Fix deprecation warning in Python 3

This PR fixed the second failed test case in #2737. The following line caused the failure,

    drop_idx = active.pop(idx)

type of `idx` is `numpy.ndarray`, and `pop` operation raised 

    DeprecationWarning: converting an array with ndim > 0 to an index will result in an error in the future

To fix it, just using `active.pop(idx[0])`.

This PR also changed `floating point division` to `floor division`. `Floating point division` caused `numpy` warning, 

    DeprecationWarning: using a non-integer number instead of an integer will result in an error in the future 

in `Python 3`