`test_parallelize` fails on local tests and is flaky

[selmanozleyen]

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my local run results. we need to also check whats wrong here #1105

~/projects/squidpy feat/device-settings !1 > pytest tests/utils/test_parallelize.py                                                                                                                                                               27s py squidpy 14:14:25
========================================================================================================================== test session starts ===========================================================================================================================
platform darwin -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0
rootdir: /Users/selman/projects/squidpy
configfile: pyproject.toml
plugins: anyio-4.12.1, mock-3.15.1, fast-array-utils-1.3.1, xdist-3.8.0, timeout-2.4.0, typeguard-4.4.4, zarr-3.1.5, cov-7.0.0
collected 12 items                                                                                                                                                                                                                                                       

tests/utils/test_parallelize.py Fatal Python error: Aborted

Thread 0x0000000174ff3000 (most recent call first):
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/multiprocessing/pool.py", line 579 in _handle_results
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 995 in run
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 1044 in _bootstrap_inner
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 1015 in _bootstrap

Thread 0x0000000173fe7000 (most recent call first):
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 995 in run
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 1044 in _bootstrap_inner
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 1015 in _bootstrap

Thread 0x0000000172fdb000 (most recent call first):
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/selectors.py", line 398 in select
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/multiprocessing/connection.py", line 1148 in wait
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 995 in run
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 1044 in _bootstrap_inner
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 1015 in _bootstrap

Thread 0x0000000171fcf000 (most recent call first):
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/multiprocessing/connection.py", line 648 in SocketClient
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/multiprocessing/connection.py", line 525 in Client
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/multiprocessing/managers.py", line 814 in _connect
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/multiprocessing/managers.py", line 827 in _callmethod
  File "<string>", line 2 in put
  File "/Users/selman/projects/squidpy/tests/utils/test_parallelize.py", line 50 in mock_runner
  File "/Users/selman/projects/squidpy/src/squidpy/_utils.py", line 63 in _callback_wrapper
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/joblib/parallel.py", line 607 in __call__
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/joblib/_utils.py", line 109 in __call__
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/multiprocessing/pool.py", line 125 in worker
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 995 in run
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 1044 in _bootstrap_inner
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 1015 in _bootstrap

Current thread 0x0000000170fc3000 (most recent call first):
  File "/Users/selman/projects/squidpy/tests/utils/test_parallelize.py", line 22 in wrap_numba_check
  File "/Users/selman/projects/squidpy/tests/utils/test_parallelize.py", line 48 in mock_runner
  File "/Users/selman/projects/squidpy/src/squidpy/_utils.py", line 63 in _callback_wrapper
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/joblib/parallel.py", line 607 in __call__
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/joblib/_utils.py", line 109 in __call__
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/multiprocessing/pool.py", line 125 in worker
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 995 in run
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 1044 in _bootstrap_inner
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 1015 in _bootstrap

Thread 0x000000016ffb7000 (most recent call first):
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/multiprocessing/connection.py", line 395 in _recv
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/multiprocessing/connection.py", line 430 in _recv_bytes
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/multiprocessing/connection.py", line 250 in recv
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/multiprocessing/managers.py", line 831 in _callmethod
  File "<string>", line 2 in get
  File "/Users/selman/projects/squidpy/src/squidpy/_utils.py", line 164 in update
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 995 in run
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 1044 in _bootstrap_inner
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 1015 in _bootstrap

Thread 0x000000016efab000 (most recent call first):
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 363 in wait
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 660 in wait
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/tqdm/_monitor.py", line 60 in run
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 1044 in _bootstrap_inner
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/threading.py", line 1015 in _bootstrap

