[Bioperl-l] Jason and Ewan's TODO list

[Ewan Birney]

On Tue, 29 Jan 2002, Brian Osborne wrote:

> Ewan et al,
> 
> >> Proposed 1.0alpha1 with at least top level documentation additions around
> >> Feb 15th (Brian and Peter - can we make this?)
> 
> Not wanting to sound "smart" but what do you mean by "top level
> documentation"? At the very top I see Seq, PrimarySeq, SeqIO, and not much
> else. One could argue that Blast, meaning StandAloneBlast and BPlite, is
> somewhere up there but I think that these are well-documented, the trouble
> we get into with Blast is too many modules, not too little documentation.
> Speaking of which, is SearchIO at the very top now? I'd have to profess
> nearly complete ignorance of this one.
> 
> Off the top of my head I'd say I could do work on POD-module documentation
> and have something reasonable by the 15th, yes, but you should share your
> views on what's required. There are certainly some interesting modules in
> there that aren't as well documented as they could be, Structure::*, for
> example. There are others. Also, I may have missed this but is the module
> for neophytes, Bioperl.pm, going to be in 1.0?


The main thing is in my view

bptutorial.pl

removing one of bioperl.pod or biostart.pod or whatever it is....

making sure the README points to the right documentation

handling Bio::Seq and Bio::SeqIO.pm to make sure the "first script" moment
is good


looking into Bio::Perl.pm for the true newbie


I know it is a long list, but I think doable in time...



> 
> What I'll be doing over the next few days is working on Seq.pm,
> PrimarySeq.pm, and SeqIO.pm modules, with an aim of answering the sorts of
> questions that real novices may ask, I would like important things to be a
> little more obvious. I'm also adding L<> tags here and there, I think the
> POD-as-HTML documentation is a bit hyperlink-poor, just my personal sense.
> 
> Brian O.
> 
> 
> 
> ----- Original Message -----
> From: "Ewan Birney" <birney@ebi.ac.uk>
> To: <bioperl-l@bioperl.org>
> Sent: Tuesday, January 29, 2002 6:43 PM
> Subject: [Bioperl-l] Jason and Ewan's TODO list
> 
> 
> >
> >
> > We are enjoying tuscon over here, and mainly to use the mailing list as a
> > filing system here is our TODO list.
> >
> >
> > (a) top level docs
> >
> > Peter + Brian (any dates on this?)
> >
> >
> > (b) final code changes (Jason... maybe Ewan)
> >
> > Remove Bio::Tools::BLAST
> > Bio::UnivAln
> > Bio::Tools::Fasta
> > Clean up Bio::Root:: stuff which is not needed anymore
> >
> > (c) Module review:
> >
> > SYNOPSIS - test cut-and-paste code
> >
> > Description - points to associated modules, warns if a user
> > should not read this module directly
> >
> > new method - documented and parameters are correct
> >
> > Bio::Root::Root inheritance, no RootI
> >
> > Interfaces inheriet from Bio::Root::RootI
> >
> > Document all useful looking methods
> >
> >
> > Areas -
> >
> > (NB authors should not review their own code)
> >
> > Bio::SearchIO::*    Ewan
> > Bio::SeqFeature::*  Jason
> > Bio::SeqIO::*       Lincoln
> > Bio::Structure      SteveC
> > Bio::DB             Elia (proposed - Elia - do you have time)
> > Bio::TreeIO         Hilmar (proposed --- can you do this?)
> > Bio::* (top level)  Heikki (proposed)
> > Bio::Annotation::   James Gilbert (proposed)
> > Bio::Tools::*       Ewan (or someone else if they want to)
> >
> >
> > If people want to volunteer to help out, please shout. If you are not
> > confident about the code, just helping with documentation is a a great
> > starting point.
> >
> >
> >
> > Proposed 1.0alpha1 with at least top level documentation additions around
> > Feb 15th (Brian and Peter - can we make this?)
> >
> >
> >
> > Any views on this?
> >
> >
> >
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>.
> > -----------------------------------------------------------------
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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