Command-Line Interface

Open up your favorite terminal and enter the cerebellar-models --help command to verify you correctly installed the software.

The list of cerebellar-models commands are listed below.

Note

Parameters included between angle brackets are example values, parameters between square brackets are optional, leave off the brackets in the actual command.

Retrieve a canonical circuit configuration

Warning

For the time being, this command has to be run inside the cerebellar-models folder.

cerebellar-models configure [--output_folder <./path>] [--species <mouse>] [--extension <yaml>] [--microzones]

This command will construct a BSB configuration file based on the canonical cerebellar circuit developed by the DBBS.

You will be presented with a list of forms to fill directly in the terminal. Use the up and down arrows of your keyboard to select an option that you want to modify, then press tab to select it.

Options can either be a list or an entry to manually fill (for text or number). For lists, you would have to select one or many items. An item can be chosen with the up and down arrow, selected by pressing the right arrow and validated with the enter key.

  • --species: Species to build the configuration from.

  • --output_folder: Path to the output folder where the configuration will be stored.

  • --extension: File extension for the configuration. Can be either json or yaml.

  • --microzones: Flag to split your circuit into 2 separated microzones (not set by default).

Note

When selecting a NEST simulation via the CLI, the output configuration will also contain an additional simulation based on the associated stimulation protocol (see NEST paradigms).

Re-compile NESTML neuron models

cerebellar-models build-nestml [--model_dir <path>] [--build_dir <path>] [--module_name <name>]

This command forces a full re-compilation of the NESTML neuron models used by the NEST simulator. It is equivalent to calling _build_nest_models(redo=True) programmatically: the existing build cache is cleared and PyNESTML re-generates the C++ source code and reinstalls the NEST module cerebmodule.

Running this command is useful when:

  • you have updated or added a .nestml model file and want to force the rebuild without clearing the cache manually;

  • the cached module has become stale after a NEST or PyNESTML upgrade.

Note

This command requires a working NEST and PyNESTML installation (install with pip install cerebellar-models[nest]).

  • --model_dir: Directory that contains the .nestml source files. Defaults to the nest_models folder inside the installed package.

  • --build_dir: Directory where the compiled NEST module will be written. Defaults to the user-level cache directory managed by the package (appdirs.user_cache_dir("cerebellar_models")).