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

Nathan S. Haigh n.haigh at sheffield.ac.uk
Thu Jun 14 12:36:37 EDT 2007


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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?
> 

I can fix these - although I'm still trying to get my new Debian 4.0
system up-to-speed so it might take me a little while! RE the
PodSyntax.t, I've got it silently skipping the tests if Test::Pod isn't
installed. However, would it be better to have Test::Pod in t/lib so
that it runs on the user's system during installation or leave it as is?

Nath
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