How to Write Good Scientific Software

August 19, 2020
#science
#software
#coding

This is a lightly edited transcript of a talk I delivered at MLSS South Africa on 16 January 2019.

In this post, I will define scientific software, describe how it is different from other types of software, and discuss the social, mechanical, and scholarly disciplines required for making it the best it can be.

Upfront, I should note that these are all rough guidelines, but that the context in which software is developed and used will affect the extent to which they apply. I make some generalizations to get my point across.

What is Scientific Software?

Scientific software is typically computational in nature, and aids us in our understanding of the world, often by processing observational measurements. Because scientific software aims to uncover truths, accuracy is of paramount importance. Of course, accuracy is important in many industrial applications too—you do not want a parcel delivered to the wrong address, or an email sent to the wrong recipient—but in science errors invariably invalidate the work.

Here, I consider a subset of scientific software: that which is written to aid in reproducibility. This software has to be reusable1—particularly by those who did not write the software. Even if reproducibility is not explicitly targeted, eventually most scientific codes become associated with research outputs, such as published papers. At this point, ideally, the software should be open for inspection, so that the science can be verified. The vast majority of research code has not historically fallen into this category2, but I would argue that there are systematic changes underway that will place more and more emphasis on openness.

Purpose

We write software for different purposes, and that changes the amount of rigor applied. Just as you may make some initial calculations on a napkin, code is sometimes used to improve your understanding of a problem, without any intent of using that code in future scenarios.

Apart from this type of “scratch” code, in increasing levels of maturity we have: experimental code for private use, experimental code that will be published, and algorithmic or infrastructure code with an eye towards reusability.

I would argue that the first type—experimental code that never leaves the room—is to be avoided at all cost. This code cannot be verified, and is in some sense no better than a black box that takes some arguments and spits out an answer. Is it a good answer that reflects an underlying truth? There is no way for anyone on the outside to tell.

Experimental code should be tracked, just as you would fastidiously keep a lab notebook in a chemical laboratory.

Now, let us examine the mechanisms we can use to improve the quality of our software. I want to start with a higher-level concept: that of the social environment in which you develop software, and then move on to more specific technical mechanisms.

Social Software

One day, while I was a postdoc at Berkeley’s Helen Wills Neuroscience Institute, I walked into my office to find the DiPy—that is, Diffusion Imaging in Python—team, busy finalizing their new API design after an entire day’s work.

I happened to be implementing identical functionality for my research, not realizing that their library covered similar ground. So, curious—and excited about the prospect of being able to collaborate and leverage their work—I started asking them about their new design, with my own use case in mind.

It soon became clear that the software would not yet be able to address my needs. To the team’s credit, despite some tired and exasperated looks, they worked with me for the rest of the weekend to refine their design until we had a general enough interface that addressed all of our needs.

For the next two years, I worked very closely with this team, helping them build out the package. That software—which serves a niche purpose in MRI—now has more than 450 citations.

The takeaway for me was that, here, an extra pair of eyes made a difference to the general utility of that software, and because of the newly discovered synergy the development team grew, which in turn led to many further hours of productive collaboration.

There is a large and ever-growing volume of research that shows the advantages of group work. For example, about an April 2006 article in the Journal of Personality and Social Psychology, author Patrick Laughlin from the University of Illinois says:

“We found that groups of size three, four, and five outperformed the best individuals and attribute this performance to the ability of people to work together to generate and adopt correct responses, reject erroneous responses, and effectively process information.”

This emphasizes the quality of work a team can do. Other similar experiments compare, e.g., teams of students against their professors.

For a team to work well, however, it has to have certain qualities, such as the right size and culture.

Jeff Sutherland, the co-inventor of SCRUM and co-author of the Agile Manifesto, said at the Global Scrum Gathering 2017 that he believed the optimal team size is 5.

But he also observe something remarkable3: that while individual developers different in productivity with a ratio of as much as 1:10, the difference can be orders of magnitude larger when it comes to teams.

In 2012, Google launched Project Aristotle to determine what makes a good team successful. One of their key findings was that group norms are a key to success. In other words, it makes a difference when team members feel comfortable enough to take risks, make mistakes, and voice their opinions.

There are also some further straightforward connections with teams and better work:

In summary: find good and varied collaborators; your software will be better because of it.

Technical Mechanisms for Higher Quality Software

We now turn to more straightforward technical mechanisms, techniques, and disciplines for improving the quality of your software.

While working on a large open source project, we had a collaborator who did not “believe” in testing. That person also happened to be a very talented programmer; still, I made a point of writing a test for each piece of functionality they included. Invariably, almost every single contribution performed incorrectly on some corner case of the data.

I knew at this point already that almost all the code I wrote was flawed in some way, and that it only improved through iterative refinement. But it was an eye-opener to see that the best programmers still made mistakes—and frequently.

Just like when you drive a car, you have certain blind spots while programming. And just like you check that blind spot on the road, there are techniques we can use to make software development safer.

Let me highlight a few of those mechanisms:

Test your software

At a very minimum, your software has to be run, frequently. This does not guarantee correct results, but at least allows you to go back and re-run earlier steps of an analysis, as needed. You’d be surprised how many researchers are stuck in a situation where they cannot explore new ideas, because parts of their pipelines are stuck in an unrunnable state. This is bad news: bad for your research, bad for reproducibility, and bad for any papers that rely on these stagnant results.

Ideally, however, your code will be tested thoroughly. While, or immediately after, writing code, you will examine corner cases, generate (by hand if needed) test data, and compare output against pre-calculated results. The formula is simple: if I execute f(x), do I get y as expected?

