[Biopython-dev] Port Biopython documentation to Sphinx

[Eric Talevich]

On Fri, Apr 29, 2011 at 3:55 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> Re: Feature #3219: Port Biopython documentation to Sphinx
> https://redmine.open-bio.org/issues/3219
>
> and this thread last year:
> http://portal.open-bio.org/pipermail/biopython-dev/2010-July/007977.html
>
> On Fri, Apr 29, 2011 at 8:37 AM, Kristian Rother <krother at rubor.de> wrote:
> >
> > Hi,
> >
> > I've seen Sphinx being used on several projects (see e.g.
> > http://pycogent.sourceforge.net/cookbook/index.html) and tried it on one
> > myself (2009). The system for mixing text+code and testing code examples
> > is gorgeous!
> >
> > What I didn't like is that all Sphinx sites seem to look the same
> > (including font sizes and colours). There probably is a place to apply a
> > CSS stylesheet, but it was not easy to find. There might be some work at
> > this point.
> >
> > Is someone trying to make a proof-of-concept on GIT or are we looking for
> > a volunteer?
> >
> > Best regards,
> >   Kristian
>
> I think there was an experimental branch on github already... by Eric
> and/or
> Vince, but his repository seems to have gone:
> https://github.com/vsbuffalo/
>
>
I don't have a branch for this yet, but I filed the bugs on Redmine to get
this big to-do item out of my head and onto the web. I expect to have a
little bit more time this summer to work on Bio.Phylo and Bio.PDB/Struct,
and I'm going to start by converting the docstrings in Bio.Phylo to
reStructuredText. This won't take much time, and once we merge that branch
and make the Docutils dependency official (for building Epydoc
documentation), that will reduce the activation energy for porting the rest
of our docstrings.

If anyone else wants to port some docstrings independently, that's cool too,
and I don't think it will cause any conflict in the code base.

Once that's done, we can start seriously considering the switch from Epydoc
to Sphinx. Sound like a plan?

Cheers,
Eric