Andreas Tille pushed to branch master at Debian Med / iva
Commits:
5b125ef3 by Andreas Tille at 2026-07-08T14:35:05+02:00
Restrictions: allow-stderr
- - - - -
f7c43cc0 by Andreas Tille at 2026-07-08T14:36:25+02:00
Work around a Cython issue
- - - - -
859f44f8 by Andreas Tille at 2026-07-08T14:45:55+02:00
Upload to unstable
- - - - -
4 changed files:
- debian/changelog
- + debian/patches/fork-context-workaround.patch
- debian/patches/series
- debian/tests/control
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-iva (1.0.11+ds-7) UNRELEASED; urgency=medium
+iva (1.0.11+ds-7) unstable; urgency=medium
[ Sascha Steinbiss ]
* Update the salsa-ci.yml file with the current Debian Med one.
@@ -15,7 +15,7 @@ iva (1.0.11+ds-7) UNRELEASED; urgency=medium
* Adapt to forkserver in Python3.14
Closes: #1141283
- -- Andreas Tille <[email protected]> Wed, 08 Jul 2026 11:47:22 +0200
+ -- Andreas Tille <[email protected]> Wed, 08 Jul 2026 14:37:40 +0200
iva (1.0.11+ds-6) unstable; urgency=medium
=====================================
debian/patches/fork-context-workaround.patch
=====================================
@@ -0,0 +1,37 @@
+Description: Use the fork multiprocessing context explicitly
+ Python 3.14 made "forkserver" the default multiprocessing start
+ method on Linux. There is a known CPython regression
+ (https://github.com/python/cpython/issues/144503, present in at
+ least 3.14.3/3.13.12) in forkserver's daemon bootstrap that can
+ surface as "ConnectionResetError: [Errno 104] Connection reset by
+ peer" during the initial authentication handshake, unrelated to
+ anything this script does.
+ .
+ This script only uses multiprocessing.Process for two short-lived,
+ trivial parallel calls to pyfastaq.tasks.to_fasta() and has no
+ threading concerns that would make "fork" unsafe, so request the
+ "fork" context explicitly for these two Process objects rather than
+ relying on the (currently broken in some 3.14 point releases)
+ forkserver default.
+ .
+ This is a workaround for an upstream Python bug, not a long-term
+ design choice; it can be dropped once the relevant Python versions
+ in Debian carry the fix for cpython#144503.
+Author: Andreas Tille <[email protected]>
+Bug: https://github.com/python/cpython/issues/144503
+Last-Update: 2026-07-08
+
+--- a/scripts/iva
++++ b/scripts/iva
+@@ -185,8 +185,9 @@ else:
+ fq_to_convert_to_fa_1 = reads_for_trimming_1
+ fq_to_convert_to_fa_2 = reads_for_trimming_2
+
+- p1 = multiprocessing.Process(target=pyfastaq.tasks.to_fasta,
args=(fq_to_convert_to_fa_1, reads_1), kwargs={'line_length':0})
+- p2 = multiprocessing.Process(target=pyfastaq.tasks.to_fasta,
args=(fq_to_convert_to_fa_2, reads_2), kwargs={'line_length':0})
++ mp_ctx = multiprocessing.get_context('fork')
++ p1 = mp_ctx.Process(target=pyfastaq.tasks.to_fasta,
args=(fq_to_convert_to_fa_1, reads_1), kwargs={'line_length':0})
++ p2 = mp_ctx.Process(target=pyfastaq.tasks.to_fasta,
args=(fq_to_convert_to_fa_2, reads_2), kwargs={'line_length':0})
+ p1.start()
+
+ if options.threads == 1:
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ python3.12.patch
syntax-warning.patch
check-test-data-and-altdir.patch
fix_python3.14_forkserver.patch
+fork-context-workaround.patch
=====================================
debian/tests/control
=====================================
@@ -1,4 +1,4 @@
Tests: run-unit-test
Depends: @, trimmomatic, python3-packaging
-Restrictions: skip-not-installable
+Restrictions: skip-not-installable, allow-stderr
# Currently kmc is only available for amd64
View it on GitLab:
https://salsa.debian.org/med-team/iva/-/compare/14deaa90204151c2e5081da30b9a9b4b54966473...859f44f85eb9928349b2b9267f64d4a64a25e929
--
View it on GitLab:
https://salsa.debian.org/med-team/iva/-/compare/14deaa90204151c2e5081da30b9a9b4b54966473...859f44f85eb9928349b2b9267f64d4a64a25e929
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