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

[redmine at redmine.open-bio.org]

Issue #3220 has been updated by Eric Talevich.


I posted about Sphinx on the parent issue.

For this bug, I reckon the best approach is to convert the rest of the docstrings to reStructuredText, removing Epytext markup wherever we find it. Going further, we could try using "restructuredtext" instead of "plaintext" as the default format when running Epydoc, and fix any errors or abominations that appear. If we can get that to work, then we'll know it's all safe to pull into Sphinx with the automodule command.
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Feature #3220: Port Biopython docstrings to reStructuredText
https://redmine.open-bio.org/issues/3220

Author: Eric Talevich
Status: In Progress
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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