[Biopython-dev] Biopython 1.61 release

[Peter Cock]

On Tue, Feb 5, 2013 at 6:22 PM, Wibowo Arindrarto
<w.arindrarto at gmail.com> wrote:
> Hi Peter,
>
>> Bow - the `backtick` markup doesn't do anything in epydoc, but
>> perhaps for the next release we can turn the SearchIO markup
>> into restructuredtext instead?
>>
>> I think last time I didn't have the docutils dependency installed
>> in order for epydoc to try and parse the restructuredtext (used
>> in Bio.Phylo). Running epydoc also showed a few more epydoc
>> formatting errors, fixed in git - I will now regenerate the installers,
>> and tag this in git etc.
>
> Hmm..IIRC, I did wrote the entire SearchIO doc using reStructuredText
> markup; in hindsight probably not wise since we still rely on epydoc.
> Using rSt for the next release sounds good.

Using reStructuredText (like Eric did with Bio.Phylo) would have
been (and is) fine, however you had __docformat__ = 'epytext en'
in the file.

> On a related not, do we have any solid plans to move out of epydoc
> (and into Sphinx?) for the next release?

Not yet - but moving all the docstrings to reStructuredText is a
very good step towards that, and a chance to review/update
all the plain text docstrings in particular to look nicer and be
more consistent.

Peter