fix: add missing self to reindex_subcomponent_taxa

src/dendropy/datamodel/taxonmodel.py

@@ -407,7 +407,7 @@ def reindex_taxa(self, taxon_namespace=None, clear=False):
         self.reindex_subcomponent_taxa()
         return self.taxon_namespace
 
-    def reindex_subcomponent_taxa():
+    def reindex_subcomponent_taxa(self):
         """
         DEPRECATED: Use :meth:`reconstruct_taxon_namespace()` instead.
         Derived classes should override this to ensure that their various

src/dendropy/datamodel/treecollectionmodel.py

@@ -1019,7 +1019,7 @@ def poll_taxa(self, taxa=None):
             tree.poll_taxa(taxa)
         return taxa
 
-    def reindex_subcomponent_taxa():
+    def reindex_subcomponent_taxa(self):
         raise NotImplementedError()
 
    ##############################################################################

tests/unittests/test_datamodel_tree_list.py

@@ -25,6 +25,7 @@
 import collections
 import dendropy
 import random
+import warnings
 import os
 import sys
 sys.path.insert(0, os.path.dirname(__file__))
@@ -1011,6 +1012,22 @@ def test_migrate_taxon_namespace_unifying_case_insensitive(self):
                 case_sensitive_label_mapping=False,
                 original_tns=original_tns)
 
+    def test_reindex_subcomponent_taxa_raises_not_implemented(self):
+        # Regression: the stub was defined without a `self` parameter, so
+        # calling it as an instance method raised TypeError instead of the
+        # intended NotImplementedError.
+        with self.assertRaises(NotImplementedError):
+            self.tree_list.reindex_subcomponent_taxa()
+
+    def test_reindex_taxa_raises_not_implemented(self):
+        # `reindex_taxa` is deprecated and delegates to
+        # `reindex_subcomponent_taxa`; it should surface NotImplementedError
+        # rather than a TypeError about positional argument counts.
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore")
+            with self.assertRaises(NotImplementedError):
+                self.tree_list.reindex_taxa()
+
 class TestTreeListAppend(
         curated_test_tree.CuratedTestTree,
         unittest.TestCase):