[Bioperl-l] new Bio::Object -> Bio::Object->new()

Chris Fields cjfields at uiuc.edu
Thu Jun 14 12:35:21 EDT 2007


The genbank commit was mine so I'll look into it; may be that I  
hadn't finished up the bug work.  If if have time I'll look into  
Sopma as well (unless you get to it first).

chris

On Jun 14, 2007, at 10:34 AM, Sendu Bala wrote:

> Sendu Bala wrote:
>> It is preferable to have ->new syntax over new Object syntax, as
>> outlined here:
>> http://www.bioperl.org/wiki/Bioperl_Best_Practices#BioPerl_Object- 
>> oriented_programming_and_modules
>>
>> I propose making this syntax change in all Bioperl POD  
>> documentation, so
>> that the bad syntax is no longer suggested/encouraged. Any  
>> objections?
>> If not, I'll go ahead and commit the changes.
>>
>> (affects 907 modules in live)
>
> It was actually 515 modules & test scripts from live, 48 from run, 21
> from db and 2 from network.
>
> Now committed. Before and after my changes these were failing:
>
>
> Failed Test     Stat Wstat Total Fail  List of Failed
> ---------------------------------------------------------------------- 
> ---------
> t/BioGraphics.t    3   768    38    3  3-5
> t/PodSyntax.t      9  2304  2195    9  378 614 660 1023 1197 1512 1558
>                                         1932 2106
> t/Sopma.t          2   512    16    2  8 15
> t/genbank.t        2   512   247    2  122-123
>
>
> BioGraphics failure caused by Graphics Panel.pm 1.135 -> 1.136
> (unintentional?).
>
> Sopma may not be a bug: results from server might have changed.
>
> genbank caused by genbank.t 1.20 -> 1.21 and presumably genbank.pm  
> 1.163
> -> 1.164 not doing what the new tests expect.
>
> PodSyntax is new and obviously a bunch of POD needs fixing: Nathan,  
> are
> you working on that, or can I fix those errors?
>
> Anyone care to look into those things?
>
> Cheers,
> Sendu.
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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