Documentation#

This section provides an overview of documentation standards for ARTKIT, including the README, Sphinx, and docstrings.

README#

The README file for the repo is formatted as .rst instead of the traditional markdown format. This facilitates incorporation of README content into the Home page of the documentation during the Sphinx build, which minimizes code duplication and ensures updates to our README are reflected in the Sphinx documentation.

Sphinx Build#

Documentation for ARTKIT is built using sphinx. Before building the documentation ensure the artkit-develop environment is active as the documentation build has a number of key dependencies specified in the environment.yml file, specifically:

  • sphinx

  • pydata-sphinx-theme

  • nbsphinx

  • sphinx-autodoc-typehints

To generate the Sphinx documentation locally, navigate to /sphinx and run

./make.py html

By default this will clean any previous build. The generated Sphinx documentation for ARTKIT can then be found at sphinx/build/html.

Documentation versioning is managed via the release process – see the section on Package Builds.

Sphinx Folder Structure#

The sphinx folder in the root directory contains the following:

  • a make.py script for executing the documentation build via python

  • a source directory containing predefined .rst files for the documentation build and other required elements (see below for more details)

  • a base folder which contains

    • the make_base.py and conf_base.py scripts with nearly all configuration for make.py and conf.py

    • _static directory, containing logos, icons, javascript and css used for documentation builds

    • _templates directory, containing autodoc templates used in generating and formatting the modules and classes for the API documentation

The sphinx/source folder contains:

  • a conf.py script that is the build configuration file needed to customize the input and output behavior of the Sphinx documentation build (see below for further details)

  • the essential files used for the documentation build, which are:

    • index.rst: definition of the high-level documentation structure which mainly references the other .rst files in this directory

    • user_guide/*: pages containing a detailed user guide for artkit.

    • examples/*: pages containing end-to-end examples of using artkit for specific use cases.

    • contributor_guide/*: pages containing detailed information on contributing to artkit.

    • faqs.rst: contains answers to frequently asked questions

    • api_landing.rst: contains the API landing page preamble. This information will appear on the API landing page in the documentation build after the description in src/__init__.py. This is incorporated in the documentation build via the custom-module-template.rst

  • _static contains additional material used in the documentation build, in this case, logos and icons

The two key scripts are make.py and conf.py.

make.py#

All base configuration comes from artkit/sphinx/make/make_base.py, which includes defined commands for key steps in the documentation build. Briefly, the key steps for the documentation build are:

  • Clean: remove the existing documentation build

  • FetchPkgVersions: fetch the available package versions with documentation

  • ApiDoc: generate API documentation from sources

  • Html: run Sphinx build to generate HTML documentation

The two other commands are Help and PrepareDocsDeployment.

conf.py#

All base configuration comes from artkit/sphinx/make/conf_base.py. This build configuration file is a requirement of Sphinx and is needed to customize the input and output behavior of the documentation build. In particular, this file highlights key extensions needed in the build process, of which some key ones are as follows:

  • intersphinx (external links to other documentations built with Sphinx: matplotlib, numpy, …)

  • viewcode to include source code in the documentation, and links to the source code from the objects documentation

  • imgmath to render math expressions in doc strings. Note that a local latex installation is required (e.g., MiKTeX for Windows)

Docstrings#

The API documentation is generated from docstrings in the source code. Before writing your own, take some time to study the existing code documentation and emulate the same style. Describe not only what the code does, but also why, including the rationale for any design choices that may not be obvious. Provide examples wherever this helps explain usage patterns.

  • A docstring is mandatory for all of the following entities in the source code, except when they are protected/private (i.e. the name starts with a leading _ character):

    • modules

    • classes

    • functions/methods

    • properties

    • attributes

  • Docstrings are not necessary for non-public methods, but you should have a comment that describes what the method does.

  • Docstrings must use reStructuredText syntax, the default syntax for Sphinx.

  • Write docstrings for functions and methods in the imperative style, e.g.,

    def fit():
"""Fit the model."""

    but not

    def fit():
"""This is a function that fits the model."""

    which is too wordy and not imperative.

  • Write docstrings for modules, classes, modules, and attributes starting with a descriptive phrase (as you would expect in a dictionary entry). Be concise and avoid unnecessary or redundant phrases. For example:

    class Inspector:
    """
    Explains the inner workings of a predictive model using the SHAP approach.

    The inspector offers the following analyses:

    - ...
    - ...

    but not

    class Inspector:
    """
    This is a class that provides the functionality to inspect models
    ...

    as this is too verbose, and explains the class in terms of its name which does not add any information.

  • Properties should be documented as if they were attributes, not as methods, e.g.,

    @property
def children(self) -> Foo:
    """The child nodes of the tree."""
    pass

    but not

    @property
def foo(self) -> Foo:
    """:return: the foo object"""
    pass

  • Start full sentences and phrases with a capitalised word and end each sentence with punctuation, e.g.,

    """Fit the model."""

    but not

    """fit the model"""

  • For multi-line docstrings, insert a line break after the leading triple quote and before the trailing triple quote, e.g.,

    def fit():
    """
    Fit the model.

    Use the underlying estimator's ``fit`` method
    to fit the model using the given training sample.

    :param sample: training sample
    """

    but not

    def fit():
    """Fit the model.

    Use the underlying estimator's ``fit`` method
    to fit the model using the given training sample.

    :param sample: training sample"""

  • For method arguments, return value, and class parameters, one must hint the type using the typing module. Do not specify the parameter types in the docstrings, e.g.,

    def f(x: int) -> float:
  """
  Do something.

  :param x: input value
  :return: output value
  """

    but not

    def f(x: int) -> float:
  """
  Do something.

  :param int x: input value
  :return float: output value
  """
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