[med-svn] [Git][med-team/kleborate][master] 2 commits: Remove distutils to work with Python3.12

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / kleborate


Commits:
8ebe3373 by Andreas Tille at 2024-02-02T06:43:42+01:00
 Remove distutils to work with Python3.12

- - - - -
bbe4b5b4 by Andreas Tille at 2024-02-02T07:19:12+01:00
routine-update: Ready to upload to unstable

- - - - -


3 changed files:

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


Changes:

=====================================
debian/changelog
=====================================
@@ -1,12 +1,17 @@
-kleborate (2.4.1-2) UNRELEASED; urgency=medium
+kleborate (2.4.1-2) unstable; urgency=medium
 
+  [ Étienne Mollier ]
   * use_debian_installed_kaptive.patch: update.
     Remove another reference to the kaptive package in setup.py, in an
     attempt to fix build failures in particular contexts such as Salsa CI.
   * d/salsa-ci.yml: disable build on i386.
     mash is a missing dependency and not expected to make it to 32-bit.
 
- -- Étienne Mollier <emollier at debian.org>  Sat, 13 Jan 2024 18:20:25 +0100
+  [ Andreas Tille ]
+  * Remove distutils to work with Python3.12
+    Closes: #1061805
+
+ -- Andreas Tille <tille at debian.org>  Fri, 02 Feb 2024 07:05:54 +0100
 
 kleborate (2.4.1-1) unstable; urgency=medium
 


=====================================
debian/patches/python3.12.patch
=====================================
@@ -0,0 +1,35 @@
+Description: Remove distutils to work with Python3.12
+Bug-Debian: https://bugs.debian.org/1061805
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 02 Feb 2024 06:40:50 +0100
+
+--- a/kleborate/__main__.py
++++ b/kleborate/__main__.py
+@@ -13,7 +13,7 @@ not, see <http://www.gnu.org/licenses/>.
+ """
+ 
+ import argparse
+-import distutils.spawn
++import shutil
+ import gzip
+ import os
+ import pathlib
+@@ -174,14 +174,14 @@ def check_inputs_and_programs(args):
+             header, seq = record
+             if len(seq) == 0:
+                 sys.exit('Error: invalid FASTA file (contains a zero-length sequence): ' + assembly)
+-    if not distutils.spawn.find_executable('makeblastdb'):
++    if not shutil.which('makeblastdb'):
+         sys.exit('Error: could not find makeblastdb')
+-    if not distutils.spawn.find_executable('blastn'):
++    if not shutil.which('blastn'):
+         sys.exit('Error: could not find blastn')
+     if args.resistance:
+-        if not distutils.spawn.find_executable('blastx'):
++        if not shutil.which('blastx'):
+             sys.exit('Error: could not find blastx')
+-    if not distutils.spawn.find_executable('mash'):
++    if not shutil.which('mash'):
+         sys.exit('Error: could not find mash')
+     major, minor, patch = get_blast_version()
+     if major < 2 or (major == 2 and minor < 7):


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 python3.patch
 use_debian_installed_kaptive.patch
 bigendian.patch
+python3.12.patch



View it on GitLab: https://salsa.debian.org/med-team/kleborate/-/compare/c8acd73b2d35893d52b24a99d44a36cd5359770a...bbe4b5b4560fe5f4198ca57986f10b2e0a2ae886

-- 
View it on GitLab: https://salsa.debian.org/med-team/kleborate/-/compare/c8acd73b2d35893d52b24a99d44a36cd5359770a...bbe4b5b4560fe5f4198ca57986f10b2e0a2ae886
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