Scientific simulation codes are public property sustained by the community. Modern technology allows anyone to join scientific software projects, from anywhere, remotely via the internet. The phonopy and phono3py codes are widely used open-source phonon calculation codes. This review describes a collection of computational methods and techniques implemented in these codes and shows their implementation strategies as a whole, aiming to be useful for the community. Some of the techniques presented here are not limited to phonon calculations and may therefore be useful in other areas of condensed matter physics.