[Biopython-dev] Running pylint over Biopython

[Eric Talevich]

2010/2/23 Peter <biopython at maubp.freeserve.co.uk>

> Hi all,
>
> Those following @Biopython on twitter or subscribed to the github RSS
> feed for our repository will know this already, but I've been using
> pylint today to spot some errors in Biopython.
> http://www.logilab.org/project/pylint
>
> This was prompted by Eric trying this on Bio.PDB for Bug 3013 and
> finding some issues - thank Eric, this was a valuable suggestion.
>
> Glad I could help. :)


> Eric, I don't have all the dependencies installed by pylint does
> appear to dislike a few things in Bio.Phylo on the trunk:
>

Pylint hates the way I wrote Bio.Phylo, in particular the way TreeMixin
assumes it will be mixed with a class that has 'root' and 'is_terminal'
attributes, and the __dict__ hack in the PhyloXML class __init__ methods --
it can't figure out where the attributes are coming from.

The last error was real, and I've pushed a fix to the trunk. Thanks for
catching it.

One thing this exercise has shown is that we still need to do some
> work on the unit test coverage.
>

Agreed. I also added a unit test for get_alignment (finally), and should get
to TreeMixin.prune and .split soon. Then Bio.Phylo will have essentially
100% unit test coverage.

Cheers
-Eric