Where does this come from: -*- coding: utf-8 -*-

This way of specifying the encoding of a Python file comes from PEP 0263 - Defining Python Source Code Encodings.

It is also recognized by GNU Emacs (see Python Language Reference, 2.1.4 Encoding declarations), though I don't know if it was the first program to use that syntax.

# -*- coding: utf-8 -*- is a Python 2 thing.

In Python 3.0+ the default encoding of source files is already UTF-8 so you can safely delete that line, because unless it says something other than some variation of "utf-8", it has no effect. See Should I use encoding declaration in Python 3?

pyupgrade is a tool you can run on your code to remove those comments and other useless leftovers from Python 2, like having all your classes inherit from object.

This is so called file local variables, that are understood by Emacs and set correspondingly. See corresponding section in Emacs manual - you can define them either in header or in footer of file

In PyCharm, I'd leave it out. It turns off the UTF-8 indicator at the bottom with a warning that the encoding is hard-coded. Don't think you need the PyCharm comment mentioned above.