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

Hilmar Lapp hlapp at gmx.net
Wed Apr 18 12:00:49 EDT 2007


sounds good to me - the less cruft the better. -hilmar
On Apr 18, 2007, at 7:48 AM, Sendu Bala wrote:

> Alex Lancaster wrote:
>> In packaging bioperl-run for Fedora, I think I stumbled across a bug
>> in the bioperl-run package.  It appears from this edit:
>>
>> http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/Bio/Root/ 
>> Attic/AccessorMaker.pm?hideattic=0&cvsroot=bioperl
>>
>> that Bio::Root::AccessorMaker was removed in bioperl 1.5.x, but
>> bioperl-run 1.5.2_100 still contains modules that use this module:
>>
>> $ cd bioperl-run-1.5.2_100
>> $ grep -r AccessorMaker  *
>> Bio/Tools/Run/Phylo/Forester/SDI.pm:use Bio::Root::AccessorMaker (
>> Bio/Tools/Run/JavaRunner.pm:use Bio::Root::AccessorMaker ('$'=>[qw 
>> (jar
>> class min_version)]);
>> Bio/Tools/Run/AbstractRunner.pm:use Bio::Root::AccessorMaker
>> ('$'=>[qw(input_file output_file)]);
>
> 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.
>
> 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]
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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