[Bioperl-l] Immediate-effect deprecations (was: bioperl-run and Bio::Root::AccessorMaker)

Chris Fields cjfields at uiuc.edu
Wed Apr 18 08:43:45 EDT 2007

On Apr 18, 2007, at 6:48 AM, Sendu Bala wrote:

> It looks like I've implemented a similar idea to AccessorMaker and
> AbstractRunner in Bio::Root::Root->_set_from_args() and
> Bio::Tools::Run::WrapperBase->_setparams(). Since nothing uses
> AbstractRunner I propose deprecating it immediately.

JavaRunner is-a AbstractRunner, but what you propose below takes care  
of that.

> Forester::SDI and JavaRunner have no tests which is why we didn't  
> notice
> the problem. Since they've been out of use for a number of years now I
> also propose their immediate deprecation. Alternatively, it may not be
> too difficult to just update them to use _set_from_args and  
> _setparams,
> but I've nothing to test against (and JavaRunner is self-described as
> "probably incomplete").
> I can remove the modules from cvs and create bioperl-run-1.5.2_101,
> resolving the packaging issue. I plan on doing precisely this  
> within the
> next seven days unless someone puts a hand up to stop me.
> [BCC: author, Juguang Xiao]

I suppose you could just remove the modules from the branch for now,  
but (as you point out) the code appears largely incomplete, so might  
as well deprecate the entire lot.  The code will be in the 'attic'  
once removed if anyone's really interested in it.

You've forwarded the author and the mail list so let's see what the  
response is (if any)...


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