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pyxem / kikuchipy

Toolbox for analysis of electron backscatter diffraction (EBSD) patterns
https://kikuchipy.org
GNU General Public License v3.0
78 stars 30 forks source link

Segmentation fault #634

Closed ericpre closed 1 year ago

ericpre commented 1 year ago

Occured first time 2 days ago in that build: https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/4549395766

Reading package lists...
Building dependency tree...
Reading state information...
xvfb is already the newest version (2:21.1.3-2ubuntu2.7).
0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
Fatal Python error: Segmentation fault

Thread 0x00007f555608a640 (most recent call first):
  File "/usr/share/miniconda3/lib/python3.10/socket.py", line 293 in accept
  File "/usr/share/miniconda3/lib/python3.10/site-packages/pytest_rerunfailures.py", line 470 in run_server
  File "/usr/share/miniconda3/lib/python3.10/threading.py", line 953 in run
  File "/usr/share/miniconda3/lib/python3.10/threading.py", line 1016 in _bootstrap_inner
  File "/usr/share/miniconda3/lib/python3.10/threading.py", line 973 in _bootstrap

Current thread 0x00007f5557d9c740 (most recent call first):
  File "/usr/share/miniconda3/lib/python3.10/site-packages/llvmlite/binding/ffi.py", line [15](https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/4559704609/jobs/8043937522#step:17:16)1 in __call__
  File "/usr/share/miniconda3/lib/python3.10/site-packages/llvmlite/binding/executionengine.py", line 92 in finalize_object
  File "/usr/share/miniconda3/lib/python3.10/site-packages/numba/core/codegen.py", line 1060 in wrapper
  File "/usr/share/miniconda3/lib/python3.10/site-packages/numba/core/codegen.py", line 999 in _finalize_specific
  File "/usr/share/miniconda3/lib/python3.10/site-packages/numba/core/codegen.py", line 797 in _finalize_final_module
  File "/usr/share/miniconda3/lib/python3.10/site-packages/numba/core/codegen.py", line 765 in finalize
  File "/usr/share/miniconda3/lib/python3.10/site-packages/numba/core/runtime/nrtdynmod.py", line 213 in compile_nrt_functions
  File "/usr/share/miniconda3/lib/python3.10/site-packages/numba/core/runtime/nrt.py", line 41 in initialize
  File "/usr/share/miniconda3/lib/python3.10/site-packages/numba/core/compiler_lock.py", line 35 in _acquire_compile_lock
  File "/usr/share/miniconda3/lib/python3.10/site-packages/numba/core/cpu.py", line 59 in init
  File "/usr/share/miniconda3/lib/python3.10/site-packages/numba/core/compiler_lock.py", line 35 in _acquire_compile_lock
  File "/usr/share/miniconda3/lib/python3.10/site-packages/numba/core/base.py", line 257 in __init__
  File "/usr/share/miniconda3/lib/python3.10/site-packages/numba/core/cpu.py", line 40 in __init__
  File "/usr/share/miniconda3/lib/python3.10/site-packages/numba/core/registry.py", line 31 in _toplevel_target_context
  File "/usr/share/miniconda3/lib/python3.10/functools.py", line 981 in __get__
  File "/usr/share/miniconda3/lib/python3.10/site-packages/numba/core/registry.py", line 47 in target_context
  File "/usr/share/miniconda3/lib/python3.10/site-packages/numba/core/dispatcher.py", line 824 in __init__
  File "/usr/share/miniconda3/lib/python3.10/site-packages/numba/core/decorators.py", line 208 in wrapper
  File "/usr/share/miniconda3/lib/python3.10/site-packages/pyebsdindex/rotlib.py", line 77 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 883 in exec_module
  File "<frozen importlib._bootstrap>", line 688 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1006 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1027 in _find_and_load
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1078 in _handle_fromlist
  File "/usr/share/miniconda3/lib/python3.10/site-packages/pyebsdindex/band_vote.py", line 32 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 883 in exec_module
  File "<frozen importlib._bootstrap>", line 688 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1006 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1027 in _find_and_load
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1078 in _handle_fromlist
