pyrates

export.pyrates

PyRates Integration Module

Provides modular conversion between TVBO Dynamics/Network models and PyRates YAML format.

PyRates uses a YAML-based template system with: - OperatorTemplate: Contains equations and variables (dynamics) - NodeTemplate: Contains one or more operators (node) - EdgeTemplate: Defines edge operators (coupling) - CircuitTemplate: Contains nodes and edges (network)

TVBO Templates (modular): - tvbo-pyrates-model.yaml.mako: OperatorTemplate only (dynamics) - tvbo-pyrates-network.yaml.mako: NodeTemplate + CircuitTemplate (topology) - tvbo-pyrates-experiment.yaml.mako: Complete runnable YAML (model + network)

Example

from tvbo import Dynamics model = Dynamics(“JansenRitModel”)

Export model only (OperatorTemplate)

operator_yaml = to_pyrates_model_yaml(model)

Export network only (Node + Circuit)

network_yaml = to_pyrates_network_yaml(model)

Export complete experiment (ready to run)

experiment_yaml = model.to_yaml(format=“pyrates”) model.to_yaml(format=“pyrates”, filepath=“mymodel.yaml”)

Load a PyRates model

model = Dynamics.from_pyrates(“mymodel.yaml”)

Export a Network (circuit) to PyRates

from tvbo.knowledge.simulation import Network network = Network(connectome) network.to_yaml(format=“pyrates”, filepath=“circuit.yaml”)

References

• PyRates documentation: https://pyrates.readthedocs.io/

Functions

Name	Description
from_pyrates_yaml	Load a PyRates YAML file and return dict for Dynamics constructor.
from_pyrates_yaml_all	Load a PyRates YAML file and return dict of all Dynamics.
network_to_pyrates_yaml_string	Export a TVBO Network to complete PyRates experiment YAML.
to_pyrates_model_yaml	Export a Dynamics model to PyRates OperatorTemplate YAML (model only).
to_pyrates_network_yaml	Export to PyRates NodeTemplate + CircuitTemplate YAML (network topology only).
to_pyrates_yaml_string	Export to complete PyRates experiment YAML (model + network, ready to run).

from_pyrates_yaml

export.pyrates.from_pyrates_yaml(filepath, operator_key=None)

Load a PyRates YAML file and return dict for Dynamics constructor.

Parameters

filepath : str Path to PyRates YAML file. operator_key : str, optional Name of the specific OperatorTemplate to load (without _op suffix). If None, loads the first OperatorTemplate found.

Returns

dict Dictionary suitable for Dynamics(**dict) constructor.

Raises

ValueError If operator_key is specified but not found in the file.

from_pyrates_yaml_all

export.pyrates.from_pyrates_yaml_all(filepath)

Load a PyRates YAML file and return dict of all Dynamics.

Parameters

filepath : str Path to PyRates YAML file.

Returns

dict[str, dict] Dictionary mapping operator names to Dynamics-compatible dicts. Keys are the clean names (without _op suffix).

network_to_pyrates_yaml_string

export.pyrates.network_to_pyrates_yaml_string(network, filepath=None)

Export a TVBO Network to complete PyRates experiment YAML.

Alias for to_pyrates_yaml_string(network=network, filepath=filepath).

to_pyrates_model_yaml

export.pyrates.to_pyrates_model_yaml(dynamics, filepath=None)

Export a Dynamics model to PyRates OperatorTemplate YAML (model only).

This generates ONLY the OperatorTemplate (dynamics/equations). Use to_pyrates_network_yaml for topology, or to_pyrates_yaml_string for complete.

Parameters

dynamics : Dynamics TVBO Dynamics model to export. filepath : str, optional Path to write the YAML file. If None, returns the YAML string.

Returns

str YAML string (or filepath if written to file).

to_pyrates_network_yaml

export.pyrates.to_pyrates_network_yaml(
    dynamics=None,
    network=None,
    filepath=None,
)

Export to PyRates NodeTemplate + CircuitTemplate YAML (network topology only).

This generates ONLY the network structure (nodes, edges, circuit). Operators are referenced but not defined.

Parameters

dynamics : Dynamics, optional TVBO Dynamics model for single-node circuit. network : Network, optional TVBO Network for multi-node circuit. filepath : str, optional Path to write the YAML file. If None, returns the YAML string.

Returns

str YAML string (or filepath if written to file).

to_pyrates_yaml_string

export.pyrates.to_pyrates_yaml_string(
    dynamics=None,
    network=None,
    filepath=None,
)

Export to complete PyRates experiment YAML (model + network, ready to run).

This generates a self-contained YAML with OperatorTemplate, NodeTemplate, and CircuitTemplate - everything needed to run with PyRates.

Parameters

dynamics : Dynamics or dict[str, Dynamics], optional TVBO Dynamics model for single-node experiment, or a dictionary of dynamics models keyed by name for heterogeneous networks. network : Network, optional TVBO Network for multi-node experiment. filepath : str, optional Path to write the YAML file. If None, returns the YAML string.

Returns

str YAML string (or filepath if written to file).