funlib.persistence

Interfaces for data (arrays and graphs) and storage formats (databases and file formats)

Documentation: https://funkelab.github.io/funlib.persistence

Install

pip install funlib.persistence    # or: uv add funlib.persistence

Contributing

The commands below are the ones CI runs, so a green local run means a green PR.

git clone https://github.com/funkelab/funlib.persistence
cd funlib.persistence
uv sync                                             # Python, dependencies, dev tools (from uv.lock)
uv run pytest                                       # tests with coverage
uv run pytest --no-cov tests/<file>.py              # one file, without the coverage floor
uv run ruff check . && uv run ruff format --check . # lint and formatting
uv run ty check src tests                           # types
uv run --group docs sphinx-build -W docs/source docs/build/html   # docs

The graph-database tests need a PostgreSQL server (CI starts one as a service, PGUSER=postgres); they are skipped when none is reachable.

uv.lock pins the development environment; the lock-upgrade workflow refreshes it monthly and opens a pull request.