Updating old tsinfer tree sequences to the improved 0.3.0 style, with multiple roots

[hyanwong]

If you used tsinfer prior to version 0.3.0, you would have created a single long root node. This can cause problems for dating, and the behaviour was changed in 0.3.0. If you have an old tree sequence which you wish to convert, you can convert it using tsinfer.post_process(). Here is some code to check and convert:

import json
import tsinfer
print(json.loads(inferred_ts.provenance(0).record)['software']  # old versions will have a version < 0.3.0)
print(tsinfer.__version__)  # should be 0.3.0 or greater
assert tsinfer.has_single_edge_over_grand_root(ts)  # check ts in in old style format - this is the ts before simplifying / dating
new_ts = tsinfer.post_process(ts, warn_if_unexpected_format=True)

You should now get better results when e.g. dating the new_ts:

import tsdate
dated_ts = tsdate.date(new_ts, population_size=..., mutation_rate=...)