[Debian-med-packaging] Bug#1055687: khmer ftbfs with Python 3.12

[Olivier Gayot]

Package: khmer
Followup-For: Bug #1055687
User: ubuntu-devel at lists.ubuntu.com
Usertags: origin-ubuntu noble ubuntu-patch
Control: tags -1 patch

Dear Maintainer,

In Ubuntu, the attached patch was applied to achieve the following:

  * Fix build against Python 3.12 (LP: #2044383).


Thanks for considering the patch.


-- System Information:
Debian Release: trixie/sid
  APT prefers mantic-updates
  APT policy: (500, 'mantic-updates'), (500, 'mantic-security'), (500, 'mantic')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 6.1.0-16-generic (SMP w/8 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
-------------- next part --------------
diff -Nru khmer-3.0.0~a3+dfsg/debian/patches/python3.12-support.patch khmer-3.0.0~a3+dfsg/debian/patches/python3.12-support.patch
--- khmer-3.0.0~a3+dfsg/debian/patches/python3.12-support.patch	1970-01-01 01:00:00.000000000 +0100
+++ khmer-3.0.0~a3+dfsg/debian/patches/python3.12-support.patch	2023-11-23 15:24:51.000000000 +0100
@@ -0,0 +1,24 @@
+Description: Add support for Python 3.12
+ Ever since Python 3.2, configparser.SafeConfigParser has been deprecated in
+ favor of configparser.ConfigParser. An alias existed for backward compability
+ but the alias was dropped from Python 3.12.
+Author: Olivier Gayot <olivier.gayot at canonical.com>
+Bug-Ubuntu: https://launchpad.net/bugs/2044383
+Bug-Debian: https://bugs.debian.org/1055687
+Forwarded: https://github.com/dib-lab/khmer/pull/1922
+Last-Update: 2023-11-23
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+Index: khmer-3.0.0~a3+dfsg/versioneer.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/versioneer.py	2019-03-13 14:42:12.000000000 +0100
++++ khmer-3.0.0~a3+dfsg/versioneer.py	2023-11-23 15:19:50.025827413 +0100
+@@ -339,7 +339,7 @@
+     # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
+     # the top of versioneer.py for instructions on writing your setup.cfg .
+     setup_cfg = os.path.join(root, "setup.cfg")
+-    parser = configparser.SafeConfigParser()
++    parser = configparser.ConfigParser()
+     with open(setup_cfg, "r") as f:
+         parser.readfp(f)
+     VCS = parser.get("versioneer", "VCS")  # mandatory
diff -Nru khmer-3.0.0~a3+dfsg/debian/patches/series khmer-3.0.0~a3+dfsg/debian/patches/series
--- khmer-3.0.0~a3+dfsg/debian/patches/series	2023-09-09 08:30:33.000000000 +0200
+++ khmer-3.0.0~a3+dfsg/debian/patches/series	2023-11-23 15:19:31.000000000 +0100
@@ -17,3 +17,4 @@
 stringio-buffer.patch
 refresh_cython
 find_object_files_at_right_loc.patch
+python3.12-support.patch