[med-svn] [Git][med-team/mcaller][master] 4 commits: d/watch: version=5

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / mcaller


Commits:
1e892d3c by Andreas Tille at 2026-06-30T21:51:55+02:00
d/watch: version=5

- - - - -
400c7252 by Andreas Tille at 2026-06-30T20:52:11+01:00
Remove redundant Priority: optional from source stanza.

Changes-By: lintian-brush
Fixes: lintian: source: redundant-priority-optional-field
See-also: https://lintian.debian.org/tags/redundant-priority-optional-field.html

- - - - -
a5d54f39 by Andreas Tille at 2026-06-30T21:52:59+02:00
Update standards version to 4.7.4, no changes needed.

Upgrade checklist verified:
 4.6.1 → 4.6.2:
  * Package does not provide x-window-manager alternative
 4.6.2 → 4.7.0:
  * Package does not use dpkg-divert
 4.7.0 → 4.7.1:
  * Package does not install to non-/usr paths
 4.7.3 → 4.7.4:
  * Package is not in non-free-firmware

Changes-By: lintian-brush
Fixes: lintian: source: ancient-standards-version 4.6.0 (released 2021-08-18) (current is 4.7.4.1)
See-also: https://lintian.debian.org/tags/ancient-standards-version.html

- - - - -
cdd58c2c by Andreas Tille at 2026-06-30T22:09:13+02:00
Fix multiprocessing with Python3.14 Closes: #1140947

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/python3.14_multiprocessing.patch
- debian/patches/series
- debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+mcaller (1.0.3+git20210624.b415090-4) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * d/watch: version=5
+  * Remove redundant Priority: optional from source stanza.
+  * Update standards version to 4.7.4, no changes needed.
+  * Fix multiprocessing with Python3.14
+    Closes: #1140947
+
+ -- Andreas Tille <tille at debian.org>  Tue, 30 Jun 2026 21:52:47 +0200
+
 mcaller (1.0.3+git20210624.b415090-3) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -1,6 +1,5 @@
 Source: mcaller
 Section: science
-Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Steffen Moeller <moeller at debian.org>
 Build-Depends: debhelper-compat (= 13),
@@ -11,7 +10,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-biopython,
                python3-numpy,
                python3-sklearn
-Standards-Version: 4.6.0
+Standards-Version: 4.7.4
 Vcs-Browser: https://salsa.debian.org/med-team/mcaller
 Vcs-Git: https://salsa.debian.org/med-team/mcaller.git
 Homepage: https://github.com/al-mcintyre/mCaller


=====================================
debian/patches/python3.14_multiprocessing.patch
=====================================
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-06-30
+Bug-Debian: https://bugs.debian.org/1140947
+Description: Fix multiprocessing with Python3.14
+
+--- a/mCaller.py
++++ b/mCaller.py
+@@ -22,6 +22,8 @@ from load_mCaller_data import tsv2matrix
+ 
+ warnings.filterwarnings("ignore", module="sklearn")
+ 
++multiprocessing.set_start_method('fork')
++
+ def distribute_threads(positions_list,motif,tsvname,read2qual,refname,num_refs,base,mod,nprocs,nvariables,train,modelfile,skip_thresh,qual_thresh,classifier,training_tsv,plot_training):
+     """ distributes list of genomic positions across processes then adds resulting signals to matrix if training"""
+     outdir='/'.join(tsvname.split('/')[:-1])


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 shebang.patch
 python2to3.patch
 prefixes.patch
+python3.14_multiprocessing.patch


=====================================
debian/watch
=====================================
@@ -1,4 +1,6 @@
-version=4
-opts="mode=git,pretty=1.0.3+git%cd.%h" https://github.com/al-mcintyre/mCaller.git HEAD
-#opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%mcaller-$1.tar.gz%" \
-#   https://github.com/al-mcintyre/mCaller/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz
+Version: 5
+
+Source: https://github.com/al-mcintyre/mCaller.git
+Matching-Pattern: HEAD
+Mode: git
+Git-Pretty: 1.0.3+git%cd.%h



View it on GitLab: https://salsa.debian.org/med-team/mcaller/-/compare/4886ee5d3a0cc7639c461952cae778b79dae0893...cdd58c2c6247e6bcf35ce700c0cb4d862d0a22bb

-- 
View it on GitLab: https://salsa.debian.org/med-team/mcaller/-/compare/4886ee5d3a0cc7639c461952cae778b79dae0893...cdd58c2c6247e6bcf35ce700c0cb4d862d0a22bb
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