CHBH CLI Tool for neuroimagers.

To use the tool download the repo and place the files in the directory you wish to start your project.

Installing tool

This will download the script and making it executable from anywhere in your terminal.

git clone https://github.com/chbh-opensource/chbh-cli.git
cd chbh-cli
bash ./chbh install

Setting up an M/EEG environment

You can create new python environments using the chbh command. This will copy a template pyproject.toml file into your working directory and initialise a new virtual environment with a range of common tools installed in it.

cd /path/to/my/working/directory
chbh venv meeg
source .venv/bin/activate

This works using UV, and can be further customised after install using uv add full docs here.

For example, if we want to include seaborn.

uv add seaborn

The package will be added to the virtual environment and the dependencies syncronised.

Full Usage

CHBH environment manager

Usage:
  chbh install
      Install the chbh command and environment template.

  chbh version
      Show the version of the installed CHBH environment template.

  chbh bear-modules
      Load the basic BlueBEAR modules recommended for Python by CHBH.

  chbh summarise-logs <log-directory>
      Summarise SLURM logs in the specified directory.
      This may install a python instance the first time it runs after install.

  chbh venv <group> [group ...]
      Create or update a UV environment in the current directory.

Available venv groups:
  meeg     EEG, MEG and electrophysiology tools
  mri      MRI and neuroimaging tools
  sleep    Sleep analysis tools
  dev      Development and code-quality tools

Examples:
  chbh install

  chbh version

  chbh bear-modules

  chbh summarise-logs ./logs

  chbh venv meeg

  chbh venv mri

  chbh venv meeg mri

  chbh venv meeg sleep

  chbh venv meeg mri sleep dev

Notes:
  - A .venv is created in the current working directory.
  - If no pyproject.toml exists, the CHBH template is copied into
    the current directory.
  - Existing pyproject.toml files are preserved and used as-is.
  - Activate the environment with:

        source .venv/bin/activate