feat: Add cophenetic_distances function to rust and integrate binding

[lsetiawan]

Overview

Currently, there is a cophenetic_distances function in the python package:

phylo2vec/py-phylo2vec/phylo2vec/metrics/pairwise.py

Lines 7 to 47 in 50811ab

	def cophenetic_distances(v, unrooted=False):
	# Should be very similar to dist_nodes in ape
	# Ancestry
	A = _get_ancestry(v)
	if unrooted:
	A[-1, -1] = A.max() - 1
	n_leaves = len(v) + 1
	# Distance matrix
	D = np.zeros((2 * n_leaves - 1, 2 * n_leaves - 1), dtype=np.uint32)
	# Keep track of visited nodes
	all_visited = []
	for i in range(n_leaves - 1):
	c1, c2, p = A[n_leaves - i - 2, :]
	for visited in all_visited[:-1]:
	dist_from_visited = D[p, visited] + 1
	# c1 to visited
	D[c1, visited] = dist_from_visited
	D[visited, c1] = dist_from_visited
	# c2 to visited
	D[c2, visited] = dist_from_visited
	D[visited, c2] = dist_from_visited
	# c1 to c2: path length = 2
	D[c1, c2] = 2
	D[c2, c1] = 2
	# c1 to parent: path length = 1
	D[c1, p] = 1
	D[p, c1] = 1
	# c2 to parent: path length = 1
	D[c2, p] = 1
	D[p, c2] = 1
	all_visited.extend([c1, c2, p])
	return D[:n_leaves, :n_leaves]

We need to port this over to Rust -> Create Binding -> Integrate back to Python.