Fix index_unique argument for concatenating

anndata/_core/anndata.py

@@ -1690,6 +1690,7 @@ def concatenate(
             batch_categories=batch_categories,
             uns_merge=uns_merge,
             fill_value=fill_value,
+            index_unique=index_unique,
         )
 
         # Backwards compat, ordering columns:

anndata/_core/merge.py

@@ -432,32 +432,27 @@ def concat(
     if batch_categories is None:
         batch_categories = np.arange(len(adatas)).astype(str)
 
-    # Combining indexes
-    obs_names = pd.Index(
-        np.concatenate(
-            [
-                pd.Series(a.obs_names) + f"{index_unique}{batch}"
-                for batch, a in zip(batch_categories, adatas)
-            ]
-        )
+    # Batch column
+    batch = pd.Categorical.from_codes(
+        np.repeat(np.arange(len(adatas)), [a.n_obs for a in adatas]),
+        categories=batch_categories,
     )
+
+    # Combining indexes
+    obs_names = pd.concat([pd.Series(a.obs_names) for a in adatas], ignore_index=True)
+    if index_unique is not None:
+        obs_names = obs_names.str.cat(batch.map(str), sep=index_unique)
+    obs_names = pd.Index(obs_names)
+
     var_names = resolve_index([a.var_names for a in adatas], join=join)
     reindexers = [
         gen_reindexer(var_names, a.var_names, fill_value=fill_value) for a in adatas
     ]
 
     # Obs
-    # fmt: off
-    batch = (
-        pd.Series(
-            np.repeat(np.arange(len(adatas)), [a.n_obs for a in adatas]), dtype="category"
-        )
-        .map(dict(zip(np.arange(len(adatas)), batch_categories)))
-    )
-    # fmt: on
     obs = pd.concat([a.obs for a in adatas], ignore_index=True)
     obs.index = obs_names
-    obs[batch_key] = batch.values
+    obs[batch_key] = batch
 
     # Var
     var = merge_dataframes(

anndata/tests/test_concatenate.py

@@ -46,7 +46,6 @@ def fix_known_differences(orig, result):
     orig = orig.copy()
     result = result.copy()
 
-    result.obs_names = result.obs_names.str.extract(r"^(.*)-\d+$", expand=False)
     result.obs.drop(columns=["batch"], inplace=True)
     result.strings_to_categoricals()  # Should this be implicit in concatenation?
 
@@ -76,7 +75,9 @@ def test_concatenate_roundtrip(join_type, array_type):
         subsets.append(adata[subset_idx])
         remaining = remaining.difference(subset_idx)
 
-    result = subsets[0].concatenate(subsets[1:], join=join_type, uns_merge="same")
+    result = subsets[0].concatenate(
+        subsets[1:], join=join_type, uns_merge="same", index_unique=None
+    )
 
     # Correcting for known differences
     orig, result = fix_known_differences(adata, result)