Testing is my primary concern around Jupyter notebooks for serious science. They can be tested, but it is hard, and the mechanisms are not widely available. They also encourage the use of global state, instead of functions. As such, I strongly discourage my students from using them other than for scratch experiments, or as a by-product of research to allow others to explore data and results.

To automate your tests, you may make use of continuous integration systems such as Travis-CI, Azure Pipelines, et cetera. (See, e.g., PR #3584 from NumPy, and its test results on Travis-CI.)

Track your progress

Using a revision control system is a must, and I recommend Git. This lets you track the history of your software as it evolves, reduces the need to keep hundreds of backup copies, and allows other developers to take part in development. See revision control as the equivalent of your lab notebook, but for your software. You’ll never need to worry about lost code again, and your stress levels the day before publishing will thank you for it.

In “The Toyota Way: 14 Principles From The World’s Greatest Manufacturer”, Jeffrey Liker describes their 5S program for effective and productive workspaces. Three of these are: Sort, Straighten, and Shine. That is, sort out unneeded items, have a place for everything, and keep your workspace clean. Git provides the software tools to do this.

Document your code

Your code may never see another pair of eyes, but even for your own benefit: document your code. I suggest identifying a documentation template, such as the one we use for the NumPy project. Here, we decide beforehand the types of things that should be documented, so that each function has the same information. For example, you can describe: the intent of the function, input parameters, return values, usage examples, and notes and references.

Keep it simple

We all know that moment. Huzzah! Ten lines of code condensed into a one-liner. It’s a divine piece of art, beautifully compact.

And, yet, so utterly incomprehensible to future you.

I don’t know where the following idea originated, but Robert Martin states it well in “Clean Code”. He writes: “Indeed, the ratio of time spent reading versus writing is well over 10 to 1. We are constantly reading old code as part of the effort to write new code. …[Therefore,] making it easy to read makes it easier to write.”

In addition, Martin Fowler wrote: “Any fool can write code that a computer can understand. Good programmers write code that humans can understand.”

Making code shorter does not necessarily mean making it simpler to understand. Strive for clarity of expression, instead.

I’ll also note here that object orientation is a great distraction to new programmers, when functional design would suffice for the majority of cases.

Algorithm over optimization

We all know the Donald Knuth quote: “Premature optimization is the root of all evil”.

I experienced this first-hand while writing a library to calculate discrete pulse transforms of images. I spent weeks on this project, utilizing every trick in the book: I wrote a library in C, cached every intermediate calculation, and invented a new sparse data-structure. I felt good about this code; it was clever and fast.

One day, an old professor walked into my office. “Oh, by the way,” he said, “I wrote an implementation of the discrete pulse transform this weekend.” I ran his code: it executed correctly, and was at least as fast as mine. Confused, I examined his work more closely: 80 lines of pure Python. No particular optimizations. Just: the right idea, aided by the appropriate built-in data structures (priority queues, in this case).

It turns out the professor was the one who invented the algorithm, and he knew a thing or two about it. This experience taught me a valuable lesson: get the execution order right. You can write your code in assembler, and your $\mathcal{O}(N^2)$ algorithm still won’t beat $\mathcal{O}(N)$ runtime on a large enough dataset. Worry about implementing the correct algorithm, instead of optimizing the wrong one.

Automate everything

As far as possible, automate all processes: building of your software, testing, producing figures for papers, the works. When you automate a process, you have one place to go to make a fix that affects all of your work. Otherwise, you will be very tempted to only fix the outputs that urgently require attention.

The Japanese has the practice of Kaizen (改善), or “continual improvement”. Small changes, applied many times over, can result in great progress.

As an example of a fully automated publication, see Elegant SciPy.

Be consistent

There is no single best way to structure and format code. Pick a style you like, and stick to it. Structure your entire code base the same way, and ask that collaborators use the same standards. In the Python world, we have PEP8; but use whatever your community recommends.

Publication

Finally, your scientific code will likely be of better quality if it gets made public. Why? Because if you know your code is going to be published, you will take better care in its construction, documentation, and testing. No one wants to have others look at their poor quality work!

There are several ways to make code public. The easiest is to publish it in a public git repository on, e.g., GitHub or GitLab. This also allows external developers to submit changes for your consideration.

If that is not an option, a copy of the software can be uploaded to a public repository, where it will receive a Digital Object Identifier, or DOI—essentially a snapshot, that shows the state of the software at a specific point in time.

A third option is to simply upload the software to your website. It’s the way we used to do it, but we now have better mechanisms.

Whichever medium you use, remember to add a license to your software. Without a license, your software cannot be reused by others. It is not simply public domain without a license; quite the contrary.

Conclusion

Scientific software has the potential to change our understanding of the world. Discoveries, however, depend on accurate results, which are more likely to arise from high quality code. We suggest you write your code in teams—it is not only more fun, but likely to be more widely usable. At a minimum, ensure that your code is tested and documented. Aim for reusability. Then, publish your work: it will make science more transparent, and it will make your code better.

Notes

A friend reviewing my talk pointed me to this article by Patrick Beukema that covers similar ground. Looks like we’re in agreement!

  1. Gaël Varoquaux, Beyond Computational Reproducibility, Let Us Aim for Reusability, IEEE CIS TC Cognitive and Developmental Systems (volume 32, number 2, 2016). ↩︎

  2. Why Most Published Research Findings Are False, https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.0020124 ↩︎

  3. Jeff Sutherland, Doing Twice the Work in Half the Time, Chapter 3 ↩︎