IndexArchivesAtomRSS

Testing and data analysis in Python

Something that occurred to me more frequently than I would like to admit while I was writing code to analyze data back in graduate school was that I would start a computationally intensive process, only to find that it would terminate at the penultimate step due to a simple bug in my code. At the time, I knew nothing about testing frameworks or test-driven development. I had a variety of approaches of dealing with this problem:

  • Go through statements one by one in the REPL (the ones that I could run quickly, anyway)
  • Make sure I could check on interim progress through standard output or output files
  • Split up my scripts into smaller units

None of these really substitute for the confidence you have with test coverage, however. Since I've returned to wrangling with data on my current client project, I've sought to incorporate testing into my workflow.

Most data scientists endorse the use of notebooks as a form of reproducible research. Indeed, it's a good way to explore a data set and share your analysis. I've been treating what I do in notebooks as a spike; it's a good place for one-off code and getting familiar with new APIs or libraries.

But when I find myself repeating a block of code over and over again, I move to the text editor and start writing tests for a reusable function. These functions then assemble into modules that I can import as necessary to carry out any lengthy processes or computations. I'm not quite at the stage when the final script I run only makes calls to test-covered functions, but I'm getting there. And certainly, the bugs I'm experiencing now tend to happen in the parts of the script that use untested functions.

I use pytest to run my tests. I find the output easier to read and interpret than the built-in unittest. Other people recommend nose2, which I haven't tried yet.

At the current stage of my project, I've been using the APIs from various social media platforms to collect data. While testing the functions I use to call these APIs and parse the JSON responses, I try to avoid directly interacting with those APIs (especially because they might have rate limits!) and create small mock APIs to pass to my functions instead. I found one library that was particularly good for mocking out HTTP requests and JSON responses, called appropriately enough responses. Note that if you're having trouble with the mocks, make sure you have the match_querystring boolean set to True. Otherwise, any query parameters you add to the URI of your request won't be matched. (That's not within the documentation anywhere, and I had to go into the source code to figure out that parameter existed.)

I haven't heard much about testing frameworks or TDD in data science circles. People do talk a lot about validation, but that's not of the code itself but of its output. I think it's because data science doesn't focus so much on building software; most of the code we write is procedural and not necessarily extensively reused. Since we may work primarily or only with third-party libraries (which hopefully are already well-tested before release), the need for testing the code ourselves we write probably does not seem as urgent. Nonetheless, taking the time to write tests, even for a simple series of statements that you don't plan to use again, can help you be confident that the scripts you're running won't fail on some easily preventable bug.

© Hana Lee. Built using Pelican. Theme adapted from Giulio Fidente's pelican-svbhack. Member of the Internet Defense League.