[Bioperl-l] BioPerl 1.6 RC1
valiente at lsi.upc.edu
Mon Jan 5 06:20:49 EST 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,
> 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
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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