[med-svn] [Git][med-team/iva][master] 4 commits: Python3.12 compatibility by avoiding usage of distutils

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / iva


Commits:
e423cca2 by Andreas Tille at 2024-02-01T13:33:56+01:00
Python3.12 compatibility by avoiding usage of distutils

- - - - -
5e931208 by Andreas Tille at 2024-02-01T13:34:42+01:00
routine-update: Build-Depends: s/dh-python/dh-sequence-python3/

- - - - -
e4d4df67 by Andreas Tille at 2024-02-01T13:34:44+01:00
Remove patch reduce-ram.patch that is missing from debian/patches/series.

Changes-By: lintian-brush
Fixes: lintian: patch-file-present-but-not-mentioned-in-series
See-also: https://lintian.debian.org/tags/patch-file-present-but-not-mentioned-in-series.html

- - - - -
9a12b109 by Andreas Tille at 2024-02-01T13:42:46+01:00
routine-update: Ready to upload to unstable

- - - - -


6 changed files:

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


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+iva (1.0.11+ds-5) unstable; urgency=medium
+
+  * Python3.12 compatibility by avoiding usage of distutils
+    Closes: #1061804
+  * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
+  Remove patch reduce-ram.patch that is missing from debian/patches/series.
+
+ -- Andreas Tille <tille at debian.org>  Thu, 01 Feb 2024 13:34:57 +0100
+
 iva (1.0.11+ds-4) unstable; urgency=medium
 
   * Enable building twice in a row.


=====================================
debian/control
=====================================
@@ -6,11 +6,11 @@ Uploaders: Andreas Tille <tille at debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
-               dh-python,
+               dh-sequence-python3,
                libssl-dev,
                bioperl,
                fastaq,
-               kmc (>= 3.1),
+               kmc,
                help2man,
                mummer,
                python3,


=====================================
debian/patches/python3.12.patch
=====================================
@@ -0,0 +1,16 @@
+Description: Python3.12 compatibility by avoiding usage of distutils
+Bug-Debian: https://bugs.debian.org/1061804
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 01 Feb 2024 13:32:00 +0100
+
+--- a/iva/external_progs.py
++++ b/iva/external_progs.py
+@@ -16,7 +16,7 @@ import shutil
+ import subprocess
+ import re
+ import sys
+-from distutils.version import LooseVersion
++from packaging.version import Version as LooseVersion
+ import pyfastaq
+ from iva import common
+ 


=====================================
debian/patches/reduce-ram.patch deleted
=====================================
@@ -1,13 +0,0 @@
---- a/iva/kcount.py
-+++ b/iva/kcount.py
-@@ -111,6 +111,10 @@
-         if verbose:
-             print('First try of running kmc failed. Trying again with -m4 instead of -m32...', flush=True)
-         ran_ok = _run_kmc_with_script('run_kmc.sh', reads, kmer_counts_file, kmer, min_count, max_count, 4, verbose, False, threads=threads)
-+        if not ran_ok:
-+            if verbose:
-+                print('Second try of running kmc failed. Trying again with -m2 instead of -m4...', flush=True)
-+            ran_ok = _run_kmc_with_script('run_kmc.sh', reads, kmer_counts_file, kmer, min_count, max_count, 2, verbose, False, threads=threads)
- 
-     os.chdir(original_dir)
-     shutil.rmtree(tmpdir)


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ disable-multithreaded-test.patch
 perl-shebang.patch
 samtools1.10
 disable-ram-test.patch
+python3.12.patch


=====================================
debian/rules
=====================================
@@ -10,7 +10,7 @@ gage_dir := $(CURDIR)/iva/gage
 ratt_dir := $(CURDIR)/iva/ratt
 
 %:
-	dh $@ --with python3 --buildsystem=pybuild
+	dh $@ --buildsystem=pybuild
 
 override_dh_auto_build:
 	chmod a-x $(read_trim_dir)/adapters.fasta



View it on GitLab: https://salsa.debian.org/med-team/iva/-/compare/ba7045a3e74e1ad521ede6b6feea3607677a7c23...9a12b109d031b5406f552d3fe89dfff45ceafdc1

-- 
View it on GitLab: https://salsa.debian.org/med-team/iva/-/compare/ba7045a3e74e1ad521ede6b6feea3607677a7c23...9a12b109d031b5406f552d3fe89dfff45ceafdc1
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