Possible solutions include

1. using weakref.finalize() (as you also suggested)
2. cythonize everything, make all classes cdef'd, and switch from __del__ to __dealloc__
3. using a lightweight shutdown detection hack (see, e.g., Memory Leak in libllvmlite.so when using Numba numba/numba#9731 (comment) and numba/llvmlite@7347d77)

Originally posted by @leofang in #87 (comment)