Contributing to the Documentation#

This is the contributors guide for the documentation of Mitiq, the Python toolkit for implementing error mitigation on quantum computers.

Requirements#

Our documentation is generated with Sphinx. The necessary packages can be installed, from the root Mitiq directory with the command

make install

Sphinx extensions used to build the docs#

You can check that Sphinx is installed with sphinx-build --version.

The configuration file#

Since the documentation is already created, you need not to generate a configuration file from scratch (this is done with sphinx-quickstart). Meta-data, extensions and other custom specifications are accounted for in the conf.py file.

Add/change Sphinx features in the conf.py file#

To add specific feature to the documentation, Sphinx extensions can be added to the build. As and example, to add classes and functions to the API doc, make sure that autodoc extension is enabled in the conf.py file.

extensions = ['sphinx.ext.autodoc']

Updating the Documentation#

Documentation is found in docs/source, and is divided into the following sections:

  • a guide, whose content needs to be written from scratch,

  • examples which can be either jupyter notebooks or MyST formatted notebooks, and

  • an API-doc part, which is (mostly) automatically generated.

Information in the docs should be added as markdown files using the MyST markdown syntax. If you are adding a new file (as opposed to editing an existing one), ensure to add it to an associated TOC so that it is discoverable.

The main table of contents (TOC) file for the docs is index.md. It includes guide\guide.md and apidoc.md, among other files. To add a new file to the base TOC, make sure it gets listed in the toctree directive like this:

```{toctree}
---
maxdepth: 2 
caption: Contents
---
file.md
```

Tip

If you use VS Code as your text editor there is a nice extension that does syntax highlighting for MyST: https://marketplace.visualstudio.com/items?itemName=ExecutableBookProject.myst-highlight

Including other files in the docs#

To include .md files outside of the documentation source directory, you can add a stub *.md file to the toctree inside the docs/source directory that contains:

```{include} path/to/file.md
:relative-docs: docs/
:relative-images:
```

where file.md is the one to be added. For more information on including files external to the docs, see the MyST docs.

Adding files to the user guide#

To add information in the guide, please add markdown (.md) files to the docs/guide directory. Remember to add new files to the guide’s TOC file docs/source/guide/guide.md.

Adding workflow images to the user guide#

To insert a workflow to the user’s guide of some new technique, a template is available (shown below as a png). This template is also available in svg format at mitiq_template.svg.

The svg will require edits to the items listed below:

  • One word description of the first step of the new technique in (Edit Step 1). For example, if the new technique requires sampling of the input quantum program, you will edit the text to 1. Sampling.

  • Make changes to Description of circuit generated by mitiq to instead briefly provide information about how mitiq is manipulating the input circuit.

  • Feel free to change the color scheme in mitiq.new_technique of the svg file.

_images/mitiq_workflow_template.png

The diagram shows the workflow template of a new technique in Mitiq.#

Adding code examples#

All code examples, besides explanations on the use of core software package features, live in the examples directory under docs/source. You can add Jupyter notebooks (.ipynb) or MyST markdown notebooks, but MyST formatting will be preferred as it is much easier to diff in version control.

If you have a notebook you want to add, and want to automatically convert it from the .ipynb to .md, you can use a great Python command line tool called jupytext. To convert from an IPython notebook to markdown file, run jupytext your_filename.ipynb --to myst and find the converted file at your_filename.md.

Futher, not only can jupytext convert between the formats on demand, but once you install it, you can configure it to manage both a Jupyter and Markdown version of your file, so you don’t have to remember to do conversions (for more details, see the jupytext docs on paired notebooks. Using the paired notebooks you can continue your development in the notebooks as normal, and just commit to git the markdown serialized version when you want to add to the docs. You can even add this tool as a git pre-commit hook if you want!

Tip

There is a sample markdown formatted notebook in the examples directory for you to take a look at as you write your own!

Automatically add information from the API docs#

New modules, classes and functions can be added by listing them in the appropriate file (such as apidoc.md or a child), e.g.,

## New Module
```{eval-rst}
.. automodule:: mitiq.new_module
   :members:
```

will add all elements of the mitiq.new_module module with a subtitle “New Module.” You can hand-pick classes and functions to add, to comment them, as well as exclude them.

Warning

The eval-rst directive must be used for now as myst-parser only supports parsing docstrings as RST. Once executablebooks/MyST-Parser#228 is closed, we can migrate to markdown docstrings.

Tip

If you are adding new features to Mitiq, make sure to add API docs in the source code, and to the API page apidoc.md.

Adding references#

To add references to the Mitiq bibliography, the first step is to add the reference to docs/source/refs.bib which is organized alphabetically. For formatting, please see BibTeX documentation for articles, books, and others.

Once the reference has been added to the docs/source/refs.bib file, cite the reference in the file by using:

{cite}`title of entry`

Build the documentation locally#

The easiest way to build the docs is to run make docs from the project root directory, which builds the html docs output.

Tip

If you want a fresh build with no caching, run make docs-clean!

To call sphinx directly, cd into the docs directory and run

sphinx-build -b html source build

These commands generate the docs/build folder, which is ignore by the .gitignore file. Once the documentation is generated you can view it by opening it in your browser.

Testing the Documentation#

When writing a new code example in the docs, you can use different directives to include code blocks.

Just the code, don’t evaluate#

If you want to include a code snippet that doesn’t get run (but has syntax highlighting), use the code-block directive:

```{code-block} python
   1+1        # simple example
```

View the documentation from a PR build#

To preview the documentation (mitiq.readthedocs.io) from a specific build in a PR, click Details on the docs/readthedocs.org:mitiq line of the pull request’s merge box in the PR’s Conversation timeline. It may be necessary to scroll down to find the docs/readthedocs.org:mitiq line.

RTD of PR

If the Read the Docs build failed, it is still possible to see the documentation from the build by clicking Details and then clicking on the View docs link on the right side of screen under the time it took for the build to complete.

RTD failed

Additional information#

Here are some notes on how to build docs.

The MyST syntax guide is a cheat sheet for the extended Markdown formatting that applies to both Markdown files as well as Markdown in Jupyter notebooks.

The MyST-NB Notebook guide can help you get you write or convert your notebook content for the docs.