Use atexit for cleanup of Python-extended prototypes

Use standard atexit handler to remove Python-extended prototype
objects from C++ registry.  Ensure cleanup is truly executed
instead of relying on garbage collector to call `__del__`.

This prevents the following error message on Python exit

    Fatal Python error: PyThreadState_Get: the function must be called
    with the GIL held, but the GIL is released (the current Python
    thread state is NULL)

Author: pavoljuhas

src/diffpy/srreal/_cleanup.py

@@ -27,6 +27,7 @@ class prototypes is implemented in libdiffpy.  Any Python-extended classes
 """
 
 
+import atexit
 import weakref
 
 
@@ -62,7 +63,7 @@ def add(self, obj):
         return
 
 
-    def __del__(self):
+    def clean(self):
         while self._references:
             wr = self._references.pop()
             obj = wr()
@@ -75,7 +76,8 @@ def __del__(self):
 
 # create singleton instance of the cleanup handler
 _cleanup_handler = _DerivedClassesCleanUpHandler()
-del _DerivedClassesCleanUpHandler
+atexit.register(_cleanup_handler.clean)
 
+del _DerivedClassesCleanUpHandler
 
 # End of file.