Support ellipsis indexing

[nc1m]

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In 1.5.1 sklearn changed their _array_indexing method to use ellipsis indexing/slicing:
https://github.com/scikit-learn/scikit-learn/blob/1.5.1/sklearn/utils/_indexing.py#L33

Running train_test_split on AnnData now results in an IndexError.

Code:

import anndata
import session_info
from sklearn.model_selection import train_test_split
import scanpy as sc

session_info.show(html=False, dependencies=True)

adata = sc.datasets.ebi_expression_atlas("E-MTAB-4888")
adata_val, adata_test = train_test_split(adata, test_size=0.5, stratify=adata.obs['Sample Characteristic[cell type]'])

Traceback:

Traceback (most recent call last):
  File "/home/user/project/src/data/test.py", line 6, in <module>
    adata_val, adata_test = train_test_split(adata, test_size=0.5, stratify=adata.obs['Sample Characteristic[cell type]'])
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/.conda/envs/env/lib/python3.12/site-packages/sklearn/utils/_param_validation.py", line 213, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/.conda/envs/env/lib/python3.12/site-packages/sklearn/model_selection/_split.py", line 2805, in train_test_split
    return list(
           ^^^^^
  File "/home/user/.conda/envs/env/lib/python3.12/site-packages/sklearn/model_selection/_split.py", line 2807, in <genexpr>
    (_safe_indexing(a, train), _safe_indexing(a, test)) for a in arrays
     ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/.conda/envs/env/lib/python3.12/site-packages/sklearn/utils/_indexing.py", line 267, in _safe_indexing
    return _array_indexing(X, indices, indices_dtype, axis=axis)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/.conda/envs/env/lib/python3.12/site-packages/sklearn/utils/_indexing.py", line 33, in _array_indexing
    return array[key, ...] if axis == 0 else array[:, key]
           ~~~~~^^^^^^^^^^
  File "/home/user/.conda/envs/env/lib/python3.12/site-packages/anndata/_core/anndata.py", line 1021, in __getitem__
    oidx, vidx = self._normalize_indices(index)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/.conda/envs/env/lib/python3.12/site-packages/anndata/_core/anndata.py", line 1002, in _normalize_indices
    return _normalize_indices(index, self.obs_names, self.var_names)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/.conda/envs/env/lib/python3.12/site-packages/anndata/_core/index.py", line 39, in _normalize_indices
    ax1 = _normalize_index(ax1, names1)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/.conda/envs/env/lib/python3.12/site-packages/anndata/_core/index.py", line 109, in _normalize_index
    raise IndexError(f"Unknown indexer {indexer!r} of type {type(indexer)}")
IndexError: Unknown indexer Ellipsis of type <class 'ellipsis'>

I'm not sure if this behavior is intended.

Versions

-----
anndata             0.10.9
scanpy              1.10.2
session_info        1.0.0
sklearn             1.5.1
-----
PIL                 10.3.0
cffi                1.17.1
colorama            0.4.6
cycler              0.12.1
cython_runtime      NA
dateutil            2.9.0
h5py                3.11.0
igraph              0.11.6
joblib              1.4.2
kiwisolver          1.4.7
legacy_api_wrap     NA
leidenalg           0.10.2
llvmlite            0.43.0
matplotlib          3.9.2
mpl_toolkits        NA
natsort             8.4.0
numba               0.60.0
numpy               1.26.4
packaging           24.1
pandas              2.2.2
pyparsing           3.1.4
pytz                2024.1
scipy               1.14.1
six                 1.16.0
texttable           1.7.0
threadpoolctl       3.5.0
torch               2.4.1
torchgen            NA
tqdm                4.66.5
typing_extensions   NA
yaml                6.0.2
-----
Python 3.12.3 | packaged by conda-forge | (main, Apr 15 2024, 18:38:13) [GCC 12.3.0]
Linux-6.1.0-25-amd64-x86_64-with-glibc2.36

[ilan-gold]

@nc1m I think this is then a feature because I don't think we ever supported Ellipsis indexing. But this should be simple enough.

[flying-sheep]

Ehrdata could benefit from allowing 3D data in .X too: theislab/ehrdata#24

Seems like we already support 3D data in .layers, so latest in the .X-.layers unification (#244) we’d need to do this.