[Biopython-dev] Bio.Motif breaks epydoc?

[Peter]

On Wed, Apr 15, 2009 at 12:34 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 [...]
> 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.

The shadowing issue with GenomeDiagram should be OK in CVS now - this was
an accidental side effect of renaming the internal modules as part of
integrating
GenomeDiagram into Biopython.  I discussed this with Leighton (off list) and we
agreed that renaming the modules with the simplest solution, and opted
for adding
an underscore which makes it explicit that the modules concerned are intended to
be private.  This doesn't affect the (intended) public API for GenomeDiagram.

Peter