[Bioperl-l] Backward compatibility mode for Bio::Root::RootI

[Lincoln Stein]

Without the backward compatibility patch that Ewan discussed, any of your 
scripts which directly "use Bio::Root::RootI" will fail.  However, most 
end-user scripts don't do this, but load other modules, like BPLite, etc, and 
these won't break at all.

Lincoln

On Monday 10 December 2001 06:03, gert thijs wrote:
> I have a question concerning the installation of the modules which use this
> new Bio::Root::Root object.
> Well, I have done a 'make clean; cvs update -dP' in my bioperl-live dir and
> then I have done a 'make' and 'make test'. Almost every test passes (except
> something about connecting to GenBank), which is good. So in the scripts I
> am writing now, I insert a 'use lib' statement  that refers to
> 'bioperl-live/blib/lib' to use the Bio::Root::Root object.
> However, I would like to refer to the installed modules, when distributing
> these scripts. But, given that I just recently installed the 0.7.2 release
> of bioperl and the old scripts are running smoothly, how reasonable is it
> to do a 'make install' from the bioperl-live dir?
>
> Gert Thijs
>
> Ewan Birney wrote:
> > I basically like the split of Bio::Root::RootI interface away
> > from implementation, but it does give us a backward compatibility
> > problem.
> >
> > Some (external) modules written using Bioperl - in particular large
> > tracks of Ensembl (say - 50 modules) - now break as they assumme that
> > Bio::Root::RootI new works.
> >
> > There is alot of active ensembl's out there with the current code base,
> > and we are not going to be able to change these code bases (they are off
> > the stable branch of ensembl) by Janurary.
> >
> > What I would like to do is reintroduce a new function to RootI (blesses
> > an anonymous hash) with a strong "deprecated" warning being thrown.
> >
> > Jason/Lincoln/anyone else - do you think this ok?
> >
> > ewan
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l

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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY

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