[Bioperl-l] bioperl-dev or branch?

Hilmar Lapp hlapp at gmx.net
Thu May 21 17:00:46 EDT 2009

To quote from the thread:

"The idea behind bioperl-dev, as I understand from Chris, is to  
provide a sort of sandbox for experimental code. Adventuresome users  
should feel free to play with the code there, but not expect much in  
the way of support, bug fixes, and the like. There be dragons there.  
When a bioperl-dev module graduates to the core, then the usual  
support mechanisms kick in."

I.e., there is a possibility, but no expectation to graduate to core.  
I think that's important.

My sense is that we all agree that we don't want to abandon svn  
branches (or do we?). To I'll state the question again: what  
disqualifies a development project from going into the main trunk  
(thanks to Sendu for keeping this on the table), and what disqualifies  
it from going onto a branch, with the remaining resort being bioperl- 

I'm worried about fragmentation here - historically we've been a crowd  
that has been rather inviting of new contributions into the main code  
base and tolerant of those additions needing time to mature, and we  
have been lazy on committing on behalf of other people (which merging  
patches, branches, and separate repositories on behalf of someone else  
is) and hence liberal in giving out commit access, and commit to main  
trunk access.


On May 21, 2009, at 4:26 PM, Mark A. Jensen wrote:

> These are key points. I do believe (and think in these terms) that  
> bioperl-dev modules are intended for the trunk, as soon as they are  
> not so broken as to be testable by users. (my interp). See this  
> thread to refresh memory: http://lists.open-bio.org/pipermail/bioperl-l/2009-March/029661.html
> ----- Original Message ----- From: "Hilmar Lapp" <hlapp at duke.edu>
> To: "Chase Miller" <chmille4 at gmail.com>
> Cc: "BioPerl List" <bioperl-l at lists.open-bio.org>
> Sent: Thursday, May 21, 2009 4:00 PM
> Subject: Re: [Bioperl-l] bioperl-dev or branch?
>> Moving this question to the BioPerl list, which is where we need  
>> to  discuss this I think. Can someone refresh my memory on what  
>> the  Bioperl-dev repository is or was meant for? It doesn't seem  
>> documented  on the wiki.
>> My (admittedly vague) recollection is that bioperl-dev is  
>> basically  for highly experimental changes or functionality.
>> I'm not clear why everything else shouldn't go either into the  
>> main  trunk or into a branch. If there is a realistic expectation  
>> for  something to be folded into the main trunk sooner or later,  
>> what would  be the reasons for not putting it into a branch of the  
>> main  repository? If we are putting it into a separate repository,  
>> we're  waiving a lot of svn's support for merging and resolving  
>> concurrent  edits.
>> I would also go actually go a step further and suggest that even  
>> if  this GSoC project starts out on a branch (which I can see good  
>> reasons  for, such as eliminating fear to disrupt something), there  
>> should be a  plan to move to main trunk before the end of the  
>> project. We've had a  good tradition in BioPerl of developing  
>> directly on the main trunk. It  sometimes leads to occasional  
>> disruptions when lots of tests seem  failing, but it also  
>> encourages development discipline and make new  code to melt into  
>> the BioPerl code base without requiring any extra  steps by someone.
>> Any and all thoughts or comments welcome and appreciated!
>> -hilmar
>> On May 21, 2009, at 11:26 AM, Chase Miller wrote:
>>> This brings me to a question about where I should have my code   
>>> repository.  Originally, I was going to use Bioperl-dev, but it  
>>> was  brought to my attention that that repository does not  
>>> normally  receive daily updates and it might not be the right  
>>> place for my day  to day development.  An alternative would be to  
>>> use something like  google code on a daily basis and commit to  
>>> Bioperl-dev on a weekly  basis.
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
>> ===========================================================
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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