Scripts Repository

A collection of useful BrainGlobe related scripts. This repo consists of the following directories:

Scripts

Scripts organised by package to aid in the use of BrainGlobe tools.

Skills

Various skills which may be useful for matters relating to BrainGlobe without necessarily being Python scripts.

Usage

Python scripts

Instructions for macOS / Linux / Windows users

Most scripts list their dependencies in an inline metadata block at the top of the file, so they are best run with uv, which installs them for you.

In case it is not installed, on macOS and Linux install uv with the following command:

$ curl -LsSf https://astral.sh/uv/install.sh | sh

and on Windows:

> powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

On an HPC cluster it may be available as a module instead:

$ module load uv

Then, you can run a script by running the following command in your terminal:

$ uv run script.py

uv creates an isolated environment with the script's dependencies the first time, and reuses it afterwards. Scripts that only use the standard library can also be run with plain Python:

$ python script.py

Scripts that take arguments print their options with:

$ uv run script.py --help