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

Hilmar Lapp hlapp at gmx.net
Sat Jun 16 14:40:08 UTC 2007

Just as an aside, even if we can't keep anonymous cvs working, I  
would think that using apache URL rewriting and a small CGI script  
that returns an appropriate page redirect we can without too much  
trouble keep the hyperlinks functional that people may have bookmarked


On Jun 15, 2007, at 6:23 PM, Jason Stajich wrote:

> Sounds like a plan, I'll be curious to see if we can still get keep  
> anonymous CVS working as I'd like to not have to pull the plug on  
> that.  There are some threads out on the web about how to do this  
> with a commit rule on SVN.
> Also, can someone who is close enough to all the SVN benefits  
> please elaborate how it is going to help _this_ project?
> Perhaps you would be willing to put a few words up -- like on (a to  
> be created):
> http://bioperl.org/wiki/BioPerl:Version_control_changeover
> This way if anonymous CVS is broken and/or developers who haven't  
> been paying attention come back to commit code ask why things  
> changed we don't have to compose long emails... =)
> -jason
> On Jun 15, 2007, at 3:10 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
>>>>> _______________________________________________
>>>>> 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 :
>> ===========================================================
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> --
> Jason Stajich
> jason at bioperl.org
> http://jason.open-bio.org/

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

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