CI: new failures: segfault in free-threaded, linprog invalid value encountered in dot #22700
Description
Describe your issue.
CI is failing with a segfault in the free-threaded job; see e.g. gh-22698.
I'm also seeing a failure in the mypy job, e.g. gh-22695.
Reproducing Code Example
NAError message
In free-threaded(1):
...
scipy/sparse/tests/test_matrix_io.py ....... [ 99%]
scipy/sparse/tests/test_minmax1d.py ............ [ 99%]
Fatal Python error: Segmentation fault
Current thread 0x00007f379c41eb80 (most recent call first):
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/traceback.py", line 200 in _safe_string
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/traceback.py", line 1053 in __init__
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/traceback.py", line 1134 in __init__
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/traceback.py", line 176 in format_exception_only
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/_code/code.py", line 592 in exconly
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/_code/code.py", line 884 in get_exconly
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/_code/code.py", line 872 in get_source
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/_code/code.py", line 938 in repr_traceback_entry
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/_code/code.py", line 992 in repr_traceback
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/_code/code.py", line 1058 in repr_excinfo
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/_code/code.py", line 690 in getrepr
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/nodes.py", line 456 in _repr_failure_py
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/python.py", line 1669 in repr_failure
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/reports.py", line 376 in from_item_and_call
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/runner.py", line 368 in pytest_runtest_makereport
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/pluggy/_callers.py", line 103 in _multicall
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/pluggy/_manager.py", line 120 in _hookexec
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/pluggy/_hooks.py", line 513 in __call__
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/runner.py", line 244 in call_and_report
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/runner.py", line 132 in runtestprotocol
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/runner.py", line 113 in pytest_runtest_protocol
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/pluggy/_callers.py", line 103 in _multicall
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/pluggy/_manager.py", line 120 in _hookexec
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/pluggy/_hooks.py", line 513 in __call__
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/main.py", line 362 in pytest_runtestloop
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/pluggy/_callers.py", line 103 in _multicall
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/pluggy/_manager.py", line 120 in _hookexec
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/pluggy/_hooks.py", line 513 in __call__
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/main.py", line 337 in _main
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/main.py", line 283 in wrap_session
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/main.py", line 330 in pytest_cmdline_main
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/pluggy/_callers.py", line 103 in _multicall
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/pluggy/_manager.py", line 120 in _hookexec
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/pluggy/_hooks.py", line 513 in __call__
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/_pytest/config/__init__.py", line 175 in main
File "/home/runner/work/scipy/scipy/build-install/lib/python3.13t/site-packages/scipy/_lib/_testutils.py", line 131 in __call__
File "/home/runner/work/scipy/scipy/dev.py", line 830 in scipy_tests
File "/home/runner/work/scipy/scipy/dev.py", line 852 in run
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/doit/action.py", line 461 in execute
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/doit/task.py", line 473 in execute
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/doit/runner.py", line 176 in execute_task
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/doit/runner.py", line 220 in run_tasks
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/doit/runner.py", line 254 in run_all
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/doit/cmd_run.py", line 265 in _execute
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/doit/cmd_base.py", line 570 in execute
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/doit/cmd_base.py", line 150 in parse_execute
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/doit/api.py", line 50 in run_tasks
File "/home/runner/work/scipy/scipy/dev.py", line 252 in run_doit_task
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/pydevtool/cli.py", line 267 in callback
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/click/core.py", line 788 in invoke
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/click/core.py", line 1443 in invoke
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/click/core.py", line 1697 in invoke
