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Fix setting on Dataset2D without specificed coord #1990

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Open
3 tasks done
ilan-gold opened this issue May 15, 2025 · 0 comments · May be fixed by #1992
Open
3 tasks done

Fix setting on Dataset2D without specificed coord #1990

ilan-gold opened this issue May 15, 2025 · 0 comments · May be fixed by #1992
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Bug 🐛 type: xarray 🧊

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@ilan-gold
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Please make sure these conditions are met

  • 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.

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Code:

adata.obs["y"] = np.array(...)

should not add a coord when .obs is a Dataset2D (and the current behavior allows adding it as a coord if it is not the normal xarray tuple syntax). When you do this at the moment, you run into our check against having multiple dimensions

anndata/src/anndata/_core/xarray.py

Lines 38 to 39 in ec65081

msg = f"xarray Dataset should not have more than 1 dims, found {len(self.sizes)} {self.sizes}, {self}"
raise ValueError(msg)
if you then try to use adata.obs subsequently.

Traceback:

N/A

Versions

numpy   2.1.3
dask    2025.1.0
----    ----
hatch-vcs       0.4.0
prompt_toolkit  3.0.50
PyYAML  6.0.2
pluggy  1.5.0
jaraco.functools        4.0.1
tblib   3.0.0
h5py    3.13.0
asttokens       3.0.0
msgpack 1.1.0
natsort 8.4.0
decorator       5.1.1
psutil  7.0.0
parso   0.8.4
hatchling       1.27.0
distributed     2025.1.0
zstandard       0.23.0
tornado 6.4.2
ipython 8.32.0
jaraco.collections      5.1.0
zarr    3.0.6
numcodecs       0.15.1
wcwidth 0.2.13
scanpy  1.11.0
more-itertools  10.3.0
python-dateutil 2.9.0.post0
traitlets       5.14.3
pandas  2.2.3
executing       2.2.0
rich    13.9.4
wrapt   1.17.2
awkward 2.7.4
Deprecated      1.2.18
session-info2   0.1.2
scipy   1.15.2
pytz    2025.1
locket  1.0.0
setuptools      75.8.0
jedi    0.19.2
cloudpickle     3.1.1
zict    3.0.0
legacy-api-wrap 1.4.1
stack-data      0.6.3
typing_extensions       4.12.2
fsspec  2025.2.0
MarkupSafe      3.0.2
pathspec        0.12.1
donfig  0.8.1.post1
jaraco.context  5.3.0
pyarrow 19.0.1
awkward_cpp     44
crc32c  2.7.1
Jinja2  3.1.5
jaraco.text     3.12.1
click   8.1.8
pure_eval       0.2.3
toolz   1.0.0
setuptools-scm  8.1.0
packaging       24.2
charset-normalizer      3.4.1
xarray  2025.4.0
attrs   25.3.0
six     1.17.0
sortedcontainers        2.4.0
Pygments        2.19.1
----    ----
Python  3.12.6 (main, Sep  9 2024, 22:11:19) [Clang 18.1.8 ]
OS      Linux-5.15.0-134-generic-x86_64-with-glibc2.35
Updated 2025-05-15 14:12
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Bug 🐛 type: xarray 🧊
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(fix): setting on Dataset2D "just works" (like Dataframes) and is thoroughly checked scverse/anndata
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@flying-sheep @ilan-gold