The following failure mode relates to HocObjects, which are provided by the neuron package: > > > nseg = np.sum([s.nseg for s in self._hobj.all]) > > E TypeError: Not an iterable HocObject > > > > bmtk/simulator/bionet/morphology.py:117: TypeError
I observe that with python3.13, there is an error output about neuron failing to find mechanisms in a directory that is supposed to have some .mod files: > > ============================= test session starts > > ============================== > > platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0 > > rootdir: /build/reproducible-path/bmtk-1.1.1+ds > > plugins: typeguard-4.4.1 > > NEURON mechanisms not found in > > /build/reproducible-path/bmtk-1.1.1+ds/.pybuild/cpython3_3.13/build/bmtk/tests/simulator/bionet/components/mechanisms. > > collected 399 items / 1 skipped > > > > bmtk/tests/builder/auxi/test_edge_connectors.py .. [ > > 0%] The failing test is related to the simulator bionet, which does suggest that the neuron error at the beginning of the test may be related: > > bmtk/tests/simulator/bionet/test_morphology.py F.FFFs..FF [ > > 28%] In the meantime, there were no issues with python3.12: > > ============================= test session starts > > ============================== > > platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 > > rootdir: /build/reproducible-path/bmtk-1.1.1+ds > > plugins: typeguard-4.4.1 > > collected 361 items / 5 skipped > > > > bmtk/tests/builder/auxi/test_edge_connectors.py .. [ > > 0%] I'm not sure of the root cause yet. I don't witness differences at the end of the build between the two mechanisms/ directories between the python3.12 and python3.13 builds. There could be something about one of neuron or bmtk not supporting well dealing with both Python version during the time of the transition, but in this case 6 test failures out of 400 tests seems a bit light. Anyway, checkpointing my thoughts for future self or for others benefit, have a nice day, :) -- .''`. Étienne Mollier <[email protected]> : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/2, please excuse my verbosity `- on air: Van der Graaf Generator - My Room (Waiting For…
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