The bsb-nest from dbbs-lab

Feature request: Randomness

At the moment, there are no way to randomize the initial state of the NEST network with BSB.
NEST has some random function implemented that could be used to randomize the values of certain parameters (e.g. V_m for neurons).
There should be a way to set the seed of the NEST simulation too.

`synapse_models` attribute error

With NEST 3.1:

Traceback (most recent call last):
  File "/home/emiliano/Documenti/nest_31/bsb-nest31/bin/bsb", line 8, in <module>
    sys.exit(handle_cli())
  File "/home/emiliano/Documenti/nest_31/bsb-core/bsb/cli/__init__.py", line 11, in handle_cli
    handle_command(sys.argv[1:], exit=True)
  File "/home/emiliano/Documenti/nest_31/bsb-core/bsb/cli/__init__.py", line 31, in handle_command
    namespace.handler(namespace, dryrun=dryrun)
  File "/home/emiliano/Documenti/nest_31/bsb-core/bsb/cli/commands/__init__.py", line 98, in execute_handler
    self.handler(context)
  File "/home/emiliano/Documenti/nest_31/bsb-core/bsb/cli/commands/_commands.py", line 207, in handler
    result = network.run_simulation(sim_name)
  File "/home/emiliano/Documenti/nest_31/bsb-core/bsb/profiling.py", line 158, in decorated
    return f(*args, **kwargs)
  File "/home/emiliano/Documenti/nest_31/bsb-core/bsb/core.py", line 425, in run_simulation
    return adapter.simulate(simulation)[0]
  File "/home/emiliano/Documenti/nest_31/bsb-nest/bsb_nest/adapter.py", line 65, in simulate
    return super().simulate(simulation)
  File "/home/emiliano/Documenti/nest_31/bsb-core/bsb/simulation/adapter.py", line 76, in simulate
    data = self.prepare(simulation)
  File "/home/emiliano/Documenti/nest_31/bsb-nest/bsb_nest/adapter.py", line 80, in prepare
    self.connect_neurons(simulation)
  File "/home/emiliano/Documenti/nest_31/bsb-nest/bsb_nest/adapter.py", line 175, in connect_neurons
    raise NestConnectError(f"{connection_model} error during connect.")
bsb.exceptions.NestConnectError: <bsb_nest.connection.NestConnection object 'mossy_fibers_to_glomerulus' at 0x7fe7d0902020> error during connect.
Traceback (most recent call last):
  File "/home/emiliano/Documenti/nest_31/bsb-nest/bsb_nest/adapter.py", line 171, in connect_neurons
    ] = connection_model.create_connections(
  File "/home/emiliano/Documenti/nest_31/bsb-nest/bsb_nest/connection.py", line 63, in create_connections
    if syn_spec["synapse_model"] not in nest.synapse_models:
AttributeError: module 'nest' has no attribute 'synapse_models'

Installation of Nest takes too much github Action time

Every push on this repository requires the unit tests to pass, which makes sense. However, this means that Github needs to install NEST for the 3 maintained python versions. This takes a lot of dbbs allocation time for the Github action.

Note that we noticed this issue only recently, when we pushed new features. This should not happen very often.

While we wait for NEST to be pip installable, should we adapt the actions or install NEST differently?

Feature request: multimeter

As a user, I need to record neurons' membrane potential during Nest simulation with bsb. This corresponds to the multimeter tool in Nest.

dbbs-lab / bsb-nest Goto Github PK

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bsb-nest's Issues

Feature request: Randomness

`synapse_models` attribute error

Installation of Nest takes too much github Action time

Feature request: multimeter

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