Testing issue: py-elephant
Summary
| Summary | Spack package test failure |
| Package info |
py-elephant (py-quantities?) |
| System | |
| Related |
The py-elephant tests were sucessfull the last time they run, so this probably has to do with the latest version of py-quantities that was just installed, py-quantities@0.14.0.
Steps to reproduce the issue
$ spack spack install --test root py-elephant@0.11.2
==> Installing py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr
==> No binary for py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr found: installing from source
==> Using cached archive: /mnt/spack_v0.18.1_t/var/spack/cache/_source-cache/archive/f8/f8759fff0bbb136ae4ffc8d1eacadeea8ba56610d705c3bf207de87ada3ba240.tar.gz
==> No patches needed for py-elephant
==> py-elephant: Executing phase: 'install'
==> Error: ProcessError: Command exited with status 1:
'/mnt/spack_v0.18.1_t/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0/py-pytest-6.2.5-zebzseziv7gfxyr6cjduxuchrd2vnz77/bin/pytest'Error message
The test error message (first 1000 lines) from spack-build-out.txt is the following:
Error message
Successfully installed elephant-0.11.2
Removed build tracker: '/tmp/pip-req-tracker-_ck5jyn3'
==> Testing package py-elephant-0.11.2-hzvoyj6
==> [2023-02-14-05:39:45.459867] Running install-time tests
==> [2023-02-14-05:39:45.460095] ('RUN-TESTS: install-time tests [test]',)
==> [2023-02-14-05:39:56.181488] '/mnt/spack_v0.18.1_t/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0/py-pytest-6.2.5-zebzseziv7gfxyr6cjduxuchrd2vnz77/bin/pytest'
============================= test session starts ==============================
platform linux -- Python 3.8.11, pytest-6.2.5, py-1.11.0, pluggy-0.13.0
rootdir: /tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src
collected 675 items
elephant/test/test_asset.py ssssssssssssssssssssssssssss [ 4%]
elephant/test/test_causality.py ................ [ 6%]
elephant/test/test_cell_assembly_detection.py ... [ 6%]
elephant/test/test_change_point_detection.py ............ [ 8%]
elephant/test/test_conversion.py ....................................... [ 14%]
......... [ 15%]
elephant/test/test_csd.py .......... [ 17%]
elephant/test/test_cubic.py ... [ 17%]
elephant/test/test_gpfa.py sssssssssssss [ 19%]
elephant/test/test_icsd.py ................... [ 22%]
elephant/test/test_kcsd.py ....... [ 23%]
elephant/test/test_kernels.py ...................... [ 26%]
elephant/test/test_neo_tools.py ........................................ [ 32%]
.......................... [ 36%]
elephant/test/test_pandas_bridge.py .................................... [ 41%]
...................... [ 45%]
elephant/test/test_parallel.py . [ 45%]
elephant/test/test_phase_analysis.py ................... [ 48%]
elephant/test/test_signal_processing.py ................................ [ 52%]
................. [ 55%]
elephant/test/test_spade.py s....s...... [ 57%]
elephant/test/test_spectral.py ............... [ 59%]
elephant/test/test_spike_train_correlation.py ......................... [ 63%]
elephant/test/test_spike_train_dissimilarity.py ....... [ 64%]
elephant/test/test_spike_train_generation.py ........................... [ 68%]
.......... [ 69%]
elephant/test/test_spike_train_surrogates.py ........................... [ 73%]
....... [ 74%]
elephant/test/test_spike_train_synchrony.py .................... [ 77%]
elephant/test/test_sta.py ............................. [ 81%]
elephant/test/test_statistics.py ....................................... [ 87%]
.........F.................................... [ 94%]
elephant/test/test_unitary_event_analysis.py .......................... [ 98%]
elephant/test/test_utils.py .. [ 98%]
elephant/test/test_waveform_features.py ......... [100%]
=================================== FAILURES ===================================
_____________________ LVRTestCase.test_lvr_with_quantities _____________________
self = <elephant.test.test_statistics.LVRTestCase testMethod=test_lvr_with_quantities>
def test_lvr_with_quantities(self):
seq = pq.Quantity(self.test_seq, units='ms')
assert_array_almost_equal(statistics.lvr(seq), self.target, decimal=9)
seq = pq.Quantity(self.test_seq, units='ms').rescale('s')
assert_array_almost_equal(statistics.lvr(seq), self.target, decimal=9)
E AssertionError:
E Arrays are not almost equal to 9 decimals
E
E x and y nan location mismatch:
E x: array(nan)
E y: array(2.184536346)
elephant/test/test_statistics.py:414: AssertionError
=============================== warnings summary ===============================
elephant/test/test_neo_tools.py:24
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/test/test_neo_tools.py:24: DeprecationWarning: Importing from numpy.testing.utils is deprecated since 1.15.0, import from numpy.testing instead.
