Tests all pass with OS X on python 3.8, but on 3.9 there are multiple failures. The first I get, from running python3 -m pytest -vs -n0 is in tests/test_cli.py::TestCommandsDefaults::test_augment_ancestors:
python3 -m pytest -vs -n0
================================================================ test session starts =================================================================
platform darwin -- Python 3.9.0, pytest-6.1.2, py-1.9.0, pluggy-0.13.1 -- /usr/local/anaconda3/envs/python39/bin/python3
cachedir: .pytest_cache
rootdir: /Users/yan/Documents/Research/BDI/tsinfer, configfile: pytest.ini, testpaths: tests
plugins: xdist-2.1.0, cov-2.10.1, forked-1.3.0
collected 598 items
tests/test_cli.py::TestMain::test_cli_main PASSED
tests/test_cli.py::TestMain::test_main PASSED
tests/test_cli.py::TestDefaultPaths::test_get_default_path PASSED
tests/test_cli.py::TestDefaultPaths::test_get_ancestors_path PASSED
tests/test_cli.py::TestDefaultPaths::test_get_ancestors_trees_path PASSED
tests/test_cli.py::TestDefaultPaths::test_get_output_trees_path PASSED
tests/test_cli.py::TestCommandsDefaults::test_augment_ancestors Fatal Python error: Segmentation fault
Current thread 0x0000000118bb1dc0 (most recent call first):
File "/Users/yan/Documents/Research/BDI/tsinfer/tsinfer/inference.py", line 1095 in __complete_epoch
File "/Users/yan/Documents/Research/BDI/tsinfer/tsinfer/inference.py", line 1122 in __match_ancestors_single_threaded
File "/Users/yan/Documents/Research/BDI/tsinfer/tsinfer/inference.py", line 1169 in match_ancestors
File "/Users/yan/Documents/Research/BDI/tsinfer/tsinfer/inference.py", line 370 in match_ancestors
File "/Users/yan/Documents/Research/BDI/tsinfer/tests/test_cli.py", line 132 in setUp
File "/usr/local/anaconda3/envs/python39/lib/python3.9/unittest/case.py", line 547 in _callSetUp
File "/usr/local/anaconda3/envs/python39/lib/python3.9/unittest/case.py", line 589 in run
File "/usr/local/anaconda3/envs/python39/lib/python3.9/unittest/case.py", line 653 in __call__
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/_pytest/unittest.py", line 278 in runtest
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/_pytest/runner.py", line 163 in pytest_runtest_call
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/callers.py", line 187 in _multicall
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/manager.py", line 84 in <lambda>
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/manager.py", line 93 in _hookexec
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/hooks.py", line 286 in __call__
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/_pytest/runner.py", line 256 in <lambda>
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/_pytest/runner.py", line 310 in from_call
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/_pytest/runner.py", line 255 in call_runtest_hook
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/_pytest/runner.py", line 216 in call_and_report
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/_pytest/runner.py", line 127 in runtestprotocol
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/_pytest/runner.py", line 110 in pytest_runtest_protocol
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/callers.py", line 187 in _multicall
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/manager.py", line 84 in <lambda>
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/manager.py", line 93 in _hookexec
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/hooks.py", line 286 in __call__
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/_pytest/main.py", line 338 in pytest_runtestloop
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/callers.py", line 187 in _multicall
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/manager.py", line 84 in <lambda>
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/manager.py", line 93 in _hookexec
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/hooks.py", line 286 in __call__
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/_pytest/main.py", line 313 in _main
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/_pytest/main.py", line 257 in wrap_session
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/_pytest/main.py", line 306 in pytest_cmdline_main
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/callers.py", line 187 in _multicall
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/manager.py", line 84 in <lambda>
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/manager.py", line 93 in _hookexec
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pluggy/hooks.py", line 286 in __call__
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/_pytest/config/__init__.py", line 164 in main
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/_pytest/config/__init__.py", line 187 in console_main
File "/usr/local/anaconda3/envs/python39/lib/python3.9/site-packages/pytest/__main__.py", line 5 in <module>
File "/usr/local/anaconda3/envs/python39/lib/python3.9/runpy.py", line 87 in _run_code
File "/usr/local/anaconda3/envs/python39/lib/python3.9/runpy.py", line 197 in _run_module_as_main
zsh: segmentation fault python3 -m pytest -vs -n0
maximum crashed workers reached: 16
====================================================================== FAILURES ======================================================================
_________________________________________________________________ tests/test_cli.py __________________________________________________________________
[gw1] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw1' crashed while running 'tests/test_cli.py::TestCommandsDefaults::test_infer_from_ts'
_________________________________________________________________ tests/test_cli.py __________________________________________________________________
[gw2] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw2' crashed while running 'tests/test_cli.py::TestCommandsDefaults::test_augment_ancestors'
_________________________________________________________________ tests/test_cli.py __________________________________________________________________
[gw3] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw3' crashed while running 'tests/test_cli.py::TestCommandsDefaults::test_infer'
_________________________________________________________________ tests/test_cli.py __________________________________________________________________
[gw0] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw0' crashed while running 'tests/test_cli.py::TestCommandsDefaults::test_infer_bad_file'
______________________________________________________________ tests/test_inference.py _______________________________________________________________
[gw6] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw6' crashed while running 'tests/test_inference.py::TestAugmentedAncestorsRoundTrip::test_simple_example'
______________________________________________________________ tests/test_inference.py _______________________________________________________________
[gw7] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw7' crashed while running 'tests/test_inference.py::TestMissingDataRoundTrip::test_random_data_invariant_sites_ancestral_state'
______________________________________________________________ tests/test_inference.py _______________________________________________________________
[gw5] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw5' crashed while running 'tests/test_inference.py::TestUnfinalisedErrors::test_match_samples_unfinalised'
______________________________________________________________ tests/test_inference.py _______________________________________________________________
[gw8] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw8' crashed while running 'tests/test_inference.py::TestAlgorithmsExactlyEqualPrecision24::test_four_samples'
______________________________________________________________ tests/test_inference.py _______________________________________________________________
[gw9] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw9' crashed while running 'tests/test_inference.py::TestExtractAncestors::test_simple_simulation'
______________________________________________________________ tests/test_evaluation.py ______________________________________________________________
[gw10] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw10' crashed while running 'tests/test_evaluation.py::TestPerfectInference::test_single_tree_defaults'
______________________________________________________________ tests/test_inference.py _______________________________________________________________
[gw4] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw4' crashed while running 'tests/test_inference.py::TestAugmentedAncestorsRoundTrip::test_random_data_large_example'
______________________________________________________________ tests/test_evaluation.py ______________________________________________________________
[gw11] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw11' crashed while running 'tests/test_evaluation.py::TestPerfectInference::test_small_smc_path_compression'
______________________________________________________________ tests/test_inference.py _______________________________________________________________
[gw13] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw13' crashed while running 'tests/test_inference.py::TestSparseAncestorsRoundTrip::test_single_locus_two_samples'
______________________________________________________________ tests/test_inference.py _______________________________________________________________
[gw14] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw14' crashed while running 'tests/test_inference.py::TestGeneratedAncestors::test_no_recombination'
______________________________________________________________ tests/test_inference.py _______________________________________________________________
[gw12] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw12' crashed while running 'tests/test_inference.py::TestAugmentedAncestorsRoundTrip::test_single_locus'
______________________________________________________________ tests/test_inference.py _______________________________________________________________
[gw15] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw15' crashed while running 'tests/test_inference.py::TestMatchSamples::test_partial_bad_indexes'
______________________________________________________________ tests/test_inference.py _______________________________________________________________
[gw16] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw16' crashed while running 'tests/test_inference.py::TestPathCompressionSamplesCEngine::test_simulation_with_error'
______________________________________________________________ tests/test_evaluation.py ______________________________________________________________
[gw18] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw18' crashed while running 'tests/test_evaluation.py::TestMeanSampleAncestry::test_random_data_inferred_no_simplify'
______________________________________________________________ tests/test_evaluation.py ______________________________________________________________
[gw17] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw17' crashed while running 'tests/test_evaluation.py::TestCountSampleChildEdges::test_inferred_simplify'
______________________________________________________________ tests/test_evaluation.py ______________________________________________________________
[gw19] darwin -- Python 3.9.0 /usr/local/anaconda3/envs/python39/bin/python3
worker 'gw19' crashed while running 'tests/test_evaluation.py::TestNodeSpan::test_inferred'
Tests all pass with OS X on python 3.8, but on 3.9 there are multiple failures. The first I get, from running python3 -m pytest -vs -n0 is in tests/test_cli.py::TestCommandsDefaults::test_augment_ancestors:
Running in parallel identifies at least these others as problems