Thread 0x00000001fd92ec40 (most recent call first):
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/joblib/parallel.py", line 1800 in _retrieve
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/joblib/parallel.py", line 1682 in _get_outputs
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/joblib/parallel.py", line 2072 in __call__
  File "/Users/selman/projects/squidpy/src/squidpy/_utils.py", line 192 in wrapper
  File "/Users/selman/projects/squidpy/tests/utils/test_parallelize.py", line 104 in test_parallelize
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/_pytest/python.py", line 166 in pytest_pyfunc_call
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/pluggy/_callers.py", line 121 in _multicall
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/pluggy/_hooks.py", line 512 in __call__
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/_pytest/python.py", line 1720 in runtest
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/_pytest/runner.py", line 179 in pytest_runtest_call
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/pluggy/_callers.py", line 121 in _multicall
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/pluggy/_hooks.py", line 512 in __call__
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/_pytest/runner.py", line 245 in <lambda>
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/_pytest/runner.py", line 353 in from_call
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/_pytest/runner.py", line 244 in call_and_report
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/_pytest/runner.py", line 137 in runtestprotocol
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/_pytest/runner.py", line 118 in pytest_runtest_protocol
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/pluggy/_callers.py", line 121 in _multicall
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/pluggy/_hooks.py", line 512 in __call__
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/_pytest/main.py", line 396 in pytest_runtestloop
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/pluggy/_callers.py", line 121 in _multicall
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/pluggy/_hooks.py", line 512 in __call__
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/_pytest/main.py", line 372 in _main
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/_pytest/main.py", line 318 in wrap_session
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/_pytest/main.py", line 365 in pytest_cmdline_main
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/pluggy/_callers.py", line 121 in _multicall
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/pluggy/_hooks.py", line 512 in __call__
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/_pytest/config/__init__.py", line 199 in main
  File "/Users/selman/miniforge3/envs/squidpy/lib/python3.13/site-packages/_pytest/config/__init__.py", line 223 in console_main
  File "/Users/selman/miniforge3/envs/squidpy/bin/pytest", line 7 in <module>

