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Population-scale genomics
I think the documentation of migrations could use a bit more detail here: [migration table section of the docs](https://tskit.readthedocs.io/en/latest/data-model.html#sec-migration-table-definition). Specifically, the docs read: > Migrations are performed by individual ancestors,...
#1067 was a good reminder that there are unexpected consequences of changing things and there's actually quite a lot of software out there that needs to stay working when tskit...
#391 changed the TreeSequence.samples method to return a numpy array. Change the ``.trees()`` method to use a numpy array without first changing to a python list. Needs an update to...
Add provenance recording for operations on the ``TableCollection`` class that change the state, e.g., ``simplify``, ``sort``, ``compute_mutation_parents`` and ``deduplicate_sites``. Also include a ``record_provenance=True`` parameter like ``TreeSequence.simplify``.
Fixes https://github.com/tskit-dev/tskit/issues/2637 - I remembered this issue when writing some recent tutorial material. I went for the absolute size rather than percentage, and simply appended the codec type, rather than...
This should equivalent to ``` all_descendants = [] for tree in ts.trees(): all_descendants = np.union1d( all_descendants, np.sort(tree.preorder(alpha_origin["node_id"]))) ``` But in graph preorder. I think the algorithm is here: https://github.com/tskit-dev/tskit/discussions/2869#discussioncomment-7535830 We...
As discussed in #2911 we have the ``skip`` option now in Tree.seek (and seek_index) which will use a more efficient algorithm when doing long-range seeking. We haven't really characterised how...
Found these work with no modification, all other skips reviewed and look good. Closes #3192