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

[Jeet Sukumaran]

Hi Andreas,

Sorry. it seems like this would be the best approach for now.

For the longer term, I am confident that it can be fixed, and that the 
problem is with the unicode-decoding of the file ... but without being 
able to replicate the problem, I am not sure how to fix it and test that 
it works. If you are willing for some email back and forth, we can try 
to fix it by me pushing changes to an experiemntal branch and you 
checking out the experimental branch and trying the tests. Obviously, 
there will be some trial and error here.

-- ejet

On 8/9/15 1:39 AM, Andreas Tille wrote:
> Hi Jeet,
>
> I did not received any answer from you to this mail.
>
> I'm tempted to ignore these errors for the moment and upload the package
> to Debian experimental.  It will take some time to pass the Debian new
> queue anyway.
>
> Kind regards
>
>         Andreas.
>
> On Fri, Jul 31, 2015 at 10:49:39PM +0200, Andreas Tille wrote:
>> 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/
>>> --------------------------------------
>>>
>>>
>>
>> --
>> http://fam-tille.de
>

-- 



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