Andreas Tille pushed to branch master at Debian Med / metastudent
Commits: e5b8b08a by Andreas Tille at 2026-07-18T06:48:30+02:00 Force fork start method for the propagatePrediction worker pool Closes: #1131795 - - - - - 1eda0e98 by Andreas Tille at 2026-07-18T06:52:56+02:00 Use Github as Homepage Closes: #1141363 - - - - - e953c9b2 by Andreas Tille at 2026-07-18T07:01:33+02:00 debian/upstream/signing-key.asc: removed - - - - - b0627b39 by Andreas Tille at 2026-07-18T07:06:04+02:00 d/watch: Upstream seems to be inactive, but point watch file to Github anyway - - - - - 0e723237 by Andreas Tille at 2026-07-18T07:06:23+02:00 Ignore broken test-uscan CI test - - - - - 3d988a52 by Andreas Tille at 2026-07-18T06:06:56+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 - - - - - 4ece056a by Andreas Tille at 2026-07-18T07:08:22+02:00 Standards-Version: 4.7.4 - - - - - 6 changed files: - debian/changelog - debian/control - + debian/patches/python3.14_multiprocessing.patch - debian/patches/series - debian/salsa-ci.yml - debian/watch Changes: ===================================== debian/changelog ===================================== @@ -1,11 +1,23 @@ metastudent (2.0.1-11) UNRELEASED; urgency=medium + [ Michael R. Crusoe ] * Team upload. * d/control: consolidate all build dependencies (no need for a separate Build-Depends-Indep). * Switch to using dh-sequence-{javahelper,python3} * d/clean: use this instead of a dh_auto_clean override in d/rules + [ Andreas Tille ] + * Force fork start method for the propagatePrediction worker pool + Closes: #1131795 + * Use Github as Homepage + Closes: #1141363 + * debian/upstream/signing-key.asc: removed + * d/watch: Upstream seems to be inactive, but point watch file to Github + anyway + * Remove redundant Priority: optional from source stanza. + * Standards-Version: 4.7.4 + -- Michael R. Crusoe <[email protected]> Tue, 10 Sep 2024 12:27:34 +0200 metastudent (2.0.1-10) unstable; urgency=medium ===================================== debian/control ===================================== @@ -3,17 +3,16 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Tobias Hamp <[email protected]>, Laszlo Kajan <[email protected]> Section: science -Priority: optional Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all, python3-setuptools, default-jdk, dh-sequence-javahelper -Standards-Version: 4.6.2 +Standards-Version: 4.7.4 Vcs-Browser: https://salsa.debian.org/med-team/metastudent Vcs-Git: https://salsa.debian.org/med-team/metastudent.git -Homepage: https://rostlab.org/owiki/index.php/Metastudent +Homepage: https://github.com/Rostlab/MetaStudent Rules-Requires-Root: no Package: metastudent ===================================== debian/patches/python3.14_multiprocessing.patch ===================================== @@ -0,0 +1,28 @@ +Description: Force fork start method for the propagatePrediction worker pool +Author: Andreas Tille <[email protected]> +Bug-Debian: https://bugs.debian.org/1131795 +Last-Update: 2026-07-18 + +--- a/metastudentPkg/commons.py ++++ b/metastudentPkg/commons.py +@@ -9,6 +9,7 @@ import os + import sys + import shlex + import time ++import multiprocessing + from multiprocessing.pool import Pool + from functools import reduce + +@@ -346,7 +347,11 @@ class GOPrediction: + global go + go = self.go + +- p = Pool(processes=10) ++ # Explicit fork context: workers must inherit the module-level ++ # `go` global set just above via copy-on-write fork semantics. ++ # Since Python 3.14 defaults to forkserver on Linux, which ++ # spawns workers before `go` is set, this must be forced. ++ p = multiprocessing.get_context("fork").Pool(processes=10) + results = p.map(makeCompletePrediction, inputs, chunksize=20) + p.close() + p.join() ===================================== debian/patches/series ===================================== @@ -1,3 +1,4 @@ use_setuptools 2to3.patch 01_fix_blastp.patch +python3.14_multiprocessing.patch ===================================== debian/salsa-ci.yml ===================================== @@ -1,4 +1,7 @@ --- include: - - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml - - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/recipes/debian.yml + +# Ignore broken test-uscan CI test +test-uscan: + allow_failure: true ===================================== debian/watch ===================================== @@ -1,6 +1,6 @@ -version=4 -opts=dversionmangle=s/.*/0.No-Site/ \ -https://people.debian.org/~eriberto/ FakeWatchNoUpstreamSiteForThisPackage-(\d\S+)\.gz +Version: 5 -# Asked for release tags -# https://github.com/Rostlab/MetaStudent/issues/13 +Source: https://github.com/Rostlab/MetaStudent.git +Matching-Pattern: HEAD +Mode: git +Git-Pretty: 2.0.1~git%cd.%h View it on GitLab: https://salsa.debian.org/med-team/metastudent/-/compare/18bc425e77dd5ff965cd17c9d547467741564707...4ece056ae4662131810031bf77ef6868db65fdef -- View it on GitLab: https://salsa.debian.org/med-team/metastudent/-/compare/18bc425e77dd5ff965cd17c9d547467741564707...4ece056ae4662131810031bf77ef6868db65fdef You're receiving this email because of your account on salsa.debian.org. 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