[Biopython-dev] 1.62b test coverage report

[Eric Talevich]

On Fri, Aug 2, 2013 at 2:31 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> Thanks for these details Ben - it sounds like a mixture of real
> test failures, and mere warnings that an external tool wasn't
> found.
>
> On Fri, Aug 2, 2013 at 3:20 AM, Ben Fulton <ben at benfulton.net> wrote:
> > My test machine was running Ubuntu 12.04.
>
[...]
> > I downloaded version 130708 of Prank from
> > http://code.google.com/p/prank-msa/downloads/list. The error is on line
> 165
> > of the test file:
> >
> > AssertionError:
> > -----------------
> >  PRANK v.130708:
> > -----------------
> >
> > Input for the analysis
> >  - converting 'Quality/example.fasta' to 'temp with space.phy'
>
> This sounds like a minor change in the stdout with recent
> versions of PRANK.
>
>
It's more exciting than that: Old versions of Prank created .xml and .dnd
files by default, and had "-noxml" and "-notree" options to avoid creating
them (or clean them up, whichever). New Pranks do not create these files by
default, but do have "-showxml" and "-showtree" flags if you want them.

I removed the use of these flags in the unit test. One of the tests used
the set_parameter method, so I substituted the "-dots" flag for "-notree".
It passes on my machine now:
https://github.com/biopython/biopython/commit/30d7bcfb6eab8283a53372b2ad64b59be7461eb3

The doctests in Bio/Align/Applications/_Prank.py should probably change,
too, since the same flags are used there. (I have not done this.)

-Eric