PointsModel warning
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- Dominant language
- Python
- Stars
- 394
- Forks
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- Avg merge
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- Merged PRs (30d)
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Description
Hello!
I got this warning when running:
sdata = sdio.xenium(
"/path/to/my/folder",
nucleus_boundaries=False,
cells_boundaries=False,
)
WARNING The `feature_key` column feature_name is categorical with unknown categories. Please ensure the categories
are known before calling `PointsModel.parse()` to avoid significant performance implications due to the
need for dask to compute the categories. If you did not use PointsModel.parse() explicitly in your code
(e.g. this message is coming from a reader in `spatialdata_io`), please report this finding.
It said to report this finding.
Thank you!
- OS: macOS
- Context: loading data from Google Drive folder
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 by reproducing the warning with the shown sdata.xenium call and the Google Drive folder context. Read the PointsModel.parse() path and the spatialdata_io reader mentioned in the warning; done means identifying why feature_name has unknown categories and confirming the warning no longer occurs or is appropriately handled.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 42/100