[Biopython-dev] 1.62b test coverage report

[Peter Cock]

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?

Peter