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

Spiros Denaxas spiros at lokku.com
Fri Jun 15 17:40:32 EDT 2007


On 6/15/07, rvos <rvos at interchange.ubc.ca> wrote:
> Hi,
>
> 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.
>
> Rutger
>

I second that, SVN seems like the reasonable choice. I would be more
than happy to help out as well.

Spiros

>
> -----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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> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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