[Bioperl-l] Test overhaul complete

Chris Fields cjfields at uiuc.edu
Wed Jun 27 15:31:44 EDT 2007


On Jun 27, 2007, at 2:16 PM, Nathan S. Haigh wrote:

> ...
>
> Just to put the feelers out to see what people think.
>
> It seems (to me at least) that Bioperl modules could/should? be  
> released
> as individual modules and that "bioperl" would really constitute a
> "bundle" of all these modules - in terms of CPAN anyway. Am I  
> correct in
> this thinking? The Bio::ASN1::EntrezGene could simply require a
> particular module rather than the whole of bioperl - might get out of
> the circular dependency theoretically!?
>
> I'm not suggesting moving in this direction, but just wondered what
> others thought about this concept?
>
> Nath

Well, Steve suggested splitting some of core into distinct groups,  
which I tend to agree with in some respects (speed up releases for  
those modules, such as SearchIO, DB, Graphics).  The problem we have  
yet to solve is what we consider 'core'.  Is it Bio::Seq and  
related?  Should it include Bio::DB*?  Should it just be Bio::*  
modules with no or very few external dependencies?  And so on...,   
probably not a decision we want to make immediately (until after svn  
migration, tests finished, maybe a release or two, a beer)...

The Bioperl module dependency that Bio::ASN1::EntrezGene has is  
Bio::Index::AbstractSeq.  You could try a test build of  
Bio::ASN1::EntrezGene to see what happens.

chris




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