Normal reStructuredText Files

This is a normal RST file.

Note

Those still work!

Links to Notebooks (and Other Sphinx Source Files)

Links to Sphinx source files can be created like normal Sphinx hyperlinks, just using a relative path to the local file: link.

using a relative path to the local file: link_.

.. _link: subdir/a-notebook-in-a-subdir.ipynb

If the link text has a space (or some other strange character) in it, you have to surround it with backticks: a notebook link.

surround it with backticks: `a notebook link`_.

.. _a notebook link: subdir/a-notebook-in-a-subdir.ipynb

You can also use an anonymous hyperlink target, like this: link. If you have multiple of those, their order matters!

like this: link__.

__ subdir/a-notebook-in-a-subdir.ipynb

Finally, you can use Embedded URIs, like this link.

like this `link <subdir/a-notebook-in-a-subdir.ipynb>`_.

Note

These links should also work on Github and in other rendered reStructuredText pages.

Links to subsections are also possible by adding a hash sign (#) and the section title to any of the above-mentioned link variants. You have to replace spaces in the section titles by hyphens. For example, see this subsection.

For example, see this subsection_.

.. _subsection: subdir/a-notebook-in-a-subdir.ipynb#A-Sub-Section

Links to Notebooks, Ye Olde Way

In addition to the way shown above, you can also create links to notebooks (and other Sphinx source files) with :ref:. This has some disadvantages:

• It is arguably a bit more clunky.

• Because :ref: is a Sphinx feature, the links don’t work on Github and other rendered reStructuredText pages that use plain old docutils.

It also has one important advantage:

• The link text can automatically be taken from the actual section title.

A link with automatic title looks like this: Notebooks in Sub-Directories.

:ref:`/subdir/a-notebook-in-a-subdir.ipynb`

But you can also provide your own link title.

:ref:`your own link title </subdir/a-notebook-in-a-subdir.ipynb>`

However, if you want to use your own title, you are probably better off using the method described above in Links to Notebooks (and Other Sphinx Source Files).

Links to subsections are also possible, e.g. A Sub-Section (the subsection title is used as link text) and alternative text.

These links were created with:

:ref:`/subdir/a-notebook-in-a-subdir.ipynb#A-Sub-Section`
:ref:`alternative text </subdir/a-notebook-in-a-subdir.ipynb#A-Sub-Section>`

Note

• The paths have to be relative to the top source directory and they have to start with a slash (/).

• Spaces in the section title have to be replaced by hyphens!

Sphinx Directives for Info/Warning Boxes

Warning

This is an experimental feature! Its usage may change in the future or it might disappear completely, so don’t use it for now.

With a bit of luck, it will be possible (some time in the future) to create info/warning boxes in Markdown cells, see https://github.com/jupyter/notebook/issues/1292. If this ever happens, nbsphinx will provide directives for creating such boxes. For now, there are two directives available: nbinfo and nbwarning. This is how an info box looks like:

Note

This is an info box.

It may include nested formatting, even another info/warning box:

Warning: You should probably not use nested boxes!

Domain Objects

example_python_function(foo)

This is just for testing domain object links.

Parameters:

foo (str) – Example string parameter

See also

Links to Domain Objects

References

There are different ways of handling references, for example you could use the standard Sphinx citations, but it might be more practical to use the sphinxcontrib.bibtex extension.

After installing the sphinxcontrib.bibtex extension, you have to enable it in your conf.py and select the BibTeX file(s) you want to use:

extensions = [
    'nbsphinx',
    'sphinxcontrib.bibtex',
    # Probably more extensions here ...
]

bibtex_bibfiles = ['my-references.bib']
bibtex_reference_style = 'author_year'

Afterwards all the references defined in the bibliography file(s) can be used throughout the Jupyter notebooks and other source files as detailed in the following.

Citations

You can create citations like [Pérez et al., 2011]:

:cite:`perez2011python`

You can also create so-called in-text citations, where the names of the authors, for example Pérez et al. [2011], are part of the sentence:

:cite:t:`perez2011python`

You can create similar citations in Jupyter notebooks with a special HTML syntax, see the section about citations in Markdown cells.

You can create a list of references in any reStructuredText file (or reST cell in a notebook) like this:

.. bibliography::

For an example, see the file doc/references.rst.

Footnote citations

With a sphinxcontrib.bibtex version of >= 2.0.0 it is possible to create footnote bibliographies with footnote citations like [1].

:footcite:`perez2011python`

In-text citations like Kluyver et al.[2] can be created like this:

:footcite:t:`kluyver2016jupyter`

Also footnote citations can be used within Jupyter notebooks with a special HTML syntax, see the section about footnote citations in Markdown cells. Footnote citations are restricted to their own source file and the assembly of the bibliography is (analogously to normal citations) invoked with the

.. footbibliography::

directive. For example, a footnote bibliography might look like this (in HTML output):

[1]

Fernando Pérez, Brian E. Granger, and John D. Hunter. Python: an ecosystem for scientific computing. Computing in Science Engineering, 13(2):13–21, 2011. doi:10.1109/MCSE.2010.119.

[2]

Thomas Kluyver, Benjamin Ragan-Kelley, Fernando Pérez, Brian Granger, Matthias Bussonnier, Jonathan Frederic, Kyle Kelley, Jessica Hamrick, Jason Grout, Sylvain Corlay, Paul Ivanov, Damián Avila, Safia Abdalla, Carol Willing, and Jupyter Development Team. Jupyter Notebooks—a publishing format for reproducible computational workflows. In Fernando Loizides and Birgit Schmidt, editors, Positioning and Power in Academic Publishing: Players, Agents and Agendas, pages 87–90. IOS Press, 2016. doi:10.3233/978-1-61499-649-1-87.

In the LaTeX/PDF output, there is no list of references appearing right here. Instead, the footnote citations are placed into the footnotes of their respective pages.

Thumbnail Link Galleries (HTML only)

In some case it is desired to create thumbnail links to existing notebooks, already included in a toctree. This can be used e.g. to link to a subset of notebooks from API documentation to highlight the use of some functionality. For this there is a dedicated nblinkgallery directive.

The following example gallery was created using:

.. nblinkgallery::
    :caption: A few links
    :name: rst-link-gallery

    gallery/multiple-outputs
    gallery/no-thumbnail
    gallery/cell-metadata
    orphan

A few links

Choosing from Multiple Outputs

A Notebook without Thumbnail

Using Cell Metadata to Select a Thumbnail

An Orphan Notebook (HTML Only)

See also

Link Galleries in Jupyter Notebooks

Thumbnail Galleries

With nbsphinx you can create thumbnail galleries in notebook files as described in Gallery With Nested Documents. If you like, you can also create such galleries in reST files using the nbgallery directive. It takes the same parameters as the toctree directive.

Note

The notes regarding LaTeX in Gallery With Nested Documents and Using toctree In A Notebook also apply here!

The following example gallery was created using:

.. nbgallery::
    :caption: This is a thumbnail gallery:
    :name: rst-gallery
    :glob:
    :reversed:

    gallery/*-rst

This is a thumbnail gallery:

Dummy Notebook 1 for Gallery

Dummy Notebook 2 for Gallery