[Bioperl-l] Bio::Root::Utilities.pm

Chris Fields cjfields at uiuc.edu
Tue Feb 13 22:41:31 EST 2007


On Feb 13, 2007, at 5:00 PM, Steve Chervitz wrote:

> I noticed that Bio::Root::Utilities was purged from bioperl-live  
> for the
> 1.5.2 release, but I'd like us to consider adding it back. I agree  
> that the
> other purged Root modules were ancient relics of the past, but  
> Bio::Root::
> Utilities.pm still has signs of life (at least I still find  
> occasion to use
> it, or refer to code in it).
>
> I know that it's not currently used by any other modules in  
> Bioperl, but
> there are likely some legacy scripts out there that rely on it.  
> Probably
> most of those scripts are ones I've written, but there have been  
> substantive
> commits by others in the not-to-distant past (Dec 2005), so at  
> least some
> folks besides myself are using it and may hesitate to upgrade their  
> bioperl
> installation if it's absent.
>
> I'm all for avoiding bloat in the codebase and am eager to see  
> Bioperl be
> more lean and mean, but I'd like to keep this module around. I'll  
> agree to
> add some tests for it as well as clean some things up (e.g., use
> Bio::Root::IO to get temp file name).
>
> Cheers,
> Steve
> --
> Steve Chervitz
> sac at bioperl.org

I don't have a problem with adding it back, esp. if tests are added.   
Everything in Bio::Root* not tied to a module was yanked out when no  
one spoke up about cleaning up Bio::Root* modules:

http://thread.gmane.org/gmane.comp.lang.perl.bio.general/12792/ 
focus=12839

Maybe others disagree?

chris


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