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Any tips to help a scientist become a better programmer? (iusearchlinux.fyi)

submitted 8 months ago by [email protected] to c/[email protected]

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Hey there!

I'm a chemical physicist who has been using python (as well as matlab and R) for a lot of different tasks over the last ~10 years, mostly for data analysis but also to automate certain tasks. I am almost completely self-taught, and though I have gotten help and tips from professors throughout the completion of my degrees, I have never really been educated in best practices when it comes to coding.

I have some friends who work as developers but have a similar academic background as I do, and through them I have become painfully aware of how bad my code is. When I write code, it simply needs to do the thing, conventions be damned. I do try to read up on the "right" way to do things, but the holes in my knowledge become pretty apparent pretty quickly.

For example, I have never written a class and I wouldn't know why or where to start (something to do with the init method, right?). I mostly just write functions and scripts that perform the tasks that I need, plus some work with jupyter notebooks from time to time. I only recently got started with git and uploading my projects to github, just as a way to try to teach myself the workflow.

So, I would like to learn to be better. Can anyone recommend good resources for learning programming, but perhaps that are aimed at people who already know a language? It'd be nice to find a guide that assumes you already know more than a beginner. Any help would be appreciated.

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[–] [email protected] 16 points 8 months ago (2 children)

The O'Reilly "In a Nutshell" and "Pocket Guide to" books are great for folks who can already code, and want to pick up a related tool or a new language.

The Pocket Guide to Git is an obvious choice in your situation, if you don't already have it.

As others have mentioned, you're allowed to ignore the team stuff. In git this means you have my permission to commit directly to the 'main' branch, particularly while you're learning.

Lessons that I've learned the hard way, that apply for someone scripting alone:

git will save your ass. Get in the habit of using if for everything ASAP, and it'll be there when you need it
find that one friend who waxes poetic about git, and keep them close. Usually listening politely to them wax poetically about git will do the trick. Five minutes of their time can be a real life saver later. As that friend, I know when you're using me for my git-fu, and I don't mind. It's hard for me to make friends, perhaps because I constantly wax poetically about git.
every code swan starts as an ugly duck that got the job done.
print(f"debug: {what_the_fuck_is_this}") is a valid pattern that seasoned professionals still turn to. If you're in a code environment that doesn't support it, then it's a bad code environment.
one peer who reads your code regularly will make you a minimum of 5x more effective. It's awkward as hell to get started, but incredibly worth it. Obviously, you traditionally should return the favor, even though you won't feel qualified. They don't really feel qualified either, so it works out. (Soure: I advise real scientists about their code all the time. It's still wild to me that they, as actual scientists, listen to me - even after I see how much benefit I provide.)

[–] [email protected] 3 points 8 months ago (1 children)

print(f"debug: {what_the_fuck_is_this}") is a valid pattern that seasoned professionals still turn to. If you’re in a code environment that doesn’t support it, then it’s a bad code environment.

I've been known to print things to the console during development, but it's like eating junk food. It's better to get in the habit of using a logging framework. Insufficient logging has been in the OWASP Top 10 for a while so you should be logging anyway. Why not logger.debug("{what_the_fuck_is_this}") or get fancy with some different frameworks and logger.log(SUPER_LOW_LVL, "{really_what_the_fuck_is_this}")

You also get the bonus of not going back and cleaning up all the print statements afterward. All you have to do is set the running log level to INFO or something to turn all that off. There was a reason you needed to see that stuff in the first place. If you ever need to see all that stuff again the change the log level to whatever grain you need it.

[–] [email protected] 3 points 8 months ago* (last edited 8 months ago)

Absolutely true.

And you make a great point that: print(f"debug: {what_the_fuck_is_this}") should absolutely be maturing into logger.log(SUPER_LOW_LVL, "{really_what_the_fuck_is_this}")

Unfortunately I have found that when print("debug") isn't working, usually logging isn't setup correctly either.

In a solidly built system, a garbage print line will hit the logs and raise several alerts because it's poorly formatted - making it easy for the developer to find.

Sadly, I often see the logging setup so that poorly formatted logs go nowhere, rather than raising alerts until they're fixed. This inevitably leads to both debug logs being lost and critical but slightly misformatted logs being lost.

Your point is particularly valuable when it's time to get the system fixed, because it's easier to say "logging needs to work" than "fix my stupid printf", even though they're roughly equivalent.

Edit: And getting back to the scripting scientist context, scripting scientists still have my formal official permission to just say "just make my print('debug') work".

[–] [email protected] 3 points 8 months ago (1 children)

Along a similar vain to making a git friend, buy your sysadmins/ops people a box of doughnuts once in a while. They (generally) all code and will have some knowledge of what you are working on.

[–] [email protected] 1 points 8 months ago

That is great advice that has served me well, as well!