[Bioperl-l] pod syntax check on branch-07 starting

[Heikki Lehvaslaiho]

The pod syntax in branch-07 is now ready for release.

To recheck the POD syntax, run the following commands in the bioperl root
directory (in Linux):

	podchecker *pod 
	find . -name '*.pm' -exec podchecker '{}'  ';' 


In several files, I've added line 

  # documentation needed

under '=head1 SYNOPSIS' which should not be empty. The only warnings issued
by podchecker at the moment are:

./Bio/SeqIO/game/featureHandler.pm does not contain any pod commands.
./Bio/SeqIO/game/idHandler.pm does not contain any pod commands.
./Bio/SeqIO/game/seqHandler.pm does not contain any pod commands.

It would be nice to have game parsing docs at some point.

	-Heikki

Heikki Lehvaslaiho wrote:
> 
> I am getting tired and decided to call it a day.
> Only Bio/Tools directory is left. I'll tackle it tomorrow.
> 
> If someone can meanwhile have a look at Bio::Tools::Blast module I'd be
> much obliged: I do not understand where warnings like
> 
> *** WARNING: collapsing newlines to blanks at line 240 in file Blast.pm*
> 
> are coming from.
> 
>         -Heikki
> 
> Heikki Lehvaslaiho wrote:
> >
> > There was a bug report on pod syntax errors on one of my modules a few days
> > ago.
> > I ran podchecker and fould loads more in almost all bioperl modules.
> >
> > I'll clean everything I can during the weekend. I'll do it on branch-07
> > hoping that once the release is out we can merge those changes back into
> > the main trunk. 8-)
> >
> >         -Heikki
> >

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________