[Biopython-dev] Good progress on replacing epydoc with Sphinx for API docs

Peter Cock p.j.a.cock at googlemail.com
Wed Nov 1 21:25:25 UTC 2017

Dear Biopythoneers,

For those not subscribed to GitHub alerts, I wanted to mention
I have made good progress on building the Biopython API
documentation (drawing on our reStructuredText formatted
docstrings) using sphinx-apidoc instead of epydoc. See:


(The tool epydoc is no longer maintained, and the HTML
it produces is quite old fashioned with no search support

I'm hoping we can use this for Biopython 1.71, our next

Do people have any strong preference between:

- Having both epydoc and sphinx versions online at
  the same time (at least in the short term, useful for
  comparison and identifying any regressions).

- Dropping epydoc, replacing its old HTML pages with
  redirects to sphinx equivalent pages.

Also, do people have any strong preference between
continuing to host the API docs under biopython.org
(using GitHub Pages) versus using a third party site
like readthedocs.org (or both)?

Either way, we can likely keep a copy of the docs for
each Biopython release online for historical reference.



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