[Biopython-dev] Tutorial & Cookbook

[Peter]

On Mon, Apr 13, 2009 at 2:16 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Speaking of doctests, we should do more of those in our docstrings.
> For our online API documentation at
> http://biopython.org/DIST/docs/api/ it would be nice to have the
> python examples within the docstrings (including the doctests) shown
> with syntax colouring.  See
> http://epydoc.sourceforge.net/manual-epytext.html#doctest-blocks for
> an example, and compare this to
> http://biopython.org/DIST/docs/api/Bio.Seq-module.html - maybe we need
> to adjust our indentation?

We currently explicitly use plain text for epydoc, rather than the
default epytext markup language.  If we switch to epytext (or at least
a very simple subset of it, as some of the markup doesn't lend itself
to friendly human readable docstrings) then we do get python syntax
colouring on the doctests.  However, this will require some effort to
fine tune the docstrings, and right now it makes a mess of in some
cases.

Peter