adding_to_the_api_documentation.rst

Adding to the API Documentation

Documentation is an integral part of every collaborative software project. Good documentation not only encourages users of the package to try out different functionalities, but it also makes maintaining and expanding code significantly easier. Every code contribution to the package must come with appropriate documentation of the API. This guide details how to do this.

Docstrings

The main form of documentation are docstrings, multi-line comments beneath a class or function definition with a specific syntax, which detail its functionality. This package uses the NumPy docstring format. As a rule, all functions which are exposed to the user must have appropriate docstrings. Below is an example of a docstring for a probabilistic numerical method named problinsolve defined in _problinsolve.py in the linalg subpackage.

../../../src/probnum/linalg/_problinsolve.py

General Rules

• Cover Parameters, Returns, Raises and Examples, if applicable, in every publicly visible docstring—in that order.
• Examples are tested via doctest. Ensure doctest does not fail by running the test suite.
• Include appropriate References, in particular for probabilistic numerical methods.
• Do not use docstrings as a clutch for spaghetti code!

Parameters

• Parameter types are automatically documented via type hints in the function signature.
• Always provide shape hints for objects with a .shape attribute in the following form:

"""
Parameters
----------
arr
    *(shape=(m, ) or (m, n))* -- Parameter array of an example function.
"""

• Hyperparameters should have default values and explanations on how to choose them.
• For callables provide the expected signature as part of the docstring: foobar(x, y, z, \*\*kwargs). Backslashes remove semantic meaning from special characters.

Style

• Stick to the imperative style of writing in the docstring header (i.e.: first line).

  • Yes: “Compute the value”.
  • No: “This function computes the value / Let’s compute the value”.

  The rest of the explanation talks about the function, e. g. “This function computes the value by computing another value”.

• Use full sentences inside docstrings when describing something.
  • Yes: “This value is irrelevant, because it is not being passed on”
  • No: “Value irrelevant, not passed on”.
• When in doubt, more explanation rather than less. A little text inside an example can be helpful, too.
• A little maths can go a long way, but too much usually adds confusion.

Interface Documentation

Which functions and classes actually show up in the documentation is determined by an __all__ statement in the corresponding __init__.py file inside a module. The order of this list is also reflected in the documentation. For example, linalg has the following __init__.py:

../../../src/probnum/linalg/__init__.py

If you are documenting a subclass, which has a different path in the file structure than the import path due to __all__ statements, you can correct the links to superclasses in the documentation via the .__module__ attribute.

Sphinx

ProbNum uses Sphinx to parse docstrings in the codebase automatically and to create its API documentation. You can configure Sphinx itself or its extensions in the ./docs/conf.py file.

from IPython.display import Image

display(Image(filename="../assets/img/developer_guides/sphinx_logo.png", embed=True))

ProbNum makes use of a number of Sphinx plugins to improve the API documentation, for example to parse Jupyter notebooks. The full list of used packages can be found in ./docs/sphinx-requirements.txt and ./docs/notebook-requirements.txt.

Building and Viewing the Documentation

In order to build the documentation locally and view the HTML version of the API documentation, simply run:

tox -e docs

This creates a static web page under ./docs/_build/html/ which you can view in your browser by opening ./docs/_build/html/intro.html.

Alternatively, if you want to build the docs in your current environment you can manually execute

cd docs
make clean
make html

For more information on tox, check out the general development instructions.