Installation issue: py-tvb-library
Summary
| Summary | Spack package test failure |
| Package info | py-tvb-library |
| System | |
| Related |
When updating to Spack v0.23.0 this issue came up. It seems to be an incompatibility with py-scipy@1.14, so constraining the version to :1.13 works, but other packages need a more recent version.
@ldomide would it be possible to provide a patch or add a new version?
Steps to reproduce the issue
$ spack spec -I <spec>
...
$ spack spack install --test root <spec>
...Error message
The test error message (first 1000 lines) from install-time-test-log.txt is the following:
Error message
Successfully installed tvb-library-2.9.1
Removed build tracker: '/mnt/tmp/pip-build-tracker-5bczb67s'
==> [2025-02-21-06:04:39.362872] '/mnt/spack-tests/spack_instance_v0.23.0/ebrains-spack-builds/vendor/spack/opt/spack/[padded-to-128-chars]/linux-ubuntu22.04-x86_64/gcc-13.3.0/py-pytest-8.2.1-l2sxugmr4ejigggrqntmrd4sgcpirzwa/bin/pytest'
============================= test session starts ==============================
platform linux -- Python 3.11.9, pytest-8.2.1, pluggy-1.5.0
benchmark: 3.2.3 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
rootdir: /mnt/tmp/eleni/spack-stage/spack-stage-py-tvb-library-2.9.1-fz3ymiqa563smd4vabfu53s5kmnr3k77/spack-src
plugins: xdist-3.2.0, benchmark-3.2.3
collected 670 items
tvb/tests/library/basic/neotraits/_attr_test.py ....... [ 1%]
tvb/tests/library/basic/neotraits/neotraits_test.py .................... [ 4%]
..................................... [ 9%]
tvb/tests/library/datatypes/connectivity_test.py ..... [ 10%]
tvb/tests/library/datatypes/equations_test.py ............ [ 12%]
tvb/tests/library/datatypes/graph_test.py ... [ 12%]
tvb/tests/library/datatypes/mode_decompositions_test.py .. [ 12%]
tvb/tests/library/datatypes/patterns_test.py ..... [ 13%]
tvb/tests/library/datatypes/projections_test.py ... [ 14%]
tvb/tests/library/datatypes/sensors_test.py .... [ 14%]
tvb/tests/library/datatypes/spectral_test.py .... [ 15%]
tvb/tests/library/datatypes/surfaces_test.py ................ [ 17%]
tvb/tests/library/datatypes/temporal_correlations_test.py . [ 17%]
tvb/tests/library/datatypes/timeseries_test.py ...... [ 18%]
tvb/tests/library/datatypes/volumes_test.py . [ 18%]
tvb/tests/library/simulator/backend/cubackend_test.py ssssss [ 19%]
tvb/tests/library/simulator/backend/nbbackend_mpr_test.py FFFFF..F [ 20%]
tvb/tests/library/simulator/backend/nbbackend_test.py .................. [ 23%]
.....ss. [ 24%]
tvb/tests/library/simulator/backend/nbmprperf_test.py ........ [ 25%]
tvb/tests/library/simulator/backend/npbackend_test.py .................. [ 28%]
....... [ 29%]
tvb/tests/library/simulator/common_test.py ... [ 30%]
tvb/tests/library/simulator/coupling_test.py ......... [ 31%]
tvb/tests/library/simulator/descriptors_test.py .......... [ 32%]
tvb/tests/library/simulator/history_test.py . [ 33%]
tvb/tests/library/simulator/integrators_test.py ............ [ 34%]
tvb/tests/library/simulator/modelir_test.py ..... [ 35%]
tvb/tests/library/simulator/models_test.py .................. [ 38%]
tvb/tests/library/simulator/monitors_test.py ................... [ 41%]
tvb/tests/library/simulator/noise_test.py .. [ 41%]
tvb/tests/library/simulator/regionmapping_test.py . [ 41%]
tvb/tests/library/simulator/rngperf_test.py ............ [ 43%]
tvb/tests/library/simulator/simulator_step_test.py ... [ 43%]
tvb/tests/library/simulator/simulator_test.py .......................... [ 47%]
........................................................................ [ 58%]
........................................................................ [ 69%]
........................................................................ [ 80%]
........................................................................ [ 90%]
............................................................. [ 99%]
tvb/tests/library/simulator/stimulation_test.py . [100%]
=================================== FAILURES ===================================
______________________ TestNbSim.test_local_deterministic ______________________
self = <tvb.tests.library.simulator.backend.nbbackend_mpr_test.TestNbSim testMethod=test_local_deterministic>
def test_local_deterministic(self):
dt = 0.01
G = 0.
sim = simulator.Simulator(
model=models.MontbrioPazoRoxin(),
coupling=coupling.Linear(a=np.array([G])),
connectivity=self._random_network(),
conduction_speed=np.inf,
monitors=[
monitors.Raw()
],
integrator=integrators.HeunStochastic( # matching integrator
dt=dt,
noise=noise.Additive(
nsig=np.array([0.0, 0.0]),
noise_seed=42
)
)
).configure()
tvb/tests/library/simulator/backend/nbbackend_mpr_test.py:67:
self = <tvb.tests.library.simulator.backend.nbbackend_mpr_test.TestNbSim testMethod=test_local_deterministic>
N = 300, density = 0.1, low = 5, high = 250, speed = inf
def _random_network(self, N=300, density=0.1, low=5, high=250, speed=np.inf):
weights = ss.random(N,N, density=density, format='lil')
weights.setdiag(0)
weights = weights.tocsr()
lengths = weights.copy()
lengths.data[:] = np.random.uniform(low=low, high=high, size=lengths.data.shape[0])
N = weights.shape[0]
conn = connectivity.Connectivity(
weights=weights.A,
tract_lengths=lengths.A,
region_labels=np.array( [f'roi_{i}' for i in range(N)]),
centres=np.zeros(N),
speed=np.r_[speed]
)
E AttributeError: 'csr_matrix' object has no attribute 'A'
tvb/tests/library/simulator/backend/nbbackend_mpr_test.py:52: AttributeErrorInformation on your system
Additional information
Activity
added test-error label
Release
tvb-library 2.9.2is out on Pypi.I have also created this MR: !639 (merged)
If the pipeline works fine, this should be solved, I believe
assigned to @ldomide
mentioned in merge request !639 (merged)
