Software testing in science

As part of a CiSE submission I'm working on, I interviewed the lead developer on a scientific software package today. This software package is mainly used for evolutionary studies, and has a small but devoted following - ~6 developers and ~12 users locally, plus a few dozen users outside of MSU. I asked him a bunch of questions about development infrastructure and testing, and while the answers weren't surprising to me -- I've been friends with people on this team for over 15 years now and know the state of the software reasonabl well -- they did offer some food for thought.

The main testing method used for this software package is consistency tests, or what I would call regression tests: they compare assumed-good output from some old benchmark version to output from the current version. If they match, they declare victory: the current version reproduces the old results, so nothing is broken. The lead developer did say that he knew that the coverage of the consistency tests was poor, because when bugs in various parts of the code cropped up & were fixed, the consistency tests didn't often fail.

Other than that, there's essentially no unit or functional testing.

  1. How do you measure correctness in scientific software?

There's no yardstick, and often no previous results, just intuition based on what other people have discovered and predictions from mental models or mathematical models. This allows for fuzzy correspondence and isn't really a check on actual correctness, but rather on lack of obvious errors. Without going line-by-line or trying for formal proofs (neither of which academic programmers have any more patience for than any other programmer) you just have to trust that any major errors will pop up at some point.

  1. What's the incentive to be correct in scientific programming, anyway?

It boils down to "avoiding embarrassment," with a bit of "let's actually try to be useful, i.e. predictive or functional". There's no strong financial or career motivation to write correct software in academia; again, it's more an issue of avoiding obviously incorrect results. I don't mean that to sound harsh or manipulative -- it's frankly understandable, given that in research it's really difficult to figure out what the right answer should be, even when you can figure it out.

  1. What's the incentive to minimize maintenance costs?

There isn't really one, at least not for the first few years of a project. One of the main reasons I got involved in testing was in order to control maintenance costs for one of my projects; this, however, was an already rather successful scientific project, with a few hundred users. If you don't have a lot of users, why put effort into things like documentation, tutorials, testing and automated builds? Sure, you might attract users, but nobody really cares how many users you have. They care about publications.

  1. What's the measure of success?

At first (and second, and third) blush, it's "publication" -- did I produce an interesting enough result that I can publish it? Only after a fair number of publications do most scientists think about releasing their software.

Comments !

(Please check out the comments policy before commenting.)