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/rich_click/rich_command.py", line 166 in main
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/click/core.py", line 1161 in __call__
File "/opt/hostedtoolcache/Python/3.13.2/x64-freethreaded/lib/python3.13t/site-packages/rich_click/rich_command.py", line 378 in __call__
File "/home/runner/work/scipy/scipy/dev.py", line 1740 in <module>
Extension modules: numpy._core._multiarray_umath, numpy.linalg._umath_linalg, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy._lib._fpumode, 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, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg._matfuncs_expm, scipy.linalg._linalg_pythran, scipy.linalg.cython_blas, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ellip_harm_2, scipy.special._special_ufuncs, scipy.special._gufuncs, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.spatial.transform._rotation, scipy.spatial.transform._rigid_transform, scipy.cluster._vq, scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering, scipy.optimize._group_columns, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._cython_nnls, scipy._lib._uarray._uarray, scipy.linalg._decomp_interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.optimize._direct, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.interpolate._dierckx, scipy.interpolate._ppoly, scipy.interpolate._interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, scipy.interpolate._bspl, scipy.special.cython_special, scipy.stats._stats, scipy.stats._biasedurn, scipy.stats._stats_pythran, scipy.stats._levy_stable.levyst, scipy.stats._ansari_swilk_statistics, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats._rcont.rcont, scipy.stats._qmvnt_cy, scipy.ndimage._nd_image, scipy.ndimage._rank_filter_1d, _ni_label, scipy.ndimage._ni_label, scipy.fftpack.convolve, scipy.integrate._test_odeint_banded, scipy.io.matlab._mio_utils, scipy.io.matlab._streams, scipy.io.matlab._mio5_utils, scipy.io._test_fortran, scipy.ndimage._ctest, _cytest, scipy.ndimage._cytest, scipy.odr.__odrpack, scipy.optimize.cython_optimize._zeros, scipy.signal._sigtools, scipy.signal._max_len_seq_inner, scipy.signal._upfirdn_apply, scipy.signal._spline, scipy.signal._sosfilt, scipy.signal._peak_finding_utils, extending, extending_cpp (total: 121)
/home/runner/work/_temp/a8dac759-6f15-4aa4-9faa-9bab9b38bb77.sh: line 3: 9686 Segmentation fault (core dumped) python dev.py --no-build test $TEST_SUBMODULES -- --parallel-threads=4
scipy/sparse/tests/test_sparsetools.py
---
In mypy job:
=========================== short test summary info ============================
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogSimplexDefault::test_zero_column_2 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogSimplexDefault::test_unbounded_no_nontrivial_constraints_1 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogSimplexDefault::test_unbounded_no_nontrivial_constraints_2 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogSimplexDefault::test_enzo_example_c_with_unboundedness - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogSimplexBland::test_zero_column_2 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogSimplexBland::test_unbounded_no_nontrivial_constraints_1 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogSimplexBland::test_unbounded_no_nontrivial_constraints_2 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogSimplexBland::test_enzo_example_c_with_unboundedness - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogIPDense::test_zero_column_2 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogIPDense::test_unbounded_no_nontrivial_constraints_1 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogIPDense::test_unbounded_no_nontrivial_constraints_2 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogIPDense::test_enzo_example_c_with_unboundedness - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogIPSparse::test_zero_column_2 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogIPSparse::test_unbounded_no_nontrivial_constraints_1 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogIPSparse::test_unbounded_no_nontrivial_constraints_2 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogIPSparse::test_enzo_example_c_with_unboundedness - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogRSCommon::test_zero_column_2 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogRSCommon::test_unbounded_no_nontrivial_constraints_1 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogRSCommon::test_unbounded_no_nontrivial_constraints_2 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogRSCommon::test_enzo_example_c_with_unboundedness - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogRSBland::test_zero_column_2 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogRSBland::test_unbounded_no_nontrivial_constraints_1 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogRSBland::test_unbounded_no_nontrivial_constraints_2 - RuntimeWarning: invalid value encountered in dot
FAILED scipy/optimize/tests/test_linprog.py::TestLinprogRSBland::test_enzo_example_c_with_unboundedness - RuntimeWarning: invalid value encountered in dot
FAILED scipy/sparse/linalg/_isolve/tests/test_gcrotmk.py::TestGCROTMK::test_denormals - RuntimeWarning: invalid value encountered in dot
= 25 failed, 60324 passed, 3970 skipped, 192 xfailed, 13 xpassed in 337.24s (0:05:37) =SciPy/NumPy/Python version and system information
NA