[Biopython-dev] sphinx build with github source has error in Restriction.py
p.j.a.cock at googlemail.com
Sun Oct 20 14:18:42 UTC 2013
On Sat, Oct 19, 2013 at 12:43 AM, hari jayaram <harijay at gmail.com> wrote:
> Hi ,
> This is my first post here..so hope I am following the
> I am trying to create a Dash.app docset for biopython. Dash.app is a very
> fast documentation browser , sadly for OSX alone.
This one http://kapeli.com/dash ?
> One way to getting a docset built is to point it at sphinx documentation.
> I am using the sphinx-apidoc to auto-generate the documentation ( ver
> Sphinx can generate the documentation just fine for most of the source
How are you invoking Sphinx here? (i.e. what command line
so we can try to reproduce the problem locally)
> It has an issue with Restriction.py where it does not like cls.size.
> The error is:
> line 324, in __len__
> return cls.size
> AttributeError: type object 'RestrictionType' has no attribute 'size'
> I could cheat..and change it to "return 1" in the code and I got the
> documentation to build just fine.
The RestrictionType.__init__ documentation warns it is not
intended for direct use (see the auto-generated file
Restriction_Dictionary.py and associated magic to create
a class for each enzyme). It seems Sphinx is trying to call
the methods of the class.
> I dont know why sphinx cares about that line to throw an error ,
> or how to get around that without cheating.
I'm not sure either - there must be other strange Python
classes where __len__ doesn't work without special
initialisation. That might be worth asking on the Sphinx
> On a side note: The sphinx documentation , looks fine in a browser , but
> the dash2doc app could not index it to yield a docset. The problem was
> somehwere in the html , beautiful soup entered an infinite loop.
Could be a bug in the HTML output from sphinx, perhaps a
malformed tag from an unusual string in our comments?
> I could however use pydoctor to generate a docset. It seems
> to work OK..but while sphinx doc created 15,804 index entries.
> The pydoctor index had only around 5000 entries.
> Ref: http://kapeli.com/docsets
I don't know if those numbers should be the same, or if one
counts modules while the other counts classes/functions etc?
The HTML API docs we distribute are generated with epydoc,
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