Example files are found at https://github.com/phonopy/phono3py/tree/master/example. The same are found in the example directory of the phono3py package downloaded at https://github.com/phonopy/phono3py/archive/master.zip.
Examples of silicon with VASP and Pwscf as calculators are given in
example directory. An example using phono3py API is found in
example/Si-PBEsol/Si.py but the API document has not yet written.