The Living Thing / Notebooks : Python

A Swiss army knife of coding tools. Good matrix library, general scientific tools, statistics library, art tools interoperation with everything else - wraps C, C++, Fortran, comes with web servers, HTTP clients, parsers and all the other fruits of a thriving community. Fast enough, easy to debug, garbage-collected. If some bit is too slow, you compile it, otherwise, you relax. An excellent choice if you’d rather get stuff done than write code.

I do my stats and graphs in R, my user interface in javascript, my parallelism in java, and my linear algebra library is fortran but python is the thread that stitches this Frankensteinian monster together.

Of course, it could be better. Clojure is more elegant, scala is more parallelisable, julia prioritises scientific work more highly… But in terms of using a damn-well-supported language that goes on your computer right now, and requires you to reinvent few wheels, and which is transferrable across number crunching, web development, UIs, text processing, graphics and sundry other domains, and does not require heavy licensing costs… this one is a good default choice.

Python version management for weird sciency distributions

One suggestion I’ve has is to use pyenv.

apparently I should also use virtualenv, which can create different projects within a global python version.

In addition, anaconda reckons their conda command is the best.


I’m using virtualenv for now; it is the most common one and works fine.


The python-specific part of jupyter, which can also run without jupyter. Long story.

The main problem I forget here is how to debug. Let’s say there is a line in your code that keeps on failing:


In vanilla python if you want to debug the last exception (the post-mortem debugger) you do:

import pdb;

and if you want to drop into a debugger from some bit of code, you write:

import pdb; pdb.set_trace()

and if you want to use a fancier debugger (ipdb is recommended):

import ipdb; ipdb.set_trace()


import ipdb;

This doesn’t work in ipython, which has some other fancy interaction loop going on.

Here’s one manual way to drop into the debugger from code, noticed by Christoph Martin

from IPython.core.debugger import Tracer; Tracer()()

However, that’s not how you are supposed to do it. The real debugger invocation is supposed to be through so-called magics, e.g. the %debug magic to set a breakpoint.

%debug [--breakpoint filename:line_number_for_breakpoint]


Without the argument it activates post-mortem mode.

And if you want to drop automatically into the post mortem debugger for every error

%pdb on


Props to Josh Devlin for explaining this and some other handy tips.


Profile functions using cProfile.

Now visualise them using… uh…

Visualising profiles

Miscellaneous stuff I always need to look up


Not so hard, but confusing and chaotic due to many long-running disputes only lately resolving.

Python 2 v 3