Jerome Kelleher

Probably, I'm not sure without looking things up @szhan. Here's some other implementations to check against: - https://scikit-allel.readthedocs.io/en/stable/stats/diversity.html#allel.watterson_theta - http://molpopgen.github.io/pylibseq/docs/_build/html/pages/summstats.html#libsequence.thetaw

The first option sounds super interesting @petrelharp. I wonder if there's any connection with keeping track of the last time a node was updated (e.g., [here](https://github.com/tskit-dev/tskit/blob/f83ee533f3e5be7ff938435668d14215b7f5f0cc/python/tests/test_tree_stats.py#L435), which we might be...

The generalisation to individuals is trickier - how about we get an implementation of the first algorithm implemented and tested, and then think about how to generalise? The ``sample_lists`` idea...

> Sounds good. That's a different issue to this one, anyhow (which is "linear algebra tools"). Was commenting on this: >> If we knew not only sample_lists but also, say,...

It's a very strong assumption @gregorgorjanc and it definitely won't hold in general. It's only going to work for things in which the underlying generative process is based on the...

Possibly - you'd need to explain the details to me in person though.

Also Python testing of the variant state is needs beefing up. We need to test taking copies of copies, among other things.

We could consider renaming this to ``tsk_variant_frozen_copy`` (keeping the current name as an alias)

I think there's a ``samples`` argument to ``variants`` which we could also easily add to genotype matrix. That would be an easy PR, I think. Going through ``simplify`` etc seems...

> I'm interested in this, so might have a go at it soon. Great, thanks @mufernando! The first thing to do is to figure out if a Python version of...