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_foundation_logo.png)

myst-nb logo

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_foundation_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([[ 5.53795308, 35.03617076, 87.79551013, 62.5419711 , 58.62952678,
        33.49884177, 17.39910313, 59.85368359, 77.89795375, 62.78131658],
       [99.18851813, 31.62435046, 24.92921631, 28.9291576 , 80.80322318,
         4.89112715, 90.37135984, 34.53425707, 88.22927572, 16.15841829],
       [78.86645182,  8.40729962, 48.85661754, 49.83364222, 17.38035801,
        63.73025871, 52.17267352, 42.01727291, 15.73882017, 55.99348775]])

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	5.537953	99.188518	78.866452
1	35.036171	31.624350	8.407300
2	87.795510	24.929216	48.856618
3	62.541971	28.929158	49.833642
4	58.629527	80.803223	17.380358

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 0x71a427aa3e60>

../_images/efbf33976d883a038aaea4de4a272cdc8fe66693439bd2aa725a8e53d12d70fd.png

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"
    }