[Bioperl-l] SVN and ...Re: Perltidy

Chris Fields cjfields at uiuc.edu
Thu Jun 14 14:32:41 EDT 2007

To chip in on this, I only use perltidy when I need to clean bioperl  
code up for debugging (particularly if blocks are hard to see) and  
just use the defaults.  I agree it would be nice to have everything  
tidied up but it'll definitely need to be a consensus config file.

About svn, I like the idea of eventually migrating to using it over  
CVS (I think BioPython and BioJava have plans to but I'm not sure)  
but I don't really know enough to say how feasible/difficult the  
migration path would be.  Anyone know?


On Jun 14, 2007, at 12:38 PM, Mark Johnson wrote:

>     The nice thing about Perl Tidy is that everybody can have their
> own config file.  There could be a bioperl default config that gets
> applied at checkin time.  Anybody that didn't like it could script
> checkouts to get run through their own config.  Diffs might get a
> little hairy, but as long as you tidy before diffing, it shouldn't be
> too bad.  Speaking of which....coding style is controversial enough,
> but since that's already been opened, what about CVS vs Subversion? 8)
>  Some of the scripting for this sort of thing might be easer in
> Subversion.  Though maybe something like Git would fit the developer
> model better (more support for distributed development).
> On 6/14/07, Sendu Bala <bix at sendu.me.uk> wrote:
>> Nathan S. Haigh wrote:
>>> I'm just wondering if anyone passes their modules through  
>>> perltidy in
>>> order for them to have the same look/feel? If so, do you have a
>>> .perltidyrc file? Also, is it worth running the Bioperl modules  
>>> through it?
>> I don't use it, but I was contemplating the same thing. Chris uses it
>> from time to time and I think we have a similar taste in style.
>> But we'd have to hammer something out that was agreeable to everyone.
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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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