[Bioperl-l] BioPerl 1.6 RC1

Gabriel Valiente valiente at lsi.upc.edu
Mon Jan 5 11:20:49 UTC 2009

>>> 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,
>> Gabriel
> The question isn't whether they will be included within BioPerl per  
> se, but specifically within the core modules of BioPerl (see  
> below).  Judging by your response I think we can include them for  
> the 1.6 release.  It might help if we set up bug reports to be  
> passed on to you or others responsible (with the obvious constraint  
> that fixes for 1.6 won't break any API).  We can set something up  
> on bugzilla for that; just let me know what email you want reports  
> sent.

No problem, please put me (valiente at lsi.upc.edu) and also Gabriel  
Cardona (gabriel.cardona at uib.es).

> BioPerl 1.6 is to represent the last 'full' or old-style release.   
> Regarding all modules automatically being in core: we have  
> extensively discussed on the list the problem of code bloat in  
> core.  We plan on splitting off specialized modules into  
> subdistributions, similar to bioperl-db, etc, post 1.6.  This is  
> something that most (all?) core devs appear to agree on.
> Based on that I would say that post-1.6, unless the  
> Bio::PhyloNetwork modules prove to be inextricably linked to a  
> large portion of BioPerl classes, I could see these being included  
> in a specialized bioperl-phylo or similar package, kept in a  
> separate subversion repo just like the other bioperl-*  
> distributions.  Won't be up to me alone though, and anyone is  
> welcome to discuss this further on the list.

Ok. So far, Bio::PhyloNetwork is linked to Bio::Tree and Bio::TreeIO.  


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