Bug#1025116: [Debian-med-packaging] Bug#1025116: python-pybedtools: (autopkgtest) needs update for python3.11: No module named 'pysam.libchtslib'

[Étienne Mollier]

Hi Andreas,

Andreas Beckmann, on 2023-01-02:
> python3-pysam is now available for python3.11, please revert the "stick
> to python3.10" changes.

Thanks for the reminder, I think I sprinkled that "fix" in a
couple of other packages, but they should crop up as I
accompanied them with a FIXME item in the control file.

Besh wishes,  :)
-- 
Étienne Mollier 
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/tty1, please excuse my verbosity.


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Bug#1025116: python-pybedtools: (autopkgtest) needs update for python3.11: No module named 'pysam.libchtslib'

[Andreas Beckmann]

Followup-For: Bug #1025116
Control: reopen -1

python3-pysam is now available for python3.11, please revert the "stick
to python3.10" changes.


Andreas

Bug#1025116: python-pybedtools: (autopkgtest) needs update for python3.11: No module named 'pysam.libchtslib'

[Paul Gevers]

Source: python-pybedtools
Version: 0.9.0-2
Severity: serious
Tags: sid bookworm
User: debian...@lists.debian.org
Usertags: needs-update
User: debian-pyt...@lists.debian.org
Usertags: python3.11
Control: affects -1 src:python3-defaults

Dear maintainer(s),

We are in the transition of adding python3.11 as a supported Python 
version [0]. With a recent upload of python3-defaults the autopkgtest of 
python-pybedtools fails in testing when that autopkgtest is run with the 
binary packages of python3-defaults from unstable. It passes when run 
with only packages from testing. In tabular form:


   passfail
python3-defaults   from testing3.10.6-3
python-pybedtools  from testing0.9.0-2
all others from testingfrom testing

I copied some of the output at the bottom of this report.

Currently this regression is blocking the migration of python3-defaults 
to testing [1]. https://docs.python.org/3/whatsnew/3.11.html lists 
what's new in Python3.11, it may help to identify what needs to be updated.


More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[0] https://bugs.debian.org/1021984
[1] https://qa.debian.org/excuses.php?package=python3-defaults

https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-pybedtools/28750381/log.gz

Testing with python3.11:
Traceback (most recent call last):
  File "", line 1, in 
  File "/usr/lib/python3/dist-packages/pybedtools/__init__.py", line 
16, in 

from . import contrib
  File "/usr/lib/python3/dist-packages/pybedtools/contrib/__init__.py", 
line 3, in 

from . import venn_maker
  File 
"/usr/lib/python3/dist-packages/pybedtools/contrib/venn_maker.py", line 
11, in 

from pybedtools import helpers
  File "/usr/lib/python3/dist-packages/pybedtools/helpers.py", line 12, 
in 

import pysam
  File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 5, in 


from pysam.libchtslib import *
ModuleNotFoundError: No module named 'pysam.libchtslib'
autopkgtest [23:15:21]: test autodep8-python3



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