Sorry for not responding, missed the message, it seems.

Cython has to support old-style relative imports also in Py3 because that's how the user code was originally written, using Py2-style syntax and semantics. Most Cython code has not been converted to Py3 syntax/semantics, but still needs to work in Py3.

From a user perspective, it's best to switch on "__future__.absolute_import" and use explicit relative imports (or write Py3 code), because it reduces the overhead at import time.

I'm hoping to look into multi-step module initialisation this summer. As Nick noted, this might also help with this issue.