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

Sendu Bala bix at sendu.me.uk
Thu Jun 14 11:34:27 EDT 2007


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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