[bmitc]

> Academic code is about "proof of concept."

Why does he think that but presumably not the same about the paper itself and the “equations”, plots, etc. contained within?

It’s really not that hard to write pretty good code for prototypes. In fact, I can only assume that he and other professors never allowed or encouraged “proof of concept” code to be submitted as course homework or projects.

[cycomanic]

I think you don't understand the realities of work in scientific/academic organisations. Unless you work in computer science you likely never received any formal education on programming except for some numerical methods in c/matlab/fortran course during your studies (which often also focus more on the numerical methods and not the programming). So pretty much every person, just learned by doing.

Moreover you are not being paid for writing reasonable programs you're paid for doing science. Nobody would submit "prototype" papers, because they are the currency of academic work. There is lots of time spend on polishing a paper before submission, but doing that for code is generally not appreciated because nobody will see this on your CV.

[bmitc]

I understand it fine. Like I said, it’s really not that hard to write pretty good code for prototypes. I'm not saying the code needs to be architected for scale or performance or whatever else needless expectation. I don't have a formal education in programming or computer science and write clean code just fine, as do some other non-computer science people I've worked with in advanced R&D contexts. And then some (many?) don't. It's not really about educational background, it's more about just being organized. Even when someone is "just" doing science, a lot of times, the code explicitly defines what's going on and has major impacts on the results. (Not to mention that plenty of people with computer science backgrounds write horrible code.)

If code is a large part of your scientific work, then it's just as important as someone who does optics keeping their optics table organized and designed well. If one is embarrassed by that, then too bad. Embarrassment is how we learn.

Lastly, you're describing problems with the academic world as if they are excuses. They're reasons but most people know the academic world is not perfect, especially with what is prioritized and essentially gamified.

[cycomanic]

I'm not making excuses I'm just talking about the realities. For the significant majority of researchers I know about version control is still program_v1.py, program_v1.py, program_final.py, program_final2.py (and this is the good version, at least they are using python), so talking about clean code is still quite a bit away. I'm teaching PhD students and it's even hard to convince them, because they just look at how to get the next publishable result. For academics it becomes even more unrealistic, most don't even have time to go to a lab, they are just writing grants typically.

I'm actually a strong supporter of open science, release my code OSS (and actually clean it up) and data (when possible). But just saying it's easy and there is no cost, is just setting the wrong expectations. Generally unless you enjoy it, spending significant time on your code is not smart for your career. Hopefully things are changing, but it is a slow process.

Funny that you talk about optics I know some of the most productive people in my field and their optical tables are an absolute mess (as is their code btw). They don't work at universities though.

[bmitc]

I still think it’s really not that hard, and actually, it’s really not even about code. It’s really just about organization, because as you point out, not everyone is great at it. But for example, messy optics tables, labs, or whatever do in fact cause problems, like efficiency and knowing what “state” of supporting tools yielded what result and several other derivative problems. I think my push would be just applying even a modicum of organization on supposedly ancillary things will go a long way rather than accepting them as reality.

I understand the realities and have even been a part of PowerPoint development where slides are emailed back and forth. Sometimes one just has to go with things like that. But I have also seen the reality of stubbornness. I have tried introducing source code control to scientists or even stuff like wikis, all supported and already up and running by IT and used by other groups. Scientists and engineers, especially those with PhDs, can a bit rejective and set in their ways. I have been told flat out by different people that they wouldn’t use tools like a wiki or that Python and C was all they ever needed. I have even noticed physicists saying “codes” for software instead of “code”. It’s fairly rampant, and I have seen it in research papers, published books, and in industry in person. I have never seen that use of “codes” anywhere else. That alone is evidence of a certain amount of culture and institutionalization of doing things incorrectly but viewed as acceptable within the field.

I have written code in some research contexts. I get the constraints. One just needs to take it seriously. But organization, in general, often takes a back seat in basically any field. The only way to change things like this are like anything, which is to push against culture.