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 <[email protected]> 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 <[email protected]> Uploaders: Steffen Moeller <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
