Contributing to vczstore

Development setup

We use uv for dependency management.

Clone the repository and install all development dependencies:

git clone https://github.com/sgkit-dev/vczstore.git
cd vczstore
uv sync --group dev

uv run pytest

Note: some tests require bcftools to be installed (available via conda-forge and bioconda).

We use prek for pre-commit linting, configured in prek.toml. Install it as a pre-commit hook:

uv run prek install

Run all checks manually:

uv run --only-group=lint prek -c prek.toml run --all-files

If local results differ from CI, run uv run prek cache clean.