unchecked MultiIndex row index results in Pandas Error #2049
Description
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- I have checked that this issue has not already been reported.
- I have confirmed this bug exists on the latest version of anndata.
- (optional) I have confirmed this bug exists on the master branch of anndata.
Report
While anndata checks for multiindex columns, multiindex rows go unchecked and raise a pandas error due to the type cast.
Code:
import anndata as ad
import pandas as pd
df = pd.DataFrame({"x": [1,2,3]}, index=pd.MultiIndex.from_tuples([("a", 1), ("b", 2), ("c", 3)]))
ad.AnnData(df)Traceback:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In[49], line 5
2 import pandas as pd
4 df = pd.DataFrame({"x": [1,2,3]}, index=pd.MultiIndex.from_tuples([("a", 1), ("b", 2), ("c", 3)]))
----> 5 ad.AnnData(df)
File ~/micromamba/envs/dev/lib/python3.12/site-packages/legacy_api_wrap/__init__.py:82, in legacy_api.<locals>.wrapper.<locals>.fn_compatible(*args_all, **kw)
79 @wraps(fn)
80 def fn_compatible(*args_all: P.args, **kw: P.kwargs) -> R:
81 if len(args_all) <= n_positional:
---> 82 return fn(*args_all, **kw)
84 args_pos: P.args
85 args_pos, args_rest = args_all[:n_positional], args_all[n_positional:]
File ~/micromamba/envs/dev/lib/python3.12/site-packages/anndata/_core/anndata.py:242, in AnnData.__init__(self, X, obs, var, uns, obsm, varm, layers, raw, dtype, shape, filename, filemode, asview, obsp, varp, oidx, vidx)
240 self._init_as_view(X, oidx, vidx)
241 else:
--> 242 self._init_as_actual(
243 X=X,
244 obs=obs,
245 var=var,
246 uns=uns,
247 obsm=obsm,
248 varm=varm,
249 raw=raw,
250 layers=layers,
251 dtype=dtype,
252 shape=shape,
253 obsp=obsp,
254 varp=varp,
255 filename=filename,
256 filemode=filemode,
257 )
File ~/micromamba/envs/dev/lib/python3.12/site-packages/anndata/_core/anndata.py:424, in AnnData._init_as_actual(self, X, obs, var, uns, obsm, varm, varp, obsp, raw, layers, dtype, shape, filename, filemode)
421 source = "shape"
423 # annotations
--> 424 self._obs = _gen_dataframe(
425 obs, ["obs_names", "row_names"], source=source, attr="obs", length=n_obs
426 )
427 self._var = _gen_dataframe(
428 var, ["var_names", "col_names"], source=source, attr="var", length=n_vars
429 )
431 # now we can verify if indices match!
File ~/micromamba/envs/dev/lib/python3.12/functools.py:912, in singledispatch.<locals>.wrapper(*args, **kw)
908 if not args:
909 raise TypeError(f'{funcname} requires at least '
910 '1 positional argument')
--> 912 return dispatch(args[0].__class__)(*args, **kw)
File ~/micromamba/envs/dev/lib/python3.12/site-packages/anndata/_core/aligned_df.py:87, in _gen_dataframe_df(anno, index_names, source, attr, length)
85 msg = "Transforming to str index."
