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I'm writing a web-app that will take input from the user, run a long-ish calculation (say 15s) based on that input and return the output. Do I understand it correctly that this CPU usage doesn't count towards the quota? Is there a caveat I should be aware of?

Web apps are limited by number of web workers and timeout. To move computation outside web workers see https://help.pythonanywhere.com/pages/AsyncInWebApps/