Py-elephant build issue on JURECA for esd/25.05-rc
Summary
| Summary | Spack package build failure |
| Package info | |
| System | JURECA |
| Related |
Steps to reproduce the issue
$ spack spec -I <spec>
...
$ spack install --test root
...Error message
Error message
Building wheel for elephant (setup.py): finished with status 'done'
Created wheel for elephant: filename=elephant-1.1.1-cp311-cp311-linux_x86_64.whl size=1217098 sha256=13962a0914ec01675a6af12ef0e9794ac24f99befc9f353a20fa13d91078d18c
Stored in directory: /tmp/pip-ephem-wheel-cache-tgsi0yz3/wheels/4f/63/53/053708130cc56d3d22af95fcc764d72ea207507159e1f31b76
Successfully built elephant
Installing collected packages: elephant
Successfully installed elephant-1.1.1
Removed build tracker: '/tmp/pip-build-tracker-p6d4fg8o'
==> [2025-04-25-11:53:10.188676] '/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/install/linux-rocky9-zen2/gcc-13.3.0/py-pytest-8.2.1-tey5i6xssbjbtcvollvjsr3h5j42lfw2/bin/pytest' '-k' 'not test_WPLI_ground_truth_consistency_real_LFP_dataset and not test_multitaper_cohere_perfect_cohere and not test_parallel'
============================= test session starts ==============================
platform linux -- Python 3.11.10, pytest-8.2.1, pluggy-1.5.0
rootdir: /p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src
collected 726 items / 3 deselected / 723 selected
elephant/test/test_asset.py ...F.........F........................ [ 5%]
elephant/test/test_causality.py ............................ [ 9%]
elephant/test/test_cell_assembly_detection.py ... [ 9%]
elephant/test/test_change_point_detection.py ............ [ 11%]
elephant/test/test_conversion.py ....................................... [ 16%]
......... [ 17%]
elephant/test/test_cubic.py ... [ 18%]
elephant/test/test_current_source_density.py ............ [ 19%]
elephant/test/test_datasets.py ... [ 20%]
elephant/test/test_gpfa.py ................ [ 22%]
elephant/test/test_icsd.py ................... [ 25%]
elephant/test/test_kcsd.py ....... [ 26%]
elephant/test/test_kernels.py ...................... [ 29%]
elephant/test/test_neo_tools.py ........................................ [ 34%]
.......................... [ 38%]
elephant/test/test_phase_analysis.py .......................... [ 41%]
elephant/test/test_signal_processing.py ................................ [ 46%]
.................. [ 48%]
elephant/test/test_spade.py s....s....... [ 50%]
elephant/test/test_spectral.py ................................ [ 55%]
elephant/test/test_spike_train_correlation.py .......................... [ 58%]
......... [ 59%]
elephant/test/test_spike_train_dissimilarity.py ....... [ 60%]
elephant/test/test_spike_train_generation.py ........................... [ 64%]
.......... [ 65%]
elephant/test/test_spike_train_surrogates.py ........................... [ 69%]
......... [ 70%]
elephant/test/test_spike_train_synchrony.py .................... [ 73%]
elephant/test/test_sta.py ............................. [ 77%]
elephant/test/test_statistics.py ....................................... [ 83%]
..................................................... [ 90%]
elephant/test/test_total_spiking_probability_edges.py ... [ 90%]
elephant/test/test_trials.py ........................ [ 94%]
elephant/test/test_unitary_event_analysis.py .......................... [ 97%]
elephant/test/test_utils.py ....... [ 98%]
elephant/test/test_waveform_features.py ......... [100%]
=================================== FAILURES ===================================
________________ AssetTestCase.test_asset_choose_backend_opencl ________________
self = <elephant.test.test_asset.AssetTestCase testMethod=test_asset_choose_backend_opencl>
def test_asset_choose_backend_opencl(self):
class TestClassBackend(asset._GPUBackend):
def __init__(self):
super().__init__()
self.backend = self._choose_backend()
def cpu(self):
return "cpu"
def pycuda(self):
return "cuda"
def pyopencl(self):
