nrn-glia 0.1.5

Package manager for NEURON

Glia: NEURON package manager

Package manager for NEURON.

Installation

Glia can be installed from pip.

pip install nrn-glia

Usage

When Glia is imported it will check for glia packages and compile them into a library for NEURON, afterwards immediatly loading it into NEURON aswell.

from neuron import h
import glia as g

Only assets following the Glia naming convention will be included in the library and are available either directly using their namespaced name, or using glia.insert:

section = h.Section(name="soma")
# Add the default Kv1 mechanism provided in the `example` package.
section.insert("glia__example__Kv1__0")
# Preferably use glia's mechanism resolver to load your favourite Kv1 mechanism.
g.insert(section, "Kv1")

Asset management

Glia allows for multiple assets to refer to the same mechanism by giving them a unique name per package. The standard naming convention is as follows:

glia__<package-name>__<asset-name>__<variant-name>

Double underscores in packages, assets or variant names are not allowed.

This naming convention allows for multiple people to provide an implementation of the same asset, and by using variants even one package can provide multiple variations on the same mechanism.

Glia will by default use the variant 0 and if only 1 asset with the same name is found no further configuration is required. If you install multiple packages that provide the same asset, or if you would like to specify another variant you will need to instruct Glia to do so.

There are 3 different scopes for providing asset preferences:

• Global scope: Selects a default mechanism asset.
• Script scope: Selects a default mechanism asset for the remainder of the Python script.
• Single use: Selects a mechanism asset for a single glia.insert call

Single use

Whenever you call glia.insert you can append your preferences for that insert:

g.insert('Kv1', pkg='not_my_models', variant='high_activity')

Script scope

Use glia.select to select a preferred mechanism asset, similar to the single use syntax:

section_global_Kv1 = h.Section()
section_local_Kv1 = h.Section()
g.insert(section_global_Kv1, 'Kv1') # Will use your global Kv1 mechanism
g.select('Kv1', pkg='not_my_models', variant='high_activity')
g.insert(section_local_Kv1, 'Kv1') # Will use the above selected Kv1 mechanism

Global scope

Applying global scope uses the Glia command-line tool and will configure glia to always select a mechanism asset as default.

Go to your favorite command-line tool and execute:

glia select Kv1 --pkg=some_pkg_name --variant=non_default