Data structure recommendation?

[bearophileHUGS at lycos.com]

More bits from your code:

neighbours = list()
==>
neighbours = []

If you have a recent enough version of Python you can use:
candidate_is_neighbour = any(distance < n[1] for n in neighbours)
Instead of:
candidate_is_neighbour = bool([1 for n in neighbours if distance <
n[1]])

It's shorter & simpler, and it stops as soon as it finds a true
condition.

Bye,
bearophile