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The prefix context manager (and probably others that are using _setenv) don't behave as expected when not called immediately prior to __enter__(). This means that the context manager isn't usable with contextlib.nested. Here's an example:
The reason is because the new values are being stored at the time prefix is called—not when the context is entered. So, in the example above, when prefix is called the first time, it defines the context manager as setting command_prefixes to the current value () plus ['echo 1']. When it's called the second time, the current value of command_prefixes is still an empty list (because the first context hasn't been entered yet), so the context manager is defined as setting command_prefixes to ['echo 2']. Therefore, entering the second context manager clobbers any effect of entering the first.
The fix, I think, is to defer the getting of command_prefixes until the context is entered.
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Just to clarify, this bug doesn't just affect nested, but any situation in which the context managers aren't entered immediately after initialization. The test in 65647c6 contains a simple nested-less example.