Merge branch 'main' into ig/cu13

Author: ilan-gold

.github/workflows/test-gpu.yml

@@ -52,9 +52,10 @@ jobs:
       - name: Nvidia SMI sanity check
         run: nvidia-smi
 
-      - name: Install yq
+      - name: Install yq # https://cirun.slack.com/archives/C09SNDRB3A8/p1766512487317849?thread_ts=1766512112.938459&cid=C09SNDRB3A8
         run: |
-          sudo snap install yq
+          sudo wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64
+          sudo chmod +x /usr/local/bin/yq
 
       - name: Extract max Python version from classifiers
         run: |

docs/release-notes/2267.fix.md

@@ -0,0 +1 @@
+Actually copy single zarr store input in {func}`anndata.experimental.concat_on_disk` {user}`ilan-gold`

src/anndata/experimental/merge.py

@@ -618,10 +618,10 @@ def concat_on_disk(  # noqa: PLR0913
 
     if (
         len(in_files) == 1
-        and isinstance(in_files[0], str | PathLike)
+        and isinstance(in_file := in_files[0], str | PathLike)
         and is_out_path_like
     ):
-        shutil.copy2(in_files[0], out_file)
+        (shutil.copytree if in_file.is_dir() else shutil.copy2)(in_file, out_file)
         return
 
     if keys is None:

tests/test_concatenate_disk.py

@@ -278,6 +278,10 @@ def visit(key: str, arr: zarr.Array | zarr.Group):
     check_all_sharded(g)
 
 
+def test_singleton(xxxm_adatas, tmp_path, file_format):
+    assert_eq_concat_on_disk(xxxm_adatas[:1], tmp_path, file_format=file_format)
+
+
 def test_output_dir_exists(tmp_path):
     in_pth = tmp_path / "in.h5ad"
     out_pth = tmp_path / "does_not_exist" / "out.h5ad"