Clean up/Fix runtime warning messages in python unit test standard error

Currently the log of python unit test results contains thousands of lines of runtime warning / future warning / deprecation warnings, making trouble shooting during development inconvenient. Most of the warning messages are not necessary at all and could be suppressed or fixed if possible.
For example, the most popped message is hundreds of lines of 'RuntimeWarning: Mean of empty slice
return np.nanmean(a, axis, out=out, keepdims=keepdims)'
raised in dataframe tests, which could be suppressed.