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.
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 index.rst file.
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
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
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
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
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
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.
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 ist installed from the packet
Create a file named
requirements.txt(or whatever name you wish) in your repository containing the required pip packages:
You can also install directly from Github et al., using a specific branch/tag/commit, e.g.
In the “Advanced Settings” on readthedocs.org, specify the path to your
requirements.txtfile (or however you called it) in the box labeled “Requirements file”. Kinda obvious, isn’t it?
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!
Create a file named
readthedocs.ymlin the main directory of your repository, containing the name of yet another file:
conda: file: readthedocs-environment.yml
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 - sphinx>=1.6 - pandoc - nbconvert!=5.4 - ipykernel - pip: - nbsphinx
It is up to you if you want to install
pip(but note that the
condapackage might be outdated). And you can of course add further
pippackages. 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
The specification of the
conda-forge channel is recommended because it tends to have more recent package versions than the default channel.
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.
If you have a very long repository name (or branch name), you might run into this quite obscure problem: ‘placeholder too short’.
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:
- The documentation (or the official sample page) of this theme (if available; see also the documentation of the built-in Sphinx themes)
- How the
nbsphinxdocumentation looks when using this theme
- How to enable this theme using either
readthedocs.ymland theme-specific settings (in some cases)
Sphinx’s Built-In Themes¶
- sphinx_rtd_theme: example, usage
- bootstrap: example, usage
- cloud: example, usage
- sphinx_py3doc_enhanced_theme: example, usage
- basicstrap: example, usage
- dotted: example, usage
- better: example, usage
- guzzle_sphinx_theme: example, usage
- julia: example, usage
- jupyter: example, usage
Using Notebooks with Git¶
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: