[Debian-med-packaging] Bug#1148450: jellyfish: FTBFS against python 3.15rc2

[Maximiliano Curia]

Package: src:jellyfish
Version: 2.3.1-6
User: debian-python at lists.debian.org
Usertags: python3.15-default
Tags: patch, ftbfs, forky, sid
Severity: important

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/

-- 
"Can you imagine what I would do if I could do all I can?" -- Sun Tzu
Saludos /\/\ /\ >< `/
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