Rename to individuals_nodes

Author: benjeffery

bio2zarr/tskit.py

@@ -13,7 +13,7 @@ class TskitFormat(vcz.Source):
     def __init__(
         self,
         ts_path,
-        individual_nodes,
+        individuals_nodes,
         sample_ids=None,
         contig_id=None,
         isolated_as_missing=False,
@@ -25,10 +25,10 @@ def __init__(
 
         self.positions = self.ts.sites_position
 
-        self._num_samples = individual_nodes.shape[0]
+        self._num_samples = individuals_nodes.shape[0]
         if self._num_samples < 1:
-            raise ValueError("individual_nodes must have at least one sample")
-        self.max_ploidy = individual_nodes.shape[1]
+            raise ValueError("individuals_nodes must have at least one sample")
+        self.max_ploidy = individuals_nodes.shape[1]
         if sample_ids is None:
             sample_ids = [f"tsk_{j}" for j in range(self._num_samples)]
         elif len(sample_ids) != self._num_samples:
@@ -39,14 +39,14 @@ def __init__(
 
         self._samples = [vcz.Sample(id=sample_id) for sample_id in sample_ids]
 
-        self.tskit_samples = np.unique(individual_nodes[individual_nodes >= 0])
+        self.tskit_samples = np.unique(individuals_nodes[individuals_nodes >= 0])
         if len(self.tskit_samples) < 1:
-            raise ValueError("individual_nodes must have at least one valid sample")
+            raise ValueError("individuals_nodes must have at least one valid sample")
         node_id_to_index = {node_id: i for i, node_id in enumerate(self.tskit_samples)}
-        valid_mask = individual_nodes >= 0
+        valid_mask = individuals_nodes >= 0
         self.sample_indices, self.ploidy_indices = np.where(valid_mask)
         self.genotype_indices = np.array(
-            [node_id_to_index[node_id] for node_id in individual_nodes[valid_mask]]
+            [node_id_to_index[node_id] for node_id in individuals_nodes[valid_mask]]
         )
 
     @property
@@ -212,7 +212,7 @@ def generate_schema(
 def convert(
     ts_path,
     zarr_path,
-    individual_nodes,
+    individuals_nodes,
     *,
     sample_ids=None,
     contig_id=None,
@@ -224,7 +224,7 @@ def convert(
 ):
     tskit_format = TskitFormat(
         ts_path,
-        individual_nodes,
+        individuals_nodes,
         sample_ids=sample_ids,
         contig_id=contig_id,
         isolated_as_missing=isolated_as_missing,

tests/test_ts.py

@@ -324,14 +324,14 @@ def test_iter_alleles_and_genotypes_errors(self, simple_ts):
         # Test with empty ind_nodes array (no samples)
         empty_nodes = np.zeros((0, 2), dtype=np.int32)
         with pytest.raises(
-            ValueError, match="individual_nodes must have at least one sample"
+            ValueError, match="individuals_nodes must have at least one sample"
         ):
             format_obj = ts.TskitFormat(ts_path, empty_nodes)
 
         # Test with all invalid nodes (-1)
         all_invalid = np.full((2, 2), -1, dtype=np.int32)
         with pytest.raises(
-            ValueError, match="individual_nodes must have at least one valid sample"
+            ValueError, match="individuals_nodes must have at least one valid sample"
         ):
             format_obj = ts.TskitFormat(ts_path, all_invalid)