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

rvos rvos at interchange.ubc.ca
Fri Jun 15 17:08:17 EDT 2007


I would very much prefer it if bioperl moved to svn. I'm considering merging Bio::Phylo (to the extent that that's possible/practical) with bioperl and move it to an OBF repository, but I'd rather not go back to CVS.


-----Original Message-----

> Date: Fri Jun 15 07:56:23 PDT 2007
> From: "Chris Fields" <cjfields at uiuc.edu>
> Subject: Re: [Bioperl-l] SVN and ...Re:  Perltidy
> To: "Sendu Bala" <bix at sendu.me.uk>
> On Jun 15, 2007, at 5:07 AM, Sendu Bala wrote:
> >>>> ...
> >>> 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!
> >
> > Sorry, can you clarify the problem you envisage? And why would  
> > making a branch release help?
> Maybe the worry is that mass conversion in such a large codebase  
> could lead to hard-to-locate bugs.  Shouldn't occur but who knows w/o  
> trying?
> >> I agree; if we intend on doing this it should be all at once,  
> >> maybe  on a branch dedicated to ensure that code changes don't  
> >> tank tests  (they shouldn't but one never knows).  We would then  
> >> need a script up- and-running that tidies everything up prior to  
> >> commits (though what  happens if perltidy tanks?...).
> >> Sendu, up for it?
> >
> > If its going to be difficult and a hassle, for such an unnecessary  
> > thing I'm not sure its worth it. There are more pressing things to  
> > be done for Bioperl.
> >
> > If I can just run perltidy on the entire package and commit, I'd do  
> > it. If that's not appropriate, I won't.
> The choices aren't necessarily all or nothing.  What about voluntary,  
> recommended use of a perltidy config file included with the  
> distribution, with additional 'caveats'?  See my response to Sean.
> >>>> About svn
> > [snip]
> >> Stepped into that one, didn't I!  I'll look into how much effort  
> >> is  involved and try getting something going in the next month or  
> >> two,  maybe sooner if time permits.  I'm lacking on SVN-foo as  
> >> well but it  might be worth looking into.
> >
> > I'd put this in the unnecessary-but-nice category as well. If it  
> > will be as easy as my ->new change, go ahead. If not, there are  
> > more pressing matters (POD fixing, test script updating and  
> > finishing...).
> A few other open-bio projects have actively discussed a CVS->SVN  
> migration (BioRuby and I think BioPython, though the latter could be  
> wrong).  As I said, "it might be worth looking into" to weigh the  
> pros/cons, get others opinions from others who have made the  
> transition, etc.  We could, as Jason suggested, even set up a tester  
> SVN w/o making it the default codebase (lock it off to a few testers,  
> have CVS commits automatically/manually carry over to SVN, etc).
> I agree with you that it's not feasible to switch over prior to a  
> release and that there are more pressing issues, but it doesn't hurt  
> having an open discussion about it.
> chris
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