Update the Arbor backend to support Arbor 0.10.0 – 0.12.2#842
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Arbor 0.10.0 introduced breaking changes to its Python bindings that prevented the backend from importing/running. Update the backend and version pins accordingly: - Units at the user interface: physical quantities passed to decor.set_property/set_ion, threshold_detector, iclamp, the spike schedules and simulation.run must now be unit-typed (arbor.units). - Morphology loaders now return a bundle; use load_swc_neuron(f).segment_tree instead of the removed raw=True argument. - Probes now require a tag string and sampling is addressed by (gid, tag) instead of the removed cell_member index. Also fixes a latent frequency-unit bug in SpikeSourcePoisson: rate (Hz) was passed into Arbor's kHz frequency slot; it is now tagged with U.Hz, matching PyNN's Hz semantics and the NEURON/NEST backends.
Differences between these versions are handled in a new pyNN/arbor/_compat.py.
Arbor >= 0.10 requires the delay argument to arbor.connection to be a unit-typed quantity rather than a plain float; pass it in ms.
…tantiation MultiCompartmentNeuron.__init__ replaced the ion-channel and post-synaptic classes with instances in place, mutating the class-level dicts that hold them. A second instantiation of the same cell type then failed with "object is not callable", and setting ion_channels on the class in one test leaked instances into others.
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coverage: 71.713% (+0.6%) from 71.141% — apdavison:update-arbor into NeuralEnsemble:master |
# Conflicts: # test/system/scenarios/test_cell_types.py
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The Arbor backend previously required Arbor 0.9.0 and no longer worked with current Arbor releases. This PR updates it to work, from a single codebase, with every Arbor version from 0.10.0 (the version currently in the EBRAINS Software Distribution) through 0.12.2, and adds additional tests.
Arbor API changes accommodated:
arbor.units) for properties, stimuli, thresholds, schedules and run/dt;cv_policy_max_extentalso gained units in 0.12. (This also fixed a latent Hz-vs-kHzSpikeSourcePoissonbug.)load_swc_neuron(...).segment_tree.decoronto thecable_cellconstructorspike_recording.local— the global callback was broken by the 0.12 MPI rework (arbor-sim/arbor#2511).iclamp→i_clamp, anddecor.place()dropped the label for current stimuli.In addition, the catalogue
.sois now keyed onarbor.__version__to avoid stale ABIs.