Memory leak in ts.variants()

[jeromekelleher]

Benchmark:

import msprime
import time


before = time.perf_counter()
ts = msprime.sim_ancestry(
    10000,
    sequence_length=1000000,
    population_size=10_000,
    recombination_rate=1e-8,
    random_seed=1234,
)
ts = msprime.sim_mutations(ts, rate=1e-7, random_seed=1)
duration = time.perf_counter() - before
print(f"Simulation of {ts.num_trees} trees done after {duration:.2f} seconds")

for _ in range(10):
    for var in ts.variants():
        pass

Result:

This is because the version of variants introduced in #2397 always looks at ts.tables.sites.position. This was released in 0.5.1.