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Faster xenium polygon parsing via ragged arrays#365

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LucaMarconato merged 3 commits intomainfrom
performance/xenium-shapes-parsing
Feb 4, 2026
Merged

Faster xenium polygon parsing via ragged arrays#365
LucaMarconato merged 3 commits intomainfrom
performance/xenium-shapes-parsing

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Parsing polygons for Xenium is now ~9x faster thanks to using from_ragged_array() and using plain numpy instead of pandas group_by.

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codecov-commenter commented Feb 3, 2026

Codecov Report

❌ Patch coverage is 89.47368% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 63.08%. Comparing base (1431911) to head (dc8e297).
⚠️ Report is 4 commits behind head on main.

Files with missing lines Patch % Lines
src/spatialdata_io/readers/xenium.py 89.47% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #365      +/-   ##
==========================================
+ Coverage   62.98%   63.08%   +0.10%     
==========================================
  Files          27       27              
  Lines        3147     3153       +6     
==========================================
+ Hits         1982     1989       +7     
+ Misses       1165     1164       -1     
Files with missing lines Coverage Δ
src/spatialdata_io/__main__.py 87.22% <ø> (-0.08%) ⬇️
src/spatialdata_io/readers/xenium.py 73.27% <89.47%> (+0.84%) ⬆️
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@LucaMarconato LucaMarconato merged commit 28eacc9 into main Feb 4, 2026
4 of 5 checks passed
@LucaMarconato LucaMarconato deleted the performance/xenium-shapes-parsing branch February 4, 2026 10:39
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