Extension modules: numpy._core._multiarray_umath, numpy.linalg._umath_linalg, _cyutility, scipy._cyutility, 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, charset_normalizer.md, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, yaml._yaml, psutil._psutil_osx, markupsafe._speedups, scipy._lib._uarray._uarray, 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.fftpack.convolve, h5py._errors, h5py.defs, h5py._objects, h5py.h5, h5py.utils, h5py.h5t, h5py.h5s, h5py.h5ac, h5py.h5p, h5py.h5r, h5py._npystrings, h5py._proxy, h5py._conv, h5py.h5z, h5py.h5a, h5py.h5d, h5py.h5ds, h5py.h5g, h5py.h5i, h5py.h5o, h5py.h5f, h5py.h5fd, h5py.h5pl, h5py.h5l, h5py._selector, numcodecs.compat_ext, numcodecs.blosc, numcodecs.zstd, numcodecs.lz4, numcodecs._shuffle, numcodecs.jenkins, google_crc32c._crc32c, numcodecs.vlen, numcodecs.fletcher32, backports.zstd._zstd, pyarrow.lib, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pyarrow._compute, pandas._libs.ops, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, scipy.io.matlab._mio_utils, scipy.io.matlab._streams, scipy.io.matlab._mio5_utils, numba.core.typeconv._typeconv, numba._helperlib, numba._dynfunc, numba._dispatcher, numba.core.runtime._nrt_python, numba.np.ufunc._internal, numba.experimental.jitclass._box, shapely.lib, shapely._geos, shapely._geometry_helpers, pyproj._compat, pyproj._context, pyproj._network, pyproj._version, pyproj._geod, pyproj.list, pyproj._crs, pyproj.database, pyproj._transformer, pyproj._sync, PIL._imaging, kiwisolver._cext, sklearn.__check_build._check_build, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._batched_linalg, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_schur_sqrtm, 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._arpacklib, scipy.sparse.linalg._propack, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._hausdorff, scipy.spatial._distance_wrap, scipy.spatial.transform._rotation_cy, scipy.spatial.transform._rigid_transform_cy, scipy.optimize._group_columns, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._slsqplib, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, 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.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.interpolate._dierckx, scipy.interpolate._ppoly, scipy.interpolate._interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, 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.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.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, sklearn._cyutility, sklearn.utils._isfinite, sklearn.utils.sparsefuncs_fast, sklearn.utils.murmurhash, sklearn.utils._openmp_helpers, sklearn.utils._random, igraph._igraph, leidenalg._c_leiden, torch._C, torch._C._dynamo.autograd_compiler, torch._C._dynamo.eval_frame, torch._C._dynamo.guards, torch._C._dynamo.utils, torch._C._fft, torch._C._linalg, torch._C._nested, torch._C._nn, torch._C._sparse, torch._C._special, skimage.measure._moments_cy, skimage.measure._find_contours_cy, skimage.measure._marching_cubes_lewiner_cy, numba.mviewbuf, numba.types.itertools, requests.packages.charset_normalizer.md, requests.packages.chardet.md, scipy.cluster._vq, scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering, skimage.segmentation._slic, skimage.transform._warps_cy, skimage.filters._multiotsu, skimage.morphology._misc_cy, skimage.measure._ccomp, _skeletonize_lee_cy, skimage.morphology._skeletonize_lee_cy, skimage.morphology._skeletonize_various_cy, skimage._shared.geometry, skimage.measure._pnpoly, skimage.morphology._convex_hull, skimage.morphology._grayreconstruct, skimage.morphology._extrema_cy, skimage.morphology._flood_fill_cy, skimage.morphology._max_tree, skimage.segmentation._felzenszwalb_cy, sklearn.metrics.cluster._expected_mutual_info_fast, sklearn.metrics._dist_metrics, sklearn.metrics._pairwise_distances_reduction._datasets_pair, sklearn.utils._cython_blas, sklearn.metrics._pairwise_distances_reduction._base, sklearn.metrics._pairwise_distances_reduction._middle_term_computer, sklearn.utils._heap, sklearn.utils._sorting, sklearn.metrics._pairwise_distances_reduction._argkmin, sklearn.metrics._pairwise_distances_reduction._argkmin_classmode, sklearn.utils._vector_sentinel, sklearn.metrics._pairwise_distances_reduction._radius_neighbors, sklearn.metrics._pairwise_distances_reduction._radius_neighbors_classmode, sklearn.metrics._pairwise_fast, sklearn.preprocessing._csr_polynomial_expansion, sklearn.preprocessing._target_encoder_fast, sklearn.neighbors._partition_nodes, sklearn.neighbors._ball_tree, sklearn.neighbors._kd_tree, sklearn.utils.arrayfuncs, sklearn.utils._seq_dataset, sklearn.linear_model._cd_fast, _loss, sklearn._loss._loss, sklearn.linear_model._sag_fast, sklearn.svm._liblinear, sklearn.svm._libsvm, sklearn.svm._libsvm_sparse, sklearn.utils._weight_vector, sklearn.linear_model._sgd_fast, sklearn.decomposition._online_lda_fast, sklearn.decomposition._cdnmf_fast, sklearn.tree._utils, sklearn.neighbors._quad_tree, sklearn.tree._tree, sklearn.tree._partitioner, sklearn.tree._splitter, sklearn.tree._criterion, sklearn.ensemble._gradient_boosting, sklearn.ensemble._hist_gradient_boosting.common, sklearn.ensemble._hist_gradient_boosting._gradient_boosting, sklearn.ensemble._hist_gradient_boosting._binning, sklearn.ensemble._hist_gradient_boosting._bitset, sklearn.ensemble._hist_gradient_boosting.histogram, sklearn.ensemble._hist_gradient_boosting._predictor, sklearn.ensemble._hist_gradient_boosting.splitting, sklearn.utils._fast_dict, sklearn.cluster._hierarchical_fast, sklearn.cluster._k_means_common, sklearn.cluster._k_means_elkan, sklearn.cluster._k_means_lloyd, sklearn.cluster._k_means_minibatch, sklearn.cluster._dbscan_inner, sklearn.cluster._hdbscan._tree, sklearn.cluster._hdbscan._linkage, sklearn.cluster._hdbscan._reachability, sklearn._isotonic, sklearn.manifold._barnes_hut_tsne, sklearn.manifold._utils, skimage._shared.transform, skimage.feature._texture, skimage.segmentation._watershed_cy, _cffi_backend (total: 309)
[1]    94946 abort      pytest tests/utils/test_parallelize.py

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