[Biopython-dev] biopython on github

Tiago Antão tiagoantao at gmail.com
Tue Mar 17 15:09:13 EDT 2009

OK, in order to exercise and try github development I have forked a
branch to work on the PopGen code. The idea of the branch is to serve
as a platform for merging with the "official" branch. So, the idea is:

1. Official branch - The stable thingy
2. PopGen stabilizer branch - The place to merge contributions from
PopGen development branches. The idea is that people can go crazy on
their own branches and this intermediate one serves as a point to
stabilize (unit test, documentation, QA, ...) before the commit to the
official one
3. Crazy branches - Develop your crazy idea. I have 3 ideas myself:
One for Jason's structure code, one for my LDNe code and another for
statistics. Many more welcomed....

The development procedure would be like this:
A. People would have all the fun on their development branches
B. When they felt confident they would submit their code to the
stabilizer branch, where we would check that all the important things
were there: unit test, code comments, QA, documentation
C. When things were in good shape, we would propose changes to the
official branch

And, by the way, bug fixes of existing production would also be done
on the stabilizer branch.

Does this make any sense?

In my view, with things like git, a policy like this encourages both
innovation while preserving stability and robustness of the official


On Tue, Mar 17, 2009 at 6:36 PM, Giovanni Marco Dall'Olio
<dalloliogm at gmail.com> wrote:
> 2009/3/17 Peter Cock <p.j.a.cock at googlemail.com>
>> 2009/3/17 Tiago Antão <tiagoantao at gmail.com>:
>> I'd still like to have a copy of the "official" git repository running
>> on biopython.org, but this may not be that easy without some technical
>> expertise in house to do this.  From initial discussion with the OBF
>> team about the idea of running git on their servers, my impression is
>> if we can do it ourselves, we may.  Jason Stajich actually suggested
>> we use github independently.
> Well, basically it is not strictly necessary to have git installed on their
> computers to create a mirror.
> You can just create the clone on your computer, raw-ly copy the files there,
> and then you will be able to push the new changes with an ssh access.
> Since git is a distributed source control system, it doesn't require to
> configure a server part as with cvs :-)
> To my knowledge, the pygr project (also a bioinformatics suite in python)
> have an official repository hosted in gitourious, and a mirror in github to
> collect patches from there.
> --
> My blog on bioinformatics (now in English): http://bioinfoblog.it

 "A man who dares to waste one hour of time has not discovered the
value of life" - Charles Darwin

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