This notebook is part of the nbsphinx documentation: https://nbsphinx.readthedocs.io/.

Markdown Cells¶

We can use emphasis, boldface, preformatted text.

It looks like strike-out text is not supported: strikethrough.

• Red
• Green
• Blue

1. One
2. Two
3. Three

Arbitrary Unicode characters should be supported, e.g. łßō. Note, however, that this only works if your HTML browser and your LaTeX processor provide the appropriate fonts.

Equations¶

Inline equations like $\text{e}^{i\pi} = -1$ can be created by putting a LaTeX expression between two dollar signs, like this: $\text{e}^{i\pi} = -1$.

Equations can also be displayed on their own line like this: \begin{equation} \int\limits_{-\infty}^\infty f(x) \delta(x - x_0) dx = f(x_0). \end{equation}

This can be done by simply using one of the LaTeX math environments, like so:

\begin{equation}
\int\limits_{-\infty}^\infty f(x) \delta(x - x_0) dx = f(x_0)
\end{equation}

Automatic Equation Numbering¶

This is not automatically enabled in Jupyter notebooks, but you can install a notebook extension in order to enable equation numbering: https://jupyter-contrib-nbextensions.readthedocs.io/en/latest/nbextensions/equation-numbering/readme.html.

Automatic Equation Numbering is enabled on https://nbviewer.jupyter.org/, see e.g. the latest version of this very notebook at the link https://nbviewer.jupyter.org/github/spatialaudio/nbsphinx/blob/master/doc/markdown-cells.ipynb#Automatic-Equation-Numbering.

When using nbsphinx, you can use the following mathjax3_config setting in your conf.py file to enable automatic equation numbering in HTML output.

mathjax3_config = {
    'tex': {'tags': 'ams', 'useLabelIds': True},
}

This works for Sphinx version 4 (and higher), which uses MathJax version 3. For older Sphinx versions, the corresponding configuration looks like this:

mathjax_config = {
    'TeX': {'equationNumbers': {'autoNumber': 'AMS', 'useLabelIds': True}},
}

In LaTeX output, the equations are numbered by default.

You can use \label{...} to give a unique label to an equation:

\begin{equation}
\phi = \frac{1 + \sqrt{5}}{2}
\label{golden-mean}
\end{equation}

If automatic equation numbering is enabled, you can later reference that equation using its label. You can use \eqref{golden-mean} for a reference with parentheses: \eqref{golden-mean}, or \ref{golden-mean} for a reference without them: \ref{golden-mean}.

In HTML output, these equation references only work for equations within a single HTML page. In LaTeX output, equations from other notebooks can be referenced, e.g. \eqref{fibonacci-recurrence}.

Manual Equation Numbering¶

If you prefer to assign equation numbers (or some kind of names) manually, you can do so with \tag{...}:

\begin{equation}
a^2 + b^2 = c^2
\tag{99.4}
\label{pythagoras}
\end{equation}

The above equation has the number \ref{pythagoras}.

Citations¶

According to https://nbconvert.readthedocs.io/en/latest/latex_citations.html, nbconvert supports citations using a special HTML-based syntax. nbsphinx supports the same syntax.

Example: Kluyver et al. (2016).

<cite data-cite="kluyver2016jupyter">Kluyver et al. (2016)</cite>

You don't actually have to use <cite>, any inline HTML tag can be used, e.g. <strong>: Python: An Ecosystem for Scientific Computing.

<strong data-cite="perez2011python">Python: An Ecosystem for Scientific Computing</strong>

You'll also have to define a list of references, see the section about references.

There is also a Notebook extension which may or may not be useful: https://github.com/takluyver/cite2c.

Footnote citations¶

Since version 2.0.0 of sphinxcontrib-bibtex, footnote citations are possible. This generates footnotes for all foot-citations up to the point of the bibliography directive, which is typically placed at the end of the source file.

Depending on whether the documentation is rendered into HTML or into LaTeX/PDF, the citations are either placed into a bibliography as ordinary citations (HTML output) or placed into the footnotes of the citation's respective page (PDF).

Example: Pérez et al. (2011).

<cite data-footcite="perez2011python">Pérez et al. (2011)</cite>

As footnote references are restricted to their own Jupyter notebook or other source file, a raw nbconvert cell of reST format (see the section about raw cells) can be added to the notebook, containing the

.. footbibliography::

directive.

Alternatively, one can use the nbsphinx epilog by setting it to, e.g.,

nbsphinx_epilog = r"""
.. footbibliography::
"""

Code¶

We can also write code with nice syntax highlighting:

print("Hello, world!")

Tables¶

Images¶

Local image:

![Jupyter notebook icon](images/notebook_icon.png)

Remote image:

![Python logo (remote)](https://www.python.org/static/img/python-logo-large.png)

Using the HTML <img> tag¶

The aforementioned Markdown syntax for including images doesn't allow specifying the image size.

