Contributing

Contributions are welcome through GitHub Issues and pull requests. For the repository-level contributor guide, see CONTRIBUTING.md.

Helpful Contributions

• Real-world regression fixtures for sorting, fixing, scaffolding, and graph-aware gap filling.
• Documentation improvements and worked examples for new users.
• Reports from assemblies where MUMmer and minimap2 produce meaningfully different placement evidence.
• Edge cases for GFA/GAF/Hi-C-like support and ambiguous graph paths.

Development Checks

mamba env create -f environment.yml
mamba activate chromosort
make agent-check

or:

pixi install
pixi run agent-check

For a focused code check, python -m unittest discover -s tests -v and pytest both exercise the synthetic fixture suite.