return "opencl"
# check which backend is chosen if environment variable for opencl
# is not set
os.environ.pop('ELEPHANT_USE_OPENCL', None)
# create object of TestClass
backend_obj = TestClassBackend()
if HAVE_PYOPENCL:
self.assertEqual(backend_obj.backend(), 'opencl')
else:
# if environment variable is not set and no module pyopencl or
# device is found: choose cpu backend
self.assertEqual(backend_obj.backend(), 'cpu')
E AssertionError: 'cuda' != 'cpu'
E - cuda
E + cpu
elephant/test/test_asset.py:543: AssertionError
____________________ AssetTestCase.test_pmat_neighbors_gpu _____________________
self = <elephant.test.test_asset.AssetTestCase testMethod=test_pmat_neighbors_gpu>
def test_pmat_neighbors_gpu(self):
np.random.seed(12)
n_largest = 3
pmat1 = np.random.random_sample((40, 40)).astype(np.float32)
np.fill_diagonal(pmat1, 0.5)
pmat2 = np.random.random_sample((70, 23)).astype(np.float32)
pmat3 = np.random.random_sample((27, 93)).astype(np.float32)
for pmat in (pmat1, pmat2, pmat3):
for filter_size in (4, 8, 11):
filter_shape = (filter_size, 3)
with warnings.catch_warnings():
# ignore even filter sizes
warnings.simplefilter('ignore', UserWarning)
pmat_neigh = asset._PMatNeighbors(
filter_shape=filter_shape, n_largest=n_largest)
lmat_true = pmat_neigh.cpu(pmat)
if HAVE_PYOPENCL:
lmat_opencl = pmat_neigh.pyopencl(pmat)
assert_array_almost_equal(lmat_opencl, lmat_true)
if HAVE_CUDA:
lmat_cuda = pmat_neigh.pycuda(pmat)
elephant/test/test_asset.py:357:
elephant/asset/asset.py:1358: in pycuda
kernel(lmat_gpu.gpudata, mat_gpu, grid=(grid_size, 1),
func = <pycuda._driver.Function object at 0x14e858b783a0>
args = (<pycuda._driver.DeviceAllocation object at 0x14e85986b300>, <pycuda._driver.DeviceAllocation object at 0x14e85986b920>)
kwargs = {}, grid = (1, 1), stream = None, block = (1024, 1, 1), shared = 0
texrefs = [], time_kernel = False, handlers = []
arg_buf = b'\x00\x00 +\xe8\x14\x00\x00\x000 +\xe8\x14\x00\x00'
def function_call(func, *args, **kwargs):
grid = kwargs.pop("grid", (1, 1))
stream = kwargs.pop("stream", None)
block = kwargs.pop("block", None)
shared = kwargs.pop("shared", 0)
texrefs = kwargs.pop("texrefs", [])
time_kernel = kwargs.pop("time_kernel", False)
if kwargs:
raise ValueError(
"extra keyword arguments: %s" % (",".join(kwargs.keys()))
)
if block is None:
raise ValueError("must specify block size")
func._set_block_shape(*block)
handlers, arg_buf = _build_arg_buf(args)
for handler in handlers:
handler.pre_call(stream)
for texref in texrefs:
func.param_set_texref(texref)
post_handlers = [
handler for handler in handlers if hasattr(handler, "post_call")
]
if stream is None:
if time_kernel:
Context.synchronize()
from time import time
start_time = time()
func._launch_kernel(grid, block, arg_buf, shared, None)
E pycuda._driver.LaunchError: cuLaunchKernel failed: too many resources requested for launch
../../../../../install/linux-rocky9-zen2/gcc-13.3.0/py-pycuda-2023.1-wx6czukd7lrgexw74x5jr7nnoome4yum/lib/python3.11/site-packages/pycuda/driver.py:502: LaunchError
----------------------------- Captured stderr call -----------------------------
Largest neighbors CPU: 0%| | 0/33 [00:00<?, ?it/s]
Largest neighbors CPU: 100%|██████████| 33/33 [00:00<00:00, 14461.61it/s]
Largest neighbors CUDA: 0%| | 0/1 [00:00<?, ?it/s]
Largest neighbors CUDA: 100%|██████████| 1/1 [00:00<00:00, 1.98it/s]
Largest neighbors CUDA: 100%|██████████| 1/1 [00:00<00:00, 1.98it/s]
Largest neighbors CPU: 0%| | 0/25 [00:00<?, ?it/s]
Largest neighbors CPU: 100%|██████████| 25/25 [00:00<00:00, 8236.40it/s]
Largest neighbors CUDA: 0%| | 0/1 [00:00<?, ?it/s]
Largest neighbors CUDA: 0%| | 0/1 [00:00<?, ?it/s]
=============================== warnings summary ===============================
../../../../../install/linux-rocky9-zen2/gcc-13.3.0/py-neo-0.13.3-woy73ynchwos3hia4sz3ez4n2ep5pzad/lib/python3.11/site-packages/neo/core/spiketrain.py:227: 1 warning
