[Bioperl-l] Looking good.

[Brian Osborne]

Ewan et al,

>>(3) Top level documentation: We need to overhaul bioperl.pod,
>>biostart.pod, bptutorial.pl, README to all work together. Peter I assumme
>>will be doing bptutorial - Peter - do you still have time? Does anyone
>>want to work on the other modules?

I made some minor changes to biostart.pod a while back, and in so doing saw
that it was largely superceded by bptutorial.pl, though it has a nice
discussion of the Seq object. I'd be happy to work on biostart.pod but first
give me a clearer sense of what you'd like to be done. Make it more like a
true 'start' document? with various references to existing resources?
Currently it gives the impression of being unfinished....

Brian O.

----- Original Message -----
From: "Ewan Birney" <birney@ebi.ac.uk>
To: <bioperl-l@bioperl.org>
Sent: Wednesday, January 09, 2002 4:18 AM
Subject: [Bioperl-l] Looking good.


>
> Ok. We have had "make test" bascially pass on all major unix platforms
> (hurray!) but need to chase down final problems. I'm still planning on a
> 0.9.3 tar ball release on friday. I think we should call the next release
> 1.0alpha1 unless anyone objects...
>
>
> I'd like to encourage people with NT installations to start trying
> reporting tests. Do we have anyone with commit priviledges who works on NT
> who would like to lead that? (cross platform testing is such a pain
> if we don't actually have good access to the platform).
>
>
> I'd like to suggest we don't worry so much about MacPerl for MacOS <= 9,
> assumming that anyone who wants to both have a Mac and do this will do the
> sensible thing and move MacOS X. If someone could do a make test on MacOS
> X that would be great as well.
>
>
>
> Things to do:
>
>
> Code
> ----
>
> (1) Jason - are we all smoothed off for the SearchIO system? Does anything
> else needed to be added?
>
> (2) Is there anything outstanding to go in? Kris - you had some check-ins
> you wanted to put into for PDB?
>
>
>
> (3) What do we do about semi-defunct modules?
>
>   Bio/Tools/Blast.pm
>
> and
>
>   Bio/Tools/BPlite.pm
>
> and (potentialy)
>
>   Bio/Tools/HMMER.pm
>
>
> What I would like to suggest is that we have the following code in the
> "new" functions of these methods
>
>
> (In Bio::Root::RootI.pm ---
>
>     $WARN_ABOUT_DEPRECATED_MODULES = 0;
>
>
>
>  In the modules 'new'
>
>
>   if( $WARN_ABOUT_DEPRECATED_MODULES ) {
>      $self->deprecated("XXXXX has been deprecated for the new
> Bio::SearchIO framework. Please investigating porting to the new system");
>    }
>
> )
>
>
> The big global variable is so that people can move from 0.7.2 to 1.0 and
> then set that flag to 1 in their local copy to prevent endless painful
> messages arriving on their screen --- but they do have to actively switch
> off the warnings.
>
>
> Later on in the 1.0 series we might get more frantic.
>
>
> Testing
> -------
>
>
> We need broader testing against existing code bases. I will start to drum
> up larger test sites...
>
>
>
> Documentation
> -------------
>
> (1) POD stuff. Most of Heikki's POD errors are SteveC's modules - Steve -
> have you been using the wrong POD syntax for something? Any views?
>
>
> (2) Documentation on modules: We want every synopsis to be
> cut-and-paste-able as much as possible. Does anyone want to try that out?
> Volunteers? (go on...)
>
>
> (3) Top level documentation: We need to overhaul bioperl.pod,
> biostart.pod, bptutorial.pl, README to all work together. Peter I assumme
> will be doing bptutorial - Peter - do you still have time? Does anyone
> want to work on the other modules?
>
>
>
> External code
> -------------
>
>
> Someone should read all the examples/ code and check it is up to
> date (and at the very least, works). Again - any volunteers?
>
>
>
>
> This is one of those moments when lots of people can help (in particular
> with documentation!). So... it is time not to ask what bioperl can do for
> you, but what you can do for bioperl...
>
>
>
>
> ewan
>
>
>
>
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>.
> -----------------------------------------------------------------
>
>
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