Helper function to sanitize tables

[timtreis]

No description provided.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.14%. Comparing base (eb5a202) to head (b994960).
⚠️ Report is 8 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #935      +/-   ##
==========================================
+ Coverage   92.11%   92.14%   +0.03%     
==========================================
  Files          48       48              
  Lines        7429     7473      +44     
==========================================
+ Hits         6843     6886      +43     
- Misses        586      587       +1     

Files with missing lines	Coverage Δ
src/spatialdata/__init__.py	96.55% <100.00%> (+0.12%)	⬆️
src/spatialdata/_core/_utils.py	100.00% <100.00%> (ø)
src/spatialdata/_core/validation.py	100.00% <100.00%> (ø)

... and 3 files with indirect coverage changes

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Copilot]

Pull Request Overview

This PR introduces helper functions to sanitize table keys in AnnData objects and updates validation error messaging to guide users in fixing naming issues.

• Adds sanitize_name and sanitize_table in src/spatialdata/_utils.py
• Provides comprehensive tests in tests/utils/test_sanitize.py to validate various sanitization scenarios
• Updates error messages in src/spatialdata/_core/validation.py to include a remediation hint

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File	Description
tests/utils/test_sanitize.py	Adds tests covering multiple sanitization edge cases
src/spatialdata/_utils.py	Implements core sanitization logic for AnnData objects
src/spatialdata/_core/validation.py	Updates ValidationError messaging with sanitization suggestion

Comments suppressed due to low confidence (1)

src/spatialdata/_core/validation.py:382

• The error message now suggests running 'spatialdata.utils.sanitize_table(adata)'. Please verify that the module reference accurately reflects the actual location or re-export of the sanitize_table function.

raise ValidationError(

[LucaMarconato]

Thanks Tim for implementing this functionality! I corrected an edge case, made the docstring more explicit (by referencing the naming restrictions #707) and added the functions to the docs.

Please give a review of my changes and feel free to merge.

[LucaMarconato]

There was an edge case around the user of lstrip('_'). In particular:
-_valid is actually a valid string and

• _index is valid when it's not a obs or var column

Also, now I sanitize __ to _ (and the same for __________, as I basically remove one _ at the time until the string doesn't start with __ anymore).

[melonora]

We should maybe have a doc on these naming rules unless we had one already. WDYT @LucaMarconato

[LucaMarconato]

Yes, at some point we will make a doc (when working on better documenting the file format). For the moment I added a link to #707.

[melonora]

Overall looks good to me, but here and there some minor requests.

[melonora]

After applying changes based on discussion with @LucaMarconato

[LucaMarconato]

Thanks great fixes, I agree with all the changes.