[Biopython-dev] Bio.Motif breaks epydoc?

[Peter]

Hi all,

I forgot to run epydoc when I did Biopython 1.50 beta, but I've just
tried and it is failing - apparently due to an issue with Bio.Motif.

First of all there are some warnings which we should probably address
now, before the Bio.Motif API is officially released:

Warning: Module Bio.Motif.AlignAceParser is shadowed by a variable with the
         same name.
Warning: Module Bio.Motif.MEMEParser is shadowed by a variable with the
         same name.
Warning: Module Bio.Motif.Motif is shadowed by a variable with the same
         name.

Ignoring these warnings for now, epydoc then crashes for me doing
Bio.Motif.Motif.Motif-class.html - which is bigger problem.  This was
using Epydoc version 3.0.1 (with python 2.6 on Ubuntu Jaunty).  I'll
try another machine tomorrow just to make sure this isn't a local
setup issue.

Also we should probably fix these "shadowing warnings", they can make
the API confusing - in addition to confusing epydoc and making the API
doc pages confusing.  GenomeDiagram is also doing this, and we should
try and fix that too:

Warning: Module Bio.Graphics.GenomeDiagram.Diagram is shadowed by a
         variable with the same name.
Warning: Module Bio.Graphics.GenomeDiagram.FeatureSet is shadowed by a
         variable with the same name.
Warning: Module Bio.Graphics.GenomeDiagram.GraphSet is shadowed by a
         variable with the same name.
Warning: Module Bio.Graphics.GenomeDiagram.Track is shadowed by a variable
         with the same name.

However it may be a bit late to fix the main source of these warnings,
Bio.PDB, without breaking things (i.e. any fix may not be backwards
compatible).  See also this thread from when I was running epydoc for
Biopython 1.49 late last year:
http://lists.open-bio.org/pipermail/biopython-dev/2008-November/004810.html

Peter