+1 maintenance report

[Alexandre Ghiti]

Hi,

I was on +1 maintenance last week and I focused on python3-defaults regressions:

libapache2-mod-python
-------------------------------

This package must be adapted to support python 3.10, patches can be
found here https://bugs.launchpad.net/ubuntu/+source/libapache2-mod-python/+bug/1960088
However, as I explained in the above bug report (and was already
mentioned by the author), a segfault is triggered when we use the
buffer returned by PyArg_ParseTuple.

pytest
--------

Upstream patches were necessary to support 3.10 which allowed
re-enable tests that were removed (thanks to Graham)
Graham uploaded this new version and that fixed autopkgtests.

pytest-mpi
--------------

No problem with this package, simply a python deprecation warning that
is output to stderr which makes autopkgtest fail: I fixed this warning
in the tox package by simply replacing distutils.sysconfig with
sysconfig.
Graham uploaded this new version and that fixed autopkgtests.

pytest-skip-markers
--------------------------

Autopkgtests fails because of pyfakefs usage of _from_parts which
prototype is different in python 3.10: I struggled to cherry-pick
upstream patches to fix in pyfakefs package so I bumped it to version
4.5.4 and that was merged in debian by Graham.
This package synced to Ubuntu and that fixed autopkgtests.

python-dugong
--------------------

One test timeout on ppc64el: I was able to reproduce the problem
locally in a VM but not to fix it.

python-ml-collection
---------------------------

Simple fix to support python 3.10 which consisted in changing
'collections' to 'collections.abc'.
Graham uploaded this new version and that fixed autopkgtests.

python-pip
--------------

Against python 3.10, python-pip installs packages in the wrong
directory: it is installed
/usr/lib/python3.10/site-packages/world-4.1.1.dist-info whereas it is
expected to be in /usr/local/lib/python3.10/dist-packages/. A bug
report can be found here:
https://bugs.launchpad.net/ubuntu/+source/python-pip/+bug/1960608
@stefanor advised to enable a patch that was currently disabled in
python 3.10:  I rebased it and it's currently building in my PPA. I'll
keep @doko and @stefanor posted if that fixes the problem.

q2-demux
--------------

Simply a retrigger on the new version from debian, thanks Graham.

q2-cli
-------

This package is not compatible with python-click >= 8 and was asked
for removal by Graham (it was already removed in debian):
https://bugs.launchpad.net/ubuntu/+source/q2cli/+bug/1960593

shasta
---------

New version 0.8.0-1 fails because the autopkgtest VM is too 'small': I
added it to the list of big_packages, it was merged by Brian Murray
and we should retrigger its build soon. But that may not pass since in
Debian, peak memory usage showed > 9GB.
https://ci.debian.net/data/autopkgtest/testing/amd64/s/shasta/19119761/log.gz

toil
----

upstream toil does not seem to support python 3.10 yet:
https://github.com/DataBiosphere/toil/pull/3967

typer
-------

It fails autopkgtest because of DeprecationWarning on stderr from
pytest-sugar: I fixed those warnings in pytest-sugar.
Graham uploaded this new version and that fixed autopkgtests.

unicycler
------------

It fails autopkgtest because of DeprecationWarning on stderr from
spades: I fixed spades but I'm waiting for upstream feedback to make
sure the fix is ok https://github.com/ablab/spades/pull/914

Thanks,

Alex