[Biopython-dev] Bio.Motif breaks epydoc?

[Bartek Wilczynski]

Hi,

I'm working on Bio.Motif to fix this. I'll send a patch later today.

cheers
Bartek

On Wed, Apr 15, 2009 at 1:34 AM, Peter <peter at maubp.freeserve.co.uk> wrote:
> 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
>



-- 
Bartek Wilczynski
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EMBL, Furlong group
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