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

Jason Stajich jason at bioperl.org
Thu Jun 14 15:00:09 EDT 2007

On Jun 14, 2007, at 11:32 AM, Chris Fields wrote:

> 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.

Can we do any sort of massive conversion at some logical timepoint.   
Probably after a branch release or something?  Because it basically  
means we're going to have differences on nearly every line which is  
going to make diff-ing difficult when debugging old/new versions.   
Maybe it is not a problem because we aren't introducing and new bugs!

> 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?

It's doable but non-trivial.  cvs2svn (python gah!) script exists to  
help in this.  There are pros and cons to converting.   There is a  
fair amount of documentation and other pointers out there that point  
to the CVS server for getting latest code so we'd need to think about  
whether we'd support some sort of backwards compatible SVN -> CVS for  
read-only or what.

Mostly it will need someone to lead the charge - I made a go at doing  
it in the winter, but I really don't have the SVN-foo to make this  
work.  We'd need someone with SVN experience to step up and help.   
You can always try and we can play with the converted repository for  
a while without making it the new code base.


> chris
> 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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Jason Stajich
jason at bioperl.org

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