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

Chris Fields cjfields at uiuc.edu
Wed Jun 7 09:56:16 EDT 2006


Yikes!  I'll download a tarball from anon CVS and run a comparison (vs my
pre-updated bioperl-live) on WinXP and Mac OS X 10.4 (Intel) and report back
success/fail; may be a bit.

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Heikki Lehvaslaiho
> Sent: Wednesday, June 07, 2006 4:58 AM
> To: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] For CVS developers-
> potentialpitfallwith"returnundef"
> 
> Committed.
> 
> Please report any surprising changes in functionality to the list.
> 
> 	-Heikki
> 
> On Tuesday 06 June 2006 10:04, Heikki Lehvaslaiho wrote:
> > OK. I've gone through all cases where return and undef are on the same
> > lines. I've done changes in 185 files.
> >
> > My aims have ben the following:
> >
> > 1. Remove undef from return undef when not necessary.
> > 	This will make it easier to spot cases where undef matters in the
> future
> > 	Most of the changes fall into this category. The context is clearly
> > scalar.
> >
> > 2. Returning undef when user expects en empty list is bad
> >
> > ./Bio/Tools/Est2Genome.pm fixed
> > ./Bio/SearchIO/blast.pm:2330:  should return (undef, undef) for clarity?
> >                                not fixed
> > ./Bio/Matrix/PSM/SiteMatrix.pm  fixed
> > ./Bio/Matrix/PSM/Psm  fixed
> > ./Bio/DB/Taxonomy::entrez.pm fixed
> >
> > 3. If docs say method returns nothing, explicit undef is not the right
> > thing to return
> >
> > 4. do not return an explicit undef if the method is supposed to return
> > false on failure
> >
> >
> > Before I do the commit, I'd like to see number people to do 'make test'
> on
> > bioperl-live and report back after the commit they see changes. There
> are
> > quite a few tests that fail currently.
> >
> > I'll do the commit tomorrow Wednesday at 9 o'cock GMT.
> >
> > 	-Heikki
> >
> > On Friday 02 June 2006 09:52, Heikki Lehvaslaiho wrote:
> > > I've started going through the files that have 'return undef' lines.
> > > I'll report back later.
> > >
> > > Initial impression is that there are a few cases where the context
> > > indicates list to be returned but failure returns an explicit undef.
> I'll
> > > fix those.
> > >
> > > Most of the cases are much more ambiguous. Even when documentation
> says
> > > the failure returns undef, it is clearly meant to mean false. In most
> > > cases documentation does not comment on return value at all. Luckily
> the
> > > context is almost always scalar and therefore it does not matter too
> > > much.
> > >
> > > I seem to be changing 'return undef' to plain 'return' a bit
> > > overzealously, so do not take it personally.
> > >
> > > 	-Heikki
> > >
> > > On Thursday 01 June 2006 19:46, Chris Fields wrote:
> > > > ....
> > > >
> > > > > > Again, didn't do that.
> > > > >
> > > > > I'm very sorry that I allowed the ambiguity, but my comments were
> > > > > certainly not directed at your recent changes to
> > > > > Bio::Restriction::IO. In fact, I put in the above * comment to
> > > > > exclude your changes from my discussion; you changed the docs
> because
> > > > > the code never did what they said they did (the docs were bad).
> > > > > That's fine (good!). My comments were a general point, slightly
> > > > > directed at the idea of changing all the return undef;s - changing
> > > > > the code so that it no longer matches the docs of a previously
> > > > > working method. That's what I think is bad. Though in this
> particular
> > > > > case it shouldn't make any difference at all.
> > > >
> > > > Agreed.  In any case, if tests have been properly set up then they
> > > > should catch problems.  This is, of course, if they are properly set
> > > > up.
> > > >
> > > > Chris
> > > >
> > > > > _______________________________________________
> > > > > Bioperl-l mailing list
> > > > > Bioperl-l at lists.open-bio.org
> > > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > > >
> > > > _______________________________________________
> > > > Bioperl-l mailing list
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> 
> --
> ______ _/      _/_____________________________________________________
>       _/      _/
>      _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
>     _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
>    _/  _/  _/  SANBI, South African National Bioinformatics Institute
>   _/  _/  _/  University of Western Cape, South Africa
>      _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
> ___ _/_/_/_/_/________________________________________________________
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