from numpy.testing.utils import assert_array_equal
elephant/test/test_pandas_bridge.py:24
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/test/test_pandas_bridge.py:24: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
from pandas.util.testing import assert_frame_equal, assert_index_equal
elephant/pandas_bridge.py:32
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/pandas_bridge.py:32: DeprecationWarning: pandas_bridge module will be removed in Elephant v0.8.x
warnings.warn("pandas_bridge module will be removed in Elephant v0.8.x",
elephant/parallel/init.py:47
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/parallel/init.py:47: UserWarning: mpi4py package is missing. Please run 'pip install mpi4py' in a terminal to activate MPI features.
warnings.warn("mpi4py package is missing. Please run 'pip install mpi4py' "
elephant/test/test_causality.py: 16 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/causality/granger.py:288: FutureWarning: rcond parameter will change to the default of machine precision times max(M, N) where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass rcond=None, to keep using the old, explicitly pass rcond=-1.
np.linalg.lstsq(yule_walker_matrix, positive_lag_covariances)[0]
elephant/test/test_causality.py: 13 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/causality/granger.py:489: UserWarning: The value of the log determinant is at or below the tolerance level. Proceeding with computation.
warnings.warn("The value of the log determinant is at or below the "
elephant/test/test_causality.py::PairwiseGrangerTestCase::test_pairwise_granger_error_null_signals
/mnt/spack_v0.18.1_t/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0/py-numpy-1.21.6-6fewtq7oarp3vtwlxrrcofz5sxwt55s7/lib/python3.8/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
elephant/test/test_causality.py::PairwiseGrangerTestCase::test_pairwise_granger_error_null_signals
/mnt/spack_v0.18.1_t/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0/py-numpy-1.21.6-6fewtq7oarp3vtwlxrrcofz5sxwt55s7/lib/python3.8/site-packages/numpy/core/_methods.py:181: RuntimeWarning: invalid value encountered in true_divide
ret = um.true_divide(
elephant/test/test_causality.py::PairwiseGrangerTestCase::test_pairwise_granger_error_null_signals
/mnt/spack_v0.18.1_t/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0/py-numpy-1.21.6-6fewtq7oarp3vtwlxrrcofz5sxwt55s7/lib/python3.8/site-packages/numpy/linalg/linalg.py:2098: RuntimeWarning: invalid value encountered in slogdet
sign, logdet = _umath_linalg.slogdet(a, signature=signature)
elephant/test/test_cell_assembly_detection.py::CadTestCase::test_cad_msip
elephant/test/test_cell_assembly_detection.py::CadTestCase::test_cad_single_sip
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:260: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
sign_pairs_matrix = np.zeros((n_neurons, n_neurons), dtype=np.int)
elephant/test/test_cell_assembly_detection.py: 132 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:633: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
maxrate = np.int(max(max(binned_pair[0]), max(binned_pair[1])))
elephant/test/test_cell_assembly_detection.py: 132 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:637: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
par_processes = np.zeros((maxrate, 2, ntp), dtype=np.int)
elephant/test/test_cell_assembly_detection.py: 132 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:638: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
par_proc_expectation = np.zeros(maxrate, dtype=np.int)
elephant/test/test_cell_assembly_detection.py: 342 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:641: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
par_processes[i] = np.array(binned_pair > i, dtype=np.int)
elephant/test/test_cell_assembly_detection.py: 132 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:492: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
n_chunks = np.int(n_chunks)
elephant/test/test_cell_assembly_detection.py: 132 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:493: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
size_chunks = np.int(size_chunks)
elephant/test/test_cell_assembly_detection.py: 132 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:499: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
binned_pair_cut = np.array([np.zeros(length - max_lag, dtype=np.int),
elephant/test/test_cell_assembly_detection.py: 132 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:500: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.zeros(length - max_lag, dtype=np.int)])
elephant/test/test_cell_assembly_detection.py: 132 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:852: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
marginal_counts = np.zeros((nch, maxrate, 2), dtype=np.int)
elephant/test/test_cell_assembly_detection.py: 132 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:858: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
