[Biopython-dev] biopython on github

Peter biopython at maubp.freeserve.co.uk
Tue Mar 17 13:59:43 EDT 2009

I wrote:
> In the short term (at least until Biopython 1.50 beta is out, perhaps
> until Biopython 1.50 proper is out), CVS will remain the official
> repository.  ...  During this period I hope most (ideally all) our active
> developers with CVS access will create an account on github, and
> try out forking from the CVS mirror, creating their own branches,
> checking in some changes, and doing some simple merges - for
> example pulling code from other Biopython developer's public
> branches.  This should give us the confidence to trust git and
> github enough to use it for real.

Brad and I have been trying this out in practice, and it seems to work OK.

I started a fork to test the patches for Bug 2767, adding quality
parsers to Bio.SeqIO,
I made a few incremental checkins, pushed to github one by one.

Brad then took a fork of this in order to make some minor changes and
fix a typo in the documentation :

At this point the "network" diagrams showed up the two branches as
diverging.  Brad then sent me a "pull" request, suggesting I might
want to pull his work into my branch.

Using the git command line tool, I was able to pull and merge Brad's
changes (as I had made no changes in the meantime this could be done
automatically), and then push the merged version back up to github on
my branch.  At this point my branch and brad's agreed once again, and
the "network" diagram no longer shows both.  Note that my branch now
includes a commit from Brad.

At this point, Brad may choose to delete his branch, or perhaps make
further changes.

Now all this worked, but I was wondering if the github web interface
could have simplified any of this, if I'd only know where to click.
For example, does github offer any way to view a diff between to
branches?  Or, as I suspect, do they simply expect you to use the git
tools directly for this?


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