Contributing to MRI-Degad

MRI_Degad python package uses uv pacakge manager to manage its dependencies. You’ll need it installed on your machine before contributing to the software. Installation instructions can be found on the Installation Page.

MRI_Degad currently only caters to T1w gadolinium-enhanced modality images.

Note: These instructions are only recommended if you are making changes to the MRI-Degad codebase and committing these back to the repository or if you are using Snakemake’s cluster execution profiles.

Setup the development environment

Once uv is available, clone this repository and install all dependencies (including dev):

git clone https://github.com/mackenziesnyder/MRI_DeGad.git
cd MRI_Degad 
uv venv
source .venv/bin/activate  # On Windows: .venv\Scripts\activate
uv pip install -e .[dev]

Then, you can run mri_degad:

mri_degad -h

You can exit the virtual environment with:

deactivate

Running and fixing code format quality

We use a few tools, including black, snakefmt, and isort to ensure formatting and style of our codebase is consistent. There are two task runners you can use to check and fix your code, which can be invoked with:

uv run quality-fix
uv run quality-check

Questions, Issues, Suggestions, and Other Feedback

Please reach out if you have any questions, suggestions, or other feedback related to this software—either through email (m25snyde@uwaterloo.ca) or the discussions page.