maxrate_t = np.zeros(nch, dtype=np.int)
elephant/test/test_cell_assembly_detection.py: 132 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:861: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
ch_nn = np.zeros(nch, dtype=np.int)
elephant/test/test_cell_assembly_detection.py: 1320 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:872: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.int(maxrate_t[iii]))]
elephant/test/test_cell_assembly_detection.py: 1320 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:874: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
for i in range(np.int(maxrate_t[iii])):
elephant/test/test_cell_assembly_detection.py: 2682 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:876: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
(2, len(binned_pair_chunked[0])), dtype=np.int)
elephant/test/test_cell_assembly_detection.py: 2682 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:878: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
dtype=np.int)
elephant/test/test_cell_assembly_detection.py: 1320 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:880: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
for i in range(np.int(maxrate_t[iii])):
elephant/test/test_cell_assembly_detection.py: 2682 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:883: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
marginal_counts[iii][i][0] = np.int(np.sum(par_processes_a))
elephant/test/test_cell_assembly_detection.py: 2682 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/cell_assembly_detection.py:884: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
marginal_counts[iii][i][1] = np.int(np.sum(par_processes_b))
elephant/test/test_cell_assembly_detection.py: 1 warning
elephant/test/test_conversion.py: 1 warning
elephant/test/test_spade.py: 1 warning
elephant/test/test_sta.py: 9 warnings
elephant/test/test_unitary_event_analysis.py: 1 warning
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/conversion.py:1170: UserWarning: Binning discarded 1 last spike(s) of the input spiketrain
warnings.warn("Binning discarded {} last spike(s) of the "
elephant/test/test_conversion.py::BinnedSpikeTrainTestCase::test_binnend_spiketrain_different_input_units
elephant/test/test_conversion.py::BinnedSpikeTrainTestCase::test_repr
elephant/test/test_conversion.py::BinnedSpikeTrainTestCase::test_rescale
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:291: UserWarning: Correcting 2 rounding errors by shifting the affected spikes into the following bin. You can set tolerance=None to disable this behaviour.
warnings.warn(f'Correcting {num_corrections} rounding errors by '
elephant/test/test_conversion.py::BinnedSpikeTrainTestCase::test_binnend_spiketrain_different_input_units
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/test/test_conversion.py:669: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
1007, 1008, 1009, 1010], dtype=np.float
elephant/test/test_conversion.py::BinnedSpikeTrainTestCase::test_binnend_spiketrain_different_input_units
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/test/test_conversion.py:673: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
1008.5, 1009.5], dtype=np.float) * pq.ms
elephant/test/test_conversion.py::BinnedSpikeTrainTestCase::test_different_input_types
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/conversion.py:442: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
spiketrains = np.asarray(spiketrains)
elephant/test/test_conversion.py::BinnedSpikeTrainTestCase::test_get_num_of_spikes
elephant/test/test_conversion.py::BinnedSpikeTrainTestCase::test_to_spike_trains
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/conversion.py:703: UserWarning: The sparse matrix format is CSC. For better performance, specify the CSR format while constructing a BinnedSpikeTrain(sparse_format='csr')
warnings.warn("The sparse matrix format is CSC. For better "
elephant/test/test_conversion.py::BinnedSpikeTrainTestCase::test_slice
/mnt/spack_v0.18.1_t/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0/py-scipy-1.8.1-jxxra3ybzx3ltdmxs6woa3nl2k7vzx3m/lib/python3.8/site-packages/scipy/sparse/_index.py:146: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil_matrix is more efficient.
self._set_arrayXarray(i, j, x)
elephant/test/test_conversion.py: 1 warning
elephant/test/test_parallel.py: 10 warnings
elephant/test/test_spike_train_correlation.py: 2 warnings
elephant/test/test_spike_train_dissimilarity.py: 21 warnings
elephant/test/test_spike_train_generation.py: 8 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/spike_train_generation.py:1118: DeprecationWarning: 'homogeneous_poisson_process' is deprecated; use 'StationaryPoissonProcess'.
warnings.warn(
elephant/test/test_conversion.py::BinnedSpikeTrainTestCase::test_to_spike_trains
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:291: UserWarning: Correcting 1 rounding errors by shifting the affected spikes into the following bin. You can set tolerance=None to disable this behaviour.