86 warnings.warn(msg, ImplicitModificationWarning, stacklevel=2)
---> 87 anno.index = anno.index.astype(str)
88 if not len(anno.columns):
89 anno.columns = anno.columns.astype(str)
File ~/micromamba/envs/dev/lib/python3.12/site-packages/pandas/core/indexes/multi.py:3892, in MultiIndex.astype(self, dtype, copy)
3890 raise NotImplementedError(msg)
3891 if not is_object_dtype(dtype):
-> 3892 raise TypeError(
3893 "Setting a MultiIndex dtype to anything other than object "
3894 "is not supported"
3895 )
3896 if copy is True:
3897 return self._view()
TypeError: Setting a MultiIndex dtype to anything other than object is not supportedVersions
| Package | Version |
| ---------- | ------- |
| pandas | 2.3.0 |
| pytometry | 0.1.4 |
| numpy | 1.26.4 |
| matplotlib | 3.10.3 |
| pyhere | 1.0.3 |
| anndata | 0.12.0 |
| FlowKit | 1.2.3 |
| Dependency | Version |
| ------------------ | ---------------------- |
| typing_extensions | 4.14.0 |
| packaging | 24.2 |
| statsmodels | 0.14.4 |
| lxml | 6.0.0 |
| certifi | 2025.6.15 (2025.06.15) |
| setuptools | 80.9.0 |
| prompt_toolkit | 3.0.51 |
| idna | 3.10 |
| xyzservices | 2025.4.0 |
| bokeh | 3.7.3 |
| multipledispatch | 0.6.0 |
| scipy | 1.15.2 |
| platformdirs | 4.3.8 |
| pure_eval | 0.2.3 |
| Jinja2 | 3.1.6 |
| comm | 0.2.2 |
| pyct | 0.5.0 |
| zarr | 3.1.0 |
| matplotlib-inline | 0.1.7 |
| scikit-learn | 1.7.0 |
| psutil | 7.0.0 |
| pyarrow | 19.0.1 |
| ipywidgets | 8.1.7 |
| networkx | 3.5 |
| tornado | 6.5.1 |
| Brotli | 1.1.0 |
| numcodecs | 0.16.1 |
| cycler | 0.12.1 |
| six | 1.17.0 |
| msgpack | 1.1.1 |
| MarkupSafe | 3.0.2 |
| natsort | 8.4.0 |
| astroid | 3.3.10 |
| cloudpickle | 3.1.1 |
| PyYAML | 6.0.2 |
| pycparser | 2.22 |
| threadpoolctl | 3.6.0 |
| pyparsing | 3.2.3 |
| legacy-api-wrap | 1.4.1 |
| cffi | 1.17.1 |
| ipykernel | 6.29.5 |
| FlowUtils | 1.1.0 |
| Pygments | 2.19.2 |
| session-info2 | 0.1.2 |
| jaraco.collections | 5.1.0 |
| llvmlite | 0.44.0 |
| contourpy | 1.3.2 |
| kiwisolver | 1.4.8 |
| readfcs | 1.1.8 |
| executing | 2.2.0 |
| fsspec | 2025.5.1 |
| jaraco.context | 5.3.0 |
| xarray | 2025.7.1 |
| more-itertools | 10.3.0 |
| traitlets | 5.14.3 |
| zstandard | 0.23.0 |
| jaraco.text | 3.12.1 |
| debugpy | 1.8.14 |
| anytree | 2.13.0 (2.12.1) |
| stack_data | 0.6.3 |
| param | 2.2.1 |
| donfig | 0.8.1.post1 |
| h5py | 3.14.0 |
| jupyter_core | 5.8.1 |
| decorator | 5.2.1 |
| jupyter_client | 8.6.3 |
| requests | 2.32.4 |
| scanpy | 1.11.3 |
| joblib | 1.5.1 |
| toolz | 1.0.0 |
| fcsparser | 0.2.8 |
| wcwidth | 0.2.13 |
| patsy | 1.0.1 |
| numba | 0.61.2 |
| crc32c | 2.7.1 |
| PySocks | 1.7.1 |
| datashader | 0.18.1 |
| jaraco.functools | 4.0.1 |
| python-dateutil | 2.9.0.post0 |
| charset-normalizer | 3.4.2 |
| pyzmq | 27.0.0 |
| ipython | 9.4.0 |
| parso | 0.8.4 |
| colorama | 0.4.6 |
| asttokens | 3.0.0 |
| pytz | 2025.2 |
| jedi | 0.19.2 |
| FlowIO | 1.3.0 |
| seaborn | 0.13.2 |
| pillow | 11.3.0 |
| urllib3 | 2.5.0 |
| Component | Info |
| --------- | ------------------------------------------------------------------------------ |
| Python | 3.12.11 | packaged by conda-forge | (main, Jun 4 2025, 14:45:31) [GCC 13.3.0] |
| OS | Linux-5.15.0-142-generic-x86_64-with-glibc2.36 |
| Updated | 2025-07-24 11:53 |