[Biopython-dev] [Biopython - Feature #3220] Port Biopython docstrings to reStructuredText

[redmine at redmine.open-bio.org]

Issue #3220 has been updated by Peter Cock.


You linked to this on the parent bug #3319, but we should probably adopt (some of) the NumPy docstring conventions, which limit the amount of rich mark up so as not to make the plain text view too ugly. This is important when reading the API help text at the python prompt.
https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt

Also note that a large fraction of the current API docs are not even done in epytext, they are plain text.

This would also be a nice point to standardise on the layout of things like function/method argument documentation. Again, I'd suggest following NumPy by default.
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Feature #3220: Port Biopython docstrings to reStructuredText
https://redmine.open-bio.org/issues/3220

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


The first part of the effort to port Biopython's documentation to Sphinx is to convert our API docs from Epytext to reStructuredText. Plain text will generally work.

Epydoc already supports using reStructuredText as a markup language instead of the default Epytext, so this isn't as painful as it sounds. This can be done one module at a time, changing the format declaration at the top from:
<pre>
__docformat__ = "epytext en"
</pre>
to:
<pre>
__docformat__ = "restructuredtext en"
</pre>

And changing any Epytext markup in the docstrings to valid rST.

Note that this adds the dependency of Docutils when generating API docs, in addition to the current dependency on Epydoc. Since documentation is normally built ahead of the time when packaging stable Biopython releases, this shouldn't be a problem for end users, and may be a small inconvenience for developers who want to work on the documentation.

See:
http://epydoc.sourceforge.net/manual-othermarkup.html
http://docutils.sourceforge.net/rst.html


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