[Bioperl-l] Possible migration to git/github

Chris Fields cjfields at illinois.edu
Tue Apr 20 15:00:49 EDT 2010

On Apr 20, 2010, at 8:24 AM, Peter wrote:

> On Tue, Apr 20, 2010 at 11:20 AM, D. Joe Anderson <bioperl at etrumeus.com> wrote:
>> On Sat, Apr 17, 2010 at 11:18:13AM -0500, Chris Fields wrote:
>>> I wanted to get the BioPerl community's general input on a
>>> possible Subversion to git/github migration for the BioPerl
>>> repository.
>> Moving to git seems like a great good thing with few downsides.
>> Distributed revision control has been gaining ground for years,
>> and seems to have exploded with the development and adoption of
>> git.  All the cool kids are doing it.
>> Moving to github, however, brings up all the usual concerns with
>> getting locked-in to a proprietary application, since the github
>> software is not open source.  Granted, given the decentralized
>> nature of git development, the code itself would be fine.
>> However, contributor metadata and workflows could be at risk
>> from changes in github's business model down the line.
>> I realize these concerns face an uphill battle, given the
>> popularity of github in particular and of proprietary
>> software-as-a-service more generally (Google, various social
>> networking sites) and, most perniciously, the intrusion of
>> proprietary software-as-a-service into partially- or mostly-FOSS
>> projects (like Ubuntu One), but I felt they needed airing.
> Using git does not in anyway tie us to github.com - we could
> in theory host the "official" repository on the OBF servers or
> anywhere else (such as gitorious as you mentioned), and
> from a technical perspective this is easy. The authorship
> metadata would also be preserved (I don't understand your
> concern here).
> You are right there is a potential concern if the project comes
> depend on any of github's additions like the network diagram
> or commenting features, or using the github "pull request"
> notification system as part of a workflow to review code for
> merging. But a workflow is a social convention that can be
> changed as needed.
> I have no concerns over using git hosted on github from a
> vendor lock in point of view.
>> We should note here that Biopython is already using git and
>> github in some fashion:
>> http://www.biopython.org/wiki/GitUsage
> Don't forget that BioRuby has been using github for even longer,
> as I pointed out near the start of this thread:
> http://lists.open-bio.org/pipermail/bioperl-l/2010-February/032353.html
> http://github.com/bioruby/bioruby
> Also Chris mentioned (off list) that Biolib is using github too:
> http://github.com/pjotrp/biolib/
> This does seem to confirm your observation of the popularity
> of github ;)
> Peter
> (Biopython)

I do share some of D. Joe Anderson's concerns, mainly re: use of github's other tools.  However, I don't particularly see this as an insurmountable issue, just one that needs to be clarified w/ regards to how many of the github tools we intend on supporting.  I don't envision a complete migration to their wiki services or bug tools for the time being.

And glad that Gitorious was mentioned, as it was another option I wanted to raise as well.  It does have several large and very active projects (Qt, FreeBSD, etc), but very few (any?) bioperl devs on it, beyond me.


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