Contributing¶

Contributions to sssom-py are welcome! Here's how to get started.

Development setup¶

$ git clone https://github.com/mapping-commons/sssom-py
$ cd sssom-py
$ uv sync --all-extras

Running tests¶

# Run all tests
$ uv run pytest

# Run with tox (includes linting, type checking, etc.)
$ uvx tox

Code quality¶

The project uses:

black for code formatting
isort for import sorting
flake8 for linting
mypy for static type checking

Run formatting before committing:

$ uvx black src/ tests/
$ uvx isort src/ tests/

Building documentation locally¶

$ uv run --extra docs mkdocs serve

Then open http://127.0.0.1:8000 in your browser.

Project structure¶

sssom-py/
├── src/sssom/          # Main package
│   ├── cli.py          # Click CLI commands
│   ├── parsers.py      # File parsing (TSV, JSON, RDF, OBO Graphs)
│   ├── writers.py      # Output writers (TSV, OWL, RDF, JSON)
│   ├── util.py         # Core utilities (merge, diff, filter, etc.)
│   ├── io.py           # High-level I/O operations
│   ├── validators.py   # Schema validation
│   ├── rdf_util.py     # RDF utilities
│   ├── rdf_internal.py # Internal RDF serialisation
│   ├── constants.py    # Constants and schema helpers
│   ├── context.py      # Prefix map / context handling
│   ├── cliques.py      # Clique detection (requires networkx)
│   ├── sparql_util.py  # SPARQL endpoint queries
│   └── obo.epm.json    # OBO Extended Prefix Map
├── tests/              # Test suite
├── docs/               # Documentation source (mkdocs)
├── mkdocs.yml          # MkDocs configuration
├── pyproject.toml      # Project configuration
└── tox.ini             # Tox test environments