IPython tips, tricks & notes – Part 1

June 29, 2015

During the last week, I attended the Next Generation Computational Modelling (NGCM) Summer Academy at the University of Southampton. Three days were spent on a detailed IPython course, run by MinRK, one of the core IPython developers, and two days on a Pandas course taught by Skipper Seaborn and Chris Fonnesbeck.
The course was very useful, and I’m going to post a series of blog posts covering some of the things I’ve learnt. All of the posts will be written for people like me: people who already use IPython or Pandas but may not know some of the slightly more hidden tips and techniques.

Useful Keyboard Shortcuts

Everyone knows the Shift-Return keyboard shortcut to run the current cell in the IPython Notebook, but there are actually three ‘running’ shortcuts that you should know:

Shift-Return: Run the current cell and move to the cell below
Ctrl-Return: Run the current cell and stay in that cell
Opt-Return: Run the current cell, create a new cell below, and move to it

Once you know these you’ll find all sorts of useful opportunities to use them. I now use Ctrl-Return a lot when writing code, running it, changing it, running it again etc – it really speeds that process up!
Also, everyone knows that TAB does autocompletion in IPython, but did you know that Shift-TAB pops up a handy little tooltip giving information about the currently selected item (for example, the argument list for a function, the type of a variable etc. This popup box can be expanded to its full size by clicking the + button on the top right – or, by pressing Shift-TAB again.

Magic commands

Again, a number of IPython magic commands are well known: for example, %run and %debug, but there are loads more that can be really useful. A couple of really useful ones that I wasn’t aware of are:

%%writefile

This writes the contents of the cell to a file. For example:

%%writefile test.txt
This is a test file!
It can contain anything I want...

And more...

Writing test.txt

!cat test.txt

This is a test file!
It can contain anything I want...

And more...

%xmode

This changes the way that exceptions are displayed in IPython. It can take three options: plain, context and verbose. Let’s have a look at these.
First we create a simple module with a couple of functions, this basically just gives us a way to have a stack trace with multiple functions that leads to a ZeroDivisionError.

%%writefile mod.py

def f(x):
    return 1.0/(x-1)

def g(y):
    return f(y+1)

Writing mod.py

Now we’ll look at what happens with the default option of context

import mod
mod.g(0)

---------------------------------------------------------------------------
ZeroDivisionError                         Traceback (most recent call last)
<ipython-input-6-a54c5799f57e> in <module>()
      1 import mod
----> 2 mod.g(0)

/Users/robin/code/ngcm/ngcm_ipython_tutorial/Robin'sNotes/mod.py in g(y)
      4 
      5 def g(y):
----> 6     return f(y+1)

/Users/robin/code/ngcm/ngcm_ipython_tutorial/Robin'sNotes/mod.py in f(x)
      1 
      2 def f(x):
----> 3     return 1.0/(x-1)
      4 
      5 def g(y):

ZeroDivisionError: float division by zero

You’re probably fairly used to seeing that: it’s the standard IPython stack trace view. If we want to go back to plain Python we can set it to plain. You can see that you don’t get any context on the lines surrounding the exception – not so helpful!

%xmode plain

Exception reporting mode: Plain

import mod
mod.g(0)

Traceback (most recent call last):

  File "<ipython-input-8-a54c5799f57e>", line 2, in <module>
    mod.g(0)

  File "/Users/robin/code/ngcm/ngcm_ipython_tutorial/Robin'sNotes/mod.py", line 6, in g
    return f(y+1)

  File "/Users/robin/code/ngcm/ngcm_ipython_tutorial/Robin'sNotes/mod.py", line 3, in f
    return 1.0/(x-1)

ZeroDivisionError: float division by zero

The most informative option is verbose, which gives all of the information that is given by context but also gives you the values of local and global variables. In the example below you can see that g was called as g(0) and f was called as f(1).

%xmode verbose

Exception reporting mode: Verbose

import mod
mod.g(0)

---------------------------------------------------------------------------
ZeroDivisionError                         Traceback (most recent call last)
<ipython-input-10-a54c5799f57e> in <module>()
      1 import mod
----> 2 mod.g(0)
        global mod.g = <function g at 0x10899aa60>

/Users/robin/code/ngcm/ngcm_ipython_tutorial/Robin'sNotes/mod.py in g(y=0)
      4 
      5 def g(y):
----> 6     return f(y+1)
        global f = <function f at 0x10899a9d8>
        y = 0

/Users/robin/code/ngcm/ngcm_ipython_tutorial/Robin'sNotes/mod.py in f(x=1)
      1 
      2 def f(x):
----> 3     return 1.0/(x-1)
        x = 1
      4 
      5 def g(y):

ZeroDivisionError: float division by zero

%load

The load magic loads a Python file, from a filepath or URL, and replaces the contents of the cell with the contents of the file. One really useful application of this is to get example code from the internet. For example, the code %load http://matplotlib.org/mpl_examples/showcase/integral_demo.py will create a cell containing that matplotlib example.

%connect_info & %qtconsole

IPython operates on a client-server basis, and multiple clients (which can be consoles, qtconsoles, or notebooks) can connect to one backend kernel. To get the information required to connect a new front-end to the kernel that the notebook is using, run %connect_info:

%connect_info

{
  "control_port": 49569,
  "signature_scheme": "hmac-sha256",
  "transport": "tcp",
  "stdin_port": 49568,
  "key": "59de1682-ef3e-42ca-b393-487693cfc9a2",
  "ip": "127.0.0.1",
  "shell_port": 49566,
  "hb_port": 49570,
  "iopub_port": 49567
}

Paste the above JSON into a file, and connect with:
    $> ipython <app> --existing <file>
or, if you are local, you can connect with just:
    $> ipython <app> --existing kernel-a5c50dd5-12d3-46dc-81a9-09c0c5b2c974.json 
or even just:
    $> ipython <app> --existing 
if this is the most recent IPython session you have started.

There is also a shortcut that will load a qtconsole connected to the same kernel:

%qtconsole

Stopping output being printed

This is a little thing, that is rather reminiscent of Mathematica, but can be quite handy. You can suppress the output of any cell by ending it with ;. For example:

5+10

5+10;

Right, that’s enough for the first part – tune in next time for tips on figures, interactive widgets and more.

If you found this post useful, please consider buying me a coffee.
This post originally appeared on Robin's Blog.

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