README

Test of integrating jupyter with emacs org-mode

First I am going to try ob-ipython, to see if that works better than using the normal python integration

ob-ipython

Installation

• It seems I already had installed it from MELPA
• [2016-09-18 Sun 18:54] updated to the latest version

Tests

We turn this on so that the inline figs get updated immediately

(add-hook 'org-babel-after-execute-hook 'org-display-inline-images 'append)

First we import the packages we want and set up the plotting style.

%matplotlib inline
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
sns.set(context='notebook',
        style='darkgrid', 
        palette='bright',
        font_scale=1.5,
        color_codes=True)

Use SVG files instead of PNG for resolution independence.

%config InlineBackend.figure_format = 'svg'

Inspect the style parameters that we got from the darkgrid canned option.

sns.axes_style()

{'axes.axisbelow': True,
 'axes.edgecolor': 'white',
 'axes.facecolor': '#EAEAF2',
 'axes.grid': True,
 'axes.labelcolor': '.15',
 'axes.linewidth': 0.0,
 'figure.facecolor': 'white',
 'font.family': [u'sans-serif'],
 'font.sans-serif': [u'Arial',
  u'Liberation Sans',
  u'Bitstream Vera Sans',
  u'sans-serif'],
 'grid.color': 'white',
 'grid.linestyle': u'-',
 'image.cmap': u'Greys',
 'legend.frameon': False,
 'legend.numpoints': 1,
 'legend.scatterpoints': 1,
 'lines.solid_capstyle': u'round',
 'text.color': '.15',
 'xtick.color': '.15',
 'xtick.direction': u'out',
 'xtick.major.size': 0.0,
 'xtick.minor.size': 0.0,
 'ytick.color': '.15',
 'ytick.direction': u'out',
 'ytick.major.size': 0.0,
 'ytick.minor.size': 0.0}

Change the plot colours to be more suitable to a dark background.

black_style ={
 'axes.edgecolor': '#3f3f3f',
 'axes.facecolor': '#504040',
 'axes.labelcolor': '.85',
 'figure.facecolor': '#3f3f3f',
 'grid.color': 'gray',
 'xtick.color': '.85',
 'ytick.color': '.85',

}
sns.set_style(rc=black_style)

plt.hist(np.random.randn(20000), bins=50)

fig, ax = plt.subplots(1, 1)
fig.set_size_inches(5, 3)
x = np.linspace(-20.0, 20.0, 100)
ax.plot(x, np.sin(x)/x)

So we can make a plot of \[ y = \frac{sin x}{x} \] if we want to. And we can change the size of the figure.

EIN

We should also look at this

Export of this file to HTML

• Note that we run org-export on the top-level section, so go to the top and type C-c C-e C-s h o
  • This is the only way of getting the export file name to be different from the org source file name
  • We want it to export to docs/index.html so that it is served as a web page on github.io
• In order that the inline figures work in both the org file and in the exported web page, we use the following hack:
  • Figure files are specified by a relative path in the figs/ subfolder
    • E.g.,
  • But this is really a symbolic link to the docs/ folder:

    ls -ld figs
            

    lrwxr-xr-x  1 will  staff  9 Sep 19 09:09 figs -> docs/figs
            

• Configuration of MathJax for equation display
  • Use the https protocol
  • Try the Asana-Math font
• The general export options are given below (invisible in HTML export)
  • Only change from default is to remove section numbering

Issues with the export to GitHub pages

• On the whole, it works pretty well
• The main problem with using the github.io address is that the CDN takes a very long time to propagate changes. Like, several hours.
• I set up a dns forward from jupiter-org-integration.henney.org
  • Notice the typo in the name!
  • That updated faster
• There were some issues with mathjax
  • I have switched it to https to be on the safe side.
  • it worked perfectly on my iPad, but to begin with not on my iPhone
  • This turned out to be because of content blocker Purify
  • Once I white listed my site, all was fine
  • On my laptop, the change of font is not respected
    • But this may well be something I have configured