From fe4bd10a0c137a508d4fbdb6af1883aef4ca7b2f Mon Sep 17 00:00:00 2001
From: ilan-gold <ilanbassgold@gmail.com>
Date: Fri, 9 Aug 2024 15:32:33 -0400
Subject: [PATCH 1/9] (fix): disallow using dataframes with multi index columns

---
 src/anndata/_core/aligned_mapping.py | 26 ++++++++++++++++----------
 src/anndata/_core/anndata.py         | 18 ++++++++++++++++++
 src/anndata/_core/storage.py         |  5 +++++
 src/anndata/tests/helpers.py         | 11 +++++++++++
 tests/test_annot.py                  |  8 ++++++++
 tests/test_base.py                   | 20 +++++++++++++++++++-
 tests/test_obsmvarm.py               |  7 +++++++
 7 files changed, 84 insertions(+), 11 deletions(-)

diff --git a/src/anndata/_core/aligned_mapping.py b/src/anndata/_core/aligned_mapping.py
index 26c89d9f2..aafbdb0ca 100644
--- a/src/anndata/_core/aligned_mapping.py
+++ b/src/anndata/_core/aligned_mapping.py
@@ -258,16 +258,22 @@ def to_df(self) -> pd.DataFrame:
         return df
 
     def _validate_value(self, val: Value, key: str) -> Value:
-        if isinstance(val, pd.DataFrame) and not val.index.equals(self.dim_names):
-            # Could probably also re-order index if it’s contained
-            try:
-                pd.testing.assert_index_equal(val.index, self.dim_names)
-            except AssertionError as e:
-                msg = f"value.index does not match parent’s {self.dim} names:\n{e}"
-                raise ValueError(msg) from None
-            else:
-                msg = "Index.equals and pd.testing.assert_index_equal disagree"
-                raise AssertionError(msg)
+        if isinstance(val, pd.DataFrame):
+            if isinstance(val.columns, pd.MultiIndex):
+                raise ValueError(
+                    "MultiIndex columns are not supported in AnnData. "
+                    "Please use a single-level index."
+                )
+            if not val.index.equals(self.dim_names):
+                # Could probably also re-order index if it’s contained
+                try:
+                    pd.testing.assert_index_equal(val.index, self.dim_names)
+                except AssertionError as e:
+                    msg = f"value.index does not match parent’s {self.dim} names:\n{e}"
+                    raise ValueError(msg) from None
+                else:
+                    msg = "Index.equals and pd.testing.assert_index_equal disagree"
+                    raise AssertionError(msg)
         return super()._validate_value(val, key)
 
