This addresses #3398. As far as I could see I removed all of them except a couple in hmm.py which I thought wasn't worth touching since it is going away.
Remove 'DeprecationWarning: using a non-integer number instead of an …
…integer will result in an error in the future' warnings
Remove a couple more 'using a non-integer number instead of an intege…
This is good. I'll merge when travis is done!