There are MST algorithms in Python, for example in pygraph and networkx. These use their native graph formats, though, which would have meant I'd have to construct a graph from my point set.
I didn't see a way on how to do this and set the edge weights without iterating over all edges.
That would probably take longer than the computation of the MST, so I decided to do my own small implementation using numpy.
This is an instantiation of Prim's algorithm based on numpy matrices. The input is a dense matrix of distances, the output a list of edges. It is not as pretty as I would have hoped but still reasonably short. If any one has suggestions how to make this prettier, I'd love that.
 Using line_profiler I had a quick look a the code and made some minor improvements. It's now significantly faster than networkx and also a bit prettier. Most time is now spent on the argmin, which seems reasonable. It would probably be even faster if I didn't use a full matrix for representing the weights but only the upper triangle. But that seems to be some extra effort.[/edit]
Here it goes:
import numpy as np from scipy.spatial.distance import pdist, squareform import matplotlib.pyplot as plt def minimum_spanning_tree(X, copy_X=True): """X are edge weights of fully connected graph""" if copy_X: X = X.copy() if X.shape != X.shape: raise ValueError("X needs to be square matrix of edge weights") n_vertices = X.shape spanning_edges =  # initialize with node 0: visited_vertices =  num_visited = 1 # exclude self connections: diag_indices = np.arange(n_vertices) X[diag_indices, diag_indices] = np.inf while num_visited != n_vertices: new_edge = np.argmin(X[visited_vertices], axis=None) # 2d encoding of new_edge from flat, get correct indices new_edge = divmod(new_edge, n_vertices) new_edge = [visited_vertices[new_edge], new_edge] # add edge to tree spanning_edges.append(new_edge) visited_vertices.append(new_edge) # remove all edges inside current tree X[visited_vertices, new_edge] = np.inf X[new_edge, visited_vertices] = np.inf num_visited += 1 return np.vstack(spanning_edges) def test_mst(): P = np.random.uniform(size=(50, 2)) X = squareform(pdist(P)) edge_list = minimum_spanning_tree(X) plt.scatter(P[:, 0], P[:, 1]) for edge in edge_list: i, j = edge plt.plot([P[i, 0], P[j, 0]], [P[i, 1], P[j, 1]], c='r') plt.show() if __name__ == "__main__": test_mst()The algorithms basically works on a dense distance matrix and finds the best possible edge that is reachable from a set of active nodes.
All edges that connect nodes already inside the tree are set to infinity so as not to create cycles.
I haven't really benchmarked this and it probably loses against any cython implementation but I would hope it is reasonably fast and straight-forward.
The output looks something like this: