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I do this by ensuring that only one of MIDDLEWARE and MIDDLEWARE_CLASSES gets patched.
Downside: I still don't completely understand why it would flake, I know there is some kind of race in the tests happening where the insert_trace_middleware function gets called multiple times but I couldn't figure out what it is. I was starting to spend a little too much time on this, so I figured you'd at least enjoy a solution.
I just made sure that insert_trace_middleware is idempotent now.