Re: setup.py sdist permissions
Robert Collins writes: > Yah, packaging permissions are an installation problem, and setup.py > is (no longer) intended for installation. Thanks, that is what I thought too. Have followed up in the bug report. -- Brian May
Strange encoding problem in setup.py of biopython 1.71
Hi,
I imported BioPython version 1.71 into the packaging Git[1] and tried to
build it. Unfortunately I'm stumbling upon some encoding problem in
(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
...
I admit I have no idea how to fix this. Any idea?
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/python-biopython
--
http://fam-tille.de
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
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: [DPMT] Interested to joining the team
[T K Sourabh, 2018-03-28] > I am interested in contributing to python modules for Debian. Happy to help. > > Why you want to join the team: > I want to help in contributing to packaging python module. > > Your Alioth login: > sourabhtk37-guest > > I have read https://python-modules.alioth.debian.org/policy.html and accept > it. welcome :) -- GPG: 1D2F A898 58DA AF62 1786 2DF7 AEF6 F1A2 A745 7645
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: Requesting team membership for DPMT on Salsa
[Andreas Tille, 2018-03-28] > I failed to find a button to ask for membership in the Salsa web let me know if you find it (bonus points for also letting me know how to disable it) > interface for DPMT. Please add me since I contributed to some python-* > packages in the past and would like to keep on contributing. :-) > > It would be nice if the permissions would enable me creating new > projects. done :) -- GPG: 1D2F A898 58DA AF62 1786 2DF7 AEF6 F1A2 A745 7645
Re: Please add me on Salsa
Hi Nikolaus, [Nikolaus Rath, 2018-04-03] > Could someone please add me to the DPMT and DPAP teams on Salsa? My > Alioth and Salsa username is nikratio-guest. what do you think about our policy and on which packages do you want to work with us? -- GPG: 1D2F A898 58DA AF62 1786 2DF7 AEF6 F1A2 A745 7645
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: packages that use dh_python{2,3} but don't depend on dh-python
On Mon, Mar 26, 2018 at 01:32:10PM +0200, Piotr Ożarowski wrote: > http://people.debian.org/~piotr/dh_python3_without_dh-python.ddlist I've fixed Andreas Tille iva (U) kissplice (U) python-biopython (U) [ only in Git due to some other issues ] python-csb (U) sphinxcontrib-autoprogram (U) > http://people.debian.org/~piotr/dh_python2_without_dh-python.ddlist I'll work on this step by step to safe you from filing bug reports. Kind regards Andreas. -- http://fam-tille.de
Re: Requesting team membership for DPMT on Salsa
On Thu, Apr 05, 2018 at 04:40:44PM +0200, Piotr Ożarowski wrote: > [Andreas Tille, 2018-03-28] > > I failed to find a button to ask for membership in the Salsa web > > let me know if you find it (bonus points for also letting me know how to > disable it) May be it is just disabled? > > interface for DPMT. Please add me since I contributed to some python-* > > packages in the past and would like to keep on contributing. :-) > > > > It would be nice if the permissions would enable me creating new > > projects. > > done :) Thanks Andreas. -- http://fam-tille.de
Re: Requesting team membership for DPMT on Salsa
On 18-04-05 16:53:36, Andreas Tille wrote: > On Thu, Apr 05, 2018 at 04:40:44PM +0200, Piotr Ożarowski wrote: > > [Andreas Tille, 2018-03-28] > > > I failed to find a button to ask for membership in the Salsa web > > > > let me know if you find it (bonus points for also letting me know how to > > disable it) > > May be it is just disabled? If you want to make sure: Check the group settings, especially "Allow users to request access." Cheers, Georg signature.asc Description: Digital signature
Re: Requesting team membership for DPMT on Salsa
[Andreas Tille, 2018-04-05] > On Thu, Apr 05, 2018 at 04:40:44PM +0200, Piotr Ożarowski wrote: > > [Andreas Tille, 2018-03-28] > > > I failed to find a button to ask for membership in the Salsa web > > > > let me know if you find it (bonus points for also letting me know how to > > disable it) > > May be it is just disabled? FTR (if it wasn't clear) I want it disabled! I want all join requests to go to this list so that other team members can raise their concerns. -- GPG: 1D2F A898 58DA AF62 1786 2DF7 AEF6 F1A2 A745 7645
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: Please add me on Salsa
On Apr 05 2018, Piotr Ożarowski wrote: > Hi Nikolaus, > > [Nikolaus Rath, 2018-04-03] >> Could someone please add me to the DPMT and DPAP teams on Salsa? My >> Alioth and Salsa username is nikratio-guest. > > what do you think about our policy and on which packages do you want to > work with us? Huh? I have been member of the team for a few years already, I'm just not registered on Salsa yet (as far as I know Alioth memberships don't transfer automatically). But yeah, I am still committed to abide by the policy, and I am maintaining the python-llfuse and python-dugong packages. Best, -Nikolaus -- GPG Fingerprint: ED31 791B 2C5C 1613 AF38 8B8A D113 FCAC 3C4E 599F »Time flies like an arrow, fruit flies like a Banana.« signature.asc Description: PGP signature
Re: Please add me on Salsa
[Nikolaus Rath, 2018-04-05] > Huh? I have been member of the team for a few years already, I'm just > not registered on Salsa yet (as far as I know Alioth memberships don't > transfer automatically). ah, sorry, I didn't check alioth. You're now also a member on salsa. BTW, there's no need to send an email to the mailing list, if someone was a member on alioth, just send me private email or a message on IRC. -- GPG: 1D2F A898 58DA AF62 1786 2DF7 AEF6 F1A2 A745 7645
new DPMT / PAPT admin
Hi, We don't have a procedure to select a new admin (or terms / rotations unfortunately) so if you want to blame current admins for this, Ondřej Nový will share the blame now :) -- GPG: 1D2F A898 58DA AF62 1786 2DF7 AEF6 F1A2 A745 7645 signature.asc Description: PGP signature
