Backport PR #2159 on branch 0.12.x (perf: add ability to write downcasted indices)

[meeseeksmachine]

Backport PR #2159: perf: add ability to write downcasted indices

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.80%. Comparing base (172c4db) to head (1af48ee).
⚠️ Report is 19 commits behind head on 0.12.x.

Additional details and impacted files

@@            Coverage Diff             @@
##           0.12.x    #2318      +/-   ##
==========================================
- Coverage   86.84%   84.80%   -2.05%     
==========================================
  Files          46       46              
  Lines        7221     7231      +10     
==========================================
- Hits         6271     6132     -139     
- Misses        950     1099     +149     

Files with missing lines	Coverage Δ
src/anndata/_io/specs/methods.py	90.82% <100.00%> (-0.22%)	⬇️
src/anndata/_settings.py	91.95% <100.00%> (+0.04%)	⬆️

... and 6 files with indirect coverage changes

[scverse-benchmark]

Benchmark changes

Change	Before [172c4db] <0.12.8>	After [1af48ee]	Ratio	Benchmark (Parameter)
-	5.75±0.3ms	4.77±0.02ms	0.83	dataset2d.Dataset2D.time_getitem_slice('h5ad', (-1,), 'cat')
+	319±20μs	352±4μs	1.1	sparse_dataset.SparseCSRContiguousSlice.time_getitem_adata('alternating', False)

Comparison: https://github.com/scverse/anndata/compare/172c4db6d1ce5bf0d354dee14d8fdbe4a83f023d..1af48ee0498d796575db8b706b6d912fc3602185
Last changed: Thu, 29 Jan 2026 11:03:36 +0000

More details: https://github.com/scverse/anndata/pull/2318/checks?check_run_id=61849077633