[Biopython (old issues only) - Feature #3220] (Closed) Port Biopython docstrings to reStructuredText

Issue #3220 has been updated by Peter Cock.

Status changed from In Progress to Closed
% Done changed from 20 to 100

We made the switch to using reStructuredText by default with epydoc for Biopython 1.67 (although there are likely still visual glitches waiting to be reported). Closing.

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Feature #3220: Port Biopython docstrings to reStructuredText
https://redmine.open-bio.org/issues/3220#change-15295

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