warnings.warn(f'Correcting {num_corrections} rounding errors by '
elephant/test/test_csd.py::LFP_TestCase::test_lfp1d_electrodes
elephant/test/test_csd.py::CSD1D_TestCase::test_inputs_deltasplineicsd
elephant/test/test_csd.py::CSD1D_TestCase::test_inputs_standardcsd
elephant/test/test_csd.py::CSD1D_TestCase::test_inputs_stepicsd
elephant/test/test_csd.py::CSD1D_TestCase::test_inuts_kcsd
elephant/test/test_csd.py::CSD1D_TestCase::test_validate_inputs
elephant/test/test_kcsd.py::KCSD1D_TestCase::test_kcsd1d_estimate
elephant/test/test_kcsd.py::KCSD1D_TestCase::test_valid_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/utility_functions.py:253: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
ele_x = np.mgrid[xlims[0]: xlims[1]: np.complex(0, res)]
elephant/test/test_csd.py::LFP_TestCase::test_lfp2d_electrodes
elephant/test/test_csd.py::CSD2D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_kcsd2d_estimate
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_moi_estimate
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_valid_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/utility_functions.py:257: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
ele_x, ele_y = np.mgrid[xlims[0]: xlims[1]: np.complex(0, res),
elephant/test/test_csd.py::LFP_TestCase::test_lfp2d_electrodes
elephant/test/test_csd.py::CSD2D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_kcsd2d_estimate
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_moi_estimate
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_valid_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/utility_functions.py:258: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
ylims[0]: ylims[1]: np.complex(0, res)]
elephant/test/test_csd.py::LFP_TestCase::test_lfp3d_electrodes
elephant/test/test_csd.py::CSD3D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_kcsd3d_estimate
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_valid_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/utility_functions.py:263: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
ele_x, ele_y, ele_z = np.mgrid[xlims[0]: xlims[1]: np.complex(0, res),
elephant/test/test_csd.py::LFP_TestCase::test_lfp3d_electrodes
elephant/test/test_csd.py::CSD3D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_kcsd3d_estimate
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_valid_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/utility_functions.py:264: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
ylims[0]: ylims[1]: np.complex(0, res),
elephant/test/test_csd.py::LFP_TestCase::test_lfp3d_electrodes
elephant/test/test_csd.py::CSD3D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_kcsd3d_estimate
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_valid_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/utility_functions.py:265: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
zlims[0]: zlims[1]: np.complex(0, res)]
elephant/test/test_csd.py::LFP_TestCase::test_lfp3d_electrodes
elephant/test/test_csd.py::CSD3D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_kcsd3d_estimate
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_valid_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density.py:320: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
x_limits[0]: x_limits[1]: np.complex(0, resolution),
elephant/test/test_csd.py::LFP_TestCase::test_lfp3d_electrodes
elephant/test/test_csd.py::CSD3D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_kcsd3d_estimate
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_valid_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density.py:321: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
y_limits[0]: y_limits[1]: np.complex(0, resolution),
elephant/test/test_csd.py::LFP_TestCase::test_lfp3d_electrodes
elephant/test/test_csd.py::CSD3D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_kcsd3d_estimate
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_valid_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density.py:322: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
z_limits[0]: z_limits[1]: np.complex(0, resolution)
elephant/test/test_csd.py::CSD1D_TestCase::test_inuts_kcsd
elephant/test/test_kcsd.py::KCSD1D_TestCase::test_kcsd1d_estimate
elephant/test/test_kcsd.py::KCSD1D_TestCase::test_valid_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/KCSD.py:397: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
self.estm_x = np.mgrid[self.xmin:self.xmax:np.complex(0,nx)]
elephant/test/test_csd.py::CSD1D_TestCase::test_inuts_kcsd
elephant/test/test_kcsd.py::KCSD1D_TestCase::test_kcsd1d_estimate
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/utility_functions.py:74: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.complex(0, n_src)]
elephant/test/test_csd.py: 12090 warnings
elephant/test/test_kcsd.py: 7592 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/KCSD.py:320: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
B_new = np.matrix(B_train) + (lambd*I_matrix)
elephant/test/test_csd.py: 24180 warnings
elephant/test/test_kcsd.py: 15184 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/KCSD.py:322: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
