[Bioperl-l] For CVS developers - potentialpitfallwith"returnundef"

Tue May 30 22:08:26 UTC 2006

Agreed.  I would say, probably 6-12 months time, might be a good idea to try
getting something actually started, maybe under the 'bioperl-experimental'
title Jason has mentioned.  One could always try getting a Bio::Root-like
object going in Pugs/Perl6 as a starter and work up from there, with
emphasis on key areas (seq. parsing, so on).

CJF

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Rutger Vos
> Sent: Tuesday, May 30, 2006 4:58 PM
> To: bioperl list
> Subject: Re: [Bioperl-l] For CVS developers -
> potentialpitfallwith"returnundef"
> 
> I've been following the perl6 mailing lists for a while now. I think
> this time around it won't really take that long (one year?) for
> pugs/perl6 stacks to become more than just toys. I think especially
> large projects, like bioperl, will really benefit from the improved OO
> implementation in perl6, so it might be of interest to at least
> fantasize about it.
> 
> Chris Fields wrote:
> > Ha!  Or may be the 'nonexistent' bioperl-experimental.  Wonder what'll
> > happen once Perl6 comes to term?
> >
> > -CJF
> >
> >
> >> -----Original Message-----
> >> From: Rutger Vos [mailto:rvosa at sfu.ca]
> >> Sent: Tuesday, May 30, 2006 4:48 PM
> >> To: Chris Fields
> >> Subject: Re: [Bioperl-l] For CVS developers - potential
> >> pitfallwith"returnundef"
> >>
> >> Surely this will all sort itself out in bioperl6 ;-)
> >>
> >> Chris Fields wrote:
> >>
> >>> Agreed, though I think these changes should be implemented at some
> point
> >>> (Conway's argument here makes sense and it is nice for Torsten to
> check
> >>>
> >> this
> >>
> >>> out).  If proper tests are written then any changes resulting in
> errors
> >>> should be picked up by checking the appropriate test suite, though I
> >>>
> >> know it
> >>
> >>> doesn't absolutely guarantee it.  ; P
> >>>
> >>> Chris
> >>>
> >>>
> >>>
> >>>> -----Original Message-----
> >>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >>>> bounces at lists.open-bio.org] On Behalf Of Rutger Vos
> >>>> Sent: Tuesday, May 30, 2006 1:53 PM
> >>>> To: bioperl-l at lists.open-bio.org
> >>>> Subject: Re: [Bioperl-l] For CVS developers - potential pitfallwith
> >>>> "returnundef"
> >>>>
> >>>> Although I agree with the sentiment of following PBP, I'm not so sure
> >>>> changing 'return undef' to 'return' *now* will fix any bugs without
> >>>> introducing new, subtle ones.
> >>>>
> >>>> Chris Fields wrote:
> >>>>
> >>>>
> >>>>> Torsten,
> >>>>>
> >>>>> Any way you can post a list of some/all of the offending lines or
> >>>>>
> >>>>>
> >>>> modules?
> >>>>
> >>>>
> >>>>> Sounds like something to consider, but if the list is as large as
> you
> >>>>>
> >>>>>
> >>>> say we
> >>>>
> >>>>
> >>>>> made need something (bugzilla? wiki?) to track the changes and make
> >>>>>
> >> sure
> >>
> >>>>> they pass tests; I'm sure a large majority will.
> >>>>>
> >>>>> I'm guessing Jason would want this somewhere on the project priority
> >>>>>
> >>>>>
> >>>> list or
> >>>>
> >>>>
> >>>>> bugzilla, with a link to the actual list, but I'm not sure.  Maybe
> >>>>>
> >> start
> >>
> >>>> a
> >>>>
> >>>>
> >>>>> page on the wiki for proposed code changes?
> >>>>>
> >>>>> Chris
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>> -----Original Message-----
> >>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >>>>>> bounces at lists.open-bio.org] On Behalf Of Torsten Seemann
> >>>>>> Sent: Tuesday, May 30, 2006 3:19 AM
> >>>>>> To: bioperl-l at lists.open-bio.org
> >>>>>> Subject: [Bioperl-l] For CVS developers - potential pitfall with
> >>>>>> "returnundef"
> >>>>>>
> >>>>>> FYI Bioperl developers:
> >>>>>>
> >>>>>> I just audited the bioperl-live CVS and found about 450 occurrences
> >>>>>>
> >> of
> >>
> >>>>>> "return undef".
> >>>>>>
> >>>>>> Page 199 of "Perl Best Practices" by Damian Conway, and this URL
> >>>>>> http://www.perl.com/lpt/a/2006/02/23/advanced_subroutines.html
> >>>>>>
> >> suggest:
> >>
> >>>>>> "Use return; instead of return undef; if you want to return
> nothing.
> >>>>>>
> >> If
> >>
> >>>>>> someone assigns the return value to an array, the latter creates an
> >>>>>> array of one value (undef), which evaluates to true. The former
> will
> >>>>>> correctly handle all contexts."
> >>>>>>
> >>>>>> So I'm guessing at least some of these 450 occurrences *could*
> result
> >>>>>>
> >>>>>>
> >>>> in
> >>>>
> >>>>
> >>>>>> bugs and should probably be changed.
> >>>>>>
> >>>>>> Your opinion may differ :-)
> >>>>>>
> >>>>>> --
> >>>>>> Dr Torsten Seemann               http://www.vicbioinformatics.com
> >>>>>> Victorian Bioinformatics Consortium, Monash University, Australia
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Bioperl-l mailing list
> >>>>>> Bioperl-l at lists.open-bio.org
> >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>> _______________________________________________
> >>>>> Bioperl-l mailing list
> >>>>> Bioperl-l at lists.open-bio.org
> >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>> --
> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>>> Rutger Vos, PhD. candidate
> >>>> Department of Biological Sciences
> >>>> Simon Fraser University
> >>>> 8888 University Drive
> >>>> Burnaby, BC, V5A1S6
> >>>> Phone: 604-291-5625
> >>>> Fax: 604-291-3496
> >>>> Personal site: http://www.sfu.ca/~rvosa
> >>>> FAB* lab: http://www.sfu.ca/~fabstar
> >>>> Bio::Phylo: http://search.cpan.org/~rvosa/Bio-Phylo/
> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Bioperl-l mailing list
> >>>> Bioperl-l at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>>
> >> --
> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> Rutger Vos, PhD. candidate
> >> Department of Biological Sciences
> >> Simon Fraser University
> >> 8888 University Drive
> >> Burnaby, BC, V5A1S6
> >> Phone: 604-291-5625
> >> Fax: 604-291-3496
> >> Personal site: http://www.sfu.ca/~rvosa
> >> FAB* lab: http://www.sfu.ca/~fabstar
> >> Bio::Phylo: http://search.cpan.org/~rvosa/Bio-Phylo/
> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>
> >
> >
> >
> >
> >
> >
> 
> --
> ++++++++++++++++++++++++++++++++++++++++++++++++++++
> Rutger Vos, PhD. candidate
> Department of Biological Sciences
> Simon Fraser University
> 8888 University Drive
> Burnaby, BC, V5A1S6
> Phone: 604-291-5625
> Fax: 604-291-3496
> Personal site: http://www.sfu.ca/~rvosa
> FAB* lab: http://www.sfu.ca/~fabstar
> Bio::Phylo: http://search.cpan.org/~rvosa/Bio-Phylo/
> ++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> 
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