elephant/test/test_asset.py: 630 warnings
elephant/test/test_cell_assembly_detection.py: 57 warnings
elephant/test/test_change_point_detection.py: 4 warnings
elephant/test/test_conversion.py: 210 warnings
elephant/test/test_gpfa.py: 1000 warnings
elephant/test/test_neo_tools.py: 1024 warnings
elephant/test/test_phase_analysis.py: 36 warnings
elephant/test/test_spade.py: 2051 warnings
elephant/test/test_spike_train_correlation.py: 121 warnings
elephant/test/test_spike_train_dissimilarity.py: 174 warnings
elephant/test/test_spike_train_generation.py: 604 warnings
elephant/test/test_spike_train_surrogates.py: 248 warnings
elephant/test/test_spike_train_synchrony.py: 6042 warnings
elephant/test/test_sta.py: 105 warnings
elephant/test/test_statistics.py: 3575 warnings
elephant/test/test_total_spiking_probability_edges.py: 602 warnings
elephant/test/test_trials.py: 144 warnings
elephant/test/test_unitary_event_analysis.py: 1959 warnings
elephant/test/test_utils.py: 57 warnings
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/install/linux-rocky9-zen2/gcc-13.3.0/py-neo-0.13.3-woy73ynchwos3hia4sz3ez4n2ep5pzad/lib/python3.11/site-packages/neo/core/spiketrain.py:227: QuantitiesDeprecationWarning: The 'copy' argument in Quantity is deprecated and will be removed in the future. The argument has no effect since quantities-0.16.0 (to aid numpy-2.0 support).
return pq.Quantity(times, units=units, dtype=dtype, copy=copy), dim
elephant/spectral.py:1035
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/spectral.py:1035: DeprecationWarning: invalid escape sequence '\o'
"""
elephant/test/test_asset.py: 123 warnings
elephant/test/test_cell_assembly_detection.py: 23 warnings
elephant/test/test_conversion.py: 253 warnings
elephant/test/test_gpfa.py: 724 warnings
elephant/test/test_spade.py: 116 warnings
elephant/test/test_spike_train_correlation.py: 116 warnings
elephant/test/test_spike_train_surrogates.py: 20 warnings
elephant/test/test_spike_train_synchrony.py: 13 warnings
elephant/test/test_sta.py: 70 warnings
elephant/test/test_statistics.py: 36 warnings
elephant/test/test_total_spiking_probability_edges.py: 7 warnings
elephant/test/test_unitary_event_analysis.py: 77 warnings
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/conversion.py:380: QuantitiesDeprecationWarning: The 'copy' argument in Quantity is deprecated and will be removed in the future. The argument has no effect since quantities-0.16.0 (to aid numpy-2.0 support).
return pq.Quantity(self._t_start, units=self.units, copy=False)
elephant/test/test_asset.py: 123 warnings
elephant/test/test_cell_assembly_detection.py: 21 warnings
elephant/test/test_conversion.py: 255 warnings
elephant/test/test_gpfa.py: 724 warnings
elephant/test/test_spade.py: 116 warnings
elephant/test/test_spike_train_correlation.py: 116 warnings
elephant/test/test_spike_train_surrogates.py: 20 warnings
elephant/test/test_spike_train_synchrony.py: 9 warnings
elephant/test/test_sta.py: 64 warnings
elephant/test/test_statistics.py: 21 warnings
elephant/test/test_total_spiking_probability_edges.py: 7 warnings
elephant/test/test_unitary_event_analysis.py: 77 warnings
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/conversion.py:387: QuantitiesDeprecationWarning: The 'copy' argument in Quantity is deprecated and will be removed in the future. The argument has no effect since quantities-0.16.0 (to aid numpy-2.0 support).
return pq.Quantity(self._t_stop, units=self.units, copy=False)
elephant/test/test_asset.py: 29 warnings
elephant/test/test_conversion.py: 6 warnings
elephant/test/test_spike_train_synchrony.py: 10 warnings
elephant/test/test_statistics.py: 10 warnings
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/conversion.py:579: QuantitiesDeprecationWarning: The 'copy' argument in Quantity is deprecated and will be removed in the future. The argument has no effect since quantities-0.16.0 (to aid numpy-2.0 support).
