Iss1152

[ajkswamy]

Issue:

#1152

Summary:

• Writing AnnData table to zarr file now uses different methods depending on zarr format being written and anndata version installed
• A new custom Deprecation warning is thrown when writing any element to zarr format v2.
• A new hatch env config to help run all tests for combination of anndata/pandas versions

How to test:

• Use this notebook, modified from the one provided by LazDaria in Missing values in AnnData .uns DataFrame become string "nan" after SpatialData Zarr round trip #1152 to cover all cases there
• Use the hatch env added here and call hatch run test-anndata-pandas: test {args}. Check config before running, every script is run multiple times based on the matrix defined.

Related PRs

• Support sharding through config and raster_write_kwargs #1106 (comment)

[codecov]

Codecov Report

❌ Patch coverage is 90.90909% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.42%. Comparing base (eb4fb3d) to head (5f4afca).

Files with missing lines	Patch %	Lines
src/spatialdata/_io/exceptions.py	60.00%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1170      +/-   ##
==========================================
- Coverage   92.44%   92.42%   -0.02%     
==========================================
  Files          51       52       +1     
  Lines        7820     7857      +37     
==========================================
+ Hits         7229     7262      +33     
- Misses        591      595       +4     

Files with missing lines	Coverage Δ
src/spatialdata/_io/io_points.py	100.00% <100.00%> (ø)
src/spatialdata/_io/io_raster.py	89.35% <100.00%> (+0.30%)	⬆️
src/spatialdata/_io/io_shapes.py	96.34% <100.00%> (+0.18%)	⬆️
src/spatialdata/_io/io_table.py	92.72% <100.00%> (+2.25%)	⬆️
src/spatialdata/_io/exceptions.py	60.00% <60.00%> (ø)

🚀 New features to boost your workflow:

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