[Bioperl-l] BioPerl Migration to Git/GitHub

[Chris Fields]

Lincoln, 

Just an update, I've added you, as well as Dave and Florent.  Still not sure about the bioperl.org address myself, but it seems to work for Dave and others.  We posted to root-l and Chris D. to make sure that's correct or if we should be using open-bio.org instead, but I believe it is.

chris 

On May 6, 2010, at 7:01 AM, Lincoln Stein wrote:

> My github username is lstein and I've just added lstein at bioperl.org to my
> linked email addresses. I hope I have a bioperl.org address; I never use it!
> 
> Lincoln
> 
> On Wed, May 5, 2010 at 10:46 AM, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> All,
>> 
>> I would like to finalize moving over to git/github very soon.  We're sort
>> of in limbo on this, so it needs to progress forward.  We'll need to do some
>> initial cleanup after the move (Heikki is already doing a few things on the
>> test repo, which we'll need to diff over to the new one).
>> 
>> So with that in mind, here are my thoughts.  This is copied over to this
>> wiki page, in case you don't want to reply here:
>> 
>> http://www.bioperl.org/wiki/From_SVN_to_Git
>> 
>> (thanks Mark!)
>> 
>> 1) Timeline
>> 
>> When?  Sooner the better (weeks as opposed to months).  Our anon. svn is
>> down, likely permanently (
>> http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-live).
>> 
>> 2) Migration strategy
>> 
>> Now mainly worked out using svn2git, which is very fast.  We would need to
>> make the svn repo on dev read-only during this transition.  My guess is it
>> would take very little time.  Do we want to retain the git-SVN metadata on
>> commits?  This is viewable with our current read-only mirror on github:
>> 
>> 
>> http://github.com/bioperl/bioperl-live/commit/7090e24f3916346b11a6bf960371f1d903d241ca
>> 
>> 3) Developers
>> 
>> Not everyone has a github account.  Recent ones who I couldn't find on
>> github: dmessina, fangly
>> 
>> The current authors file used for mapping commit authors to emails used
>> their respective bioperl.org addresses (DEVNAME -at- bioperl.org).  I
>> think, once one has signed up with github, you can add that same address to
>> your current ones, and it should map to your github account.  If we use
>> dev.open-bio.org as our central git repo, we won't need to go through with
>> that, but we will need a viewable version of dev available somehow (mirrored
>> on github or otherwise).  Speaking of...
>> 
>> 4) Development strategy
>> 
>> Are we sticking with a single centralized repo (SVN-like)?  Will that be
>> github, or will github be a downstream repo to our work on dev?  We could
>> feasibly have github be an active, forkable repo that could be
>> bidirectionally synced with dev, but I'm not sure of the logistics on this
>> (this popped up before with svn migration and was rejected b/c it was
>> considered too difficult to maintain).
>> 
>> Git makes it very easy to make branches and merge in code to trunk.  With
>> that in mind, I would highly suggest we start working on branches for almost
>> everything and merge over to trunk.  There is very little to no overhead in
>> doing so with git.
>> 
>> I like this strategy (Mark Jensen pointed this out):
>> http://nvie.com/git-model
>> 
>> Also, several points were raised in a related project (Parrot) considering
>> a move to git/github from svn.  One in particular was that git allows
>> destructive commits.  Jonathan Leto indicated we can set up specific
>> branches that don't allow this, using commit hooks, so my guess is the
>> master branch and release branches wouldn't allow rewinds.
>> 
>> 5) Encouraging outside contributors
>> 
>> Do we want to adopt a policy similar to Moose?
>> 
>> http://search.cpan.org/dist/Moose/lib/Moose/Manual/Contributing.pod
>> 
>> This is easy with github and forks.
>> 
>> 6) SVN Read/Write to GitHub
>> 
>> It was recently announced that one can access a github repo using
>> subversion as read-only, and just yesterday experimental write to github is
>> allowed:
>> 
>> http://github.com/blog/644-subversion-write-support
>> 
>> I can see allowing read-only svn, but write support is still experimental.
>> Do we want to allow that?
>> 
>> 7) Others?
>> 
>> 
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l