::Annotation*, deprecate  
the tag methods in AnnotatableI, and go about fixing everything up.   
If that occurs (which seems to be the major impediment) and we get  
GMOD/GBrowse playing well with BioPerl then we can aim for a new  
stable release, and then institute a regular release cycle.


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