OpenFF Sphinx theme

openff-sphinx-theme

Jupyter Notebooks

The MyST-NB extension allow notebooks to be seemlessly integrated into a Sphinx website. This page demonstrates how notebooks are rendered.

Mathematics

MathJax can use used to render mathematical equations. Equations can be rendered either in their own line using double dollar signs

\[ y_{it} = \alpha_i + \gamma_t + \beta x_{it} + \epsilon_{it} \]

or inline using single dollar signs (\(\LaTeX\)).

DataFrames

pandas DataFrames are rendered with useful markup.

import numpy as np
import pandas as pd

df = pd.DataFrame({'ints': [1, 2, 3], 
                   'floats': [np.pi, np.exp(1), (1+np.sqrt(5))/2],
                   'strings': ['aardvark', 'bananarama', 'charcuterie' ]})

df

	ints	floats	strings
0	1	3.141593	aardvark
1	2	2.718282	bananarama
2	3	1.618034	charcuterie

Plots and Figures

matplotlib can be used to produce plots in notebooks

This example comes from the matplotlib gallery.

%matplotlib inline

import numpy as np
import matplotlib.pyplot as plt
from matplotlib import cm

fig, ax = plt.subplots(figsize=(12,8))

data = np.clip(np.random.randn(250, 250), -1, 1)

cax = ax.imshow(data, interpolation='nearest', cmap=cm.coolwarm)
ax.set_title('Gaussian noise with vertical colorbar', fontsize=16)
plt.tick_params(labelsize=16)

# Add colorbar, make sure to specify tick locations to match desired ticklabels
cbar = fig.colorbar(cax, ticks=[-1, 0, 1])
cbar.ax.set_yticklabels(['< -1', '0', '> 1'])  # vertically oriented colorbar
cbar.ax.tick_params(labelsize=16)

STDERR and STDOUT

raise ValueError(", ".join(str(i) for i in range(100)))

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[3], line 1
----> 1 raise ValueError(", ".join(str(i) for i in range(100)))

ValueError: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99

import sys
print("hi", file=sys.stderr)

hi

print("hi, this is stderr", file=sys.stderr)
print("hi, this is stdout", file=sys.stdout)
"this is a return value"

hi, this is stdout

hi, this is stderr

'this is a return value'

print("hi, this is stderr", file=sys.stderr)
print("hi, this is stdout", file=sys.stdout)
raise ValueError("this is an error")

hi, this is stdout

hi, this is stderr

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[6], line 3
      1 print("hi, this is stderr", file=sys.stderr)
      2 print("hi, this is stdout", file=sys.stdout)
----> 3 raise ValueError("this is an error")

ValueError: this is an error

# This cell has no output

Alerts

Alerts are the Jupyter Notebook version of admonitions

NOTE Use blue boxes for Tips and notes.

Use green boxes sparingly, and only for some specific purpose that the other boxes can't cover. For example, if you have a lot of related content to link to, maybe you decide to use green boxes for related links from each section of a notebook.

Use yellow boxes for examples that are not inside code cells, or use for mathematical formulas if needed.

In general, just avoid the red boxes.