Contributing¶

We welcome contributions of all kinds — bug reports, documentation fixes, new features, and new database connectors.

Development setup¶

git clone https://github.com/sysbio-curie/Neko.git
cd Neko
poetry install
pre-commit install

Code style¶

NeKo uses the following formatters and linters (enforced via pre-commit):

Tool	Purpose
black	Code formatting
autopep8	PEP 8 compliance
isort	Import ordering
flake8	Error / style linting
prettier	YAML / JSON / Markdown formatting

Run checks manually:

pre-commit run --all-files

Running tests¶

pytest tests/
# or with coverage:
pytest --cov=neko tests/

Docstring style¶

NeKo uses NumPy-style docstrings:

def my_function(x: int, y: float) -> str:
    """
    One-line summary.

    Longer description if needed.

    Parameters
    ----------
    x : int
        Description of x.
    y : float
        Description of y.

    Returns
    -------
    str
        Description of the return value.
    """

Pull request checklist¶

[ ] Tests pass (pytest tests/)
[ ] New code is covered by tests
[ ] Docstrings follow NumPy style
[ ] pre-commit run --all-files passes
[ ] Changelog entry added

Reporting issues¶

Open a GitHub issue and include:

NeKo version (python -c "import neko; print(neko.__version__)")
Python version
OS
Minimal reproducible example