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MAINT: test failures/segfaults against NumPy main #4481

@tylerjereddy

Description

@tylerjereddy

MDAnalysisTests/analysis/test_base.py::test_frame_slice[run_kwargs0-frames0] segfaults it seems, along with a few other tests.

Details
MDAnalysisTests/analysis/test_base.py Fatal Python error: Segmentation fault

Current thread 0x00007f86f7ea1f80 (most recent call first):
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/MDAnalysis/coordinates/XDR.py", line 249 in _read_offsets
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/MDAnalysis/coordinates/XDR.py", line 211 in _load_offsets
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/MDAnalysis/coordinates/XDR.py", line 157 in __init__
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/MDAnalysis/lib/util.py", line 2553 in wrapper
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/MDAnalysis/core/universe.py", line 580 in load_new
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/MDAnalysis/core/universe.py", line 375 in __init__
  File "/home/treddy/github_projects/mdanalysis/testsuite/MDAnalysisTests/analysis/test_base.py", line 209 in test_frame_slice
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/_pytest/python.py", line 194 in pytest_pyfunc_call
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pluggy/_callers.py", line 102 in _multicall
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pluggy/_manager.py", line 119 in _hookexec
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pluggy/_hooks.py", line 501 in __call__
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/_pytest/python.py", line 1831 in runtest
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/_pytest/runner.py", line 170 in pytest_runtest_call
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pluggy/_callers.py", line 102 in _multicall
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pluggy/_manager.py", line 119 in _hookexec
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pluggy/_hooks.py", line 501 in __call__
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/_pytest/runner.py", line 263 in <lambda>
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/_pytest/runner.py", line 342 in from_call
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/_pytest/runner.py", line 262 in call_runtest_hook
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/_pytest/runner.py", line 223 in call_and_report
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/_pytest/runner.py", line 134 in runtestprotocol
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/_pytest/runner.py", line 115 in pytest_runtest_protocol
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pluggy/_callers.py", line 102 in _multicall
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pluggy/_manager.py", line 119 in _hookexec
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pluggy/_hooks.py", line 501 in __call__
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/_pytest/main.py", line 352 in pytest_runtestloop
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pluggy/_callers.py", line 102 in _multicall
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pluggy/_manager.py", line 119 in _hookexec
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pluggy/_hooks.py", line 501 in __call__
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/_pytest/main.py", line 327 in _main
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/_pytest/main.py", line 273 in wrap_session
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/_pytest/main.py", line 320 in pytest_cmdline_main
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pluggy/_callers.py", line 102 in _multicall
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pluggy/_manager.py", line 119 in _hookexec
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pluggy/_hooks.py", line 501 in __call__
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/_pytest/config/__init__.py", line 175 in main
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/_pytest/config/__init__.py", line 198 in console_main
  File "/home/treddy/python_venvs/py_311_mda/lib/python3.11/site-packages/pytest/__main__.py", line 7 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, msgpack._cmsgpack, MDAnalysis.lib._cutil, _transformations, MDAnalysis.lib._augment, MDAnalysis.lib.nsgrid, MDAnalysis.lib.c_distances, MDAnalysis.lib.c_distances_openmp, MDAnalysis.lib.formats.cython_util, MDAnalysis.lib.formats.libmdaxdr, MDAnalysis.lib.formats.libdcd, scipy._lib._ccallback_c, 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.cython_blas, scipy.linalg._matfuncs_expm, 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._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, MDAnalysis.coordinates.timestep, gsd.fl, scipy.io.matlab._mio_utils, scipy.io.matlab._streams, scipy.io.matlab._mio5_utils (total: 67)
Segmentation fault (core dumped)

Looks like MDAnalysis/coordinates/XDR.py", line 249 in _read_offsets is troublesome.

A quick pass at debugging wasn't fully conclusive, I'll need to circle back if nobody beats me to it.

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