  File "/usr/share/miniconda3/lib/python3.10/site-packages/pyebsdindex/_ebsd_index_single.py", line 32 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 883 in exec_module
  File "<frozen importlib._bootstrap>", line 688 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1006 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1027 in _find_and_load
  File "/usr/share/miniconda3/lib/python3.10/site-packages/pyebsdindex/ebsd_index.py", line 26 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 883 in exec_module
  File "<frozen importlib._bootstrap>", line 688 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1006 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1027 in _find_and_load
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1078 in _handle_fromlist
  File "/usr/share/miniconda3/lib/python3.10/site-packages/kikuchipy/__init__.py", line 39 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 883 in exec_module
  File "<frozen importlib._bootstrap>", line 688 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1006 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1027 in _find_and_load
  File "<frozen importlib._bootstrap>", line 1050 in _gcd_import
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 992 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1027 in _find_and_load
  File "<frozen importlib._bootstrap>", line 1050 in _gcd_import
  File "/usr/share/miniconda3/lib/python3.10/importlib/__init__.py", line 126 in import_module
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/pathlib.py", line 533 in import_path
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/config/__init__.py", line 635 in _importconftest
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/config/__init__.py", line 603 in _getconftestmodules
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/main.py", line 541 in gethookproxy
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/main.py", line 577 in _collectfile
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/main.py", line 706 in collect
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/runner.py", line 370 in <lambda>
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/runner.py", line 339 in from_call
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/runner.py", line 370 in pytest_make_collect_report
  File "/usr/share/miniconda3/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/share/miniconda3/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/share/miniconda3/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/runner.py", line 538 in collect_one_node
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/main.py", line 645 in perform_collect
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/main.py", line 334 in pytest_collection
  File "/usr/share/miniconda3/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/share/miniconda3/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/share/miniconda3/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/main.py", line 323 in _main
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/main.py", line 270 in wrap_session
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/main.py", line 317 in pytest_cmdline_main
  File "/usr/share/miniconda3/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/share/miniconda3/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/share/miniconda3/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/config/__init__.py", line [16](https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/4559704609/jobs/8043937522#step:17:17)7 in main
  File "/usr/share/miniconda3/lib/python3.10/site-packages/_pytest/config/__init__.py", line [19](https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/4559704609/jobs/8043937522#step:17:20)0 in console_main
  File "/usr/share/miniconda3/lib/python3.10/site-packages/pytest/__main__.py", line 5 in <module>
  File "/usr/share/miniconda3/lib/python3.10/runpy.py", line 86 in _run_code
  File "/usr/share/miniconda3/lib/python3.10/runpy.py", line 196 in _run_module_as_main

