[Biopython-dev] [Biopython - Feature #3219] Port Biopython documentation to Sphinx

[redmine at redmine.open-bio.org]

Issue #3219 has been updated by Peter Cock.


In terms of moving the Tutorial from LaTeX to Sphinx, we'd need to update Tests/test_Tutorial.py which currently tests marked doctests within the tutorial (to ensure they are in sync with the latest code).
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Feature #3219: Port Biopython documentation to Sphinx
https://redmine.open-bio.org/issues/3219

Author: Eric Talevich
Status: In Progress
Priority: Low
Assignee: Biopython Dev Mailing List
Category: Documentation
Target version: 
URL: 


Currently we use Epydoc for the API reference documentation, and LaTeX (to PDF via pdflatex, and HTML via hevea) for the tutorial. There's some material on the wiki to consider, too.

A number of Python projects, including CPython, now use Sphinx for documentation. Content is written in reStructuredText format, and can be pulled from both standalone .rst files and Python docstrings.

This offers several advantages: (i) API documentation will be prettier and easier to navigate; (ii) the Tutorial will be easier to edit for those not fluent in LaTeX; (iii) Since the API reference and Tutorial will be written in the same markup, potentially even pulling from some shared sources, it will be easier to  address redundant or overlapping portions between the two, avoiding inconsistencies.

See:
http://sphinx.pocoo.org/
http://docutils.sourceforge.net/

Mailing list discussion:
http://lists.open-bio.org/pipermail/biopython-dev/2010-July/007977.html

Numpy's approach:
http://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt



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