[Biopython-dev] Interested in contributing to Biopython

Peter Cock p.j.a.cock at googlemail.com
Wed May 18 21:53:19 UTC 2016

Hi Mahesh,

Saying hello on this mailing list is very appropriate. Welcome!

Right now we've been busy with rebuilding the website using
GitHub pages - you've found the repository for that - have a
look at the issue tracker or just looking glitches in the website
would  be a good way to immediately help out.

(If this side of things happens to particularly interest you,
then the websites for BioSQL, BioJava, and BioPerl have
been though a similar migration - I'm currently doing BioDAS
and there are a couple more to look at after that).

On the testing side, Tiago has been looking at making it easier
for us to make sure we're testing all our code with "soft" or
optional dependencies. We're using TravisCI but haven't yet
got that working under Mac OS X too - nor have we setup a
similar system for Windows testing but such things exist.

We do have a buildbot setup as well, testing.open-bio.org,
but do need another volunteer with a Windows machine...

API documentation wise, we're still using epydoc to build
the API doc webpages from our docstrings, see:


All our docstrings *should* now be valid restructured text.
A next step would be to replac epydoc (and its ugly HTML
output) with something like Sphinx, pandoc, or the hosted
service readthedocs.org

Rather than scaring you (and anyone else reading this), I'm
trying to say there's lots of things that can be worked on
even without working directly on the code itself - so I hope
there's something that looks interesting that you'll try.

And please do ask questions,



On Wed, May 18, 2016 at 9:32 PM, Mahesh Gudapakkam
<mahesh.gudapakkam at gmail.com> wrote:
> Hi All,
> I have a feeling this may not be the right way to offer that I'd like to
> help with contributing to Biopython but I am doing so per this text on your
> website. (http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc319 -
>  The best place to express an interest is on the Biopython mailing lists –
> just let us know you are interested in coding and what kind of stuff you
> want to work on.)
> I am Web developer and UI/UX designer who is very interested in
> Bioinformatics. Ideally I'd like to contribute to modules within Biopython
> but I know that will take time and domain expertise. I will get there.
> However, I'd like to begin immediately by offering to help with the website,
> documentation and unit tests.  At present, I am reviewing both Chapter 22
> Where to go from here – contributing to Biopython as well as your github
> repo for your website https://github.com/biopython/biopython.github.io.
> Please let me know if this is the right way to get involved with this
> effort. My apologies if I did this the wrong way.
> Thanks
> Mahesh Gudapakkam
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev

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