[Bioperl-l] BioPerl 1.6 RC1

Gabriel Valiente valiente at lsi.upc.edu
Sun Jan 4 10:51:33 EST 2009

>>> Bio::PhyloNetwork [...]  Does anyone think we should leave this out?
>> I would rephrase the question. I think it's a very valuable  
>> addition to BioPerl, and the above may be understood as a vote on  
>> that, which AFAIAC is not a vote we need to have.
>> Instead, I would ask the following. Generally, i) are there any  
>> opinions on whether the Bio::XXX root namespace should be  
>> permissively expanded, and ii) should new modules that have not  
>> been reviewed yet by core devs be included in a stable release.  
>> Specifically with respect to Bio::PhyloNetwork, are there opinions  
>> on i) moving or not moving this to the Bio::Phylo::Network  
>> namespace, and on ii) harmonizing or not the API as much as  
>> possible with the Bio::Tree APIs.
> On Bio::XXX root namespace expansion: this popped up recently with  
> Bio::Microarray and was discussed on the list.  In general I think  
> any expansion of Bio::XXX should be 1) actively discussed on list  
> (i.e. not just assume a non-response means support) and 2)  
> supported by the active core devs.
> On reviewing core modules for inclusion in a stable release: we  
> simply can't support something that has an unstable API.  We are  
> planning on a separate bioperl-dev which can act as a testing  
> ground w/o stifling regular bioperl-* releases.  The plan is to  
> also move untested modules there.
> On Bio::PhyloNetwork specifically: could renaming that to  
> Bio::Phylo::Network lump or confuse these with Rutger's Bio::Phylo  
> modules?  I can't specifically speak for Bio::PhyloNetwork's API  
> and how it coordinates with Bio::Tree APIs but Gabriel or Jason  
> could possibly chime in.  They seem to use various Bio::* modules  
> but mainly inherit Bio::Root::Root.
>> (Chris - you would probably agree that the publication neither  
>> answers the above questions, nor guarantees for the API's stability.)
> Yes, 100% agree, though I feel publishing should put the onus to  
> support the module on the module author, not the core devs (which  
> makes me wonder if it would work better split off from core at some  
> point).
> I'm not sure what we should do at this point late in the game, but  
> I would support pulling it and leaving it in trunk until a decision  
> is made, then adding it back in a point release at a later point.   
> I need to know something soon, though.  I already have RC1 out; RC2  
> is to be tagged in the next day or two, and I would like to get a  
> final release out in the next few weeks (as well as create 1.6  
> branches for bioperl-db, bioperl-run, etc).

As authors of the Bio::PhyloNetwork modules, we have made every  
effort to conform to the Bio::Tree API. Nevertheless, it would be  
best if active core developers could please have a closer look. In  
any case, our motivation in publishing these modules as part of the  
BioPerl distribution was to make them available to the large  
community of BioPerl users and if you end up deciding to pull them  
from the core distribution, they won't be that visible anymore.  
Regarding renaming Bio::PhyloNetwork to Bio::Phylo::Network, I don't  
like the idea very much because the Bio::PhyloNetwork modules do not  
have much in common with Rutger's Bio::Phylo modules. Thanks,


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