oxbow 0.8.0

Read genomic file formats into data frames and more.

py-oxbow

The Python interface for oxbow.

Warning: oxbow is under active development. APIs are not yet stable and are subject to change.

Installation

pip install oxbow

To build and install the bleeding edge from GitHub (requires Rust and maturin to build the package locally):

pip install 'git+https://github.com/abdenlab/oxbow.git@main#egg=oxbow&subdirectory=py-oxbow'

Development

This is a hybrid Python/Rust project and requires uv for development, relying on maturin as a build system. Dependencies are organized into PEP 735-style dependency groups in the pyproject.toml.

By default, the development environment enables all dependency groups, ensuring that all tools and libraries required by project commands are available locally. In CI, we selectively enable groups to avoid unnecessary compilation or installation of unused dependencies for specific commands.

uv sync # Create `.venv` with all dependency groups

Building the project

To (re)build and install a local development version of oxbow into your virtual environment:

uvx maturin develop --uv # --release (for non-debug build)

Linting and formatting

We use ruff for linting and formatting Python code.

To validate the code style:

uv run ruff check

To format:

uv run ruff format

Running Tests

Tests use pytest and require only the dev dependency group (default, no --group necessary). Currently, tests must be run from within the tests directory to correctly generate manifests.

cd tests
uv run pytest

Documentation

Documentation is managed with sphinx and uses the isolated docs dependency group:

uv run --group=docs sphinx-build docs docs/_build/html       # Build docs
uv run --group=docs sphinx-autobuild docs docs/_build/html   # Live-reload server