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I have a server running a Python app. I'm updating the app's code manually via sftp. Is it safe to remove the *.pyc files that are automatically created in my app's dir?

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Yes, it's safe. Use pyclean command

Usage: pyclean [-p PACKAGE] [DIR_OR_FILE]

pyclean . 
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Command 'pyclean' not found, but can be installed with: sudo apt install python2

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