Several Cython features have been deprecated in Cython 3.0 and will
generate errors in future Cython releases. This change removes .pxi
include files, all `IF` conditional statements, and cpdef functions.
Almost all Cython 3.0 deprecation warnings were addressed, a silent
API change from Python 3.11 was mitigated, and some of the custom
Cython code for type checking was replaced by equivalent C++ code.