Configuration wizard for a Neurobagel deployment.

Development environment

Setting up a local development environment

1. Set up a Python environment. We use uv for this.

2. Clone the repository

   git clone https://github.com/neurobagel/configure-nb.git
   cd configure-nb
   

3. Install the CLI and all development dependencies in editable mode:

   uv sync --group dev
   

4. To run configure-nb during development, you can run it directly with uv:

   uv run configure-nb [OPTIONS]
   

Confirm that everything works by running the tests: uv run pytest

Setting up code formatting and linting (recommended)

pre-commit is configured in the development environment for this repository, and can be set up to automatically run a number of code linters and formatters on any commit you make according to the consistent code style set for this project.

Inside the repo, run the following to install the configured pre-commit "hooks":

uv run pre-commit install

pre-commit will now run automatically whenever you run git commit.