aind-dynamic-foraging

A repository for the Dynamic Foraging task.

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📋 General instructions

This repository follows the project structure laid out in the Aind.Behavior.Services repository.

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🔧 Prerequisites

Pre-requisites for running the project can be found here.

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🚀 Deployment

For convenience, once third-party dependencies are installed, Bonsai and python virtual environments can be bootstrapped by running:

./scripts/deploy.ps1

from the root of the repository.

⚙️ Generating settings files

The Dynamic Foraging tasks is instantiated by a set of three settings files that strictly follow a DSL schema. These files are:

• task_logic.json
• rig.json
• session.json

Examples on how to generate these files can be found in the ./Examples directory of the repository. Once generated, these are the the only required inputs to run the Bonsai workflow in ./src/main.bonsai.

The workflow can thus be executed using the Bonsai CLI:

"./bonsai/bonsai.exe" "./src/main.bonsai" -p SessionPath=<path-to-session.json> -p RigPath=<path-to-rig.json> -p TaskLogicPath=<path-to-task_logic.json>

However, for a better experiment management user experience, it is recommended to use the provided experiment launcher below.

[> ] CLI tools

The platform exposes a few CLI tools to facilitate various tasks. Tools are available via:

uv run dynamic-foraging <subcommand>

for a list of all sub commands available:

uv run dynamic-foraging -h

You may need to install optional dependencies depending on the sub-commands you run.

🔄 Regenerating schemas

DSL schemas can be modified in ./src/aind_behavior_dynamic_foraging/rig.py (or (...)/task_logic.py`).

Once modified, changes to the DSL must be propagated to json-schema and csharp API. This can be done by running:

uv run dynamic-foraging regenerate