Allow multiple input feature with the same value for gaussian processes

Fix for issue #3162. Allows to have multiple input feature with the same values for Gaussian Processes 
The message is confusing as well here. A better message might be "Repeated samples (rows in X) for noise-free modeling"  although as I am not familiar with GP either it's hard to me to tell whether this is correct or not.

Also the exception type should be a `ValueError` in this case.