Is automatic sanitisation necessary?
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- Dominant language
- Python
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Description
In several Scanpy functions sanitize_anndata() is called which converts most string columns in obs/var to categorical columns. Often this seems to be a precaution rather than really necessary and as a user it's frustrating to have things changed in a way you have no control over. Just wondering if you have considered how required this is and whether it would be better to let users control when/if this happens.
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 locating the Scanpy functions that call sanitize_anndata() and inspect how string columns in obs and var are converted to categorical columns. Determine which callers require this behavior and whether user control is feasible. Done means the necessity and desired control behavior are resolved and reflected in the relevant implementation or documentation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100