Checkpointing tests on distance matrix

[glesica]

High-level tests by checkpointing at the distance matrix step, compare against running all the way through in one go

We also want to use the naive distance calculator implementation here without any vectorization because we’re more confident that it is correct, so that will be the standard we compare against

[TW: an initial test of this confidence would be to compare distances computed by this naive approach with distances computed in Java implementation]