[Bioperl-l] Priorities for a bioperl-1.6 release

Sendu Bala bix at sendu.me.uk
Wed Feb 13 20:19:01 UTC 2008

Brian Osborne wrote:
> You should be careful about the names of these packages. For example, 
> Bio::Biblio and Bio::Restriction are not "in development" as the term 
> bioperl-dev implies. They're tried and true. And there may be sets of 
> modules that are experimental in "bioperl-dev", of course. Is it 
> possible to have 2 packages, "dev" and "tools"? Or something along those 
> lines?
> Calling things by the wrong names leads to confusion, witness the 
> Bioperl newcomers who would install an antiquated version 1.4 because it 
> was labelled 'stable'.

On the topic of confusion, I think 'bioperl-tools' is a very bad choice 
since we have Bio::Tools. Why would Bio::Microarray (for example) be in 
there? (And then we have Bio::Microarray::Tools ...)

Can all of the non Bio::Tools modules currently in the bioperl-tools 
section of the wiki page be annotated as to why they're there and not in 
core? Then maybe we can come up with a better name to categorize them 
all under.

Perhaps we could also annotate the things in core to justify why they 
should be in core? Is anyone good at creating maps so we can easily see 
what Bioperl modules are most used (by other Bioperl modules)?

Or is the split intended to be 'core' == "anything and everything that 
was in 1.4", '????' == "everything else"? In which case, what's a good 
name for "modules created after 1.4"? 'crust'? ;)

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