return pq.Quantity(bin_edges, units=self.units, copy=False)
elephant/test/test_asset.py: 36 warnings
elephant/test/test_causality.py: 2 warnings
elephant/test/test_cubic.py: 6 warnings
elephant/test/test_current_source_density.py: 19 warnings
elephant/test/test_kcsd.py: 18 warnings
elephant/test/test_phase_analysis.py: 59 warnings
elephant/test/test_signal_processing.py: 148 warnings
elephant/test/test_spectral.py: 38 warnings
elephant/test/test_spike_train_correlation.py: 63 warnings
elephant/test/test_spike_train_generation.py: 78 warnings
elephant/test/test_spike_train_synchrony.py: 9 warnings
elephant/test/test_sta.py: 113 warnings
elephant/test/test_statistics.py: 480 warnings
elephant/test/test_trials.py: 144 warnings
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/install/linux-rocky9-zen2/gcc-13.3.0/py-neo-0.13.3-woy73ynchwos3hia4sz3ez4n2ep5pzad/lib/python3.11/site-packages/neo/core/analogsignal.py:202: QuantitiesDeprecationWarning: The 'copy' argument in Quantity is deprecated and will be removed in the future. The argument has no effect since quantities-0.16.0 (to aid numpy-2.0 support).
obj = pq.Quantity(signal, units=units, dtype=dtype, copy=copy).view(cls)
elephant/test/test_asset.py: 50 warnings
elephant/test/test_conversion.py: 1 warning
elephant/test/test_spike_train_generation.py: 8 warnings
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/spike_train_generation.py:1097: DeprecationWarning: 'homogeneous_poisson_process' is deprecated; use 'StationaryPoissonProcess'.
warnings.warn(
elephant/test/test_asset.py::AssetTestIntegration::test_probability_matrix_symmetric
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/conversion.py:1130: UserWarning: Binning discarded 4 last spike(s) of the input spiketrain
warnings.warn("Binning discarded {} last spike(s) of the "
elephant/test/test_causality.py: 14 warnings
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/causality/granger.py:677: 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
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/install/linux-rocky9-zen2/gcc-13.3.0/py-numpy-1.25.2-rht64kl2m7o45med457qqayaqvbj6h3d/lib/python3.11/site-packages/numpy/core/fromnumeric.py:3504: 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
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/install/linux-rocky9-zen2/gcc-13.3.0/py-numpy-1.25.2-rht64kl2m7o45med457qqayaqvbj6h3d/lib/python3.11/site-packages/numpy/core/_methods.py:121: RuntimeWarning: invalid value encountered in divide
ret = um.true_divide(
elephant/test/test_causality.py::PairwiseGrangerTestCase::test_pairwise_granger_error_null_signals
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/install/linux-rocky9-zen2/gcc-13.3.0/py-numpy-1.25.2-rht64kl2m7o45med457qqayaqvbj6h3d/lib/python3.11/site-packages/numpy/linalg/linalg.py:2120: RuntimeWarning: invalid value encountered in slogdet
sign, logdet = _umath_linalg.slogdet(a, signature=signature)
elephant/test/test_cell_assembly_detection.py: 2 warnings
elephant/test/test_conversion.py: 166 warnings
elephant/test/test_spike_train_correlation.py: 72 warnings
elephant/test/test_spike_train_surrogates.py: 13 warnings
elephant/test/test_sta.py: 16 warnings
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/conversion.py:373: QuantitiesDeprecationWarning: The 'copy' argument in Quantity is deprecated and will be removed in the future. The argument has no effect since quantities-0.16.0 (to aid numpy-2.0 support).
return pq.Quantity(self._bin_size, units=self.units, copy=False)
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_total_spiking_probability_edges.py: 1 warning
elephant/test/test_unitary_event_analysis.py: 1 warning
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/conversion.py:1130: 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_binned_spiketrain_bin_edges
elephant/test/test_conversion.py::BinnedSpikeTrainTestCase::test_binnend_spiketrain_different_input_units
elephant/test/test_conversion.py::BinnedSpikeTrainTestCase::test_binnend_spiketrain_different_input_units
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/conversion.py:600: QuantitiesDeprecationWarning: The 'copy' argument in Quantity is deprecated and will be removed in the future. The argument has no effect since quantities-0.16.0 (to aid numpy-2.0 support).
bin_centers = pq.Quantity(bin_centers, units=self.units, copy=False)
elephant/test/test_conversion.py::BinnedSpikeTrainTestCase::test_get_num_of_spikes
elephant/test/test_conversion.py::BinnedSpikeTrainTestCase::test_to_spike_trains
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/conversion.py:664: 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
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/install/linux-rocky9-zen2/gcc-13.3.0/py-scipy-1.14.1-dkh76mdwbdoyyv3cbkckcxgmb2urnc3w/lib/python3.11/site-packages/scipy/sparse/_index.py:151: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil and dok are more efficient.
