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Documentation

We use Sphinx and ReadtheDocs to organize our documentation page. Most up-to-date documentation is typically collected in separate branch doc-patch, which can be seen here.

We utilize the following extensions to enhance the documentation ☕

  • numpydoc: We favor numpy documentation style for API documentation.
  • myst_parser: We like to write documentation and guidelines in markdown format.

Key things to remember

  • Please DON'T IGNORE any errors or warnings during the compilation stage.
  • If you have any .ipynb format notebook, please change it to .md format using jupytext <notebook>.ipynb --to myst. (You can install jupytext with pip.)
    • Make sure you excluded the input-output cells.
    • Currently, we don't use the runnable notebook directly on the documentation. If you think otherwise, please leave an issue so that we can discuss.
  • If you would like to include images (i.e. result, plot, or visualization), upload the image on cloud (Box or Google Drive) and add the URL link.

Build documentation

The sphinx is already initialized in docs directory. In order to build the documentation, you will need additional package listed in extra dependencies.

poetry install -E docs
cd docs
make clean
make html

Once the documentation building is done, open docs/_build/html/index.html to view.

Use make help for other options.

User Guide

User guidelines and tutorials are written in .rst or .md format. These files will be managed in docs directory.

API documentation

The docstring for function or modules are automatically parsed using sphinx+numpydoc. Any inline function description, such as

""" This is the form of a docstring.

... description

Attributes
----------
x : type
    x description
y : type
    y description

"""

will be parsed and displayed in API documentation. See numpydoc for more details.

ReadtheDocs

ReadtheDocs runs sphinx internally and maintain the documentation website. We will always activate the stable and latest version, and few past-documentations will also be available for the support.

@nmnaughton and @skim449 has access to the ReadtheDocs account.