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Documentation for alibi

This directory contains the sources (.md and .ipynb files) for the documentation. The main index page is defined in source/index.md. The Sphinx options and plugins are found in the source/conf.py file. The documentation is generated in full by calling make html which also automatically generates the Python API documentation from docstrings.

Building documentation locally

To build the documentation, first we need to install Python requirements:

pip install -r ../requirements/docs.txt

We also need pandoc for parsing Jupyter notebooks, the easiest way to install this is using conda:

conda install -c conda-forge pandoc=2.9.2.1

Note: the older version of pandoc is used because this is available on readthedocs.org where we host our docs, the newer version fixes a lot of bugs, but using a newer version locally is misleading as to whether the docs will render properly on RTD, also see gotchas.

We are now ready to build the docs:

make -C .. build_docs

This calls the sphinx html builder command defined in the main repo Makefile. Note this can take some time as some of the notebooks may be executed during the build process. The resulting documentation is located in the _build directory with _build/html/index.html marking the homepage.

A pdf of the docs can also be built:

make -C .. build_latex

with the resulting pdf file residing at _build/latex/alibi.pdf.

Sphinx extensions and plugins

We use various Sphinx extensions and plugins to build the documentation, including:

The full list of plugins and their options can be found in source/conf.py.

Adding new examples

All examples are Jupyter notebooks and live in the doc/source/examples directory. When you run make build_docs locally, symbolic links pointing to these notebooks are added in the top-level examples/ directory. For example, for the notebook doc/source/examples/cem_iris.ipynb, a symbolic link named cem_iris.ipynb will be added in examples/. When adding a new notebook, you should run make build_docs to generate a new symbolic link, and make sure this is also added to the new commit.

MyST format

For consistency, all docs files excluding .ipynb notebooks are written as Markedly Structured Text (MyST) files. Although still named as .md files, the files are passed through myst-parser, which processes rst-type directives contained within the .md files. This allows for more powerful functionality to be included in the docs. For example, an admonition block can be included in a .md file with:

```{admonition} My markdown link
Here is [markdown link syntax](https://jupyter.org)
```

and an image can be embedded with:

```{image} img/fun-fish.png
:alt: fishy
:class: bg-primary
:width: 200px
:align: center
```

For more details on the MyST syntax see the MyST docs.

Gotchas when writing notebooks as examples

We use Jupyter notebooks for examples and method descriptions and invoke the nbsphinx plugin, which in turn invokes pandoc for rendering the notebooks as static documentation. Generally, the Jupyter notebook is more permissive for what it can render correctly than the static documentation, so it is important to check that the content is rendered correctly in the static docs as well. Here is a list of common formatting gotchas and how to fix them:

  • When using a bullet-point list, leave a blank line before the preceding paragraph, otherwise it will fail to render
  • Always use $$ $$ or \begin{equation}\end{equation}to delimit display math.
  • Leave a blank line before and after any display math
  • For references and footnotes, the tag indicating the section needs to start with an uppercase letter, e.g. [[1]](#References) linking to a section <a id='References'></a> [1](#f_1) reference here
  • Whilst superscript (for e.g. footnotes) can be rendered in Jupyter using <sup></sup> tags, this won't work in the static docs. To avoid jarring appearence of footnote numbers in the text, wrap them in parentheses, e.g. (1) will be rendered inline as (1).
  • Avoid starting a cell with an html tag, e.g. for making hyperlinks to link back to the reference in the text <a id='ref1'></a>. The (older) version of pandoc==2.9.2.1 used both on CI and readthedocs.org machines cannot handle it and may fail to build the docs. Recommended action is to put such tags at the end of the cell.
  • Avoid using underscores in alternative text for images, e.g. instead of ![my_pic](my_pic.png) use ![my-pic](my_pic.png), this is due to the old version of pandoc==2.9.2.1 used on reathedocs.org.
  • Avoid nesting markdown markups, e.g. italicising a hyperlink, this might not render
  • When embedding images in notebooks which are linked to via a .nblink file, an extra-media key needs to be added in the .nblink file. See the nbsphinx-link docs, or alibi_detect_deploy.nblink for an example in alibi-detect. Prefer using the following to produce self-contained notebooks:
  • To add a static image to an example, use the syntax ![my-image.png](attachment:my_image.png) and execute the cell. This will embed the actual binary image into the example notebook so that the notebook is self-contained (note that some notebooks won't be self-contained due to dependencies on data or models under doc/source/examples/assets). Afterwards, ensure the image is located in the doc/source/examples/assets directory and committed to the repository.