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The values used in Flags are an implementation detail. The expected, and supported, use is naming the flags:
class Color(Flags):
 Red, Green, Blue
even custom names can be set using this method:
>>> class Color(enum.Flags):
... red, green, blue
... black = red & green & blue
... 
>>> list(Color)
[<Color.red: 1>, <Color.green: 2>, <Color.blue: 4>, <Color.black: 0>]
>>> class Color(enum.Flags):
... red, green, blue
... purple = red | blue
... 
>>> list(Color)
[<Color.red: 1>, <Color.green: 2>, <Color.blue: 4>, <Color.purple: 5>]
>>> Color(5)
<Color.purple: 5>
>>> Color(3)
<Color.red|green: 3>
I'll have to think about ensuring each bit is named -- it's only a (potential) problem if the values are specified manually.