     @property
diff --git a/src/anndata/_core/anndata.py b/src/anndata/_core/anndata.py
index 7da29e4a4..7bcd1df76 100644
--- a/src/anndata/_core/anndata.py
+++ b/src/anndata/_core/anndata.py
@@ -234,6 +234,19 @@ def __init__(
         oidx: Index1D = None,
         vidx: Index1D = None,
     ):
+        # check for any multi-indices
+        df_elems = [obs, var, X]
+        for xxxm in [obsm, varm]:
+            if xxxm is not None and not isinstance(xxxm, np.ndarray):
+                df_elems += [v for v in xxxm.values() if isinstance(v, pd.DataFrame)]
+        for attr in df_elems:
+            if isinstance(attr, pd.DataFrame) and isinstance(
+                attr.columns, pd.MultiIndex
+            ):
+                raise ValueError(
+                    "MultiIndex columns are not supported in AnnData. "
+                    "Please use a single-level index."
+                )
         if asview:
             if not isinstance(X, AnnData):
                 raise ValueError("`X` has to be an AnnData object.")
@@ -736,6 +749,11 @@ def n_vars(self) -> int:
     def _set_dim_df(self, value: pd.DataFrame, attr: str):
         if not isinstance(value, pd.DataFrame):
             raise ValueError(f"Can only assign pd.DataFrame to {attr}.")
+        if isinstance(value.columns, pd.MultiIndex):
+            raise ValueError(
+                "MultiIndex columns are not supported in AnnData. "
+                "Please use a single-level index."
+            )
         value_idx = self._prep_dim_index(value.index, attr)
         if self.is_view:
             self._init_as_actual(self.copy())
diff --git a/src/anndata/_core/storage.py b/src/anndata/_core/storage.py
index bc6a091d3..40e7e78f6 100644
--- a/src/anndata/_core/storage.py
+++ b/src/anndata/_core/storage.py
@@ -84,6 +84,11 @@ def coerce_array(
             value = value.A
         return value
     if isinstance(value, pd.DataFrame):
+        if isinstance(value.columns, pd.MultiIndex) and allow_df:
+            raise ValueError(
+                "MultiIndex columns are not supported in AnnData. "
+                "Please use a single-level index."
+            )
         return value if allow_df else ensure_df_homogeneous(value, name)
     # if value is an array-like object, try to convert it
     e = None
diff --git a/src/anndata/tests/helpers.py b/src/anndata/tests/helpers.py
index 6a30f4c32..185808b8d 100644
--- a/src/anndata/tests/helpers.py
+++ b/src/anndata/tests/helpers.py
@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import itertools
 import random
 import re
 import warnings
@@ -1000,3 +1001,13 @@ def __init__(self, *_args, **_kwargs) -> None:
             raise ImportError(
                 "zarr must be imported to create an `AccessTrackingStore` instance."
             )
+
+
+def get_multiindex_columns_df(shape):
+    return pd.DataFrame(
+        np.random.rand(shape[0], shape[1]),
+        columns=pd.MultiIndex.from_tuples(
+            list(itertools.product(["a"], range(shape[1] - (shape[1] // 2))))
+            + list(itertools.product(["b"], range(shape[1] // 2)))
+        ),
+    )
diff --git a/tests/test_annot.py b/tests/test_annot.py
index 7f4c2697e..8287add0d 100644
--- a/tests/test_annot.py
+++ b/tests/test_annot.py
@@ -8,6 +8,7 @@
 from natsort import natsorted
 
 import anndata as ad
+from anndata.tests.helpers import get_multiindex_columns_df
 
 
 @pytest.mark.parametrize("dtype", [object, "string"])
@@ -63,3 +64,10 @@ def test_non_str_to_not_categorical():
     result_non_transformed = adata.obs.drop(columns=["str_with_nan"])
 
     pd.testing.assert_frame_equal(expected_non_transformed, result_non_transformed)
+
+
+def test_error_multiindex():
+    adata = ad.AnnData(np.random.rand(100, 10))
+    df = get_multiindex_columns_df((adata.shape[0], 20))
+    with pytest.raises(ValueError, match=r"MultiIndex columns are not supported"):
+        adata.obs = df
diff --git a/tests/test_base.py b/tests/test_base.py
index 02e4eabe1..2c8367002 100644
--- a/tests/test_base.py
+++ b/tests/test_base.py
@@ -14,7 +14,7 @@
 from anndata import AnnData, ImplicitModificationWarning
 from anndata._settings import settings
 from anndata.compat import CAN_USE_SPARSE_ARRAY
-from anndata.tests.helpers import assert_equal, gen_adata
+from anndata.tests.helpers import assert_equal, gen_adata, get_multiindex_columns_df
 
 # some test objects that we use below
 adata_dense = AnnData(np.array([[1, 2], [3, 4]]))
@@ -117,6 +117,24 @@ def test_create_from_df():
     assert df.index.tolist() == ad.obs_names.tolist()
 