Extension modules: markupsafe._speedups, 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._mt199[37](https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/4559704609/jobs/8043937522#step:17:38), numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, matplotlib._c_internal_utils, PIL._imaging, matplotlib._path, kiwisolver._cext, vtkmodules.vtkCommonCore, vtkmodules.vtkCommonMath, vtkmodules.vtkCommonTransforms, vtkmodules.vtkCommonDataModel, vtkmodules.vtkCommonExecutionModel, vtkmodules.vtkCommonMisc, vtkmodules.vtkFiltersCore, vtkmodules.vtkFiltersPython, vtkmodules.vtkFiltersGeneral, vtkmodules.vtkRenderingCore, vtkmodules.vtkRenderingContext2D, vtkmodules.vtkChartsCore, vtkmodules.vtkCommonColor, vtkmodules.vtkCommonComputationalGeometry, vtkmodules.vtkFiltersExtraction, vtkmodules.vtkFiltersFlowPaths, vtkmodules.vtkFiltersGeometry, vtkmodules.vtkFiltersHybrid, vtkmodules.vtkFiltersModeling, vtkmodules.vtkFiltersSources, vtkmodules.vtkFiltersTexture, vtkmodules.vtkParallelCore, vtkmodules.vtkFiltersParallel, vtkmodules.vtkFiltersParallelDIY2, vtkmodules.vtkFiltersPoints, vtkmodules.vtkFiltersStatistics, vtkmodules.vtkFiltersVerdict, vtkmodules.vtkIOEnSight, vtkmodules.vtkIOCore, vtkmodules.vtkIOLegacy, vtkmodules.vtkIOGeometry, vtkmodules.vtkImagingCore, vtkmodules.vtkIOImage, vtkmodules.vtkIOXMLParser, vtkmodules.vtkIOXML, vtkmodules.vtkIOInfovis, vtkmodules.vtkIOPLY, vtkmodules.vtkImagingGeneral, vtkmodules.vtkImagingHybrid, vtkmodules.vtkImagingMorphological, vtkmodules.vtkInteractionWidgets, vtkmodules.vtkPythonContext2D, vtkmodules.vtkRenderingAnnotation, vtkmodules.vtkRenderingFreeType, vtkmodules.vtkRenderingHyperTreeGrid, vtkmodules.vtkRenderingUI, vtkmodules.vtkRenderingOpenGL2, vtkmodules.vtkRenderingContextOpenGL2, vtkmodules.vtkImagingFourier, vtkmodules.vtkRenderingLabel, vtkmodules.vtkRenderingVolume, vtkmodules.vtkImagingMath, vtkmodules.vtkRenderingVolumeOpenGL2, vtkmodules.vtkViewsCore, vtkmodules.vtkViewsContext2D, _nlopt, yaml._yaml, scipy._lib._ccallback_c, scipy.sparse._sparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg._cythonized_array_utils, scipy.linalg._flinalg, scipy.linalg._solve_toeplitz, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_lapack, 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.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._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy.optimize._trlib._trlib, numpy.linalg.lapack_lite, 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.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.optimize._direct, h5py._errors, h5py.defs, h5py._objects, h5py.h5, h5py.h5r, h5py.utils, h5py.h5s, h5py.h5ac, h5py.h5p, h5py.h5t, h5py._conv, h5py.h5z, h5py._proxy, h5py.h5a, h5py.h5d, h5py.h5ds, h5py.h5g, h5py.h5i, h5py.h5f, h5py.h5fd, h5py.h5pl, h5py.h5o, h5py.h5l, h5py._selector, numba.core.typeconv._typeconv, numba._helperlib, numba._dynfunc, numba._dispatcher, numba.core.runtime._nrt_python, numba.np.ufunc._internal, numba.experimental.jitclass._box (total: 1[62](https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/4559704609/jobs/8043937522#step:17:63))
Segmentation fault (core dumped)
conda list ``` conda list shell: /usr/bin/bash -l {0} env: MPLBACKEND: agg EXTENSION: kikuchipy lumispy pyxem TEST_DEPS: pytest pytest-xdist pytest-rerunfailures pytest-mpl INPUT_RUN_POST: true CONDA: /usr/share/miniconda3 CONDA_PKGS_DIR: /home/runner/conda_pkgs_dir # packages in environment at /usr/share/miniconda3: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge aiofiles 22.1.0 pyhd8ed1ab_0 conda-forge aiohttp 3.8.4 py310h1fa729e_0 conda-forge aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge aiosqlite 0.18.0 pyhd8ed1ab_0 conda-forge anyio 3.6.2 pyhd8ed1ab_0 conda-forge aom 3.5.0 