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

Usage

Sphinx Setup

In the directory with your notebook files, run this command (assuming you have Sphinx installed already):

python3 -m sphinx.cmd.quickstart

Answer the questions that appear on the screen. In case of doubt, just press the <Return> key repeatedly to take the default values.

After that, there will be a few brand-new files in the current directory. You'll have to make a few changes to the file named conf.py. You should at least check if those two variables contain the right things:

extensions = [
    'nbsphinx',
    'sphinx.ext.mathjax',
]
exclude_patterns = ['_build', '**.ipynb_checkpoints']

For an example, see this project's conf.py file.

Once your conf.py is in place, edit the file named index.rst and add the file names of your notebooks (without the .ipynb extension) to the toctree directive. For an example, see this project's doc/index.rst file.

Sphinx Configuration Values

All configuration values are described in the Sphinx documentation, here we mention only the ones which may be relevant in combination with nbsphinx.

exclude_patterns

Sphinx builds all potential source files (reST files, Jupyter notebooks, ...) that are in the source directory, whether they are linked to or not. If you want certain files not to be built, specify them in exclude_patterns. For example, you might want to ignore files in your build directory and temporary Jupyter files:

exclude_patterns = ['_build', '**.ipynb_checkpoints']

extensions

This is the only required value. You have to add 'nbsphinx' to the list of extensions, otherwise it won't work.

Other interesting extensions are:

highlight_language

Default language for syntax highlighting in reST and Markdown cells, when no language is specified explicitly.

By default, this is 'python3', while Jupyter doesn't have a default language. Set highlight_language to 'none' to get the same behavior as in Jupyter:

highlight_language = 'none'

See also nbsphinx_codecell_lexer.

As a work-around -- until https://github.com/sphinx-doc/sphinx/issues/4229 is solved -- you should set html_scaled_image_link to False:

html_scaled_image_link = False

By default, a .txt suffix is added to source files. This is only relevant if the chosen HTML theme supports source links and if html_show_sourcelink is True.

Jupyter notebooks with the suffix .ipynb.txt are normally not very useful, so if you want to avoid the additional suffix, set html_sourcelink_suffix to the empty string:

html_sourcelink_suffix = ''

latex_additional_files

latex_additional_files can be useful if you are using BibTeX files, see References.

mathjax_config

The configuration value mathjax_config can be useful to enable Automatic Equation Numbering.

nbsphinx Configuration Values

nbsphinx_allow_errors

If True, the build process is continued even if an exception occurs.

See Ignoring Errors.

nbsphinx_codecell_lexer

Default Pygments lexer for syntax highlighting in code cells. If available, this information is taken from the notebook metadata instead.

Please note that this is not the same as highlight_language, which is used for formatting code in Markdown cells!

nbsphinx_custom_formats

See Custom Notebook Formats.

nbsphinx_epilog

See Prolog and Epilog.

nbsphinx_execute

Whether to execute notebooks before conversion or not. Possible values: 'always', 'never', 'auto' (default).

See Explicitly Dis-/Enabling Notebook Execution.

nbsphinx_execute_arguments

Kernel arguments used when executing notebooks.

If you use Matplotlib for plots, this setting is recommended:

nbsphinx_execute_arguments = [
    "--InlineBackend.figure_formats={'svg', 'pdf'}",
    "--InlineBackend.rc={'figure.dpi': 96}",
]

If you don't use LaTeX/PDF output, you can drop the 'pdf' figure format.

nbsphinx_input_prompt

Input prompt for code cells. %s is replaced by the execution count.

To get a prompt similar to the Classic Notebook, use

nbsphinx_input_prompt = 'In [%s]:'

nbsphinx_kernel_name

Use a different kernel than stored in the notebook metadata, e.g.:

nbsphinx_kernel_name = 'python3'

nbsphinx_output_prompt

Output prompt for code cells. %s is replaced by the execution count.

To get a prompt similar to the Classic Notebook, use

nbsphinx_output_prompt = 'Out[%s]:'

nbsphinx_prolog

See Prolog and Epilog.

nbsphinx_prompt_width

Width of input/output prompts (HTML only).

