[Biopython-dev] Porting docs to sphinx #3220

[Eric Talevich]

On Tue, Jun 12, 2012 at 3:03 PM, Colin Lappala <lappc at u.washington.edu>wrote:

> Hi,
>
> I'd like to contribute to feature #3220. I am interested in learning more
> about the parts and details of Biopython that I haven't used yet, as well
> as getting involved in this project somehow. I am familiar with Sphinx,
> git, and parts of Biopython, and would love the chance to help out. I have
> taken a stab at using Sphinx to semi-automatically generate the
> documentation on a project in our lab (which is not in its final form yet):
> http://depts.washington.edu/cshlab/xpression/html/rnaseq.shtml.
>
> If I can help, I had a few questions first:
>
> 1) I see that you want to keep with Numpy-type rST formatting, but I
> haven't seen the current thought on how to avoid using the :class:`class`
> type of markup in the mailing list logs.
>
> 2) How should I go about dividing the task, since there may be other people
> at work on it as well? I've branched biopython on github, but wanted to
> know which modules' docstrings are being ported so I could work on the
> other ones.
>
>
Great! The only portion of the code base I'd specifically suggest you steer
clear of right now is Bio.PDB, since several people have long-running
branches with major changes to that sub-package that we hope to merge
eventually. On the other hand, the Phylo module is already supposed to be
rST-compliant, but if you find anything to fix there, feel free.

-Eric