Bug#1028354: apbs fails with python3.11: "invalid mode rU"

[Steve Langasek]

Package: apbs
Version: 3.4.1-4
Severity: grave
Tags: patch
Justification: renders package unusable
User: ubuntu...@lists.ubuntu.com
Usertags: origin-ubuntu lunar ubuntu-patch

apbs fails its autopkgtests with python3.11, revealing a bug in the
software, because it uses a mode flag to open() which has been deprecated
since python 3 and is now obsolete in python 3.11:

[...]
--------------------------------------------------------------------------------
Testing input file apbs-mol-parallel.in

Splitting the input file into 4 separate files using the inputgen utility

Test failed: invalid mode: 'rU'
Elapsed time: 0.000597 seconds
--------------------------------------------------------------------------------
[...]

(https://autopkgtest.ubuntu.com/results/autopkgtest-lunar/lunar/amd64/a/apbs/20221229_092334_1918a@/log.gz)

This is not an autopkgtest regression in Debian because the autopkgtest
itself is also buggy, using bash-specific shell syntax in a file with no
interpreter line that as a result fails under /bin/sh. (I'm not sure why it
gets farther on Ubuntu's autopkgtest infrastructure.) However, despite not
being detected as an autopkgtest regression, it shows a significant code
defect when run under python3.11 and should be fixed.

Please see the attached patch.

Thanks for considering,
--
Steve Langasek Give me a lever long enough and a Free OS
Debian Developer to set it on, and I can move the world.
Ubuntu Developer https://www.debian.org/
slan...@ubuntu.com vor...@debian.org