Re: Strange encoding problem in setup.py of biopython 1.71
I ended up doing something similar to catch any future problematic characters: https://github.com/biopython/biopython/pull/1607 Peter On Fri, Apr 6, 2018 at 10:36 AM, Peter Cock wrote: > Thanks Andreas, > > Piotr, I think your fix would be worth including in Biopython. > > Do you want to submit this as a pull request, or give me > permission to do so by email? > > We'd need you to agree to both the Biopython License Agreement > and the 3-clause BSD licence, and say if you'd like to be > acknowledged by name or not. > > Regards, > > Peter > > On Fri, Apr 6, 2018 at 8:16 AM, Andreas Tille wrote: >> Hi Peter, >> >> On Thu, Apr 05, 2018 at 04:19:50PM +0100, Peter Cock wrote: >>> >>> https://github.com/biopython/biopython/commit/6421d365a511c0de71748737ba6e1cd8518658ac >>> >>> Can you pull in that commit as a patch for the Biopython 1.71 package? >> >> Thanks. I'm using this as patch. I can confirm that this works now >> (I'm using the other patch suggested here[1] in addition to deal with >> potential other encoding issues. >> >> I'll upload soon (I had some other issues with the packaging which are >> not related). >> >> Kind regards >> >> Andreas. >> >> >> [1] https://lists.debian.org/debian-python/2018/04/msg00023.html >> >> -- >> http://fam-tille.de
Re: Strange encoding problem in setup.py of biopython 1.71
[Peter Cock, 2018-04-06] > Piotr, I think your fix would be worth including in Biopython. > > Do you want to submit this as a pull request, or give me > permission to do so by email? go ahead > We'd need you to agree to both the Biopython License Agreement > and the 3-clause BSD licence, and say if you'd like to be > acknowledged by name or not. OK (and no need to mention my name) signature.asc Description: PGP signature
Re: Strange encoding problem in setup.py of biopython 1.71
Thanks Andreas, Piotr, I think your fix would be worth including in Biopython. Do you want to submit this as a pull request, or give me permission to do so by email? We'd need you to agree to both the Biopython License Agreement and the 3-clause BSD licence, and say if you'd like to be acknowledged by name or not. Regards, Peter On Fri, Apr 6, 2018 at 8:16 AM, Andreas Tille wrote: > Hi Peter, > > On Thu, Apr 05, 2018 at 04:19:50PM +0100, Peter Cock wrote: >> >> https://github.com/biopython/biopython/commit/6421d365a511c0de71748737ba6e1cd8518658ac >> >> Can you pull in that commit as a patch for the Biopython 1.71 package? > > Thanks. I'm using this as patch. I can confirm that this works now > (I'm using the other patch suggested here[1] in addition to deal with > potential other encoding issues. > > I'll upload soon (I had some other issues with the packaging which are > not related). > > Kind regards > > Andreas. > > > [1] https://lists.debian.org/debian-python/2018/04/msg00023.html > > -- > http://fam-tille.de
Re: Strange encoding problem in setup.py of biopython 1.71
Hi Peter, On Thu, Apr 05, 2018 at 04:19:50PM +0100, Peter Cock wrote: > > https://github.com/biopython/biopython/commit/6421d365a511c0de71748737ba6e1cd8518658ac > > Can you pull in that commit as a patch for the Biopython 1.71 package? Thanks. I'm using this as patch. I can confirm that this works now (I'm using the other patch suggested here[1] in addition to deal with potential other encoding issues. I'll upload soon (I had some other issues with the packaging which are not related). Kind regards Andreas. [1] https://lists.debian.org/debian-python/2018/04/msg00023.html -- http://fam-tille.de
Re: Strange encoding problem in setup.py of biopython 1.71
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
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
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.
>>
>
>
Re: Strange encoding problem in setup.py of biopython 1.71
On 04/05/2018 04:34 PM, 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
>>> 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?
I found none :-( but looking at file content
>
> Kind regards
>
> Andreas.
>
--
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: Strange encoding problem in setup.py of biopython 1.71
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
>>> 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.
>
Re: Strange encoding problem in setup.py of biopython 1.71
[Andreas Tille, 2018-04-05]
> Traceback (most recent call last):
> File "setup.py", line 435, in
> 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
> ...
in setup.py, if you decide to keep supporting Python 2, change lines 434-435
into:
with open("README.rst", 'rb') as handle:
readme_rst = handle.read().decode('UTF-8')
or if you finally let it go, change only line 434:
with open("README.rst", encoding='UTF-8') as handle:
--
GPG: 1D2F A898 58DA AF62 1786 2DF7 AEF6 F1A2 A745 7645
Re: Strange encoding problem in setup.py of biopython 1.71
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
> > 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.
--
http://fam-tille.de
