Jupyter Sphinx Extension¶
Jupyter-sphinx is a Sphinx extension that executes embedded code in a Jupyter kernel, and embeds outputs of that code in the document. It has support for rich output such as images, Latex math and even javascript widgets, and it allows to enable thebelab for live code execution with minimal effort.
Installation¶
Get jupyter-sphinx from pip:
pip install jupyter-sphinx
or conda:
conda install jupyter_sphinx -c conda-forge
Enabling the extension¶
To enable the extension, add jupyter_sphinx
to your enabled extensions in
conf.py
:
extensions = [
'jupyter_sphinx',
]
Basic Usage¶
You can use the jupyter-execute
directive to embed code into the document:
.. jupyter-execute::
name = 'world'
print('hello ' + name + '!')
The above is rendered as follows:
name = 'world'
print('hello ' + name + '!')
hello world!
Note that the code produces output (printing the string ‘hello world!’), and the output is rendered directly after the code snippet.
Because all code cells in a document are run in the same kernel, cells later in the document can use variables and functions defined in cells earlier in the document:
a = 1
print('first cell: a = {}'.format(a))
first cell: a = 1
a += 1
print('second cell: a = {}'.format(a))
second cell: a = 2
Because jupyter-sphinx uses the machinery of nbconvert
, it is capable of rendering
any rich output, for example plots:
import numpy as np
from matplotlib import pyplot
%matplotlib inline
x = np.linspace(1E-3, 2 * np.pi)
pyplot.plot(x, np.sin(x) / x)
pyplot.plot(x, np.cos(x))
pyplot.grid()
![_images/index_3_0.png](_images/index_3_0.png)
LaTeX output:
from IPython.display import Latex
Latex('\\int_{-\\infty}^\\infty e^{-x²}dx = \\sqrt{\\pi}')
or even full-blown javascript widgets:
import ipywidgets as w
from IPython.display import display
a = w.IntSlider()
b = w.IntText()
w.jslink((a, 'value'), (b, 'value'))
display(a, b)
It is also possible to include code from a regular file by passing the filename as argument
to jupyter-execute
:
.. jupyter-execute:: some_code.py
jupyter-execute
may also be used in docstrings within your Python code, and will be executed
when they are included with Sphinx autodoc.
Thebelab support¶
To turn on thebelab, specify its configuration directly
in conf.py
:
jupyter_sphinx_thebelab_config = {
'requestKernel': True,
'binderOptions': {
'repo': "binder-examples/requirements",
},
}
With this configuration, thebelab is activated with a button click:
By default the button is added at the end of the document, but it may also be inserted anywhere using
.. thebe-button:: Optional title
Directive options¶
You may choose to hide the code of a cell, but keep its output visible using :hide-code:
:
.. jupyter-execute::
:hide-code:
print('this code is invisible')
produces:
print('this code is invisible')
this code is invisible
this option is particularly useful if you want to embed correctness checks in building your documentation:
.. jupyter-execute::
:hide-code:
assert everything_works, "There's a bug somewhere"
This way even though the code won’t make it into the documentation, the build will fail if running the code fails.
Similarly, outputs are hidden with :hide-output:
:
.. jupyter-execute::
:hide-output:
print('this output is invisible')
produces:
print('this output is invisible')
You may also display the code below the output with :code-below:
:
.. jupyter-execute::
:code-below:
print('this code is below the output')
produces:
this code is below the output
print('this code is below the output')
You may also add line numbers to the source code with :linenos:
:
.. jupyter-execute::
:linenos:
print('A')
print('B')
print('C')
produces:
1print('A')
2print('B')
3print('C')
A
B
C
To add line numbers from a specific line to the source code, use the
lineno-start
directive:
.. jupyter-execute::
:lineno-start: 7
print('A')
print('B')
print('C')
produces:
7print('A')
8print('B')
9print('C')
A
B
C
You may also emphasize particular lines in the source code with :emphasize-lines:
:
.. jupyter-execute::
:emphasize-lines: 2,5-6
d = {
'a': 1,
'b': 2,
'c': 3,
'd': 4,
'e': 5,
}
produces:
2d = {
3 'a': 1,
4 'b': 2,
5 'c': 3,
6 'd': 4,
7 'e': 5,
8}
Controlling exceptions¶
The default behaviour when jupyter-sphinx encounters an error in the embedded code is just to
stop execution of the document and display a stack trace. However, there are many cases where it may be
illustrative for execution to continue and for a stack trace to be shown as output of the cell. This
behaviour can be enabled by using the raises
option:
.. jupyter-execute::
:raises:
1 / 0
produces:
1 / 0
---------------------------------------------------------------------------
ZeroDivisionError Traceback (most recent call last)
Cell In[13], line 1
----> 1 1 / 0
ZeroDivisionError: division by zero
Note that when given no arguments, raises
will catch all errors. It is also possible to give raises
a list of error types; if an error is raised that is not in the list then execution stops as usual:
.. jupyter-execute::
:raises: KeyError, ValueError
a = {'hello': 'world!'}
a['jello']
produces:
a = {'hello': 'world!'}
a['jello']
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
Cell In[14], line 2
1 a = {'hello': 'world!'}
----> 2 a['jello']
KeyError: 'jello'
Additionally, any output sent to the stderr
stream of a cell will result in jupyter-sphinx
producing a warning. This behaviour can be suppressed (and the stderr
stream printed as regular
output) by providing the stderr
option:
.. jupyter-execute::
:stderr:
import sys
print("hello, world!", file=sys.stderr)
produces:
import sys
print("hello, world!", file=sys.stderr)
hello, world!
