Hi!

While rebuilding the python related packages against the Python 3.15rc2
as the default version we found that jellyfish fails to build from
source [1].

This is the error:

AIL: test_add (__main__.TestHashCounter.test_add)
Traceback (most recent call last):
   File "/build/reproducible-path/jellyfish-2.3.1/swig/python/test_hash_counter.py", line 43, in test_add
     self.assertTrue(good)
AssertionError: False is not true

This failure is only present in arm64, and it happens when adding a
value that is an exact multiple of 2^val_len (where lower bits are 0),
an overflow on the large-value carry produced carry_shift == v. This
caused hash_counter::add to incorrectly assume the key was never
claimed, resulting in false duplicate detection (is_new = false) and
duplicate additions after size doubling.

I've created a patch that explicitly tracks whether the key was
claimed/found in large_hash_array instead of guessing via carry_shift ==
v. And I've also added a regression test. I've sent this patch upstream
as PR#214

I've applied this fix in the sandbox [3] to verify that it builds
successfully, please consider applying the patch to support the upcoming
3.15 version.

Setting the severity to important for now. Once Python 3.15 becomes the
default Python version this bug will become release critical.

Happy hacking,

[1]: https://debusine.debian.net/debian/r-python-python3.15/artifact/4704166/
[2]: https://github.com/gmarcais/Jellyfish/pull/214
[3]: https://debusine.debian.net/debian/r-python-python3.15/

Hello,

Bug #1148450 in jellyfish reported by you has been fixed in the
Git repository and is awaiting an upload. You can see the commit
message below and you can check the diff of the fix at:

https://salsa.debian.org/med-team/jellyfish/-/commit/c1339f0e4de59baf4266d701eabda2459e5d6e78

(this message was generated automatically)
-- 
Greetings

https://bugs.debian.org/1148450

We believe that the bug you reported is fixed in the latest version of
jellyfish, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1148450@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated jellyfish package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Tue, 22 Sep 2026 16:22:58 +0200
Source: jellyfish
Architecture: source
Version: 2.3.1-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 1105388 1148450
Changes:
 jellyfish (2.3.1-7) unstable; urgency=medium
 .
   [ Maximiliano Curia ]
   * Fix key claim tracking during hash resizing on carry overflow
     Closes: #1148450
 .
   [ Andreas Tille ]
   * Standards-Version: 4.7.4 (routine-update)
   * Reflow Uploaders field (cme)
   * Remove Priority field (cme)
   * Apply multi-arch hints.
     + libjellyfish-2.0-dev: Add Multi-Arch: same.
   * Fix FTBFS with make --shuffle=reverse
     Closes: #1105388
Checksums-Sha1:
 dc5f1a20a296aef9544c2a55d29bb0ec0eb9c77c 2759 jellyfish_2.3.1-7.dsc
 1f8d2114a1333a83911d5568a23a9d849ace4f7c 15564 jellyfish_2.3.1-7.debian.tar.xz
 8a0d9b69d46bd7a66de29e84d8c6479f2c37aa08 12306 jellyfish_2.3.1-7_amd64.buildinfo
Checksums-Sha256:
 333139c0f31a8b548e6880880eb188f4bb976c4f09f6feef6cdb22d8993a45e5 2759 jellyfish_2.3.1-7.dsc
 5d8f125bba8ecff92c4ca8a740f34c0e9583cdb5c5c1eb41b495422a95ec2e82 15564 jellyfish_2.3.1-7.debian.tar.xz
 92117a3d4955394eef43a1b730a8a43d62282fab07b42e46c2c1e5c32b9f48e9 12306 jellyfish_2.3.1-7_amd64.buildinfo
Files:
 2106d524a65ddf2ebea0f7413df7616f 2759 science optional jellyfish_2.3.1-7.dsc
 96186d916ab051123ea1be85771b843d 15564 science optional jellyfish_2.3.1-7.debian.tar.xz
 5ebd1ffc62c6d63b54a8f02dea60a8a0 12306 science optional jellyfish_2.3.1-7_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----
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=SZ5I
-----END PGP SIGNATURE-----