 
+def test_error_create_from_multiindex_df():
+    df = get_multiindex_columns_df((100, 20))
+    with pytest.raises(ValueError, match=r"MultiIndex columns are not supported"):
+        AnnData(df)
+
+
+def test_error_with_obs_multiindex_df():
+    df = get_multiindex_columns_df((100, 20))
+    with pytest.raises(ValueError, match=r"MultiIndex columns are not supported"):
+        AnnData(X=np.random.rand(100, 10), obs=df)
+
+
+def test_error_with_obsm_multiindex_df():
+    df = get_multiindex_columns_df((100, 20))
+    with pytest.raises(ValueError, match=r"MultiIndex columns are not supported"):
+        AnnData(X=np.random.rand(100, 10), obsm={"df": df})
+
+
 def test_create_from_sparse_df():
     s = sp.random(20, 30, density=0.2)
     obs_names = [f"obs{i}" for i in range(20)]
diff --git a/tests/test_obsmvarm.py b/tests/test_obsmvarm.py
index 92f5b8fa0..4ef9187f7 100644
--- a/tests/test_obsmvarm.py
+++ b/tests/test_obsmvarm.py
@@ -7,6 +7,7 @@
 from scipy import sparse
 
 from anndata import AnnData
+from anndata.tests.helpers import get_multiindex_columns_df
 
 M, N = (100, 100)
 
@@ -137,3 +138,9 @@ def test_shape_error(adata: AnnData):
         ),
     ):
         adata.obsm["b"] = np.zeros((adata.shape[0] + 1, adata.shape[0]))
+
+
+def test_error_set_multiindex_df(adata: AnnData):
+    df = get_multiindex_columns_df((adata.shape[0], 20))
+    with pytest.raises(ValueError, match=r"MultiIndex columns are not supported"):
+        adata.obsm["df"] = df

From 2c361667cec874c8f78cb8384db8e9e7eba6cadb Mon Sep 17 00:00:00 2001
From: ilan-gold <ilanbassgold@gmail.com>
Date: Fri, 9 Aug 2024 15:34:58 -0400
Subject: [PATCH 2/9] (chore): release note

---
 docs/release-notes/0.10.9.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/release-notes/0.10.9.md b/docs/release-notes/0.10.9.md
index f1a3dec9c..9604c72ac 100644
--- a/docs/release-notes/0.10.9.md
+++ b/docs/release-notes/0.10.9.md
@@ -9,6 +9,7 @@
 * Upper bound {mod}`numpy` for `gpu` installation on account of https://github.com/cupy/cupy/issues/8391 {pr}`1540` {user}`ilan-gold`
 * Fix writing large number of columns for `h5` files {pr}`1147` {user}`ilan-gold` {user}`selmanozleyen`
 * Upper bound dask on account of https://github.com/scverse/anndata/issues/1579 {pr}`1580` {user}`ilan-gold`
+* Disallow using {class}`~pandas.DataFrame`s with mutli-index columns {pr}`1589` {use}`ilan-gold`
 
 #### Documentation
 

From bf4a9314ced9453108fdcf0ebe81578dfc769d4a Mon Sep 17 00:00:00 2001
From: ilan-gold <ilanbassgold@gmail.com>
Date: Sun, 11 Aug 2024 23:45:07 -0400
Subject: [PATCH 3/9] (refactor): make `util`.

---
 src/anndata/_core/aligned_mapping.py | 14 ++++++++------
 src/anndata/_core/anndata.py         | 22 +++++++++-------------
 src/anndata/_core/storage.py         | 13 +++++++------
 src/anndata/utils.py                 |  8 ++++++++
 4 files changed, 32 insertions(+), 25 deletions(-)

diff --git a/src/anndata/_core/aligned_mapping.py b/src/anndata/_core/aligned_mapping.py
index aafbdb0ca..7727fa39c 100644
--- a/src/anndata/_core/aligned_mapping.py
+++ b/src/anndata/_core/aligned_mapping.py
@@ -13,7 +13,13 @@
 
 from .._warnings import ExperimentalFeatureWarning, ImplicitModificationWarning
 from ..compat import AwkArray
-from ..utils import axis_len, convert_to_dict, deprecated, warn_once
+from ..utils import (
+    axis_len,
+    convert_to_dict,
+    deprecated,
+    raise_value_error_if_multiindex_columns,
+    warn_once,
+)
 from .access import ElementRef
 from .index import _subset
 from .storage import coerce_array
@@ -259,11 +265,7 @@ def to_df(self) -> pd.DataFrame:
 
