cd4-histone-paper-code VS 3d-reorganization-prostate-canc

FWIW, this is how I've released the crappy barely-working "academic quality" code for a paper in the past:

https://github.com/DarwinAwardWinner/cd4-histone-paper-code

The main points are that I made only a minimal attempt to organize it, and I made the state of the code clear in the README. I don't recall anyone complaining about the code or even mentioning it during review. (I also don't recall whether I published the code before or after the paper was accepted.)

You're right, it is substantially more work to clean and organize the code for publishing. Being open about your work does make the attack surface much larger and more likely to be nitpicked, criticized, have an error found, etc.

But it is more honest. Whatever you think about the effort required to do this, there's value in honesty.

Here is an example of my own scientific work:

- paper [0]

- preprint [1]

- GitHub [2]

It certainly wasn't easy to get all of this done. But doing this can also be a guide for others. They get to see exactly what you've done so that they don't waste months on the exact implementation. They can see where maybe you've made some mistakes to avoid them. They can see so much of the implicit knowledge that is left out of your paper and learn from it. Your code isn't going to be perfect, but what paper is, either?

Everyone will be a critic, anyway, so make it easy to pick up criticism of the stuff you feel the least confident in and do better next time. You won't get better if no one sees your code.

[0]: https://cancerres.aacrjournals.org/content/81/23/5833

[1]: https://www.biorxiv.org/content/10.1101/2021.01.05.425333v2

[2]: https://github.com/LupienLab/3d-reorganization-prostate-canc...