SSN implementation in BMTK

[shixnya]

A new PopNet option based on Stabilized Supralinear Network.

Simulating 4 population will be 0.2ms per simulated second.
A network simulation example as well as parameter optimization tutorial notebook is provided.

[Copilot]

Pull Request Overview

Adds support for a Stabilized Supralinear Network (SSN) option in PopNet by introducing new simulation modules, integrating SSN into the PopNet API, and updating related utilities.

• Introduce SimulatorMod base class and SSN modules (RatesRecorderMod, InitStatesMod, ExternalRatesMod) for recording rates, initializing states, and applying external inputs.
• Register default SSN activation functions and expose them via the package.
• Integrate SSN target into PopNetwork/PopSimulator, extend DIPDE compatibility, update core SONATA reader and node sets, and enhance the plot_rates analyzer to handle CSV/HDF5.

Reviewed Changes

Copilot reviewed 15 out of 74 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
bmtk/simulator/popnet/ssn/modules/sim_module.py	Adds SimulatorMod base class for lifecycle hooks in SSN simulations
bmtk/simulator/popnet/ssn/modules/rates_recorder.py	Implements RatesRecorderMod for exporting firing rates to CSV or HDF5
bmtk/simulator/popnet/ssn/modules/initial_states.py	Implements InitStatesMod with multiple initialization backends (CSV, function)
bmtk/simulator/popnet/ssn/modules/external_inputs.py	Implements ExternalRatesMod for loading external input streams
bmtk/simulator/popnet/ssn/default_setters/activation_functions.py	Registers a default ReLU (relu2) activation function via add_activation_function
bmtk/simulator/popnet/ssn/init.py	Exports SSN entry points (PopNetwork, PopSimulator, function caches)
bmtk/simulator/popnet/dipde/popsimulator.py	Adds from_json helper and imports SimulationConfig for DIPDE simulator
bmtk/simulator/popnet/dipde/popnetwork.py	Adds target_simulator property and fixes import paths for DIPDE
bmtk/simulator/core/sonata_reader/node_adaptor.py	Extends model_type handling to include 'rate_population'
bmtk/simulator/core/node_sets.py	Implements __len__ for NodeSet
bmtk/analyzer/firing_rates.py	Adds a new plot_rates function supporting CSV and HDF5 rate files

Comments suppressed due to low confidence (2)

bmtk/simulator/popnet/ssn/modules/initial_states.py:103

• [nitpick] The exception message 'AAAA' is not descriptive. Provide a clear message explaining the unsupported distribution type.

                raise Exception("AAAA")

bmtk/simulator/popnet/ssn/modules/initial_states.py:29

• self.__name__ is undefined on instances; use self.__class__.__name__ (or similar) to reference the class name in the error message.

            raise ValueError(f'{self.__name__}: Error in {self._name} input module, no valid module [options: csv, constant, random, function]')