[Biopython-dev] 1.62b test coverage report

[Eric Talevich]

On Fri, Aug 16, 2013 at 2:31 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Fri, Aug 16, 2013 at 12:44 AM, Eric Talevich wrote:
> > On Fri, Aug 2, 2013 at 2:31 AM, Peter Cock wrote:
> >> On Fri, Aug 2, 2013 at 3:20 AM, Ben Fulton wrote:
> >> > 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.
>
> Well that API break is a bit annoying, but your test changes make sense.
>
> Do we need to add these new switches to the wrapper itself?
>

Here's the commit to add those switches to the wrapper:
https://github.com/biopython/biopython/commit/cc234b75e6e82cf9f51e3384a4fbfa1e888a3af1

I suppose it would be helpful if the wrapper detected the version of Prank
and handled the show(tree|xml) flags appropriately to avoid errors. But
that would require running the executable first, I think, which is not
something our wrappers normally do. (And then it would make sense to cache
the result for the duration of the running process.)

-Eric