Emacs IPython Notebook and the shaving of a Yak

It was this week during the project pitch exercise here at the Data Science For Social Good that I fell down a rabbit hole.  I wanted to get summary statistics on foreclosures and land values for each of Chicago’s 50 wards.  Of course I was not doing that when the well known data scientist and volunteer mentor Max Shron approached me I was fiddling with my editor. He politely introduced me to the concept of a “Yak Shave.”  As the definitive source of programming slang, the Jargon file defines it:


[MIT AI Lab, after 2000: orig. probably from a Ren & Stimpy episode.] Any seemingly pointless activity which is actually necessary to solve a problem which solves a problem which, several levels of recursion later, solves the real problem you’re working on.

Now there is some disagreement over whether this is a term of derision. Wikitionary includes an alternate meaning:

The actually useless activity you do that appears important when you are consciously or unconsciously procrastinating about a larger problem.

I thought I’d get more work done if I just fixed a problem with my .emacs file, but then I spent the whole afternoon yak shaving.


This was what Max was gently chiding me for.  After all, I am a PhD student our lives are devoted to the idea of Yak Shaving, even if we don’t have a name for it.  We all want to make our projects work without admitting to our advisers that we are stuck on step 3 of our weekly 50 part research assignment.  So I put down my fiddling and went to the meeting but I did not forget about it.  The culture of our group is nothing if not polite and friendly.

Now the truth is that this piece of out is slightly over 1 GB and I could have done all of my data cleaning in R.  However we all know that Python and Pandas are the better tools and we are trying to come up to speed quickly.  (For those of us on twitter, John Myles White, has been working on the next interpreted language to enter the speed wars, Julia). This idea of yak-shaving had me giggling for an hour.  I am a recent convert to gnu/linux and  the gnu part of that partnership is FREE Software with deep collectivist roots and installation procedures reminiscent of Dostoevsky novel if it works or years in Gulag if they don’t.  Their GNU mascot looks like a close relative of the Yak.

IpythonNotebookInEmacsEven the Wikitionary entry on useless yak shaving mentions the notoriously arcane .emacs file that needs to be constantly configured. These days may be coming to an end.  Not that I did not spend the better part of a sick day fiddling with it to get two pieces of canonical free software virtuosity, Fernando Perez‘s IPython and Richard Stallman‘s Emacs to play together well.  First, I found the brilliant ein library by Takafumi Arakaki.  But that alone did not shave the Yak.  I had to abandon my ad-hoc plugins for emacs and come to terms with Emacs’ three package managers.  It was MELPA tutorial from the indefatigable Xah Lee that worked for me.  Details will follow but here is a screen shot so you know that it is possible you to shave this Yak! …And in a lot less time than it took me.


Learning environments for data analysis software

Welcome to my blog

This is my first blog post using the iPython notebook. I am very excited about the things it can do. Here is what I want to cover:

  • Who I am
  • What the blog will cover
  • Why I named it Measure of Justice

Evan Misshula

I am a PhD student in Criminal Justice. I try to use social networks and data mining to help people make rational decisions about public safety. I care passionately about people that the world writes off. It is no shock. There have been many times when I have been written off.

Math, Computing, Causality, Networks, Security and Ethics

Early in my graduate career, I was struck that we spend a great deal of effort policing minority communities for drug use which has little effect on the non-involved but spend way less effort protecting the banking system from hackers. I also thought that there was a lot to learn about managing threats from inside by looking at both intrusion detection and counter- intelligence. Not suprisingly, I believe in second chances. Who gets those chances and when they come are an area of great interest.

What’s in a name?

When I studied Stochastic Control, Girsanov’s Theorem governed which measures
were deformable into each other. Two measures needed to have the same sets of measure zero, to equivilent. In other words it is what we think that is impossible, not unlikely that is important.

My favorite new toy

I am excited about blogging again because I can now put code and math in the blog. I have spent a lot of time in graduate school learning new tools. This blog will hopefully document some of the challenges and help others find their way. Others blogs have certainly helped me.

We can assign variables in the ipython notebook.

In [28]:

print a

In [30]:

b=9 a+b 


But you can also reach into the operating system and execute bash commands.

In [31]:




In [32]:

120907-Blogging with the IPython Notebook.ipynb EvanNB1.html old/
121120-Back from PyCon Canada 2012.ipynb EvanNB1.ipynb EvanNB1_header.html fig/

This is a markdown cell

You can italicize and use boldface. It allows us to comment code and create interactive presentations. You can build lists of your favorite tools. Here are mine.

