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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 this variable contains the right things:

extensions = [
    'nbsphinx',
    'sphinx.ext.mathjax',
]

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.

Alternatively, you can delete the file index.rst and replace it with your own notebook called index.ipynb which will serve as main page. In this case you can create the main toctree in index.ipynb.

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 (including any sub-directories), whether you want to use them or not. If you want certain source files not to be built, specify them in exclude_patterns. For example, you might want to ignore source files in your build directory:

exclude_patterns = ['_build']

Note that the directory .ipynb_checkpoints is automatically added to exclude_patterns by nbsphinx.

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.

html_css_files

See Custom CSS and html_css_files.

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.

suppress_warnings

Warnings can be really helpful to detect small mistakes, and you should consider invoking Sphinx with the -W option, which turns warnings into errors. However, warnings can also be annoying, especially if you are fully aware of the “problem”, but you simply don’t care about it for some reason. In this case, you can use suppress_warnings to silence specific types of warnings.

If you want to suppress all warnings from nbsphinx, use this:

suppress_warnings = [
    'nbsphinx',
]

You can also be more specific:

suppress_warnings = [
    'nbsphinx.localfile',
    'nbsphinx.gallery',
    'nbsphinx.thumbnail',
    'nbsphinx.notebooktitle',
    'nbsphinx.ipywidgets',
]

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.

See Configuring the Kernels.

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'

See Configuring the Kernels.

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).

If a prompt is wider than that, it protrudes into the left margin.

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_thumbnails

A dictionary mapping from a document name (i.e. source file without suffix but with subdirectories) – optionally containing wildcards – to a thumbnail path to be used in a thumbnail gallery.

See Specifying Thumbnails.

nbsphinx_timeout

Controls when a cell will time out. The timeout is given in seconds. Given -1, cells will never time out, which is also the default.

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.

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 which of those should be created.

Note

If you want to execute notebooks (see Controlling Notebook Execution), you’ll need to install the appropriate Jupyter kernel. In the examples below, the IPython kernel is installed from the packet ipykernel.

Using requirements.txt

  1. Create a file named .readthedocs.yml in the main directory of your repository with the following contents:

    version: 2
    formats: all
    python:
      version: 3
      install:
        - requirements: doc/requirements.txt
      system_packages: true
    

    For further options see https://docs.readthedocs.io/en/latest/config-file/.

  2. Create a file named doc/requirements.txt (or whatever you chose in the previous step) 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/nbsphinx.git@master
    

Using conda

  1. Create a file named .readthedocs.yml in the main directory of your repository with the following contents:

    version: 2
    formats: all
    conda:
      file: doc/environment.yml
    

    For further options see https://docs.readthedocs.io/en/latest/config-file/.

  2. Create a file named doc/environment.yml (or whatever you chose in the previous step) describing a conda environment like this:

    channels:
      - conda-forge
    dependencies:
      - python>=3
      - pandoc
      - ipykernel
      - pip
      - 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/nbsphinx.git@master
    

Note

The specification of the conda-forge channel is recommended because it tends to have more recent package versions than the default channel.

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

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:

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