     def _validate_value(self, val: Value, key: str) -> Value:
         if isinstance(val, pd.DataFrame):
-            if isinstance(val.columns, pd.MultiIndex):
-                raise ValueError(
-                    "MultiIndex columns are not supported in AnnData. "
-                    "Please use a single-level index."
-                )
+            raise_value_error_if_multiindex_columns(val)
             if not val.index.equals(self.dim_names):
                 # Could probably also re-order index if it’s contained
                 try:
diff --git a/src/anndata/_core/anndata.py b/src/anndata/_core/anndata.py
index 7bcd1df76..2c0874854 100644
--- a/src/anndata/_core/anndata.py
+++ b/src/anndata/_core/anndata.py
@@ -26,7 +26,12 @@
 from .._settings import settings
 from ..compat import DaskArray, SpArray, ZarrArray, _move_adj_mtx
 from ..logging import anndata_logger as logger
-from ..utils import axis_len, deprecated, ensure_df_homogeneous
+from ..utils import (
+    axis_len,
+    deprecated,
+    ensure_df_homogeneous,
+    raise_value_error_if_multiindex_columns,
+)
 from .access import ElementRef
 from .aligned_df import _gen_dataframe
 from .aligned_mapping import AlignedMappingProperty, AxisArrays, Layers, PairwiseArrays
@@ -240,13 +245,8 @@ def __init__(
             if xxxm is not None and not isinstance(xxxm, np.ndarray):
                 df_elems += [v for v in xxxm.values() if isinstance(v, pd.DataFrame)]
         for attr in df_elems:
-            if isinstance(attr, pd.DataFrame) and isinstance(
-                attr.columns, pd.MultiIndex
-            ):
-                raise ValueError(
-                    "MultiIndex columns are not supported in AnnData. "
-                    "Please use a single-level index."
-                )
+            if isinstance(attr, pd.DataFrame):
+                raise_value_error_if_multiindex_columns(attr)
         if asview:
             if not isinstance(X, AnnData):
                 raise ValueError("`X` has to be an AnnData object.")
@@ -749,11 +749,7 @@ def n_vars(self) -> int:
     def _set_dim_df(self, value: pd.DataFrame, attr: str):
         if not isinstance(value, pd.DataFrame):
             raise ValueError(f"Can only assign pd.DataFrame to {attr}.")
-        if isinstance(value.columns, pd.MultiIndex):
-            raise ValueError(
-                "MultiIndex columns are not supported in AnnData. "
-                "Please use a single-level index."
-            )
+        raise_value_error_if_multiindex_columns(value)
         value_idx = self._prep_dim_index(value.index, attr)
         if self.is_view:
             self._init_as_actual(self.copy())
diff --git a/src/anndata/_core/storage.py b/src/anndata/_core/storage.py
index 40e7e78f6..eeccdd513 100644
--- a/src/anndata/_core/storage.py
+++ b/src/anndata/_core/storage.py
@@ -20,7 +20,11 @@
     ZappyArray,
     ZarrArray,
 )
-from ..utils import ensure_df_homogeneous, join_english
+from ..utils import (
+    ensure_df_homogeneous,
+    join_english,
+    raise_value_error_if_multiindex_columns,
+)
 from .sparse_dataset import BaseCompressedSparseDataset
 
 if TYPE_CHECKING:
@@ -84,11 +88,8 @@ def coerce_array(
             value = value.A
         return value
     if isinstance(value, pd.DataFrame):
-        if isinstance(value.columns, pd.MultiIndex) and allow_df:
-            raise ValueError(
-                "MultiIndex columns are not supported in AnnData. "
-                "Please use a single-level index."
-            )
+        if allow_df:
+            raise_value_error_if_multiindex_columns(value)
         return value if allow_df else ensure_df_homogeneous(value, name)
     # if value is an array-like object, try to convert it
     e = None
diff --git a/src/anndata/utils.py b/src/anndata/utils.py
index 177115d26..e8b923b22 100644
--- a/src/anndata/utils.py
+++ b/src/anndata/utils.py
@@ -400,3 +400,11 @@ def is_hidden(attr) -> bool:
             for item in type.__dir__(cls)
             if not is_hidden(getattr(cls, item, None))
         ]
+
+
+def raise_value_error_if_multiindex_columns(df: pd.DataFrame):
+    if isinstance(df.columns, pd.MultiIndex):
+        raise ValueError(
+            "MultiIndex columns are not supported in AnnData. "
+            "Please use a single-level index."
+        )

From 9b8a864b00cfd71f1af686e12cfb7bef14c1bdaf Mon Sep 17 00:00:00 2001
From: ilan-gold <ilanbassgold@gmail.com>
Date: Mon, 12 Aug 2024 00:18:13 -0400
Subject: [PATCH 4/9] (fix): `user`

---
 docs/release-notes/0.10.9.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/release-notes/0.10.9.md b/docs/release-notes/0.10.9.md
index 9604c72ac..f7ba67041 100644
--- a/docs/release-notes/0.10.9.md
+++ b/docs/release-notes/0.10.9.md
@@ -9,7 +9,7 @@
 * Upper bound {mod}`numpy` for `gpu` installation on account of https://github.com/cupy/cupy/issues/8391 {pr}`1540` {user}`ilan-gold`
 * Fix writing large number of columns for `h5` files {pr}`1147` {user}`ilan-gold` {user}`selmanozleyen`
 * Upper bound dask on account of https://github.com/scverse/anndata/issues/1579 {pr}`1580` {user}`ilan-gold`
-* Disallow using {class}`~pandas.DataFrame`s with mutli-index columns {pr}`1589` {use}`ilan-gold`
+* Disallow using {class}`~pandas.DataFrame`s with mutli-index columns {pr}`1589` {user}`ilan-gold`
 
 #### Documentation
 

From 41168a80d579cc317aea3e9aaf5c3e950133aa25 Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Mon, 12 Aug 2024 08:55:26 +0200
Subject: [PATCH 5/9] Simplify

---
 src/anndata/_core/anndata.py | 12 ++++--------
 src/anndata/utils.py         |  3 ++-
 2 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/src/anndata/_core/anndata.py b/src/anndata/_core/anndata.py
index 2c0874854..2bdd7bbdd 100644
--- a/src/anndata/_core/anndata.py
+++ b/src/anndata/_core/anndata.py
@@ -236,15 +236,11 @@ def __init__(
         *,
         obsp: np.ndarray | Mapping[str, Sequence[Any]] | None = None,
         varp: np.ndarray | Mapping[str, Sequence[Any]] | None = None,
-        oidx: Index1D = None,
-        vidx: Index1D = None,
+        oidx: Index1D | None = None,
+        vidx: Index1D | None = None,
     ):
-        # check for any multi-indices
-        df_elems = [obs, var, X]
-        for xxxm in [obsm, varm]:
-            if xxxm is not None and not isinstance(xxxm, np.ndarray):
-                df_elems += [v for v in xxxm.values() if isinstance(v, pd.DataFrame)]
-        for attr in df_elems:
+        # check for any multi-indices that aren’t later checked in coerce_array
+        for attr in [obs, var, X]:
             if isinstance(attr, pd.DataFrame):
                 raise_value_error_if_multiindex_columns(attr)
         if asview:
diff --git a/src/anndata/utils.py b/src/anndata/utils.py
index e8b923b22..9467b72c2 100644
--- a/src/anndata/utils.py
+++ b/src/anndata/utils.py
@@ -404,7 +404,8 @@ def is_hidden(attr) -> bool:
 
 def raise_value_error_if_multiindex_columns(df: pd.DataFrame):
     if isinstance(df.columns, pd.MultiIndex):
-        raise ValueError(
+        msg = (
             "MultiIndex columns are not supported in AnnData. "
             "Please use a single-level index."
         )
+        raise ValueError(msg)

From 31b333bea23215529ac6803674693c55ec202a1d Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Mon, 12 Aug 2024 08:56:00 +0200
Subject: [PATCH 6/9] typo