Any CSS length can be specified.

nbsphinx_requirejs_options

Options for loading RequireJS. See nbsphinx_requirejs_path.

nbsphinx_requirejs_path

URL or local path to override the default URL for RequireJS.

If you use a local file, it should be located in a directory listed in html_static_path.

Set to empty string to disable loading RequireJS.

nbsphinx_responsive_width

If the browser window is narrower than this, input/output prompts are on separate lines (HTML only).

Any CSS length can be specified.

nbsphinx_timeout

Controls when a cell will time out. Defaults to 30; use -1 for no timeout.

See Cell Execution Timeout.

nbsphinx_widgets_options

Options for loading Jupyter widgets resources. See nbsphinx_widgets_path.

nbsphinx_widgets_path

URL or local path to override the default URL for Jupyter widgets resources. See Interactive Widgets (HTML only)).

If you use a local file, it should be located in a directory listed in html_static_path.

For loading the widgets resources, RequireJS is needed, see nbsphinx_requirejs_path.

If nbsphinx_widgets_path is not specified, widgets resources are only loaded if at least one notebook actually uses widgets. If you are loading the relevant JavaScript code by some other means already, you can set this option to the empty string to avoid loading it a second time.

Running Sphinx

To create the HTML pages, use this command:

python3 -m sphinx <source-dir> <build-dir>

If you have many notebooks, you can do a parallel build by using the -j option:

python3 -m sphinx <source-dir> <build-dir> -j<number-of-processes>

For example, if your source files are in the current directory and you have 4 CPU cores, you can run this:

python3 -m sphinx . _build -j4

Afterwards, you can find the main HTML file in _build/index.html.

Subsequent builds will be faster, because only those source files which have changed will be re-built. To force re-building all source files, use the -E option.

**Note:** By default, notebooks will be executed during the Sphinx build process only if they do not have any output cells stored. See [Controlling Notebook Execution](executing-notebooks.ipynb).

To create LaTeX output, use:

python3 -m sphinx <source-dir> <build-dir> -b latex

If you don't know how to create a PDF file from the LaTeX output, you should have a look at Latexmk (see also this tutorial).

Sphinx can automatically check if the links you are using are still valid. Just invoke it like this:

python3 -m sphinx <source-dir> <build-dir> -b linkcheck

Watching for Changes with sphinx-autobuild

If you think it's tedious to run the Sphinx build command again and again while you make changes to your notebooks, you'll be happy to hear that there is a way to avoid that: sphinx-autobuild!

It can be installed with

python3 -m pip install sphinx-autobuild --user

You can start auto-building your files with

python3 -m sphinx_autobuild <source-dir> <build-dir>

This will start a local webserver which will serve the generated HTML pages at http://localhost:8000/. Whenever you save changes in one of your notebooks, the appropriate HTML page(s) will be re-built and when finished, your browser view will be refreshed automagically. Neat!

You can also abuse this to auto-build the LaTeX output:

python3 -m sphinx_autobuild <source-dir> <build-dir> -b latex

However, to auto-build the final PDF file as well, you'll need an additional tool. Again, you can use latexmk for this (see above). Change to the build directory and run

latexmk -pdf -pvc

If your PDF viewer isn't opened because of LaTeX build errors, you can use the command line flag -f to force creating a PDF file.

Automatic Creation of HTML and PDF output on readthedocs.org

There are two different methods, both of which are described below.

In both cases, you'll first have to create an account on https://readthedocs.org/ and connect your GitLab/Github/Bitbucket account. Instead of connecting, you can also manually add any publicly available Git/Subversion/Mercurial/Bazaar repository.

After doing the steps described below, you only have to "push" to your repository, and the HTML pages and the PDF file of your stuff are automagically created on readthedocs.org. Awesome!

You can even have different versions of your stuff, just use Git tags and branches and select in the readthedocs.org settings (under "Admin", "Versions") which of those should be created.