beta_new = np.dot(np.matrix(B_new).I, np.matrix(V_train))
elephant/test/test_csd.py: 12090 warnings
elephant/test/test_kcsd.py: 7592 warnings
elephant/test/test_spike_train_correlation.py: 9 warnings
/mnt/spack_v0.18.1_t/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0/py-numpy-1.21.6-6fewtq7oarp3vtwlxrrcofz5sxwt55s7/lib/python3.8/site-packages/numpy/matrixlib/defmatrix.py:69: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
return matrix(data, dtype=dtype, copy=False)
elephant/test/test_csd.py::CSD1D_TestCase::test_validate_inputs
elephant/test/test_csd.py::CSD1D_TestCase::test_validate_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:93: DeprecationWarning: 'coords' is deprecated; use 'coordinates'
warnings.warn(f"'{old}' is deprecated; use '{new}'",
elephant/test/test_csd.py::CSD2D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_kcsd2d_estimate
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_moi_estimate
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_valid_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/KCSD.py:561: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
self.estm_x, self.estm_y = np.mgrid[self.xmin:self.xmax:np.complex(0,nx),
elephant/test/test_csd.py::CSD2D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_kcsd2d_estimate
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_moi_estimate
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_valid_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/KCSD.py:562: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
self.ymin:self.ymax:np.complex(0,ny)]
elephant/test/test_csd.py::CSD2D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_kcsd2d_estimate
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_moi_estimate
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/utility_functions.py:109: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.complex(0, nx),
elephant/test/test_csd.py::CSD2D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_kcsd2d_estimate
elephant/test/test_kcsd.py::KCSD2D_TestCase::test_moi_estimate
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/utility_functions.py:111: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.complex(0, ny)]
elephant/test/test_csd.py::CSD3D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_kcsd3d_estimate
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_valid_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/KCSD.py:851: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
self.estm_x, self.estm_y, self.estm_z = np.mgrid[self.xmin:self.xmax:np.complex(0,nx),
elephant/test/test_csd.py::CSD3D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_kcsd3d_estimate
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_valid_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/KCSD.py:852: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
self.ymin:self.ymax:np.complex(0,ny),
elephant/test/test_csd.py::CSD3D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_kcsd3d_estimate
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_valid_inputs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/KCSD.py:853: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
self.zmin:self.zmax:np.complex(0,nz)]
elephant/test/test_csd.py::CSD3D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_kcsd3d_estimate
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/utility_functions.py:189: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.complex(0, nx),
elephant/test/test_csd.py::CSD3D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_kcsd3d_estimate
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/utility_functions.py:191: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.complex(0, ny),
elephant/test/test_csd.py::CSD3D_TestCase::test_kcsd2d_init
elephant/test/test_kcsd.py::KCSD3D_TestCase::test_kcsd3d_estimate
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/current_source_density_src/utility_functions.py:193: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.complex(0, nz)]
elephant/test/test_phase_analysis.py: 11994 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/phase_analysis.py:177: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
interpolation = (1 - z) * np.exp(np.complex(0, p1)) \
elephant/test/test_phase_analysis.py: 11994 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/phase_analysis.py:178: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
+ z * np.exp(np.complex(0, p2))
elephant/test/test_signal_processing.py::ZscoreTestCase::test_zscore_list_inplace
elephant/test/test_signal_processing.py::ZscoreTestCase::test_zscore_list_inplace
elephant/test/test_signal_processing.py::ZscoreTestCase::test_zscore_single_inplace
elephant/test/test_signal_processing.py::ZscoreTestCase::test_zscore_single_inplace_int
elephant/test/test_signal_processing.py::ZscoreTestCase::test_zscore_single_multidim_inplace
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/signal_processing.py:170: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
if inplace and not np.issubdtype(np.float, sig.dtype):
