Closed ntolley closed 1 year ago
Renaming this issue to reflect problems that came up during #318
Here are the major points that should be addressed in a followup PR
_Connectivity
a proper class wit public and private attributes.drop(probability, src_gids, target_gids)
.plot
net.connectivity
list: conns = pick_connecitivity(conns, src=‘L2_pyramidal')
plot_connectivity(net, conn)
@kenloi this is the issue I was describing earlier about verbose warnings. This would also be a good opportunity to learn about what is considered a "valid" connection in the canonical microcircuit.
what's left here @ntolley ?
I recall from an older discussion that we moved away from making _Connectivity
it's own class. Also #419 was the major goal for adding more verbose warnings so I think it's save to close this issue!
This was raised by @rythorpe in #276. The current connectivity API allows for duplicates of the same connection when specified through
net.add_connection()
. Currently connectivity information is stored undernet.connectivity
as a list, so implementing this check would require looping through the entire list every time a new connection as added which seems like an unnecessary overhead. I think this check will require convertingnet.connectivity
to easily lookup/index existing connections between cells.Another much needed check is ensuring valid cell-cell connections are specified. Currently invalid connection types (inhibitory synapses on L2 proximal/distal dendrites for example) only throw an error when the network is built. Ideally this will be caught in
add_connection()
. This should also come with clear documentation of what constitutes valid cell-cell connections.