Instructions to generate documentation with Sphinx

One-time setup

Install sphinx.
Create a docs/ directory in your project's directory.
In a terminal, go to the docs/ directory and run sphinx-quickstart to generate a conf.py and index.rst, make sure you:
- say yes to separate source and build directories
- keep the source file suffix as .rst
- say yes to autodoc: automatically insert docstrings from modules
- say yes to doctest
Now you can generate html by running make html to check the build succeeded.
To create a run configuration for this in PyCharm, add a new run configuration from Python Docs > Sphinx Task, set the directory that contains conf.py as input (probably docs/source/, and select the directory containing generated html files (probably docs/build/html) as output.

Uncomment the following lines in docs/source/conf.py (probably lines 15-17):

import os
import sys
sys.path.insert(0, os.path.abspath('.'))

and change the last line to:

sys.path.insert(0, os.path.abspath('../..'))

Add each package to the table of contents, the toctree in index.rst. In this example that would be the noodles and the spaghetti packages (subpackages will be automatically included):
```
.. toctree::
   :maxdepth: 2

   noodles
   spaghetti
```
Make sure each package and subpackage you want to have in the documentation contains a __init__.py file, including the src directory if you have it.

After changing/adding files/packages: Run in a terminal in your project's top-level directory sphinx-apidoc -M -T -E -f -o docs/source . to generate a .rst file for each package. You can find what each option does in the apidocdocumentation. Do this every time you change something in your code/docstrings.
After changing documentation in the code: Run the run configuration or make html to create the html.