Use the supplied chromosome ID for an implicit complement group

ruranges/numpy.py

@@ -1476,6 +1476,10 @@ def _dispatch_unary(
 
     if prefix == "complement_numpy":
         chrom_ids = _normalize_groups(extra_kw["chrom_len_ids"], name="chrom_len_ids")
+        if groups is None:
+            if len(chrom_ids) != 1:
+                raise ValueError("`groups=None` requires exactly one chromosome in `chrom_len_ids`.")
+            groups = np.full(len(starts_arr), chrom_ids[0], dtype=np.uint32)
         extra_kw["chrom_len_ids"] = chrom_ids
         chrom_lens = _as_1d_array(extra_kw["chrom_lens"], name="chrom_lens")
         pos_extra_arrays.append(("chrom_lens", chrom_lens))

tests/test_complement_implicit_groups.py

@@ -0,0 +1,27 @@
+import numpy as np
+import pytest
+
+from ruranges.numpy import complement
+
+
+@pytest.mark.parametrize("chromosome", [0, 1, 23, 24, 2**32 - 1])
+@pytest.mark.parametrize("include_first", [False, True])
+def test_implicit_group_uses_the_supplied_chromosome(chromosome, include_first):
+    kwargs = dict(
+        starts=np.array([30, 10]),
+        ends=np.array([40, 20]),
+        chrom_len_ids=np.array([chromosome], dtype=np.uint64),
+        chrom_lens=np.array([100]),
+        include_first_interval=include_first,
+    )
+    implicit = complement(groups=None, **kwargs)
+    explicit = complement(groups=np.full(2, chromosome, dtype=np.uint32), **kwargs)
+    for actual, expected in zip(implicit, explicit):
+        np.testing.assert_array_equal(actual, expected)
+    n = 3 if include_first else 2
+    np.testing.assert_array_equal(implicit[0], [chromosome] * n)
+    np.testing.assert_array_equal(implicit[1], [0, 20, 40] if include_first else [20, 40])
+    np.testing.assert_array_equal(implicit[2], [10, 30, 100] if include_first else [30, 100])
+    assert implicit[0].dtype == np.uint32
+    # The attribution index identifies the group, not a specific interval.
+    assert np.all(implicit[3] < len(kwargs["starts"]))