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@jencake This is a general limitation when using jupyter magic syntax that manipulates the ipython kernel state at runtime and using static linters.
The problem is that magic commands aren't regular python code, so it does not translate to the equivalent python AST that flake8 uses to lint code.
The only way to fix this would require flake8 to use a different AST parser that supports jupyter magic syntax, which I'm not aware even exists and even if I don't see flake8 changing to it.
For variables are defined in another notebook and imported via %run. flake8_nb still gives me the variable is undefined error.
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