Adding documentation

Documentation for PyOpenWorm is housed in two locations:

  1. In the top-level project directory as and
  2. As a Sphinx project under the docs directory

By way of example, to add a page about useful facts concerning C. elegans to the documentation, include an entry in the list under toctree in docs/index.rst like:


and create the file worm-facts.rst under the docs directory and add a line:

.. _worm-facts:

to the top of your file, remembering to leave an empty line before adding all of your wonderful worm facts.

You can get a preview of what your documentation will look like when it is published by running sphinx-build on the docs directory:

sphinx-build -w sphinx-errors docs build_destination

The docs will be compiled to html which you can view by pointing your web browser at build_destination/index.html. If you want to view the documentation locally with the ReadTheDocs theme you’ll need to download and install it.

API Documentation

API documentation is generated by the Sphinx autodoc extension. The format should be easy to pick up on, but a reference is available here. Just add a docstring to your function/class/method and add an automodule line to PyOpenWorm/ and your class should appear among the other documented classes.


Project-wide substitutions can be (conservatively!) added to allow for easily changing a value over all of the documentation. Currently defined substitutions can be found in in the rst_epilog setting. More about substitutions


If you’d like to add a convention, list it here and start using it. It can be reviewed as part of a pull request.

  1. Narrative text should be wrapped at 80 characters.
  2. Long links should be extracted from narrative text. Use your judgement on what ‘long’ is, but if it causes the line width to stray beyond 80 characters that’s a good indication.