After some reading and trying rsync copy over only certain types of files using include option I can't get seem to get it to work.
I run the following command:
rsync -zarv -vvv -e ssh --prune-empty-dirs --delete --include="*/" --include="*.csv"
--include="*.hdf5" --include="*.pickle" --include="*.tar.gz" --include="*.bin"
--include="*.zip" --include="*.npz" --exclude="*" . user@host.com:/rsync
But at the target it backups any file I have in the directory and subdirectories. delete-before and delete-after does not delete files like .txt or .py. I have also tried the --exclude="*" before the extension includes but I am running 2.6.9 so it should be after as far as I have understood it.
Deleting files on the host machine will just sync them again for whatever reason I don't know.