[Bioperl-l] runnable SYNOPSIS

[Heikki Lehvaslaiho]

One of the first thing most users of a module do is to check the
SYNOPSIS section of the documentation. The user should be able to copy
the synopsis or part of, set values to parameters and start building to
it. 

I've now made all bioperl core module SYNOPSIS sections runnable.
Synopsis in 96 modules had to be changed slightly. 

The new rules for SYNOPSIS:

1. It should be possible to copy the whole SYNOPSIS and the perl 
   compiler should not complain about its syntax. 

2. The only exception to the above rule is one line paragraph 
   linking to a Bio:: module with a relevant synopsis. E.g.:

=head1 SYNOPSIS

See L<Bio::DB::GFF>.

=head DESCRIPTION

All other comments should be indented (by two spaces) and preceded by
the hash '#' character. 

----------------------------------------------------


The above rules are implemented in maintenance/modules.pl and can run
by:

% ./modules --synopsis

(I've now made the path to bioperl core modules relative so that it is
possible for someone else than me to run the script. Sorry. The new
--dir option allows user to point the script to any location.)

	-Heikki

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_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
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