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Re: Strange encoding problem in setup.py of biopython 1.71

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Confirmed - not sure if my earlier email made it?

https://github.com/biopython/biopython/commit/6421d365a511c0de71748737ba6e1cd8518658ac

Can you pull in that commit as a patch for the Biopython 1.71 package?

Peter

On Thu, Apr 5, 2018 at 3:39 PM, Klaus Zimmermann
<klaus_zimmermann@gmx.de> wrote:
> Hi Andreas,
>
> here, the culprit is
> U+2019 : RIGHT SINGLE QUOTATION MARK {single comma quotation mark}
> that is used as an apostrophe in two places in "Apple's".
>
> I found this by looking for 0xe2 (from your error message) in an hexdump
> (od -A d -xc README.rst |less ) at the named position (7116).
>
> Cheers
> Klaus
>
>
> On 05/04/18 16:34, Andreas Tille wrote:
>> Hi Olivier,
>>
>> On Thu, Apr 05, 2018 at 04:19:37PM +0200, Olivier Sallou wrote:
>>>
>>> On 04/05/2018 04:10 PM, Andreas Tille wrote:
>>>> (maybe?) setup.py:
>>>>
>>>>
>>>> ...
>>>> dh_auto_clean
>>>>         pybuild --clean -i python{version} -p 2.7
>>>> I: pybuild base:217: python2.7 setup.py clean
>>>> running clean
>>>> removing '/home/andreas/debian-maintain/salsa/med-team/build-area/python-biopython-1.71+dfsg/.pybuild/cpython2_2.7/build' (and everything under it)
>>>> 'build/bdist.linux-x86_64' does not exist -- can't clean it
>>>> 'build/scripts-2.7' does not exist -- can't clean it
>>>>         pybuild --clean -i python{version} -p 3.6
>>>> I: pybuild base:217: python3.6 setup.py clean
>>>> Traceback (most recent call last):
>>>>   File "setup.py", line 435, in <module>
>>>>     readme_rst = handle.read()
>>>>   File "/usr/lib/python3.6/encodings/ascii.py", line 26, in decode
>>>>     return codecs.ascii_decode(input, self.errors)[0]
>>>> UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 7116: ordinal not in range(128)
>>>> E: pybuild pybuild:336: clean: plugin distutils failed with: exit code=1: python3.6 setup.py clean
>>>> dh_auto_clean: pybuild --clean -i python{version} -p 3.6 returned exit code 13
>>> this is usually related to non ascii characters in file (readme.rst?) ,
>>> if you find some, you can patch file to remove them.
>>
>> Is there any efficient method to seek for this kind of non-ascii
>> characters?
>>
>> Kind regards
>>
>>       Andreas.
>>
>
>

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Strange encoding problem in setup.py of biopython 1.71 Andreas Tille <andreas@an3as.eu> - 2018-04-05 16:20 +0200
  Re: Strange encoding problem in setup.py of biopython 1.71 Piotr Ożarowski <piotr@debian.org> - 2018-04-05 16:40 +0200
  Re: Strange encoding problem in setup.py of biopython 1.71 Andreas Tille <andreas@an3as.eu> - 2018-04-05 16:40 +0200
    Re: Strange encoding problem in setup.py of biopython 1.71 Klaus Zimmermann <klaus_zimmermann@gmx.de> - 2018-04-05 16:50 +0200
      Re: Strange encoding problem in setup.py of biopython 1.71 Peter Cock <p.j.a.cock@googlemail.com> - 2018-04-05 17:30 +0200
        Re: Strange encoding problem in setup.py of biopython 1.71 Andreas Tille <tille@debian.org> - 2018-04-06 09:20 +0200
          Re: Strange encoding problem in setup.py of biopython 1.71 Peter Cock <p.j.a.cock@googlemail.com> - 2018-04-06 11:40 +0200
            Re: Strange encoding problem in setup.py of biopython 1.71 Piotr Ożarowski <piotr@debian.org> - 2018-04-07 00:00 +0200
            Re: Strange encoding problem in setup.py of biopython 1.71 Peter Cock <p.j.a.cock@googlemail.com> - 2018-04-13 13:20 +0200
    Re: Strange encoding problem in setup.py of biopython 1.71 Olivier Sallou <olivier.sallou@irisa.fr> - 2018-04-05 16:50 +0200

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