self._set_arrayXarray(i, j, x)
elephant/test/test_phase_analysis.py::WeightedPhaseLagIndexTestCase::test_WPLI_ground_truth_consistency_artificial_LFP_dataset
elephant/test/test_phase_analysis.py::WeightedPhaseLagIndexTestCase::test_WPLI_is_minus_one
elephant/test/test_phase_analysis.py::WeightedPhaseLagIndexTestCase::test_WPLI_is_one
elephant/test/test_phase_analysis.py::WeightedPhaseLagIndexTestCase::test_WPLI_is_zero
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/phase_analysis.py:422: RuntimeWarning: invalid value encountered in divide
wpli = wpli_num / wpli_den
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_output_for_specific_pattern
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
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/spade.py:684: 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_spike_train_correlation.py::CovarianceTestCase::test_covariance_binned
elephant/test/test_spike_train_correlation.py::CovarianceTestCase::test_covariance_binned
elephant/test/test_spike_train_correlation.py::CovarianceTestCase::test_covariance_binned_same_spiketrains
elephant/test/test_spike_train_correlation.py::CovarianceTestCase::test_covariance_binned_short_input
elephant/test/test_spike_train_correlation.py::CovarianceTestCase::test_covariance_fast_mode
elephant/test/test_spike_train_correlation.py::CorrCoefTestCase::test_corrcoef_binned_same_spiketrains
elephant/test/test_spike_train_correlation.py::CorrCoefTestCase::test_corrcoef_binned_short_input
elephant/test/test_spike_train_correlation.py::CorrCoefTestCase::test_corrcoef_fast_mode
elephant/test/test_spike_train_correlation.py::CrossCorrelationHistogramTest::test_cross_correlation_histogram
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/install/linux-rocky9-zen2/gcc-13.3.0/py-numpy-1.25.2-rht64kl2m7o45med457qqayaqvbj6h3d/lib/python3.11/site-packages/numpy/matrixlib/defmatrix.py:70: 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_spike_train_correlation.py: 63 warnings
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/spike_train_correlation.py:806: QuantitiesDeprecationWarning: The 'copy' argument in Quantity is deprecated and will be removed in the future. The argument has no effect since quantities-0.16.0 (to aid numpy-2.0 support).
t_start = pq.Quantity((lags[0] - 0.5) * bin_size,
elephant/test/test_spike_train_correlation.py::CrossCorrelationHistogramTest::test_border_correction
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/install/linux-rocky9-zen2/gcc-13.3.0/py-neo-0.13.3-woy73ynchwos3hia4sz3ez4n2ep5pzad/lib/python3.11/site-packages/neo/core/basesignal.py:121: RuntimeWarning: invalid value encountered in divide
new_signal = f(other, *args)
elephant/test/test_spike_train_correlation.py: 13 warnings
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/spike_train_correlation.py:1077: QuantitiesDeprecationWarning: The 'copy' argument in Quantity is deprecated and will be removed in the future. The argument has no effect since quantities-0.16.0 (to aid numpy-2.0 support).
return pq.Quantity(timescale, units=binned_spiketrain.units, copy=False)
elephant/test/test_spike_train_dissimilarity.py::TimeScaleDependSpikeTrainDissimMeasuresTestCase::test_van_rossum_distance
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/spike_train_dissimilarity.py:366: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(vr_dist)
...........................................
elephant/test/test_statistics.py::ComplexityTestCase::test_complexity_pdf_deprecated
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/statistics.py:1240: 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_total_spiking_probability_edges.py::TotalSpikingProbabilityEdgesTestCase::test_total_spiking_probability_edges
elephant/test/test_unitary_event_analysis.py::UETestCase::test_Riehle_et_al_97_UE
/p/usersoftware/ebrains-sw-stack/ebrains-25.02/jurecadc/stage2025/spack-user-cache/deepu1/build-stage/spack-stage-py-elephant-1.1.1-h6ekoxnq5ymtvnin7lum7ugdd6xbpljg/spack-src/elephant/conversion.py:1130: UserWarning: Binning discarded 3 last spike(s) of the input spiketrain
warnings.warn("Binning discarded {} last spike(s) of the "
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED elephant/test/test_asset.py::AssetTestCase::test_asset_choose_backend_opencl
FAILED elephant/test/test_asset.py::AssetTestCase::test_pmat_neighbors_gpu - ...
= 2 failed, 719 passed, 2 skipped, 3 deselected, 23582 warnings in 364.76s (0:06:04) =Information on your system
Additional information
Edited by Rajalekshmi Deepu