[Bioperl-l] Bio::Species, Bio::Taxonomy::Node overhaul

Chris Fields cjfields at uiuc.edu
Sat Aug 12 14:36:57 EDT 2006

>> Do you think more is warranted?
> The thing that should be somewhere is an authoritative list of
> changes and current behavior. It looks like the bug documentation has
> that in one post but then others (and quite lengthy ones) follow, so
> it's not clear what still holds and nobody should be required to read
> through the discussion (BTW Chris/Sendu: don't discuss such things on
> bugzilla - it's by all means not meant for that purpose).
> So - maybe just add a page to the wiki? It really doesn't matter that
> much how it's called unless somebody chimes in here; the page can be
> renamed and the content be migrated if deemed necessary later.
> ...


Agreed!  Using Bugzilla was my suggestion based on its use for  
suggested code enhancements.  This was also suggested to me by  
someone else, though I can remember now who that was.  It's clogging  
up the works for Bugzilla and detracts from its primary function,  
which should be primarily for bug reports.

I think the mailing list and wiki are the best places to document  
upcoming changes (these could be linked to from the project priority  
list and the Bioperl release page).  Make an announcement on the mail  
list/new page, have a back-and-forth on the specifics, refine the  
wiki page as we go along.  It works for the Bioperl Release page.  An  
advantage of using the wiki is it holds the recent history of the  
page edits.

Sendu, as Hilmar suggests, try keeping it succinct.  The wiki allows  
you to mark up and organize information very efficiently using  
bullets and links.  If anyone has a question, point to the wiki  
page.  Instead of talking about the tons of changes in Taxonomy in  
bioperl-live/CHANGES, point to the wiki page (though you should  
provide a few sentences summarizing what was done in CHANGES).

Also, if these changes impact the other documentation or scripts  
(HOWTO, FAQ, tutorial, etc) make sure to modify those accordingly.   
It would be nice, for instance, to have a demonstration script or  
similar working code outlining what your changes accomplish.  Proper  
working code speaks volumes, impresses your friends, gets you  
dates... well, maybe not the latter    ;>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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