[med-svn] [Git][med-team/metastudent][master] 7 commits: Force fork start method for the propagatePrediction worker pool Closes: #1131795
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Jul 18 06:08:40 BST 2026
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 <crusoe at debian.org> 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 <debian-med-packaging at lists.alioth.debian.
Uploaders: Tobias Hamp <hampt at rostlab.org>,
Laszlo Kajan <lkajan at debian.org>
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 <tille at debian.org>
+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
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