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

[Jeet Sukumaran]

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/
--------------------------------------