[0.11] Segmentation fault on tests

[olebole]

Forwarding Debian#1026594: Since a few weeks, the package produces a segmentation fault when running the tests:

autopkgtest [11:23:37]: test command1: cd $AUTOPKGTEST_TMP && python3 -m pytest --pyargs fast_histogram
autopkgtest [11:23:37]: test command1: [-----------------------
============================= test session starts ==============================
platform linux -- Python 3.11.1, pytest-7.2.0, pluggy-1.0.0+repack
rootdir: /tmp/autopkgtest-lxc.adqdcee1/downtmp/autopkgtest_tmp
plugins: hypothesis-6.61.0
collected 9 items

tests/test_histogram.py FFatal Python error: Segmentation fault

Current thread 0x00007f633c836040 (most recent call first):
  Garbage-collecting
  File "/usr/lib/python3/dist-packages/hypothesis/internal/conjecture/data.py", line 850 in __init__
  File "/usr/lib/python3/dist-packages/hypothesis/internal/conjecture/engine.py", line 891 in new_conjecture_data
  File "/usr/lib/python3/dist-packages/hypothesis/internal/conjecture/engine.py", line 1031 in cached_test_function
  File "/usr/lib/python3/dist-packages/hypothesis/internal/conjecture/engine.py", line 803 in generate_mutations_from
  File "/usr/lib/python3/dist-packages/hypothesis/internal/conjecture/engine.py", line 733 in generate_new_examples
  File "/usr/lib/python3/dist-packages/hypothesis/internal/conjecture/engine.py", line 880 in _run
  File "/usr/lib/python3/dist-packages/hypothesis/internal/conjecture/engine.py", line 474 in run
  File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 884 in run_engine
  File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1292 in wrapped_test
  File "/usr/lib/python3/dist-packages/fast_histogram/tests/test_histogram.py", line 78 in test_2d_compare_with_numpy
  File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195 in pytest_pyfunc_call
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1789 in runtest
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 167 in pytest_runtest_call
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 260 in <lambda>
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 339 in from_call
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 259 in call_runtest_hook
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 220 in call_and_report
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 131 in runtestprotocol
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 112 in pytest_runtest_protocol
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 349 in pytest_runtestloop
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 324 in _main
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 270 in wrap_session
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 317 in pytest_cmdline_main
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 167 in main
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 190 in console_main
  File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 5 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.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, 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, fast_histogram._histogram_core, numpy.linalg.lapack_lite (total: 15)
Segmentation fault

This happens with both Python3.10.9 and 3.11.1. Other versions:

• hypothesis 6.60.0, 6.61.0 (6.36.0 works!)
• numpy 1.23.5, 1.24.1
• pytest 7.2.0,
• pluggy 1.0.0

This happens both when running during the build (log) and when testing with python3 -m pytest --pyargs fast_histogram on the installed package (log).

[olebole]

Any idea here? This seems to be a regression with newer "hypothesis" versions; however hypothesis itself is a pure Python package and therefore should not cause a segfault. fast-histogram is used by quite a few packages; I'd like to keep it (and the packages that depend on it) in Debian. Shall I just pragmatically disable the tests?

[astrofrog]

Will try and investigate shortly - I am guessing this is a new hypothesis test case that is segfaulting

[kecnry]

Running into a similar issue in https://github.com/spacetelescope/jdaviz/pull/2498 when using the histogram viewer from glue-jupyter. If this isn't directly related, feel free to split into a separate issue.

Current thread 0x00007f4c96c5ec40 (most recent call first):
  File "/home/runner/work/jdaviz/jdaviz/.tox/py311-test-alldeps-cov/lib/python3.11/site-packages/fast_histogram/histogram.py", line 58 in histogram1d
  File "/home/runner/work/jdaviz/jdaviz/.tox/py311-test-alldeps-cov/lib/python3.11/site-packages/glue/core/data.py", line 2021 in compute_histogram
  File "/home/runner/work/jdaviz/jdaviz/.tox/py311-test-alldeps-cov/lib/python3.11/site-packages/glue/viewers/histogram/state.py", line 254 in update_histogram
  File "/home/runner/work/jdaviz/jdaviz/.tox/py311-test-alldeps-cov/lib/python3.11/site-packages/glue/viewers/histogram/state.py", line 217 in histogram
  File "/home/runner/work/jdaviz/jdaviz/.tox/py311-test-alldeps-cov/lib/python3.11/site-packages/glue_jupyter/bqplot/histogram/layer_artist.py", line 51 in _calculate_histogram
  File "/home/runner/work/jdaviz/jdaviz/.tox/py311-test-alldeps-cov/lib/python3.11/site-packages/glue_jupyter/bqplot/histogram/layer_artist.py", line 142 in _update_histogram
  File "/home/runner/work/jdaviz/jdaviz/.tox/py311-test-alldeps-cov/lib/python3.11/site-packages/glue_jupyter/bqplot/histogram/layer_artist.py", line 153 in update
  ...

[astrofrog]

@kecnry would you be able to print out or save the arguments being passed to histogram1d that are causing the segfault?

[kecnry]

It seems that it was caused (on our end) by passing arrays of length 1 to the histogram. We can just prevent passing these for now with a workaround, but it would be great if this could either be gracefully handled or raise an error instead of resulting in a segfault.