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

Chris Fields cjfields at uiuc.edu
Sat Jun 16 01:50:09 UTC 2007

I'll help out to the extent I can w/o having the SVN know-how.  We  
need (as Jason points out) someone who can detail the benefits and  
maybe keep an updated journal on the wiki.

I believe at least one or two of the other Bio* contemplated moving  
over to SVN, which may be worth checking out.


On Jun 15, 2007, at 5:10 PM, Hilmar Lapp wrote:

> 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
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> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
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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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