PCA fails sometimes (maybe if nodes are not 0...n?) #3443
Description
Consider the following code:
ts = msprime.sim_ancestry(3)
ts = msprime.sim_mutations(ts, rate=1)
t = ts.dump_tables()
t.nodes.clear()
for n in ts.nodes():
t.nodes.append(n.replace(flags=1 if (n.id > 2 and n.id < 6) else 0))
ts.pca(num_components=2)
Traceback (most recent call last):
File "<python-input-10>", line 1, in <module>
ts.pca(num_components=2)
~~~~~~^^^^^^^^^^^^^^^^^^
File "/home/peter/projects/tskit-dev/tskit/python/tskit/trees.py", line 9537, in pca
U[i], D[i], Q[i], E[i] = _rand_svd(
~~~~~~~~~^
operator=_G,
^^^^^^^^^^^^
...<4 lines>...
range_sketch=range_sketch[i],
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/peter/projects/tskit-dev/tskit/python/tskit/trees.py", line 9479, in _rand_svd
Q = _rand_pow_range_finder(
operator,
...<4 lines>...
Q=range_sketch,
)
File "/home/peter/projects/tskit-dev/tskit/python/tskit/trees.py", line 9463, in _rand_pow_range_finder
Q = operator(Q)
File "/home/peter/projects/tskit-dev/tskit/python/tskit/trees.py", line 9518, in _G
high = _f_high(
arr=x,
...<3 lines>...
windows=windows[i : i + 2],
)
File "/home/peter/projects/tskit-dev/tskit/python/tskit/trees.py", line 9229, in _genetic_relatedness_vector_node
x = self._expand_indices(x, indices)
File "/home/peter/projects/tskit-dev/tskit/python/tskit/trees.py", line 9216, in _expand_indices
y[indices] = x
~^^^^^^^^^
IndexError: index 3 is out of bounds for axis 0 with size 3