---
 docs/release-notes/0.10.9.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/release-notes/0.10.9.md b/docs/release-notes/0.10.9.md
index f7ba67041..0c57f830c 100644
--- a/docs/release-notes/0.10.9.md
+++ b/docs/release-notes/0.10.9.md
@@ -9,7 +9,7 @@
 * Upper bound {mod}`numpy` for `gpu` installation on account of https://github.com/cupy/cupy/issues/8391 {pr}`1540` {user}`ilan-gold`
 * Fix writing large number of columns for `h5` files {pr}`1147` {user}`ilan-gold` {user}`selmanozleyen`
 * Upper bound dask on account of https://github.com/scverse/anndata/issues/1579 {pr}`1580` {user}`ilan-gold`
-* Disallow using {class}`~pandas.DataFrame`s with mutli-index columns {pr}`1589` {user}`ilan-gold`
+* Disallow using {class}`~pandas.DataFrame`s with multi-index columns {pr}`1589` {user}`ilan-gold`
 
 #### Documentation
 

From 7bfb920f41f0caec7b38f15e631048580846e2b0 Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Mon, 12 Aug 2024 09:08:55 +0200
Subject: [PATCH 7/9] parametrize

---
 tests/test_base.py | 18 ++++--------------
 1 file changed, 4 insertions(+), 14 deletions(-)

diff --git a/tests/test_base.py b/tests/test_base.py
index 2c8367002..277e8c8ab 100644
--- a/tests/test_base.py
+++ b/tests/test_base.py
@@ -117,22 +117,12 @@ def test_create_from_df():
     assert df.index.tolist() == ad.obs_names.tolist()
 
 
-def test_error_create_from_multiindex_df():
+@pytest.mark.parametrize("attr", ["X", "obs", "obsm"])
+def test_error_create_from_multiindex_df(attr):
     df = get_multiindex_columns_df((100, 20))
+    val = df if attr != "obsm" else {"df": df}
     with pytest.raises(ValueError, match=r"MultiIndex columns are not supported"):
-        AnnData(df)
-
-
-def test_error_with_obs_multiindex_df():
-    df = get_multiindex_columns_df((100, 20))
-    with pytest.raises(ValueError, match=r"MultiIndex columns are not supported"):
-        AnnData(X=np.random.rand(100, 10), obs=df)
-
-
-def test_error_with_obsm_multiindex_df():
-    df = get_multiindex_columns_df((100, 20))
-    with pytest.raises(ValueError, match=r"MultiIndex columns are not supported"):
-        AnnData(X=np.random.rand(100, 10), obsm={"df": df})
+        AnnData(**{attr: val}, shape=(100, 10))
 
 
 def test_create_from_sparse_df():

From 3416668710dc5c8654d8e8b8329bc45faa8dac5c Mon Sep 17 00:00:00 2001
From: ilan-gold <ilanbassgold@gmail.com>
Date: Mon, 12 Aug 2024 12:21:38 -0400
Subject: [PATCH 8/9] (chore): add attr to message

---
 src/anndata/_core/aligned_mapping.py | 2 +-
 src/anndata/_core/anndata.py         | 8 ++++----
 src/anndata/_core/storage.py         | 2 +-
 src/anndata/utils.py                 | 4 ++--
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/anndata/_core/aligned_mapping.py b/src/anndata/_core/aligned_mapping.py
index 7727fa39c..4bb8ca831 100644
--- a/src/anndata/_core/aligned_mapping.py
+++ b/src/anndata/_core/aligned_mapping.py
@@ -265,7 +265,7 @@ def to_df(self) -> pd.DataFrame:
 
