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

[Brian Osborne]

Ewan et  al,

> The main thing is in my view
>
> bptutorial.pl

I've added and amended here, but I think of this as Peter's baby....

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

Already done. I will do a bit more to make sure all the *pod's make
something coherent. This is important. And bioback.pod needs some work as
well, I'll see what I can do.

>
> making sure the README points to the right documentation

Yes, one of my concerns as well, I think of the README as a sort of TOC...


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

Working on this...


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

I'll take a look, as should the authors.

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

It's not that bad. If mid-February is alpha, then the "real" release is a
few weeks after.


Brian O.


>
>

----- Original Message -----
From: "Ewan Birney" <birney@ebi.ac.uk>
To: "Brian Osborne" <b_i_osborne@hotmail.com>
Cc: "Bioperl" <bioperl-l@bioperl.org>
Sent: Tuesday, January 29, 2002 7:12 PM
Subject: Re: [Bioperl-l] Jason and Ewan's TODO list


> 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>.
> -----------------------------------------------------------------
>
>