[Bioperl-l] Looking good.

[Ewan Birney]

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




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