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  • Nora Abi Akar's avatar
    Gap Junction mechanisms (#1682) · dc371e5d
    Nora Abi Akar authored
    Adds support for user-defined gap junction mechanisms. Fixes #1600.
    
    - API Change: Wrap `mechanism_desc` in one of `density`, `synapse`, `junction` to be able to differentiate the kind of placed mechanism between point and junction mechanisms. 
    - API Change: The `ggap` parameter of a `gap_junction_connection` renamed to `weight` and is not a unit-less parameter. 
    - Mechanism ABI change: New `peer_index` vector which stores the indices of the peer sites of a gap-junction-connection. New mechanism kind. 
    - Internal API change: `shared_state` no longer controls the gap junction current contribution, that is now handled in the mechanism callbacks.
    - Modcc change: Add `JUNCTION_PROCESS` and `v_peer` keywords to nmodl, the first to identify a gap-junction mechanism, the second to access the peer voltage of a gap-junction connection. Modify modcc to be able to compile nmodl and generate correct code.
    - Behavior change: gap-junctions now contribute to both the current and conductance of a CV as opposed to just the current.
    - Add new "gj" mechanism, to replace the built-in constant-conductance based linear gap-junction implementation.
    - Fix unit tests.
    - Fix python wrapper. 
    - Fix docs. 
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