     def _validate_value(self, val: Value, key: str) -> Value:
         if isinstance(val, pd.DataFrame):
-            raise_value_error_if_multiindex_columns(val)
+            raise_value_error_if_multiindex_columns(val, f"{self.attrname}.{key}")
             if not val.index.equals(self.dim_names):
                 # Could probably also re-order index if it’s contained
                 try:
diff --git a/src/anndata/_core/anndata.py b/src/anndata/_core/anndata.py
index 2bdd7bbdd..49d47665d 100644
--- a/src/anndata/_core/anndata.py
+++ b/src/anndata/_core/anndata.py
@@ -240,9 +240,9 @@ def __init__(
         vidx: Index1D | None = None,
     ):
         # check for any multi-indices that aren’t later checked in coerce_array
-        for attr in [obs, var, X]:
+        for attr, key in [(obs, "obs"), (var, "var"), (X, "X")]:
             if isinstance(attr, pd.DataFrame):
-                raise_value_error_if_multiindex_columns(attr)
+                raise_value_error_if_multiindex_columns(attr, key)
         if asview:
             if not isinstance(X, AnnData):
                 raise ValueError("`X` has to be an AnnData object.")
@@ -742,10 +742,10 @@ def n_vars(self) -> int:
         """Number of variables/features."""
         return len(self.var_names)
 
-    def _set_dim_df(self, value: pd.DataFrame, attr: str):
+    def _set_dim_df(self, value: pd.DataFrame, attr: Literal["obs", "var"]):
         if not isinstance(value, pd.DataFrame):
             raise ValueError(f"Can only assign pd.DataFrame to {attr}.")
-        raise_value_error_if_multiindex_columns(value)
+        raise_value_error_if_multiindex_columns(value, attr)
         value_idx = self._prep_dim_index(value.index, attr)
         if self.is_view:
             self._init_as_actual(self.copy())
diff --git a/src/anndata/_core/storage.py b/src/anndata/_core/storage.py
index eeccdd513..15630122f 100644
--- a/src/anndata/_core/storage.py
+++ b/src/anndata/_core/storage.py
@@ -89,7 +89,7 @@ def coerce_array(
         return value
     if isinstance(value, pd.DataFrame):
         if allow_df:
-            raise_value_error_if_multiindex_columns(value)
+            raise_value_error_if_multiindex_columns(value, name)
         return value if allow_df else ensure_df_homogeneous(value, name)
     # if value is an array-like object, try to convert it
     e = None
diff --git a/src/anndata/utils.py b/src/anndata/utils.py
index 9467b72c2..3ff844054 100644
--- a/src/anndata/utils.py
+++ b/src/anndata/utils.py
@@ -402,10 +402,10 @@ def is_hidden(attr) -> bool:
         ]
 
 
-def raise_value_error_if_multiindex_columns(df: pd.DataFrame):
+def raise_value_error_if_multiindex_columns(df: pd.DataFrame, attr: str):
     if isinstance(df.columns, pd.MultiIndex):
         msg = (
             "MultiIndex columns are not supported in AnnData. "
-            "Please use a single-level index."
+            f"Please use a single-level index for {attr}."
         )
         raise ValueError(msg)

From d062a7e714668dc40bdbf163aacf9bc6752f6dc3 Mon Sep 17 00:00:00 2001
From: Ilan Gold <ilanbassgold@gmail.com>
Date: Mon, 26 Aug 2024 11:50:20 +0200
Subject: [PATCH 9/9] Update src/anndata/_core/aligned_mapping.py

Co-authored-by: Philipp A. <flying-sheep@web.de>
---
 src/anndata/_core/aligned_mapping.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/anndata/_core/aligned_mapping.py b/src/anndata/_core/aligned_mapping.py
index 4bb8ca831..e2f6e4352 100644
--- a/src/anndata/_core/aligned_mapping.py
+++ b/src/anndata/_core/aligned_mapping.py
@@ -265,7 +265,7 @@ def to_df(self) -> pd.DataFrame:
 
     def _validate_value(self, val: Value, key: str) -> Value:
         if isinstance(val, pd.DataFrame):
-            raise_value_error_if_multiindex_columns(val, f"{self.attrname}.{key}")
+            raise_value_error_if_multiindex_columns(val, f"{self.attrname}[{key!r}]")
             if not val.index.equals(self.dim_names):
                 # Could probably also re-order index if it’s contained
                 try: