dist.py

import math


def dist(xs, ys):
    return math.sqrt(sum((x-y)**2 for (x, y) in zip(xs, ys)))

links.py

get_weight = operator.itemgetter(2)

links = []
for (i, (w0, rows0)) in enumerate(by_word):
    for (j, (w1, rows1)) in enumerate(by_word):
        if w0 == w1:
            continue
        weights0 = (get_weight(w) for w in rows0)
        weights1 = (get_weight(w) for w in rows1)
        links.append({
            'source': i,
            'target': j,
            'weight': dist(weights0, weights1),
            })