elephant/test/test_signal_processing.py::ButterTestCase::test_butter_filter_function
elephant/test/test_signal_processing.py::ButterTestCase::test_butter_filter_function
elephant/test/test_signal_processing.py::ButterTestCase::test_butter_filter_function
elephant/test/test_signal_processing.py::ButterTestCase::test_butter_invalid_filter_function
elephant/test/test_signal_processing.py::ButterTestCase::test_butter_missing_cutoff_freqs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:93: DeprecationWarning: 'highpass_freq' is deprecated; use 'highpass_frequency'
warnings.warn(f"'{old}' is deprecated; use '{new}'",
elephant/test/test_signal_processing.py::ButterTestCase::test_butter_filter_function
elephant/test/test_signal_processing.py::ButterTestCase::test_butter_filter_function
elephant/test/test_signal_processing.py::ButterTestCase::test_butter_filter_function
elephant/test/test_signal_processing.py::ButterTestCase::test_butter_missing_cutoff_freqs
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:93: DeprecationWarning: 'lowpass_freq' is deprecated; use 'lowpass_frequency'
warnings.warn(f"'{old}' is deprecated; use '{new}'",
elephant/test/test_signal_processing.py::HilbertTestCase::test_hilbert_pad_type_error
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:93: DeprecationWarning: 'N' is deprecated; use 'padding'
warnings.warn(f"'{old}' is deprecated; use '{new}'",
elephant/test/test_signal_processing.py: 13 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/signal_processing.py:720: DeprecationWarning: np.complex is a deprecated alias for the builtin complex. To silence this warning, use complex by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.complex128 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
wavelet_fts = np.empty([len(freqs), n], dtype=np.complex)
elephant/test/test_signal_processing.py: 21 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/signal_processing.py:676: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
heaviside = np.array(freqs > 0., dtype=np.float)
elephant/test/test_signal_processing.py::WaveletTestCase::test_wavelet_errors
elephant/test/test_signal_processing.py::WaveletTestCase::test_wavelet_errors
elephant/test/test_signal_processing.py::WaveletTestCase::test_wavelet_errors
elephant/test/test_signal_processing.py::WaveletTestCase::test_wavelet_errors
elephant/test/test_signal_processing.py::WaveletTestCase::test_wavelet_errors
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:93: DeprecationWarning: 'freq' is deprecated; use 'frequency'
warnings.warn(f"'{old}' is deprecated; use '{new}'",
elephant/test/test_signal_processing.py::WaveletTestCase::test_wavelet_errors
elephant/test/test_signal_processing.py::WaveletTestCase::test_wavelet_errors
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:93: DeprecationWarning: 'fs' is deprecated; use 'sampling_frequency'
warnings.warn(f"'{old}' is deprecated; use '{new}'",
elephant/test/test_signal_processing.py::WaveletTestCase::test_wavelet_errors
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:93: DeprecationWarning: 'nco' is deprecated; use 'n_cycles'
warnings.warn(f"'{old}' is deprecated; use '{new}'",
elephant/test/test_spade.py::SpadeTestCase::test_parameters
elephant/test/test_spade.py::SpadeTestCase::test_parameters_3d
elephant/test/test_spade.py::SpadeTestCase::test_spade_msip
elephant/test/test_spade.py::SpadeTestCase::test_spade_msip_3d
elephant/test/test_spade.py::SpadeTestCase::test_spade_msip_spiketrainlist
elephant/test/test_spade.py::SpadeTestCase::test_spade_raise_error
elephant/test/test_spade.py::SpadeTestCase::test_spade_spectrum_cpp
elephant/test/test_spade.py::SpadeTestCase::test_spectrum
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/spade.py:679: UserWarning: Optimized C implementation of FCA (fim.so/fim.pyd) not found in elephant/spade_src folder, or not compatible with this Python version. You are using the pure Python implementation of fast fca.
warnings.warn(
elephant/test/test_spade.py::SpadeTestCase::test_parameters
elephant/test/test_spade.py::SpadeTestCase::test_parameters_3d
elephant/test/test_spade.py::SpadeTestCase::test_spade_msip
elephant/test/test_spade.py::SpadeTestCase::test_spade_msip_3d
elephant/test/test_spade.py::SpadeTestCase::test_spade_msip_spiketrainlist
/mnt/spack_v0.18.1_t/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0/py-numpy-1.21.6-6fewtq7oarp3vtwlxrrcofz5sxwt55s7/lib/python3.8/site-packages/numpy/testing/_private/utils.py:706: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
x = np.asanyarray(x)
elephant/test/test_spade.py::SpadeTestCase::test_parameters
elephant/test/test_spade.py::SpadeTestCase::test_parameters_3d
elephant/test/test_spade.py::SpadeTestCase::test_spade_msip
elephant/test/test_spade.py::SpadeTestCase::test_spade_msip_3d
elephant/test/test_spade.py::SpadeTestCase::test_spade_msip_spiketrainlist
/mnt/spack_v0.18.1_t/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0/py-numpy-1.21.6-6fewtq7oarp3vtwlxrrcofz5sxwt55s7/lib/python3.8/site-packages/numpy/testing/_private/utils.py:707: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
y = np.asanyarray(y)
elephant/test/test_spectral.py::WelchPSDTestCase::test_welch_psd_errors
