Package: apbs Version: 3.4.1-4 Severity: grave Tags: patch Justification: renders package unusable User: ubuntu-de...@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/ slanga...@ubuntu.com vor...@debian.org
diff -Nru apbs-3.4.1/debian/patches/open-U-obsolete.patch apbs-3.4.1/debian/patches/open-U-obsolete.patch --- apbs-3.4.1/debian/patches/open-U-obsolete.patch 1969-12-31 16:00:00.000000000 -0800 +++ apbs-3.4.1/debian/patches/open-U-obsolete.patch 2023-01-09 13:27:36.000000000 -0800 @@ -0,0 +1,21 @@ +Description: Drop obsolete "U" mode passed to open() + The "U" mode has been deprecated in python since python3 and has had no + effect. In python 3.11, it is now disallowed. Drop this mode flag that + causes runtime failures. +Author: Steve Langasek <steve.langa...@ubuntu.com> +Last-Update: 2023-01-09 +Forwarded: no + +Index: apbs-3.4.1/tools/manip/inputgen.py +=================================================================== +--- apbs-3.4.1.orig/tools/manip/inputgen.py ++++ apbs-3.4.1/tools/manip/inputgen.py +@@ -311,7 +311,7 @@ + file (string) + """ + nproc = 0 +- file = open(filename, "rU") ++ file = open(filename, "r") + text = "" + while 1: + line = file.readline() diff -Nru apbs-3.4.1/debian/patches/series apbs-3.4.1/debian/patches/series --- apbs-3.4.1/debian/patches/series 2022-06-04 00:58:09.000000000 -0700 +++ apbs-3.4.1/debian/patches/series 2023-01-09 13:26:06.000000000 -0800 @@ -5,3 +5,4 @@ python3.patch cmake.patch docs.patch +open-U-obsolete.patch
