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

rvos rvos at interchange.ubc.ca
Sat Jun 16 06:37:11 EDT 2007


I can volunteer some time to help out with this.

Rutger

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

> Date: Fri Jun 15 15:10:25 PDT 2007
> From: "Hilmar Lapp" <hlapp at gmx.net>
> Subject: Re: [Bioperl-l] SVN and ...Re: Perltidy
> To: spiros at lokku.com
>
> So should we set up a sandbox svn repository and those who would like  
> to help out
> 
> - take shots at migrating bioperl (any current cvs snapshot will do)  
> to svn
> 
> - you document what you find yourself having to do in trying to make  
> it work
> 
> - you report back when you think you have a working repository
> 
> - we all get a defined amount of time to test to our hearts' content,  
> say 2 weeks
> 
> - you fix issues that were encountered
> 
> - report back when done, followed by retesting for, say 1 week
> 
> - iterate previous 2 steps until no issues and no objections to  
> migration
> 
> - two more weeks of warning period to all developers to commit all  
> outstanding changes, or reapply them to a future svn checkout
> 
> - pull the trigger by locking down cvs, applying the migration as  
> worked out before, and announcing that BioPerl is now on svn
> 
> - get free beer at next BOSC (I'll pay if no one else does)
> 
> This may not be precisely the plan that needs to be executed, but  
> it's probably somewhere along those lines.
> 
> If there are volunteers who would like to spearhead this, then power  
> to you - I think everyone is in favor and the advantages of svn don't  
> need to be debated. The only reason it hasn't happened yet is because  
> no one has stepped forward who would have the energy.
> 
> I'm sure ChrisD will gladly create the svn sandbox if we have  
> volunteers lined up to get going.
> 
> 	-hilmar
> 
> On Jun 15, 2007, at 5:40 PM, Spiros Denaxas wrote:
> 
> > 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
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
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> 
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
> 
> 
> 
> 
> 
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