Dev guide

Installation¶

Install natto from source, with the extras for tests and documentation:

git clone https://github.com/wengroup/natto.git
cd natto
pip install -e ".[test,doc]"

Run the tests with pytest.

Build the docs¶

The documentation is built with Jupyter Book 2. Its pages are notebooks, so pass --execute to run their code and show the results. From the docs directory, start a live preview with

jupyter-book start --execute

or build the static site into docs/_build/html with

jupyter-book build --html --execute

A push to main builds the documentation and deploys it to GitHub Pages, at https://wengroup.github.io/natto/.

Code style¶

• Python code is linted and formatted with Ruff, and YAML files with prettier.

• Docstrings follow the Google style.

• The documentation is written in MyST Markdown.

pre-commit runs all the checks, and fixes what it can:

pip install pre-commit
pre-commit run --all-files --show-diff-on-failure

To run them on every commit, install them as a git hook with pre-commit install, and remove it with pre-commit uninstall. GitHub Actions runs the same checks, and the tests, on every push and pull request.