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Perspective for (2): it's because no one in graduate training really cares about code quality. Your PI focuses more of your attention on scientific writing, and so there's little to not time to polish your work. The incentives just don't support this work at the graduate training level.

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I agree. The only incentive to write neat code is to save yourself the pain and suffering of having to go back through it yourself to fix or add things. I am currently doing data analysis in MATLAB for my PhD, and I know nobody will ever use my code besides me.

I’d like to learn to do my due diligence, but without someone training me, it just takes so much time to learn things like git. I’d rather be recording more data and submitting my paper so I can get the hell out of here

Actually the pi doesn't even know about the concept of code quality. Or even your code at all.

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