  • linux
  • emacs
  • r statistical language
  • Emacs Speaks Statistics
  • Org-mode
  • LaTeX
  • Sweave
  • Ggplot

What is most important is to LaTeX support. My favorite math equation is $e^{i\pi}+1=0$. It can also render math numbered equations:

The browser displays

The program can display the numeric or character output of programs.

In [33]:

print "hi Doug"
hi Doug

In [9]:




It can also display graphs:

In [34]:

%pylab inline
Welcome to pylab, a matplotlib-based Python environment [backend: module://IPython.zmq.pylab.backend_inline].
For more information, type 'help(pylab)'.



In [35]:

x = linspace(0, 3*pi)
plot(x, 0.5*sin(x), label=r'$\sin(x)$') plot(x, cos(x), 'ro', label=r'$\cos(x)$') title(r'Two familiar functions')



Symbolic Manipulation

The ipython notebook can also make symbolic calculations and solve complex algebraic equations:

In [36]:

%load_ext sympyprinting import sympy as sym
from sympy import *
x, y, z = sym.symbols("x y z")
The sympyprinting extension is already loaded. To reload it, use: %reload_ext sympyprinting

In [37]:

Rational(3,2)*pi + exp(I*x) / (x**2 + y**2) 


$$\frac{3}{2} \pi + \frac{e^{\mathbf{\imath} x}}{x^{2} + y^{2}}$$

In [38]:

eq = ((x+y)**3 * (x+3)) eq


$$\left(x + 3\right) \left(x + y\right)^{3}$$

In [39]:



$$x^{4} + 3 x^{3} y + 3 x^{3} + 3 x^{2} y^{2} + 9 x^{2} y + x y^{3} + 9 x y^{2} + 3 y^{3}$$

Ipython can even calculate the derivative!!

In [40]:

diff(cos(x**2)**2 / (1+x)**2, x)


$$- 4 \frac{x \operatorname{sin}\left(x^{2}\right)
\operatorname{cos}\left(x^{2}\right)}{\left(x + 1\right)^{2}} – 2 \frac{\operatorname{cos}^{2}\left(x^{2}\right)}{\left(x +

It can also display pictures and videos…

In [19]:

from IPython.display import Image


In [20]:

from IPython.display import YouTubeVideo


We can even use other languages (including R)!!

This is because ipython communicates between the kernel and the browser so it knows how to send data to
another interpreter.

In [41]:

%%ruby puts "Hello from Ruby #{RUBY_VERSION}"
Hello from Ruby 1.9.3

In [42]:

%%bash echo "hello from $BASH" 
hello from /bin/bash

In [23]:

import rpy2;
from rpy2 import robjects; robjects.r("version")


platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
major 2
minor 15.2
year 2012
month 10
day 26
svn rev 61015
language R
version.string R version 2.15.2 (2012-10-26)
nickname Trick or Treat 

In [24]:

%load_ext rmagic
The rmagic extension is already loaded. To reload it, use: %reload_ext rmagic

In [25]:

X = np.array([0,1,2,3,4]) Y = np.array([3,5,4,6,7])

In [26]:

%%R -i X,Y -o XYcoef
XYlm = lm(Y~X)
XYcoef = coef(XYlm)
lm(formula = Y ~ X)

1 2 3 4 5
-0.2 0.9 -1.0 0.1 0.2

Estimate Std. Error t value Pr(>|t|)
(Intercept) 3.2000 0.6164 5.191 0.0139 *
X 0.9000 0.2517 3.576 0.0374 *
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.7958 on 3 degrees of freedom
Multiple R-squared: 0.81,	Adjusted R-squared: 0.7467
F-statistic: 12.79 on 1 and 3 DF, p-value: 0.03739

In [27]:



[ 3.2  0.9]

There is more to come. Ipython does d3 interactive graphs but I have not been able to get them to work. It also handles cython (python wrapped c-code) and
mpi parallel code. More later. It is time for bed.

Intro and iPython

So I was able to get this to post to my Measure of Justice. However I was not able to get it to work here. Since then, to my surprise I have found myself working less with the visually amazing, but temperamental iPython and more with Emacs org-mode.

The ability to toggle between thirty different languages and output to html or LaTeX is pretty overwhelming. This is not to say that I have had no trouble at all. Python sessions were broken for a while. Overall it has been a pleasant experience. If you are interested start with the article in the Journal of Statistical Software. But that is just the advertisement for what it can do. To master the usage you should go to the supplementary materials. You can download both the source code for the paper and the babel library. None of this is behind a pay-wall.

Here are the tricks:

1. The paper uses an initialization file, but you don’t need to do that. I generally just put an elisp block in the paper and execute that.

2. They defined a Journal of statistical software class to comply with formating requirement. You will generally just output to LaTeX

3. Any questions, just reach out to me on Twitter @emisshula