Support generic SONATA modoverride synapses via helper HOC - #91
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darshanmandge wants to merge 4 commits into
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Support generic SONATA modoverride synapses via helper HOC#91darshanmandge wants to merge 4 commits into
darshanmandge wants to merge 4 commits into
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- Relax ConnectionOverrides.mod_override from Literal["GluSynapse"] to str
- Add bluecellulab.synapse.synapse_helpers.load_synapse_helper for
neurodamus-style auto-loading of {SUFFIX}Helper.hoc via HOC_LIBRARY_PATH
- Add GenericSpikeSynapse class that constructs the point process via the
helper HOC template, matching neurodamus calling convention
- Wire SynapseFactory to dispatch to GenericSpikeSynapse when ModOverride
is set to a non-builtin SUFFIX
- Make U_SYN scaling tolerant of missing properties for non-AMPANMDA
mechanisms
Read the SONATA `modoverride` key when constructing connection overrides, while retaining `mod_override` as a backward-compatible fallback. Add regression coverage for the standard key and connections without a modoverride.
Keep Exp2Syn connection overrides on the built-in synapse path instead of requiring a nonexistent Exp2SynHelper.hoc template. Also fix reStructuredText formatting in the generic synapse docstrings so the documentation build passes with warnings treated as errors.
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Summary
ConnectionOverrides.mod_overrideto support any compiled NEURON mechanism SUFFIX.GenericSpikeSynapse.modoverridekey.mod_overridespelling.Motivation
BlueCelluLab previously restricted
mod_overrideto the built-inGluSynapsemechanism and did not correctly read the SONATA-standardmodoverridekey. As a result, custom mechanisms that reference processes could not be selected via SONATA connection overrides.This change enables SONATA circuits to select arbitrary compiled NMODL mechanisms together with their companion helper HOC templates.
Changes
Generic mod override support
ConnectionOverrides.mod_overridefrom aLiteral["GluSynapse"]tostr | None.GenericSpikeSynapse.GluSynapsepath.Helper HOC loading
Add
bluecellulab.synapse.synapse_helperswith:load_synapse_helper(suffix)helper_available(suffix)The loader follows the Neurodamus convention:
SUFFIX.modSUFFIXHelper.hoc