(feat): support ellipsis indexing

docs/release-notes/1729.feature.md

@@ -0,0 +1 @@
+Add support for ellipsis indexing of the {class}`~anndata.AnnData` object {user}`ilan-gold`

src/anndata/_core/index.py

@@ -3,6 +3,7 @@
 from collections.abc import Iterable, Sequence
 from functools import singledispatch
 from itertools import repeat
+from types import EllipsisType
 from typing import TYPE_CHECKING
 
 import h5py
@@ -47,7 +48,8 @@
     | str
     | Sequence[bool | int | np.integer]
     | np.ndarray
-    | pd.Index,
+    | pd.Index
+    | EllipsisType,
     index: pd.Index,
 ) -> slice | int | np.ndarray:  # ndarray of int or bool
     if not isinstance(index, pd.RangeIndex):
@@ -72,6 +74,8 @@
         return slice(start, stop, step)
     elif isinstance(indexer, np.integer | int):
         return indexer
+    elif isinstance(indexer, EllipsisType):
+        return slice(None)
     elif isinstance(indexer, str):
         return index.get_loc(indexer)  # int
     elif isinstance(
@@ -107,8 +111,7 @@
                     "are not valid obs/ var names or indices."
                 )
             return positions  # np.ndarray[int]
-    else:
-        raise IndexError(f"Unknown indexer {indexer!r} of type {type(indexer)}")
+    raise IndexError(f"Unknown indexer {indexer!r} of type {type(indexer)}")
 
 
 def _fix_slice_bounds(s: slice, length: int) -> slice:

src/anndata/compat/__init__.py

@@ -10,6 +10,7 @@
 from importlib.util import find_spec
 from inspect import Parameter, signature
 from pathlib import Path
+from types import EllipsisType
 from typing import TYPE_CHECKING, TypeVar
 from warnings import warn
 
@@ -46,7 +47,7 @@ class Empty:
     pass
 
 
-Index1D = slice | int | str | np.int64 | np.ndarray
+Index1D = slice | int | str | np.int64 | np.ndarray | EllipsisType
 Index = Index1D | tuple[Index1D, Index1D] | scipy.sparse.spmatrix | SpArray
 H5Group = h5py.Group
 H5Array = h5py.Dataset

tests/test_views.py

@@ -786,6 +786,14 @@ def test_dataframe_view_index_setting():
     assert a2.obs.index.values.tolist() == ["a", "b"]
 
 
+def test_ellipsis_index(adata, subset_func, matrix_type):
+    adata = gen_adata((10, 10), X_type=matrix_type, **GEN_ADATA_DASK_ARGS)
+    subset_obs_names = subset_func(adata.obs_names)
+    subset_ellipsis = adata[subset_obs_names, ...]
+    subset = adata[subset_obs_names, :]
+    assert_equal(subset_ellipsis, subset)
+
+
 # @pytest.mark.parametrize("dim", ["obs", "var"])
 # @pytest.mark.parametrize(
 #     ("idx", "pat"),