[Bioperl-l] Possible migration to git/github

Peter biopython at maubp.freeserve.co.uk
Tue Apr 20 09:24:22 EDT 2010

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:


Also Chris mentioned (off list) that Biolib is using github too:

This does seem to confirm your observation of the popularity
of github ;)


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