[Bioperl-l] BioPerl 1.6 RC1

Hilmar Lapp hlapp at gmx.net
Fri Jan 2 22:52:54 UTC 2009

On Jan 2, 2009, at 10:40 AM, Chris Fields wrote:

> 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.

(Chris - you would probably agree that the publication neither answers  
the above questions, nor guarantees for the API's stability.)

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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