This PR includes all of the machinery to hook in a new chaining algorithm that can handle bridge components as well as simple bubbles, which should make it work better in graphs with more complex local structure (like the ones generated by verkko). It's all unit tested, but I haven't done any work to benchmark it on real data. It's also not yet exposed at the command line for phase_contacts_with_monte_carlo, but the machinery is all there to switch off between the new and old chainers.
This PR includes all of the machinery to hook in a new chaining algorithm that can handle bridge components as well as simple bubbles, which should make it work better in graphs with more complex local structure (like the ones generated by verkko). It's all unit tested, but I haven't done any work to benchmark it on real data. It's also not yet exposed at the command line for
phase_contacts_with_monte_carlo, but the machinery is all there to switch off between the new and old chainers.Edit: I have now added a CLI option as well.