h27087fc_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py310h5764c6d_3 conda-forge arrow-cpp 11.0.0 ha770c72_13_cpu conda-forge asciitree 0.3.3 py_2 conda-forge asteval 0.9.29 pyhd8ed1ab_0 conda-forge asttokens 2.2.1 pyhd8ed1ab_0 conda-forge async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge attrs 22.2.0 pyh71513ae_0 conda-forge aws-c-auth 0.6.26 hf365957_1 conda-forge aws-c-cal 0.5.21 h48707d8_2 conda-forge aws-c-common 0.8.14 h0b41bf4_0 conda-forge aws-c-compression 0.2.16 h03acc5a_5 conda-forge aws-c-event-stream 0.2.20 h00877a2_4 conda-forge aws-c-http 0.7.6 hf342b9f_0 conda-forge aws-c-io 0.13.19 h5b20300_3 conda-forge aws-c-mqtt 0.8.6 hc4349f7_12 conda-forge aws-c-s3 0.2.7 h909e904_1 conda-forge aws-c-sdkutils 0.1.8 h03acc5a_0 conda-forge aws-checksums 0.1.14 h03acc5a_5 conda-forge aws-crt-cpp 0.19.8 hf7fbfca_12 conda-forge aws-sdk-cpp 1.10.57 h17c43bd_8 conda-forge babel 2.12.1 pyhd8ed1ab_1 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.0 pyha770c72_0 conda-forge bleach 6.0.0 pyhd8ed1ab_0 conda-forge blosc 1.21.3 hafa529b_0 conda-forge bokeh 2.4.3 pyhd8ed1ab_3 conda-forge brotli 1.0.9 h166bdaf_8 conda-forge brotli-bin 1.0.9 h166bdaf_8 conda-forge brotlipy 0.7.0 py310h5764c6d_1005 conda-forge brunsli 0.1 h9c3ff4c_0 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge c-blosc2 2.8.0 hf91038e_0 conda-forge ca-certificates 2022.12.7 ha878542_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge certifi 2022.12.7 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py310h255011f_3 conda-forge cfitsio 4.2.0 hd9d235c_0 conda-forge charls 2.4.1 hcb278e6_0 conda-forge charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge click 8.1.3 unix_pyhd8ed1ab_2 conda-forge cloudpickle 2.2.1 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge comm 0.1.3 pyhd8ed1ab_0 conda-forge conda 23.1.0 py310hff52083_0 conda-forge conda-package-handling 2.0.2 pyh38be061_0 conda-forge conda-package-streaming 0.7.0 pyhd8ed1ab_1 conda-forge contourpy 1.0.7 py310hdf3cbec_0 conda-forge cryptography 40.0.1 py310h34c0648_0 conda-forge curl 7.88.1 hdc1c0ab_1 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge cytoolz 0.12.0 py310h5764c6d_1 conda-forge dask 2023.3.2 pyhd8ed1ab_0 conda-forge dask-core 2023.3.2 pyhd8ed1ab_0 conda-forge dav1d 1.0.0 h166bdaf_1 conda-forge debugpy 1.6.6 py310heca2aa9_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge diffpy.structure 3.1.0 pyhd8ed1ab_0 conda-forge diffsims 0.5.1 pyhd8ed1ab_0 conda-forge dill 0.3.6 pyhd8ed1ab_1 conda-forge distributed 2023.3.2 pyhd8ed1ab_0 conda-forge double-conversion 3.2.0 h27087fc_1 conda-forge eigen 3.4.0 h4bd325d_0 conda-forge elfutils 0.189 hde5d1a3_0 conda-forge entrypoints 0.4 pyhd8ed1ab_0 conda-forge exceptiongroup 1.1.1 pyhd8ed1ab_0 conda-forge execnet 1.9.0 pyhd8ed1ab_0 conda-forge executing 1.2.0 pyhd8ed1ab_0 conda-forge expat 2.5.0 h27087fc_0 conda-forge fabio 2022.12.1 py310h0a54255_1 conda-forge fasteners 0.17.3 pyhd8ed1ab_0 conda-forge ffmpeg 5.1.2 gpl_h8dda1f0_106 conda-forge flit-core 3.8.0 pyhd8ed1ab_0 conda-forge fmt 9.1.0 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conda-forge heapdict 1.0.1 py_0 conda-forge hyperspy-base 1.7.4 py310h1fa729e_0 conda-forge icu 72.1 hcb278e6_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge imagecodecs 2023.1.23 py310h241fb82_2 conda-forge imageio 2.27.0 pyh24c5eb1_0 conda-forge importlib-metadata 6.1.0 pyha770c72_0 conda-forge importlib_metadata 6.1.0 hd8ed1ab_0 conda-forge importlib_resources 5.12.0 pyhd8ed1ab_0 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge ipykernel 6.22.0 pyh210e3f2_0 conda-forge ipyparallel 8.5.1 pyhd8ed1ab_0 conda-forge ipython 8.11.0 pyh41d4057_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 8.0.6 pyhd8ed1ab_0 conda-forge jedi 0.18.2 pyhd8ed1ab_0 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge joblib 1.2.0 pyhd8ed1ab_0 conda-forge json5 0.9.5 pyh9f0ad1d_0 conda-forge jsoncpp 1.9.5 h4bd325d_1 conda-forge jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge jupyter_client 8.1.0 pyhd8ed1ab_0 conda-forge jupyter_core 5.3.0 py310hff52083_0 conda-forge jupyter_events 0.6.3 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h4ff8645_0 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge svt-av1 1.4.1 hcb278e6_0 conda-forge sympy 1.11.1 pypyh9d50eac_103 conda-forge tbb 2021.8.0 hf52228f_0 conda-forge tbb-devel 2021.8.0 hf52228f_0 conda-forge tblib 1.7.0 pyhd8ed1ab_0 conda-forge terminado 0.17.1 pyh41d4057_0 conda-forge threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge tifffile 2023.3.21 pyhd8ed1ab_0 conda-forge tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge toolz 0.12.0 pyhd8ed1ab_0 conda-forge tornado 6.2 py310h5764c6d_1 conda-forge tqdm 4.65.0 pyhd8ed1ab_1 conda-forge traitlets 5.9.0 pyhd8ed1ab_0 conda-forge traits 6.4.1 py310h5764c6d_1 conda-forge transforms3d 0.4.1 pyhd8ed1ab_0 conda-forge typing-extensions 4.5.0 hd8ed1ab_0 conda-forge typing_extensions 4.5.0 pyha770c72_0 conda-forge tzdata 2023b h71feb2d_0 conda-forge ucx 1.14.0 ha0ee010_0 conda-forge uncertainties 3.1.7 pyhd8ed1ab_0 conda-forge unicodedata2 15.0.0 py310h5764c6d_0 conda-forge urllib3 1.26.15 pyhd8ed1ab_0 conda-forge utfcpp 3.2.3 ha770c72_0 conda-forge vtk 9.2.6 osmesa_py310h7f736e2_103 conda-forge wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 py_1 conda-forge websocket-client 1.5.1 pyhd8ed1ab_0 conda-forge wheel 0.40.0 pyhd8ed1ab_0 conda-forge widgetsnbextension 4.0.7 pyhd8ed1ab_0 conda-forge wslink 1.10.1 pyhd8ed1ab_0 conda-forge x264 1!164.3095 h166bdaf_2 conda-forge x265 3.5 h924138e_3 conda-forge xorg-damageproto 1.2.1 h7f98852_1002 conda-forge xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-glproto 1.4.17 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.8.4 h0b41bf4_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdamage 1.1.5 h7f98852_1 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge xorg-libxrandr 1.5.2 h7f98852_1 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-libxt 1.2.1 h7f98852_2 conda-forge xorg-randrproto 1.5.0 h7f98852_1001 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-util-macros 1.19.3 h7f98852_0 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge y-py 0.5.9 py310h4426083_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge yaml-cpp 0.7.0 h27087fc_2 conda-forge yarl 1.8.2 py310h5764c6d_0 conda-forge ypy-websocket 0.8.2 pyhd8ed1ab_0 conda-forge zarr 2.14.2 pyhd8ed1ab_0 conda-forge zeromq 4.3.4 h9c3ff4c_1 conda-forge zfp 1.0.0 h27087fc_3 conda-forge zict 2.2.0 pyhd8ed1ab_0 conda-forge zipp 3.15.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge zlib-ng 2.0.7 h0b41bf4_0 conda-forge zstandard 0.19.0 py310hdeb6495_1 conda-forge zstd 1.5.2 h3eb15da_6 conda-forge ```
hakonanes commented 1 year ago

Thanks for reporting this failure in kikuchipy's test setup in HyperSpy's extension test suite, @ericpre.

Since the test setup fails before any tests are run, I assume the segmentation fault is caused by Numba's compilation of some of our CPU accelerated functions. I'll look into this later today, with hopefully a fix ready by the weekend or early next week. A fix should be released as part of a 0.8.4 patch release, where we also plan to fix #622.

hakonanes commented 1 year ago

I cannot reproduce this locally, and neither can the checks in my fork of the extension repo. I've therefore asked to re-introduce the kikuchipy extension tests.

ericpre commented 1 year ago

The issue occurs when vtk build against osmesa is installed, which doesn't seem to support running headless.

hakonanes commented 1 year ago

Thanks, this will hopefully be fixed with the new build.