[med-svn] [Git][med-team/ariba][master] 3 commits: Fix autopkgtest by replacing distutils

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / ariba


Commits:
3b8244cc by Andreas Tille at 2024-02-01T09:13:54+01:00
Fix autopkgtest by replacing distutils

- - - - -
1a06319a by Andreas Tille at 2024-02-01T09:14:20+01:00
routine-update: Build-Depends: s/dh-python/dh-sequence-python3/

- - - - -
04148719 by Andreas Tille at 2024-02-01T12:00:11+01:00
Correct fix for Python3.12

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/python3.12.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+ariba (2.14.7+ds-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Fix autopkgtest by replacing distutils
+    Closes: #1061784
+  * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
+
+ -- Andreas Tille <tille at debian.org>  Thu, 01 Feb 2024 09:12:26 +0100
+
 ariba (2.14.7+ds-1) unstable; urgency=medium
 
   * New upstream version 2.14.7+ds


=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Uploaders: Sascha Steinbiss <satta at debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
-               dh-python,
+               dh-sequence-python3,
                python3-biopython,
                python3-all-dev,
                python3-dendropy,


=====================================
debian/patches/python3.12.patch
=====================================
@@ -0,0 +1,54 @@
+Description: Fix autopkgtest by replacing distutils
+Bug-Debian: https://bugs.debian.org/1061784
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 01 Feb 2024 09:12:26 +0100
+
+--- a/ariba/external_progs.py
++++ b/ariba/external_progs.py
+@@ -1,7 +1,7 @@
+ import shutil
+ import subprocess
+ import os
+-from distutils.version import LooseVersion
++from packaging.version import Version as LooseVersion
+ import re
+ import sys
+ from ariba import common
+--- a/ariba/mapping.py
++++ b/ariba/mapping.py
+@@ -1,6 +1,6 @@
+ import os
+ import sys
+-from distutils.version import LooseVersion
++from packaging.version import Version as LooseVersion
+ import pysam
+ import pyfastaq
+ from ariba import common
+--- a/ariba/megares_data_finder.py
++++ b/ariba/megares_data_finder.py
+@@ -1,6 +1,6 @@
+ import urllib.request
+ from bs4 import BeautifulSoup
+-from distutils.version import LooseVersion
++from packaging.version import Version as LooseVersion
+ 
+ 
+ class Error (Exception): pass
+--- a/ariba/versions.py
++++ b/ariba/versions.py
+@@ -1,5 +1,5 @@
+ import sys
+-from distutils.version import LooseVersion
++from packaging.version import Version as LooseVersion
+ from ariba import external_progs
+ from ariba import __version__ as ariba_version
+ 
+@@ -43,7 +43,7 @@ def get_all_versions(raise_error=True, u
+             python_packages_ok = False
+ 
+         if version != 'NOT_FOUND':
+-            if package in package_min_versions and LooseVersion(version) < package_min_versions[package]:
++            if package in package_min_versions and LooseVersion(version) < LooseVersion(package_min_versions[package]):
+                 version += '... THIS IS TOO LOW. Needs>=' + package_min_versions[package]
+                 python_packages_ok = False
+             elif package in package_max_versions and LooseVersion(version) > package_max_versions[package]:


=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ add-testdata.patch
 disable-tests-with-internet-access.patch
 support-pymummer-0.11.patch
 run-debian-spades-wrapper.patch
+python3.12.patch


=====================================
debian/rules
=====================================
@@ -7,7 +7,7 @@ mandir := $(CURDIR)/debian/man
 debfolder := $(CURDIR)/debian
 
 %:
-	dh $@ --with python3 --buildsystem=pybuild
+	dh $@ --buildsystem=pybuild
 
 override_dh_auto_clean:
 	rm -rf $(mandir)



View it on GitLab: https://salsa.debian.org/med-team/ariba/-/compare/ecb9b56fa137953bd658c15dfb2ee9622d2dc8a8...04148719f98f5324bfd6526f5e59806b686124c8

-- 
View it on GitLab: https://salsa.debian.org/med-team/ariba/-/compare/ecb9b56fa137953bd658c15dfb2ee9622d2dc8a8...04148719f98f5324bfd6526f5e59806b686124c8
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