scverse / scverse/spatialdata-io
failure to import spatialdata_io
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 103
- Forks
- 65
- Avg merge
- 1h 8m
- Merged PRs (30d)
- 3
Description
Hello, I am running one of the tutorials and I have installed both spatialdata and spatialdata_io packages, but there is an error importing spatialdata_io. Could you help? Thank you very much!
ImportError Traceback (most recent call last)
Cell In[9], line 2
1 import spatialdata as sd
----> 2 from spatialdata_io import xenium
4 import matplotlib.pyplot as plt
5 import seaborn as sns
File /opt/anaconda3/lib/python3.12/site-packages/spatialdata_io/init.py:14
12 from spatialdata_io.readers.visium import visium
13 from spatialdata_io.readers.visium_hd import visium_hd
---> 14 from spatialdata_io.readers.xenium import (
15 xenium,
16 xenium_aligned_image,
17 xenium_explorer_selection,
18 )
20 all = [
21 "curio",
22 "seqfish",
(...)
34 "visium_hd",
35 ]
37 version = version("spatialdata-io")
File /opt/anaconda3/lib/python3.12/site-packages/spatialdata_io/readers/xenium.py:40
32 from spatialdata.models import (
33 Image2DModel,
34 Labels2DModel,
(...)
37 TableModel,
38 )
39 from spatialdata.transformations.transformations import Affine, Identity, Scale
---> 40 from xarray import DataArray, DataTree
42 from spatialdata_io._constants._constants import XeniumKeys
43 from spatialdata_io._docs import inject_docs
ImportError: cannot import name 'DataTree' from 'xarray' (/opt/anaconda3/lib/python3.12/site-packages/xarray/init.py)
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with spatialdata_io/readers/xenium.py and the failing from xarray import DataArray, DataTree import shown in the traceback. Check the installed xarray and spatialdata-io versions and the tutorial environment; done means from spatialdata_io import xenium imports successfully with the documented installation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- anaconda, python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100