Providing instructive documentation is a key part of
aeon's mission. In order to meet this,
developers are expected to follow
aeon's documentation standards.
Documenting code using NumPy docstrings and aeon conventions
aeon'sdocstring convention for public code artifacts and modules
Adding new public functionality to the api_reference and user guide
More detailed information on
aeon's documentation format is provided below.
To ensure docstrings meet expectations, aeon uses a combination of validations built into numpydoc, pydocstyle pre-commit checks (set to the NumPy convention) and automated testing of docstring examples to ensure the code runs without error. However, the automated docstring validation in pydocstyle only covers basic formatting. Passing these tests is necessary to meet the aeon docstring conventions, but is not sufficient for doing so.
To ensure docstrings meet aeon’s conventions, developers are expected to check their docstrings against numpydoc and aeon conventions and reviewer’s are expected to also focus feedback on docstring quality.
aeon Specific Conventions#
Beyond basic NumPy docstring formatting conventions, developers should focus on:
Ensuring all parameters (classes, functions, methods) and attributes (classes) are documented completely and consistently
Including an Examples section that demonstrates at least basic functionality in all public code artifacts
Adding a See Also section that references related aeon code artifacts as applicable
Including citations to relevant sources in a References section
In many cases a parameter, attribute return object, or error may be described in many docstrings across aeon. To avoid confusion, developers should make sure their docstrings are as similar as possible to existing docstring descriptions of the the same parameter, attribute, return object or error.
Accordingly, aeon estimators and most other public code artifcations should generally include the following NumPy docstring convention sections:
Attributes (classes only)
Returns or Yields (as applicable)
Raises (as applicable)
See Also (as applicable)
Notes (as applicable)
References (as applicable)
Summary and Extended Summary#
The summary should be a single line, followed by a (properly formatted) extended summary. The extended summary should include a user friendly explanation of the code artifacts functionality.
For all aeon estimators and other code artifacts that implement an algorithm (e.g. performance metrics), the extended summary should include a short, user-friendly synopsis of the algorithm being implemented. When the algorithm is implemented using multiple aeon estimators, the synopsis should first provide a high-level summary of the estimator components (e.g. transformer1 is applied then a classifier). Additional user-friendly details of the algorithm should follow (e.g. describe how the transformation and classifier work).
If a “term” already exists in the glossary and the developer wants to link it directly they can use:
:term:`the glossary term`
In other cases you’ll want to use different phrasing but link to an existing glossary term, and the developer can use:
:term:`the link text <the glossary term>`
In the event a term is not already in the glossary, developers should add the term to the glossary (aeon/docs/glossary.rst) and include a reference (as shown above) to the added term.
Likewise, a developer can link to a particular area of the user guide by including an explicit cross-reference and following the steps for referencing in Sphinx (see the helpful description on Sphinx cross-references posted by Read the Docs). Again developers are encouraged to add important content to the user guide and link to it if it does not already exist.
This section should reference other
aeon code artifcats related to the code artifact being documented by the docstring. Developers should use
judgement in determining related code artifcats. For example, rather than listin all other performance metrics, a percentage error based performance metric
might only list other percentage error based performance metrics. Likewise, a distance based classifier might list other distance based classifiers but
not include other types of time series classifiers.
The notes section can include several types of information, including:
Mathematical details of a code object or other important implementation details (using ..math or :math:`` functionality)
Links to alternative implementations of the code artifact that are external to
aeon(e.g. the Java implementation of an aeon time series classifier)
state changing methods (aeon estimator classes)
aeon estimators that implement a concrete algorithm should generally include citations to the original research article, textbook or other resource that describes the algorithm. Other code artifacts can include references as warranted (for example, references to relevant papers are included in aeon’s performance metrics).
This should be done by adding references into the references section of the docstring, and then typically linking to these in other parts of the docstring.
The references you intend to link to within the docstring should follow a very specific format to ensure they render correctly. See the example below. Note the space between the “..” and opening bracket, the space after the closing bracket, and how all the lines after the first line are aligned immediately with the opening bracket. Additional references should be added in exactly the same way, but the number enclosed in the bracket should be incremented.
..  Some research article, link or other type of citation. Long references wrap onto multiple lines, but you need to indent them so they start aligned with opening bracket on first line.
To link to the reference labeled as “”, you use “_”. This only works within the same docstring. Sometimes this is not rendered correctly if the “_” link is preceded or followed by certain characters. If you run into this issue, try putting a space before and following the “_” link.
To list a reference but not link it elsewhere in the docstring, you can leave out the “.. ” directive as shown below.
Some research article, link or other type of citation. Long references wrap onto multiple lines. If you are not linking the reference you can leave off the ".. ".
Most code artifacts in aeon should include an examples section. At a minimum this should include a single example that illustrates basic functionality. The examples should use either a built-in aeon dataset or other simple data (e.g. randomly generated data, etc) generated using an aeon dependency (e.g. NumPy, pandas, etc) and whereever possible only depend on aeon or its core dependencies. Examples should also be designed to run quickly where possible. For quick running code artifacts, additional examples can be included to illustrate the affect of different parameter settings.
Examples of Good aeon Docstrings#
Here are a few examples of aeon code artifacts with good documentation.
The source files can be found
The main configuration file for sphinx is
and the main page is
To add new pages, you need to add a new
.rst file and include it in
To build the documentation locally, you need to install a few extra dependencies listed in pyproject.toml.
To install extra dependencies from the root directory, run:
pip install .[docs]
To build the website locally, run:
cd docs make html
You may need to install pandoc to build the documentation locally.