Update multi-chain permutation and permutation unittest

[dingquanyu]

Hi @christinaflo and @jnwei

Sorry I forgot to update the unittest for multi-chain permutations after the major updates on the functions. Here I have added necessary steps to prepare fake test data for testing these functions. Now all the 3 tests can run successfully. Hope it helps.

BTW I'm now adding typing to the functions in multi_chain_permutation.py and fixing some comments in that file as well. These can however go to another PR if you prefer?

Dingquan