Can not import the package using jupyter notebook in Visual Studio Code
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 394
- Forks
- 95
- Avg merge
- 4d 3h
- Merged PRs (30d)
- 7
Description
I'm running into issues while importing the spatialdata package in visualstudio code software using jupyterlab.
ModuleNotFoundError Traceback (most recent call last)
Cell In[1], line 1
----> 1 import spatialdata, spatialdata_io
2 print("spatialdata version:", spatialdata.version)
3 print("spatialdata-io version:", spatialdata_io.version)
File ~/Projects/xenium5k/.venv/lib/python3.11/site-packages/spatialdata_io/init.py:9
7 from spatialdata_io.readers.dbit import dbit
8 from spatialdata_io.readers.generic import generic, geojson, image
----> 9 from spatialdata_io.readers.macsima import macsima
10 from spatialdata_io.readers.mcmicro import mcmicro
11 from spatialdata_io.readers.merscope import merscope
File ~/Projects/xenium5k/.venv/lib/python3.11/site-packages/spatialdata_io/readers/macsima.py:20
17 from spatialdata._logging import logger
19 from spatialdata_io._constants._enum import ModeEnum
---> 20 from spatialdata_io.readers._utils._utils import (
21 calc_scale_factors,
22 parse_channels,
23 parse_physical_size,
24 )
26 if TYPE_CHECKING:
27 from collections.abc import Mapping
File ~/Projects/xenium5k/.venv/lib/python3.11/site-packages/spatialdata_io/readers/_utils/_utils.py:7
4 from pathlib import Path
5 from typing import TYPE_CHECKING, Any, Union
----> 7 from anndata.io import read_text
8 from h5py import File
9 from ome_types import from_tiff
ModuleNotFoundError: No module named 'anndata.io'
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
Reproduce the import in the Jupyter notebook environment described in the traceback, then inspect spatialdata_io/readers/_utils/_utils.py and its anndata.io import. Confirm the dependency or import issue and verify that importing spatialdata and spatialdata_io completes successfully.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python, vscode
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100