If you want to control the size of the included image, you can use the HTML <img> element with the width attribute like this:

<img src="images/notebook_icon.png" alt="Jupyter notebook icon" width="300">

In addition to the src, alt, width and height attributes, you can also use the class attribute, which is simply forwarded to the HTML output (and ignored in LaTeX output). All other attributes are ignored.

SVG support for LaTeX¶

LaTeX doesn't support SVG images, but there are Sphinx extensions that can be used for automatically converting SVG images for inclusion in LaTeX output.

Just include one of the following options in the list of extensions in your conf.py file.

• 'sphinxcontrib.inkscapeconverter' or 'sphinxcontrib.rsvgconverter': See https://github.com/missinglinkelectronics/sphinxcontrib-svg2pdfconverter for installation instructions.

  The external programs inkscape or rsvg-convert (Debian/Ubuntu package librsvg2-bin; conda package librsvg) are needed, respectively.

• 'sphinx.ext.imgconverter': This is a built-in Sphinx extension, see https://www.sphinx-doc.org/en/master/usage/extensions/imgconverter.html.

  This needs the external program convert from ImageMagick.

  The disadvantage of this extension is that SVGs are converted to bitmap images.

If one of those extensions is installed, SVG images can be used even for LaTeX output:

![Python logo](images/python_logo.svg)

Remote SVG images can also be used (and will be shown in the LaTeX output):

![Jupyter logo](https://jupyter.org/assets/main-logo.svg)

Cell Attachments¶

Images can also be embedded in the notebook itself. Just drag an image file into the Markdown cell you are just editing or copy and paste some image data from an image editor/viewer.

The generated Markdown code will look just like a "normal" image link, except that it will have an attachment: prefix:

![a stick figure](attachment:stickfigure.png)

These are cell attachments:

In the Jupyter Notebook, there is a speciall "Attachments" cell toolbar which you can use to see all attachments of a cell and delete them, if needed.

HTML Elements (HTML only)¶

It is allowed to use plain HTML elements within Markdown cells. Those elements are passed through to the HTML output and are ignored for the LaTeX output. Below are a few examples.

HTML5 audio elements can be created like this:

<audio src="https://example.org/audio.ogg" controls>alternative text</audio>

Example:

HTML5 video elements can be created like this:

<video src="https://example.org/video.ogv" controls>alternative text</video>

Example:

The alternative text is shown in browsers that don't support those elements. The same text is also shown in Sphinx's LaTeX output.

Info/Warning Boxes¶

Until there is an info/warning extension for Markdown/CommonMark (see this issue), such boxes can be created by using HTML <div> elements like this:

<div class="alert alert-info">

Note

This is a note!

</div>

For this to work reliably, you should obey the following guidelines:

• The class attribute has to be either "alert alert-info" or "alert alert-warning", other values will not be converted correctly.
• No further attributes are allowed.
• For compatibility with CommonMark, you should add an empty line between the <div> start tag and the beginning of the content.

Links to Other Notebooks¶

Relative links to local notebooks can be used: a link to a notebook in a subdirectory, a link to an orphan notebook (latter won't work in LaTeX output, because orphan pages are not included there).

This is how a link is created in Markdown:

[a link to a notebook in a subdirectory](subdir/a-notebook-in-a-subdir.ipynb)

Markdown also supports reference-style links: a reference-style link, another version of the same link.

These can be created with this syntax:

[a reference-style link][mylink]

[mylink]: subdir/a-notebook-in-a-subdir.ipynb

Links to sub-sections are also possible, e.g. this subsection.

This link was created with:

[this subsection](subdir/a-notebook-in-a-subdir.ipynb#A-Sub-Section)

You just have to remember to replace spaces with hyphens!

BTW, links to sections of the current notebook work, too, e.g. beginning of this section.

This can be done, as expected, like this:

[beginning of this section](#Links-to-Other-Notebooks)

It's also possible to create a link to the beginning of the current page, by simply using a # character:

[link to the beginning of the current page](#)

Links to *.rst Files (and Other Sphinx Source Files)¶

Links to files whose extension is in the configuration value source_suffix, will be converted to links to the generated HTML/LaTeX pages. Example: A reStructuredText file.

This was created with:

[A reStructuredText file](a-normal-rst-file.rst)

Links to sub-sections are also possible. Example: Sphinx Directives.

This was created with:

[Sphinx Directives](a-normal-rst-file.rst#sphinx-directives-for-info-warning-boxes)

Links to Local Files¶

Links to local files (other than Jupyter notebooks and other Sphinx source files) are also possible, e.g. requirements.txt.

This was simply created with:

[requirements.txt](requirements.txt)

The linked files are automatically copied to the HTML output directory. For LaTeX output, links are created, but the files are not copied to the target directory.

Links to Domain Objects¶

Links to Sphinx domain objects (such as a Python class or JavaScript function) are also possible. For example: example_python_function().

This was created with:

[example_python_function()](a-normal-rst-file.rst#example_python_function)

This is especially useful for use with the Sphinx autodoc extension!