**Note:** If you want to execute notebooks (see [Controlling Notebook Execution](executing-notebooks.ipynb)), you'll need to install the appropriate Jupyter kernel. In the examples below, the IPython kernel ist installed from the packet `ipykernel`.

Using requirements.txt

  1. Create a file named requirements.txt (or whatever name you wish) in your repository containing the required pip packages:

     ipykernel
     nbsphinx
    
    

    You can also install directly from Github et al., using a specific branch/tag/commit, e.g.

     git+https://github.com/spatialaudio/[email protected]
  2. In the "Advanced Settings" on readthedocs.org, specify the path to your requirements.txt file (or however you called it) in the box labeled "Requirements file". Kinda obvious, isn't it?

  3. Still in the "Advanced Settings", make sure the right Python interpreter is chosen. This must be the same version (2.x or 3.x) as you were using in your notebooks!

Using conda

  1. Create a file named readthedocs.yml in the main directory of your repository, containing the name of yet another file:

     conda:
       file: readthedocs-environment.yml
  2. Create the file mentioned above. You can choose whatever name you want (it may also live in a subdirectory, e.g. doc/environment.yml), it just has to match whatever is specified in readthedocs.yml. The second file describes a conda environment and should contain something like this:

     channels:
       - conda-forge
     dependencies:
       - python>=3
       - pandoc
       - ipykernel
       - pip:
         - nbsphinx
    
    

    It is up to you if you want to install nbsphinx with conda or with pip (but note that the conda package might be outdated). And you can of course add further conda and pip packages. You can also install packages directly from Github et al., using a specific branch/tag/commit, e.g.

       - pip:
         - git+https://github.com/spatialaudio/[email protected]
**Note:** The specification of the `conda-forge` channel is recommended because it tends to have more recent package versions than the default channel.
**Note:** Most of the "Advanced Settings" on readthedocs.org will be ignored if you have a `readthedocs.yml` file. In this file you can control all the settings, see https://docs.readthedocs.io/en/latest/yaml-config.html.
**Warning:** If you have a very long repository name (or branch name), you might run into this quite obscure problem: ['placeholder too short'](https://github.com/readthedocs/readthedocs.org/issues/1902).

HTML Themes

The nbsphinx extension does not provide its own theme, you can use any of the available themes or create a custom one, if you feel like it.

The following (incomplete) list of themes contains up to three links for each theme:

  1. The documentation (or the official sample page) of this theme (if available; see also the documentation of the built-in Sphinx themes)
  2. How the nbsphinx documentation looks when using this theme
  3. How to enable this theme using either requirements.txt or readthedocs.yml and theme-specific settings (in some cases)

Sphinx's Built-In Themes

3rd-Party Themes

If you know of another Sphinx theme that should be included here, please open an issue on Github. An overview of many more themes can be found at https://sphinx-themes.org/.

Using Notebooks with Git

Git is extremely useful for managing source code and it can and should also be used for managing Jupyter notebooks. There is one caveat, however: Notebooks can contain output cells with rich media like images, plots, sounds, HTML, JavaScript and many other types of bulky machine-created content. This can make it hard to work with Git efficiently, because changes in those bulky contents can completely obscure the more interesting human-made changes in text and source code. Working with multiple collaborators on a notebook can become very tedious because of this.

It is therefore highly recommended that you remove all outputs from your notebooks before committing changes to a Git repository (except for the reasons mentioned in Pre-Executing Notebooks).

If there are no output cells in a notebook, nbsphinx will by default execute the notebook, and the pages generated by Sphinx will therefore contain all the output cells. See Controlling Notebook Execution for how this behavior can be customized.

In the Jupyter Notebook application, you can manually clear all outputs by selecting "Cell" $\to$ "All Output" $\to$ "Clear" from the menu. In JupyterLab, the menu items are "Edit" $\to$ "Clear All Outputs".

There are several tools available to remove outputs from multiple files at once without having to open them separately. You can even include such a tool as "clean/smudge filters" into your Git workflow, which will strip the output cells automatically whenever a Git command is executed. For details, have a look at those links: