[Bioperl-l] bioperl-dev or branch? : redux

Mark A. Jensen maj at fortinbras.us
Wed Jun 17 12:47:38 EDT 2009

Hi All, 

I thought I'd revisit this thread, since in the last couple weeks,
have used both techniques (bioperl-dev and branch from trunk) to
produce completed projects. My thoughts:

Using bioperl-dev was very nice for creating Bio::Search::Tiling, a
new addition to the core api. There was no pressure to conform to the
existing api there. In particular, there was no implicit insistence to
make things work through Bio::Search::Utils, and I was free to factor
it out. The Tiling api was definitely unstable until the end, when it
was ported to the core. As I made regular reports to bioperl-l,
everything was transparent and up front, and I received excellent
suggestions there (as usual). 

For Bio::Restriction, using the branch was just as natural. Here, the
existing structure was well established, and all the work needed to
happen beneath the api. All old t/Restriction tests needed to pass,
and additional ones created for the new functionality. So here, using
bioperl-dev wasn't natural, even though some "experiments" needed to
be tried (some succeeded and some failed, as you can see in the
commentary at Bug #2855). Even though the new code turned out to
require substantial effort, the effort was required to fix a true bug
in the working core, and any fixes needed to work transparently with
respect to the users for whom this bug had not been an issue. Using
the branch made it relatively easy to merge quickly back into the core
when done, and there is a certain psychological pressure too provided
by an open branch which is helpful.

Hilmar raised the very good point in the previous discussion that
(essentially) bioperl-dev shouldn't become a sandbox with lots of
unfinished code scraps and derelict stuff that doesn't work. My view
is bioperl-dev will become a sandbox only if we treat it like
one. I've filled out the Bioperl-dev page on the wiki
(http://www.bioperl.org/wiki/Bioperl-dev) with this in mind. Providing
some recognition to devs there whose modules become part of the
core may be a better way to insure that projects that are started on
bioperl-dev actually get finished, than to prescribe beforehand what
kinds of projects may get started. I believe this follows the adage of
liberality on what is accepted, and strictness on what is emitted.


----- 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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