Manually forming Jupyter cells¶
When showing code samples that are computationally expensive, access restricted resources, or have non-deterministic output, it can be preferable to not have them run every time you build. You can simply embed input code without executing it using the jupyter-input
directive expected output with jupyter-output
:
.. jupyter-input::
:linenos:
import time
def slow_print(str):
time.sleep(4000) # Simulate an expensive process
print(str)
slow_print("hello, world!")
.. jupyter-output::
hello, world!
produces:
1import time
2
3def slow_print(str):
4 time.sleep(4000) # Simulate an expensive process
5 print(str)
6
7slow_print("hello, world!")
hello, world!
Controlling the execution environment¶
The execution environment can be controlled by using the jupyter-kernel
directive. This directive takes
the name of the Jupyter kernel in which all future cells (until the next jupyter-kernel
directive) should
be run:
.. jupyter-kernel:: python3
:id: a_unique_name
jupyter-kernel
can also take a directive option :id:
that names the Jupyter session;
it is used in conjunction with the jupyter-download
roles described in the next section.
Note that putting a jupyter-kernel
directive starts a new kernel, so any variables and functions declared
in cells before a jupyter-kernel
directive will not be available in future cells.
Note that we are also not limited to working with Python: Jupyter Sphinx supports kernels for any programming language, and we even get proper syntax highlighting thanks to the power of Pygments.
Downloading the code as a script¶
Jupyter Sphinx includes 2 roles that can be used to download the code embedded in a document:
:jupyter-download-script:
(for a raw script file) and :jupyter-download-notebook:
or :jupyter-download-nb:
(for
a Jupyter notebook).
These roles are equivalent to the standard sphinx download role, except the extension of the file should not be given. For example, to download all the code from this document as a script we would use:
:jupyter-download-script:`click to download <index>`
Which produces a link like this: click to download
. The target that the role is
applied to (index
in this case) is the name of the document for which you wish to download
the code. If a document contains jupyter-kernel
directives with :id:
specified, then
the name provided to :id:
can be used to get the code for the cells belonging to the
that Jupyter session.
Styling options¶
The CSS (Cascading Style Sheet) class structure of jupyter-sphinx is the following:
- jupyter_container, jupyter_cell
- cell_input
- cell_output
- stderr
- output
If a code cell is not displayed, the output is provided without the
jupyter_container
. If you want to adjust the styles, add a new stylesheet,
e.g. custom.css
, and adjust your conf.py
to load it. How you do so depends on
the theme you are using.
Here is a sample custom.css
file overriding the stderr
background color:
.jupyter_container .stderr {
background-color: #7FFF00;
}
Alternatively, you can also completely overwrite the CSS and JS files that are added by Jupyter Sphinx by providing a full copy of a jupyter-sphinx.css
(which can be empty) file in your _static
folder.
This is also possible with the thebelab CSS and JS that is added.
Configuration options¶
Typically you will be using Sphinx to build documentation for a software package.
If you are building documentation for a Python package you should add the following
lines to your sphinx conf.py
:
import os
package_path = os.path.abspath('../..')
os.environ['PYTHONPATH'] = ':'.join((package_path, os.environ.get('PYTHONPATH', '')))
This will ensure that your package is importable by any IPython kernels, as they will inherit the environment variables from the main Sphinx process.
Here is a list of all the configuration options available to the Jupyter Sphinx extension:
jupyter_execute_default_kernel
The default kernel to launch when executing code in
jupyter-execute
directives. The default ispython3
.
render_priority_html
The priority of different output mimetypes for displaying in HTML output. Mimetypes earlier in the data priority list are preferred over later ones. This is relevant if a code cell produces an output that has several possible representations (e.g. description text or an image). Please open an issue if you find a mimetype that isn’t supported, but should be. The default is
['application/vnd.jupyter.widget-view+json', 'text/html', 'image/svg+xml', 'image/png', 'image/jpeg', 'text/latex', 'text/plain']
.
render_priority_latex
Same, as
render_priority_html
, but for latex. The default is['image/svg+xml', 'image/png', 'image/jpeg', 'text/latex', 'text/plain']
.
jupyter_execute_kwargs
Keyword arguments to pass to
nbconvert.preprocessors.execute.executenb
, which controls how code cells are executed. The default isdict(timeout=-1, allow_errors=True)
.
jupyter_sphinx_linenos
Whether to show line numbering in all
jupyter-execute
sources.
jupyter_sphinx_continue_linenos
Whether to continue line numbering from previous cell in all
jupyter-execute
sources.
Changelog¶
Release 0.4.0¶
Allow adding inputs and outputs that are not executed using
jupyter-input
andjupyter-output
directives.Improve script handling by using
nbconvert
directly.Remove deprecated enabling of the extension as
jupyter_sphinx.execute
.Implement different output priorities in HTML and LaTeX builders. In practice this allows to provide a better fallback in PDF output.
Introduce new
jupyter-download
syntax compatible with Sphinx≥4,jupyter-download-nb
,jupyter-download-notebook
, andjupyter-download-script
Do not overwrite CSS and JS if files already exist in _static/, this allows to customize the CSS and JS file.
Release 0.3.0¶
Switch the extension name to
jupyter-sphinx
, deprecatejupyter-sphinx.execute
.Miscellaneous bugfixes following the restructuring of the codebase.