Development Setup

This guide covers the complete development environment setup for NeuRodent.

Prerequisites

• Python 3.10+

• uv - Fast Python package manager (install uv)

• make (optional, for convenience commands)

Quick Start

git clone https://github.com/josephdong1000/neurodent.git
cd neurodent
make setup

This runs uv sync --all-extras (installs all dependencies) and uv run pre-commit install (sets up git hooks).

Manual Setup

If you don’t have make:

git clone https://github.com/josephdong1000/neurodent.git
cd neurodent
uv sync --all-extras
uv run pre-commit install

If you don’t have uv:

git clone https://github.com/josephdong1000/neurodent.git
cd neurodent
pip install -e ".[dev]"
pre-commit install

Makefile Commands

Command	Description
make setup	Install dependencies + pre-commit hooks
make test	Run test suite with pytest
make docs	Build documentation to docs/_build/html
make docs-live	Build docs with live reload (auto-refresh on changes)
make clean	Remove build artifacts

Pre-commit Hooks

NeuRodent uses pre-commit hooks to maintain code quality. These run automatically before each git commit.

nbstripout

Strips output cells from Jupyter notebooks before commits. This keeps git history clean and avoids merge conflicts from cell outputs and metadata.

Note

Notebooks in notebooks/ are excluded from stripping (for development use). Only docs/ notebooks are stripped.

To run hooks manually on all files:

uv run pre-commit run --all-files

Notebook Documentation

Documentation notebooks in docs/ are executed during Sphinx builds to generate figures. Outputs are stripped from git but regenerated at build time.

If a notebook cell fails during build, execution stops at that cell and preceding outputs are shown. To skip execution of specific cells, add the skip-execution tag in JupyterLab.