Skip to main content

Doctesting Python command line scripts

The purists will hate this one, but the pragmatists may not condemn me so much. I'm writing Python because I want compact, easy to understand and maintain code. If I was into writing a ton of complicated boilerplate I would have used C.

In keeping with this philosophy I love doctest for testing Python code. Many a time writing code with an eye to doctesting it has led me to more modular and functional code. Perhaps this code was a little slower than it could be, but boy was it fast to write and debug and that's the reason we are in Python, right?

One bump in the road is how do you doctest whole command line applications? Vital parts of my code consist of Python scripts that are meant to be called as command line tools. The individual parts have been tested with doctest, but there is often a need for a gestalt test, where several tools are chained and the output needs to be tested.

There is something called shell-doctest which seems to do exactly this, but it is yet another third party package and not very recently maintained, or very widely known. I'm not sure I should use it.

The creator of Python has recommended creating a main function that can be then tested with forced arguments. I like this, and may convert my 'main' sections this way, but there is something to be said to maintaing the 'conversational' style of doctest, where you simply plop down python commands as you would normally and have the correct answers as if you were in an interactive programming environment.

My current experiment is to merge the gestalt test with my instruction manual so that I'm writing the command line examples into my file which then doubles as a test file which can be executed by running python -m doctest -v

In fact, if you are in IPython, the magic function run does exactly what I want - which, is to run a complete shell command, like run arg1 arg2 arg3. Unfortunately doctest uses a vanilla python shell which does not have this facility.

My solution is to define a function I call shell early on in the document.

>>> import shlex, subprocess
>>> def shell(command):

Now, in my file I have things like:

You can run the data processing program as

>>> shell('python infile.txt outfile.txt')

Which will result in this processed data

>>> with open('outfile.txt','r') as f: print
Output Data

Which serves both as do by example documentation as well as test.


Popular posts from this blog

Flowing text in inkscape (Poster making)

You can flow text into arbitrary shapes in inkscape. (From a hint here).

You simply create a text box, type your text into it, create a frame with some drawing tool, select both the text box and the frame (click and shift) and then go to text->flow into frame.


The omnipresent anonymous asked:
Trying to enter sentence so that text forms the number three...any ideas?
The solution:
Type '3' using the text toolConvert to path using object->pathSize as necessaryRemove fillUngroupType in actual text in new text boxSelect the text and the '3' pathFlow the text

Pandas panel = collection of tables/data frames aligned by index and column

Pandas panel provides a nice way to collect related data frames together while maintaining correspondence between the index and column values:

import pandas as pd, pylab #Full dimensions of a slice of our panel index = ['1','2','3','4'] #major_index columns = ['a','b','c'] #minor_index df = pd.DataFrame(pylab.randn(4,3),columns=columns,index=index) #A full slice of the panel df2 = pd.DataFrame(pylab.randn(3,2),columns=['a','c'],index=['1','3','4']) #A partial slice df3 = pd.DataFrame(pylab.randn(2,2),columns=['a','b'],index=['2','4']) #Another partial slice df4 = pd.DataFrame(pylab.randn(2,2),columns=['d','e'],index=['5','6']) #Partial slice with a new column and index pn = pd.Panel({'A': df}) pn['B'] = df2 pn['C'] = df3 pn['D'] = df4 for key in pn.items: print pn[key] -> output …

Drawing circles using matplotlib

Use the pylab.Circle command

import pylab #Imports matplotlib and a host of other useful modules cir1 = pylab.Circle((0,0), radius=0.75, fc='y') #Creates a patch that looks like a circle (fc= face color) cir2 = pylab.Circle((.5,.5), radius=0.25, alpha =.2, fc='b') #Repeat (alpha=.2 means make it very translucent) ax = pylab.axes(aspect=1) #Creates empty axes (aspect=1 means scale things so that circles look like circles) ax.add_patch(cir1) #Grab the current axes, add the patch to it ax.add_patch(cir2) #Repeat