elephant/test/test_spectral.py::WelchPSDTestCase::test_welch_psd_errors
elephant/test/test_spectral.py::WelchCohereTestCase::test_welch_cohere_errors
elephant/test/test_spectral.py::WelchCohereTestCase::test_welch_cohere_errors
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:93: DeprecationWarning: 'len_seg' is deprecated; use 'len_segment'
warnings.warn(f"'{old}' is deprecated; use '{new}'",
elephant/test/test_spectral.py::WelchPSDTestCase::test_welch_psd_errors
elephant/test/test_spectral.py::WelchPSDTestCase::test_welch_psd_errors
elephant/test/test_spectral.py::WelchCohereTestCase::test_welch_cohere_errors
elephant/test/test_spectral.py::WelchCohereTestCase::test_welch_cohere_errors
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:93: DeprecationWarning: 'num_seg' is deprecated; use 'n_segments'
warnings.warn(f"'{old}' is deprecated; use '{new}'",
elephant/test/test_spectral.py::WelchPSDTestCase::test_welch_psd_errors
elephant/test/test_spectral.py::WelchPSDTestCase::test_welch_psd_errors
elephant/test/test_spectral.py::WelchCohereTestCase::test_welch_cohere_errors
elephant/test/test_spectral.py::WelchCohereTestCase::test_welch_cohere_errors
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:93: DeprecationWarning: 'freq_res' is deprecated; use 'frequency_resolution'
warnings.warn(f"'{old}' is deprecated; use '{new}'",
elephant/test/test_spike_train_correlation.py::CrossCorrelationHistogramTest::test_border_correction
/mnt/spack_v0.18.1_t/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0/py-neo-0.11.1-ptmlyqdy6do72xxfgsxynklwtvcfqe5g/lib/python3.8/site-packages/neo/core/basesignal.py:122: RuntimeWarning: invalid value encountered in true_divide
new_signal = f(other, *args)
elephant/test/test_spike_train_correlation.py: 10 warnings
elephant/test/test_spike_train_generation.py: 4 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/spike_train_generation.py:1221: DeprecationWarning: 'homogeneous_gamma_process' is deprecated; use 'StationaryGammaProcess'.
warnings.warn(
elephant/test/test_spike_train_dissimilarity.py: 38 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/spike_train_dissimilarity.py:378: DeprecationWarning: scipy.sqrt is deprecated and will be removed in SciPy 2.0.0, use numpy.lib.scimath.sqrt instead
return sp.sqrt(vr_dist)
elephant/test/test_spike_train_generation.py::NonStationaryPoissonProcessTestCase::test_statistics
elephant/test/test_spike_train_generation.py::NonStationaryPoissonProcessTestCase::test_statistics
elephant/test/test_spike_train_generation.py::NonStationaryPoissonProcessTestCase::test_statistics
elephant/test/test_spike_train_generation.py::NonStationaryPoissonProcessTestCase::test_statistics
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/spike_train_generation.py:1165: DeprecationWarning: 'inhomogeneous_poisson_process' is deprecated; use 'NonStationaryPoissonProcess'.
warnings.warn(
elephant/test/test_spike_train_generation.py::NonStationaryGammaTestCase::test_statistics
elephant/test/test_spike_train_generation.py::NonStationaryGammaTestCase::test_statistics
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/spike_train_generation.py:1263: DeprecationWarning: 'inhomogeneous_gamma_process' is deprecated; use 'nonStationaryGammaProcess'.
warnings.warn(
elephant/test/test_spike_train_surrogates.py::SurrogatesTestCase::test_surr_method
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/spike_train_surrogates.py:1410: DeprecationWarning: 'dither_spikes_with_refractory_period' is deprecated in favor of 'dither_spikes'
warnings.warn("'dither_spikes_with_refractory_period' is deprecated "
elephant/test/test_spike_train_synchrony.py::SynchrofactDetectionTestCase::test_binning_for_input_with_rounding_errors
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:291: UserWarning: Correcting 40 rounding errors by shifting the affected spikes into the following bin. You can set tolerance=None to disable this behaviour.
warnings.warn(f'Correcting {num_corrections} rounding errors by '
elephant/test/test_spike_train_synchrony.py::SynchrofactDetectionTestCase::test_extract
elephant/test/test_spike_train_synchrony.py::SynchrofactDetectionTestCase::test_n_equals_3
elephant/test/test_spike_train_synchrony.py::SynchrofactDetectionTestCase::test_no_synchrofacts
elephant/test/test_spike_train_synchrony.py::SynchrofactDetectionTestCase::test_spread_1
elephant/test/test_spike_train_synchrony.py::SynchrofactDetectionTestCase::test_wrong_input_errors
elephant/test/test_statistics.py::ComplexityTestCase::test_binning_for_input_with_rounding_errors
elephant/test/test_statistics.py::ComplexityTestCase::test_complexity_histogram_spread_1
elephant/test/test_statistics.py::ComplexityTestCase::test_complexity_histogram_spread_2
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:93: DeprecationWarning: 'binsize' is deprecated; use 'bin_size'
warnings.warn(f"'{old}' is deprecated; use '{new}'",
elephant/test/test_statistics.py::IsiTestCase::test_isi_with_plain_array_2d_0
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/statistics.py:153: UserWarning: ISI evaluated to negative values. Please sort the input array.
