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

Hilmar Lapp hlapp at gmx.net
Fri Jun 15 22:10:25 UTC 2007

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  

- 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.


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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