An example Jupyter Notebook

This notebook is a demonstration of directly-parsing Jupyter Notebooks into Sphinx using the MyST parser.

Markdown

Configuration

https://myst-parser.readthedocs.io/en/latest/using/intro.html#getting-started

To build documentation from this notebook, the following options are set:

myst_enable_extensions = [
    "amsmath",
    "colon_fence",
    "deflist",
    "dollarmath",
    "html_image",
]
myst_url_schemes = ("http", "https", "mailto")

Syntax

As you can see, markdown is parsed as expected. Embedding images should work as expected. For example, here’s the MyST-NB logo:

![myst-nb logo](../img/unitary_fund_logo.png)

By adding "html_image" to the myst_enable_extensions list in the sphinx configuration (see here), you can even add HTML img tags with attributes:

<img src="../img/unitary_fund_logo.png" alt="logo" width="200px" class="shadow mb-2">

Because MyST-NB is using the MyST-markdown parser, you can include rich markdown with Sphinx in your notebook. For example, here’s a note admonition block:

Note

Wow, a note! It was generated with this code (as explained here):

:::{note}
**Wow**, a note!
:::

If you wish to use “bare” LaTeX equations, then you should add "amsmath" to the myst_enable_extensions list in the sphinx configuration. This is explained here, and works as such:

\begin{equation}
\frac {\partial u}{\partial x} + \frac{\partial v}{\partial y} = - \, \frac{\partial w}{\partial z}
\end{equation}

\begin{align*}
2x - 5y &=  8 \\
3x + 9y &=  -12
\end{align*}

(1)\[\begin{equation} \frac {\partial u}{\partial x} + \frac{\partial v}{\partial y} = - \, \frac{\partial w}{\partial z} \end{equation}\]

\[\begin{align*} 2x - 5y &= 8 \\ 3x + 9y &= -12 \end{align*}\]

Also you can use features like equation numbering and referencing in the notebooks:

$$e^{i\pi} + 1 = 0$$ (euler)

(2)\[e^{i\pi} + 1 = 0\]

Euler’s identity, equation (2), was elected one of the most beautiful mathematical formulas.

You can see the syntax used for this example here in the MyST documentation.

Code cells and outputs

You can run cells, and the cell outputs will be captured and inserted into the resulting Sphinx site.

__repr__ and HTML outputs

For example, here’s some simple Python:

import matplotlib.pyplot as plt
import numpy as np
data = np.random.rand(3, 100) * 100
data[:, :10]

array([[ 1.39849631, 60.17337292, 12.15497002, 73.24277304,  4.74342838,
        42.52272142,  0.9430374 , 88.60296658, 67.58392545,  3.15985982],
       [ 5.58407154, 53.06670548, 15.39496781, 19.46055717, 24.70089623,
        10.20764344, 97.54563295, 14.65390178, 29.62695719, 65.09254846],
       [40.79800351, 37.91280458, 84.63121259, 90.22141457, 33.5609507 ,
        12.37737901, 76.61884529, 15.1687794 , 12.77230809,  6.92029623]])

This will also work with HTML outputs

import pandas as pd
df = pd.DataFrame(data.T, columns=['a', 'b', 'c'])
df.head()

	a	b	c
0	1.398496	5.584072	40.798004
1	60.173373	53.066705	37.912805
2	12.154970	15.394968	84.631213
3	73.242773	19.460557	90.221415
4	4.743428	24.700896	33.560951

as well as math outputs

from IPython.display import Math
Math(r"\sum_{i=0}^n i^2 = \frac{(n^2+n)(2n+1)}{6}")

\[\displaystyle \sum_{i=0}^n i^2 = \frac{(n^2+n)(2n+1)}{6}\]

This works for error messages as well:

print("This will be properly printed...")
print(thiswont)

This will be properly printed...

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[4], line 2
      1 print("This will be properly printed...")
----> 2 print(thiswont)

NameError: name 'thiswont' is not defined

Images

Images that are generated from your code (e.g., with Matplotlib) will also be embedded.

fig, ax = plt.subplots()
ax.scatter(*data, c=data[2])

<matplotlib.collections.PathCollection at 0x7f30945f3fe0>

Thumbnail for the Notebook

To add a thumbnail for an example notebook, first add the thumbnail image file to docs/source/_thumbnails. Next, modify the docs/source/conf.py to include the example and thumbnail in the nbsphinx_thumbnails dictionary at the end of the file. The sample below contains both a generic template and an actual example.

nbsphinx_thumbnails = {
    "examples/{EXAMPLE_FILENAME_WITHOUT_.md}": "_static/{THUMBNAIL_FILENAME_WITH_EXTENSION}",
    "examples/hamiltonians": "_static/vqe-cirq-pauli-sum-mitigation-plot.png"
    }