warnings.warn("ISI evaluated to negative values. "
elephant/test/test_statistics.py::LVRTestCase::test_lvr_raise_error
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/statistics.py:586: UserWarning: No units specified for time_intervals, assuming milliseconds (ms)
warnings.warn('No units specified for time_intervals,'
elephant/test/test_statistics.py::LVRTestCase::test_lvr_with_quantities
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/statistics.py:597: RuntimeWarning: invalid value encountered in true_divide
frac1 = 4 * time_intervals[:-1] * time_intervals[1:] / t**2
elephant/test/test_statistics.py::LVRTestCase::test_lvr_with_quantities
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/statistics.py:598: RuntimeWarning: divide by zero encountered in true_divide
frac2 = 4 * R / t
elephant/test/test_statistics.py: 18 warnings
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/statistics.py:881: UserWarning: The width of the kernel was adjusted to a minimally allowed width.
warnings.warn("The width of the kernel was adjusted to a minimally "
elephant/test/test_statistics.py::ComplexityTestCase::test_binning_for_input_with_rounding_errors
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:299: UserWarning: Correcting a rounding error in the calculation of the number of bins by incrementing the value by 1. You can set tolerance=None to disable this behaviour.
warnings.warn('Correcting a rounding error in the calculation '
elephant/test/test_statistics.py::ComplexityTestCase::test_binning_for_input_with_rounding_errors
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:291: UserWarning: Correcting 39 rounding errors by shifting the affected spikes into the following bin. You can set tolerance=None to disable this behaviour.
warnings.warn(f'Correcting {num_corrections} rounding errors by '
elephant/test/test_statistics.py::ComplexityTestCase::test_binning_for_input_with_rounding_errors
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/utils.py:291: UserWarning: Correcting 116 rounding errors by shifting the affected spikes into the following bin. You can set tolerance=None to disable this behaviour.
warnings.warn(f'Correcting {num_corrections} rounding errors by '
elephant/test/test_statistics.py::ComplexityTestCase::test_complexity_pdf
elephant/test/test_statistics.py::ComplexityTestCase::test_complexity_pdf_deprecated
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/statistics.py:1437: UserWarning: No sampling rate specified. Note that using the complexity epoch to get precise spike times can lead to rounding errors.
warnings.warn('No sampling rate specified. '
elephant/test/test_statistics.py::ComplexityTestCase::test_complexity_pdf_deprecated
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/statistics.py:1119: DeprecationWarning: 'complexity_pdf' is deprecated in favor of the Complexity class which has a 'pdf' method
warnings.warn("'complexity_pdf' is deprecated in favor of the Complexity "
elephant/test/test_unitary_event_analysis.py::UETestCase::test_Riehle_et_al_97_UE
elephant/test/test_unitary_event_analysis.py::UETestCase::test_jointJ_window_analysis
/mnt/spack_v0.18.1_t/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0/py-numpy-1.21.6-6fewtq7oarp3vtwlxrrcofz5sxwt55s7/lib/python3.8/site-packages/numpy/core/shape_base.py:121: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
ary = asanyarray(ary)
elephant/test/test_unitary_event_analysis.py::UETestCase::test_Riehle_et_al_97_UE
/tmp/spack/spack-stage/spack-stage-py-elephant-0.11.2-hzvoyj6r3tjpwkrp2ipf65746esflshr/spack-src/elephant/conversion.py:1170: UserWarning: Binning discarded 3 last spike(s) of the input spiketrain
warnings.warn("Binning discarded {} last spike(s) of the "
elephant/test/test_unitary_event_analysis.py::UETestCase::test_multiple_neurons
/mnt/spack_v0.18.1_t/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0/py-numpy-1.21.6-6fewtq7oarp3vtwlxrrcofz5sxwt55s7/lib/python3.8/site-packages/numpy/core/shape_base.py:420: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
arrays = [asanyarray(arr) for arr in arrays]
-- Docs: https://docs.pytest.org/en/stable/warnings.html
=========================== short test summary info ============================
FAILED elephant/test/test_statistics.py::LVRTestCase::test_lvr_with_quantities
==== 1 failed, 631 passed, 43 skipped, 119444 warnings in 233.72s (0:03:53) ====