[Debian-med-packaging] Bug#1093231: python-pbcommand: unable to import pbcommand with python 3.13

[Vladimir Petko]

Package: python-pbcommand
Version: 2.1.1+git20220616.3f2e6c2-3
Severity: important
Tags: patch
User: ubuntu-devel at lists.ubuntu.com
Usertags: origin-ubuntu plucky ubuntu-patch

Dear Maintainer,

Adding a simple autopkgtest `python -c "import pbcommand"` fails with the
following error:

autopkgtest [10:41:25]: test command1: python3 -c "import pbcommand"
autopkgtest [10:41:25]: test command1: [-----------------------
Traceback (most recent call last):
  File "<string>", line 1, in <module>
    import pbcommand
  File "/tmp/autopkgtest.Lo75OZ/build.glM/real-tree/pbcommand/__init__.py",
line 1, in <module>
    import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
autopkgtest [10:41:26]: test command1: -----------------------]

This is due to python 3.12 removing setuptools from the default installation.

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

  * d/p/remove-pkg-resources.patch: replace the usages of pkg_resources
    with importlib.resources for Python 3.13 compatibility (LP: #2095045).
  * d/t/control: add smoke test.


Thanks for considering the patch.


-- System Information:
Debian Release: trixie/sid
  APT prefers oracular-updates
  APT policy: (500, 'oracular-updates'), (500, 'oracular-security'), (500, 'oracular'), (100, 'oracular-backports')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 6.11.0-13-generic (SMP w/32 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_WARN, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
-------------- next part --------------
diff -Nru python-pbcommand-2.1.1+git20220616.3f2e6c2/debian/patches/remove-pkg-resources.patch python-pbcommand-2.1.1+git20220616.3f2e6c2/debian/patches/remove-pkg-resources.patch
--- python-pbcommand-2.1.1+git20220616.3f2e6c2/debian/patches/remove-pkg-resources.patch	1970-01-01 12:00:00.000000000 +1200
+++ python-pbcommand-2.1.1+git20220616.3f2e6c2/debian/patches/remove-pkg-resources.patch	2025-01-16 11:00:11.000000000 +1300
@@ -0,0 +1,24 @@
+Description: Remove usages of pkg_resources
+ pkg_resources are no longer available in Python 3.12 due to setuptools
+ removal from the default installation. This patch replaces the usages of
+ pkg_resources with importlib.resources.
+Author: Vladimir Petko <vladimir.petko at canonical.com>
+Bug: https://github.com/PacificBiosciences/pbcommand/pull/191
+Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/python-pbcommand/+bug/2095045
+Last-Update: 2025-01-16
+
+--- a/pbcommand/__init__.py
++++ b/pbcommand/__init__.py
+@@ -1,9 +1,9 @@
+-import pkg_resources
++from importlib.metadata import Distribution, PackageNotFoundError
+ import sys
+
+ try:
+-    __VERSION__ = pkg_resources.get_distribution('pbcommand').version
+-except Exception:
++    __VERSION__ = Distribution.from_name('pbcommand').version
++except PackageNotFoundError:
+     __VERSION__ = '2.4.0'
+
+ VERSION = (int(x) for x in __VERSION__.split('.'))
diff -Nru python-pbcommand-2.1.1+git20220616.3f2e6c2/debian/patches/series python-pbcommand-2.1.1+git20220616.3f2e6c2/debian/patches/series
--- python-pbcommand-2.1.1+git20220616.3f2e6c2/debian/patches/series	2024-03-23 06:58:36.000000000 +1300
+++ python-pbcommand-2.1.1+git20220616.3f2e6c2/debian/patches/series	2025-01-16 11:00:11.000000000 +1300
@@ -1,2 +1,3 @@
 python3.patch
 fix_version.patch
+remove-pkg-resources.patch
diff -Nru python-pbcommand-2.1.1+git20220616.3f2e6c2/debian/tests/control python-pbcommand-2.1.1+git20220616.3f2e6c2/debian/tests/control
--- python-pbcommand-2.1.1+git20220616.3f2e6c2/debian/tests/control	2024-03-23 06:58:36.000000000 +1300
+++ python-pbcommand-2.1.1+git20220616.3f2e6c2/debian/tests/control	2025-01-16 11:00:11.000000000 +1300
@@ -1,3 +1,7 @@
 Tests: run-unit-test
 Depends: @, python3-pytest, python3-pytest-xdist, python3-pytest-cov, python3-pbcore
 Restrictions: allow-stderr, skip-not-installable
+
+Test-Command: python3 -c "import pbcommand"
+Depends: @
+Restrictions: allow-stderr, skip-not-installable