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More robust name validation #703

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More robust name validation #703

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@aeisenbarth aeisenbarth commented Sep 9, 2024 •
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Closes #624

  • This pull request changes name validation rules:
    • allow additionally . (now allowing _-. and alphanumeric, which includes 0-9a-zA-Z but also other Unicode like ɑ and ²)
    • forbid full names ., ..
    • forbid prefix __
    • forbid names only differing in character case, like abc, Abc (only one of them allowed, no matter which case)
  • Name validation is now also applied to AnnData tables (keys/columns in obs, obsm, obsp, var, varm, varp, uns).
    • For obs and var dataframes, _index is forbidden.
  • Validation happens at construction time when adding elements to an element type dictionary (as before).
  • Additionally, validation happens before writing to Zarr.

@aeisenbarth aeisenbarth marked this pull request as draft September 9, 2024 14:41
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codecov bot commented Sep 9, 2024 •
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Codecov Report

Attention: Patch coverage is 98.85057% with 1 line in your changes missing coverage. Please review.

Project coverage is 91.90%. Comparing base (8323e15) to head (a42d698).

Files with missing lines Patch % Lines
src/spatialdata/_core/spatialdata.py 91.66% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #703      +/-   ##
==========================================
+ Coverage   91.84%   91.90%   +0.06%     
==========================================
  Files          44       45       +1     
  Lines        6791     6846      +55     
==========================================
+ Hits         6237     6292      +55     
  Misses        554      554
Files with missing lines Coverage Δ
src/spatialdata/_core/_elements.py 91.86% <100.00%> (-0.10%) ⬇️
src/spatialdata/_core/validation.py 100.00% <100.00%> (ø)
src/spatialdata/models/__init__.py 100.00% <100.00%> (ø)
src/spatialdata/models/models.py 87.71% <100.00%> (-0.11%) ⬇️
src/spatialdata/_core/spatialdata.py 90.88% <91.66%> (-0.02%) ⬇️

@aeisenbarth aeisenbarth marked this pull request as ready for review September 9, 2024 19:47
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Naming constraints break compatibility with existing datasets
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@aeisenbarth