Development¶

This page covers how to set up a development environment for contributing to OptiMHC.

Clone the Repository¶

git clone https://github.com/5h4ng/OptiMHC.git
cd OptiMHC

Install Dependencies¶

OptiMHC uses uv for dependency management (recommended):

uv sync --locked --group dev

Alternatively, using pip:

pip install -e .
pip install pytest ruff pre-commit

Running Tests¶

uv run pytest                              # All tests
uv run pytest tests/test_psm_container.py  # Single file
uv run pytest tests/ -k "test_config"      # Filter by name

Linting and Formatting¶

OptiMHC uses Ruff for linting and formatting:

uv run ruff check .          # Lint
uv run ruff format .         # Format
uv run ruff format --check . # Check without modifying

Configuration: line-length = 99, rules ["E", "F", "I"] (pycodestyle errors, pyflakes, isort). E501 (line too long) is ignored. Ruff excludes docs/ and examples/.

Pre-commit Hooks¶

uv run pre-commit install              # Install hooks
uv run pre-commit run --all-files      # Run all hooks manually

Building Documentation¶

mkdocs serve   # Local preview at http://127.0.0.1:8000
mkdocs build   # Static build to site/