Segfault in numcodecs/tests/test_vlen_bytes.py::test_encode_none

[avalentino]

I run the unit test suite in debian sid (x86_64) i get a segmentation fault:

python3.13 -m pytes -v --pyargs numcodecs
============================= test session starts ==============================
platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 -- /usr/bin/python3.13
cachedir: .pytest_cache
rootdir: /build/numcodecs-0.16.0+ds/.pybuild/cpython3_3.13_numcodecs/build
configfile: pyproject.toml
plugins: typeguard-4.4.2, cov-5.0.0
collecting ... collected 698 items / 27 deselected / 4 skipped / 671 selected

numcodecs/astype.py::numcodecs.astype.AsType PASSED                      [  0%]

[...]

numcodecs/tests/test_vlen_bytes.py::test_decode_errors PASSED            [ 96%]
numcodecs/tests/test_vlen_bytes.py::test_encode_none Fatal Python error: Aborted

Current thread 0x00007ebfefa2e100 (most recent call first):
  File "/build/numcodecs-0.16.0+ds/.pybuild/cpython3_3.13_numcodecs/build/numcodecs/tests/test_vlen_bytes.py", line 94 in test_encode_none
  File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159 in pytest_pyfunc_call
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627 in runtest
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174 in pytest_runtest_call
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242 in <lambda>
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341 in from_call
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 241 in call_and_report
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 132 in runtestprotocol
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 113 in pytest_runtest_protocol
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 362 in pytest_runtestloop
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 337 in _main
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 283 in wrap_session
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 330 in pytest_cmdline_main
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 175 in main
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 201 in console_main
  File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9 in <module>
  File "<frozen runpy>", line 88 in _run_code
  File "<frozen runpy>", line 198 in _run_module_as_main

Extension modules: numpy._core._multiarray_umath, numpy.linalg._umath_linalg, numcodecs.compat_ext, numcodecs.blosc, numcodecs.zstd, numcodecs.lz4, numcodecs._shuffle, numcodecs.jenkins, crc32c._crc32c, numcodecs.vlen, numcodecs.fletcher32, msgpack._cmsgpack, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator (total: 21)
Aborted (core dumped)

[jakirkham]

Thanks for the report! 🙏

Are you able to run the test with gdb (perhaps like so)?

[jakirkham]

Looks like this happened before on macOS ( #683 )

Appears we had skipped test on macOS in PR: #690

[jakirkham]

Was able to reproduce the issue. Did a bit more digging here: #683 (comment)

Came up with a fix that works for me locally in PR: #736

Please try it out and let us know how it goes 🙂

[avalentino]

Thanks @jakirkham or the super-fast solution.
I confirm that everything works fine with your patch.

[jakirkham]

Thanks Antonio! 🙏

Appreciate the timely retesting

Have gone ahead and merged

This will show up in the next release