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Make TreeSequence.samples args kw only #1831

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Merged
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Oct 21, 2021
Merged

Make TreeSequence.samples args kw only #1831

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3 changes: 3 additions & 0 deletions python/CHANGELOG.rst
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Expand Up @@ -34,6 +34,9 @@
- Metadata encoding errors now raise ``MetadataEncodingError``
(:user:`benjeffery`, :issue:`1505`, :pr:`1827`).

- For ``TreeSequence.samples`` all arguments after ``population`` are now keyword only
(:user:`benjeffery`, :issue:`1715`, :pr:`1831`).

**Features**

- Add ``TableCollection.sort_individuals`` to sort the individuals as this is no longer done by the
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5 changes: 5 additions & 0 deletions python/tests/test_highlevel.py
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Expand Up @@ -1187,6 +1187,11 @@ def test_samples_time_errors(self):
with pytest.raises(ValueError):
ts.samples(time=(2.4, 1))

def test_samples_args(self, ts_fixture):
ts_fixture.samples(1)
with pytest.raises(TypeError, match="takes from 1 to 2 positional arguments"):
ts_fixture.samples(1, 2)

def test_genotype_matrix_indexing(self):
num_demes = 4
ts = self.get_tree_sequence(num_demes)
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2 changes: 1 addition & 1 deletion python/tskit/trees.py
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Expand Up @@ -4851,7 +4851,7 @@ def get_samples(self, population_id=None):
# Deprecated alias for samples()
return self.samples(population_id)

def samples(self, population=None, population_id=None, time=None):
def samples(self, population=None, *, population_id=None, time=None):
"""
Returns an array of the sample node IDs in this tree sequence. If
`population` is specified, only return sample IDs from that population.
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