[Bioperl-l] A new name for Bio::Moose?

Chris Fields cjfields at illinois.edu
Mon Jul 27 16:23:03 UTC 2009


Herein lies the namespace problem.  What namespace would we inhabit  
with Bioperl 2?  Bio2::*?

We can't place anything in Bio w/o running into potential problems re:  
namespace collisions, both locally and on CPAN (yes, I do intend on  
releasing to CPAN at some point).  Bio* primary maintainer is  
BIOPERLML, so releasing a Bio::Annotation::Foo on CPAN would  
potentially collide with any BioPerl Bio::Annotation::Foo as an  
unauthorized release.  If all code is sequestered in  
Bio::Moose::Annotation::Foo, we don't have a problem beyond it  
requiring more typing, hence the request for a name change  
(preferrably something short) ;>

Anyway, for all intents and purposes, if everything works out it will  
very likely become bioperl 2.0, and the old Bio::Moose (or whatever)  
will be deprecated on CPAN in favor of this.  Until then, it is simply  
a side project to explore the feasibility of moving to a Moose-based  
framework.  We can then work on reimplementing the various split-off  
Bio::* we have been discussing elsewhere.

One main side benefit of doing this: it's incredibly freeing.  I'm  
finding numerous places where we could optimize things in BioPerl,  
even in the case should this not pan out.  For instance, memoize and  
clone locations instead of creating everything de novo.  Annotations  
and AnnotationCollections could be lightened considerably if the  
proper framework were provided, something like Data::Stag or XPath.   
Also, I have found other instances that will be beneficial to a perl6- 
based implementation (roles vs interfaces primarily).  I'll be posting  
here and blogging about these along the way.


On Jul 27, 2009, at 10:25 AM, Robert Buels wrote:

> Bioperl 2.  If the Moose business doesn't work out, throw away the  
> moose code and do something different.  But I think it would be good  
> to christen it as the embryonic bioperl 2 to get some momentum  
> around it.
> Rob
> Chris Fields wrote:
>> All,
>> Pushed by a recent suggestion by Robert, I am considering changing  
>> the name of the Bio::Moose project to something simpler.  I would  
>> like to steer away from naming this directly after the  
>> implementation and have something simpler namespace-wise.
>> I have thought of 'Alces' (the genus name for moose), which  
>> indicates both the Bio aspect and the implementation in an more  
>> indirect way (and is a bit shorter).  However, I would like to  
>> solicit suggestions for alternatives.  The shorter the better, and  
>> the 'winner' will receive a free beverage or so (on me) should we  
>> meet!
>> chris
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
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> -- 
> Robert Buels
> Bioinformatics Analyst, Sol Genomics Network
> Boyce Thompson Institute for Plant Research
> Tower Rd
> Ithaca, NY  14853
> Tel: 503-889-8539
> rmb32 at cornell.edu
> http://www.sgn.cornell.edu

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