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Clarity individual table sorting requirements before subset #3355

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10 changes: 7 additions & 3 deletions python/tskit/tables.py
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Expand Up @@ -3816,9 +3816,13 @@ def canonicalise(self, remove_unreferenced=None):
"""
This puts the tables in *canonical* form, imposing a stricter order on the
tables than :ref:`required <sec_valid_tree_sequence_requirements>` for
a valid tree sequence. In particular, the individual
and population tables are sorted by the first node that refers to each
(see :meth:`TreeSequence.subset`). Then, the remaining tables are sorted
a valid tree sequence. In particular, the population table is sorted by
the lowest ID of the nodes that refer to each population, and the
individual table is sorted to ensure that not only are the standard
:ref:`sorting requirements<sec_individual_requirements>` met but
also secondarily sorted by the lowest ID of the nodes
that refer to each individual (see :meth:`TreeSequence.subset`).
The remaining tables are sorted
as in :meth:`.sort`, with the modification that mutations are sorted by
site, then time (if known), then the mutation's node's time, then number
of descendant mutations (ensuring that parent mutations occur before
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11 changes: 7 additions & 4 deletions python/tskit/trees.py
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Expand Up @@ -7513,10 +7513,13 @@ def subset(
the ancestry of these nodes - for that, see :meth:`.simplify`.

This has the side effect that it may change the order of the nodes,
individuals, populations, and migrations in the tree sequence: the nodes
in the new tree sequence will be in the order provided in ``nodes``, and
both individuals and populations will be ordered by the earliest retained
node that refers to them. (However, ``reorder_populations`` may be set to
individuals, populations, and migrations in the tree sequence. Nodes
in the new tree sequence will be in the order provided in ``nodes``,
populations will be ordered by the lowest ID of the nodes that refer to
them, and individuals will be not only ordered so that
:attr:`~Individual.parents` come before children, but in addition
will be secondarily sorted by the lowest ID of their referring
nodes. (However, ``reorder_populations`` may be set to
False to keep the population table unchanged.)

By default, the method removes all individuals and populations not
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