[Debian-med-packaging] Some remaining test failures (Was: Please help clarifying licensed)

[Andreas Tille]

Hi,

I can confirm that Python 3.4.3 is used and that the code below does not
produce any problem.

I confirm that I totally share your consideration about the problem.

Kind regards

       Andreas.

On Fri, Jul 31, 2015 at 04:35:18PM -0400, Jeet Sukumaran wrote:
> Presumably under Python >= 3.4?
> 
> Ok, then try this:
> 
> ~~~
>     import dendropy
>     d = dendropy.StandardCharacterMatrix.get(
>             path="dendropy/test/data/chars/apternodus.chars.nexus",
>             schema="nexus")
>     print(d.as_string("nexus"))
> ~~~
> 
> Again, it seems that the common issue in all four tests is this file. The
> point of failure is specifically attempting to Unicode decode the stream of
> this file. The failure occurs at the native Python level, with a failure to
> decode a particular character. So all indications are that the file is
> mis-coded somehow.
> 
> -- jeet
> 
> On 7/31/15 4:26 PM, Andreas Tille wrote:
> >On Fri, Jul 31, 2015 at 04:09:10PM -0400, Jeet Sukumaran wrote:
> >>Sorry! Wrong filename again!
> >>
> >>	dendropy/test/data/chars/apternodus.chars.nexus
> >>
> >>Note "chars" in subpath.
> >
> >Now it can be easily read and even printed without any problem.
> >
> >Kind regards
> >
> >         Andreas.
> >
> >>-- jeet
> >>
> >>
> >>On 7/31/15 4:06 PM, Andreas Tille wrote:
> >>>On Fri, Jul 31, 2015 at 03:20:02PM -0400, Jeet Sukumaran wrote:
> >>>>Sorry, the file should be:
> >>>>
> >>>>	dendropy/test/data/trees/apternodus.chars.nexus
> >>>
> >>>Hmmm:
> >>>
> >>>    ls dendropy/test/data/trees/ap*
> >>>dendropy/test/data/trees/apternodus.tre
> >>>
> >>>also this file does not exist.  Is it possibly the result of some
> >>>processing?
> >>>
> >>>>All the errors seem to be a Unicode decoding error (at the Python level)
> >>>>while reading this particular file. Still am not sure why, but if we could
> >>>>confirm that you can reproduce the error by simply opening and trying to
> >>>>read the file in Python (i.e., without even going through DendroPy), then we
> >>>>can think about trying to recreate the data file so it will be read
> >>>>properly.
> >>>
> >>>I like this idea but somehow I need to get this file.
> >>>
> >>>Kind regards
> >>>
> >>>        Andreas.
> >>>
> >>
> >>--
> >>
> >>
> >>
> >>--------------------------------------
> >>Jeet Sukumaran
> >>--------------------------------------
> >>jeetsukumaran at gmail.com
> >>--------------------------------------
> >>Blog/Personal Pages:
> >>    http://jeetworks.org/
> >>GitHub Repositories:
> >>    http://github.com/jeetsukumaran
> >>Photographs (as stream):
> >>    http://www.flickr.com/photos/jeetsukumaran/
> >>Photographs (by galleries):
> >>    http://www.flickr.com/photos/jeetsukumaran/sets/
> >>--------------------------------------
> >>
> >>
> >
> 
> -- 
> 
> 
> 
> --------------------------------------
> Jeet Sukumaran
> --------------------------------------
> jeetsukumaran at gmail.com
> --------------------------------------
> Blog/Personal Pages:
>    http://jeetworks.org/
> GitHub Repositories:
>    http://github.com/jeetsukumaran
> Photographs (as stream):
>    http://www.flickr.com/photos/jeetsukumaran/
> Photographs (by galleries):
>    http://www.flickr.com/photos/jeetsukumaran/sets/
> --------------------------------------
> 
> 

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