perf: try out new cliping numba kernel

[ilan-gold]

• Trying out kernel from [RFC] Refactoring Scanpy's Numba Backend: C-Style Kernel Layer & Biology-Optimized Sparse Matrices #3944 (comment)
• Tests included or not required because:

• Release notes not necessary because:

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.35%. Comparing base (4c7c5c0) to head (8b3f328).
✅ All tests successful. No failed tests found.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3952      +/-   ##
==========================================
+ Coverage   78.26%   78.35%   +0.09%     
==========================================
  Files         117      117              
  Lines       12633    12637       +4     
==========================================
+ Hits         9887     9902      +15     
+ Misses       2746     2735      -11     

Flag	Coverage Δ
hatch-test.low-vers	77.60% <100.00%> (+<0.01%)	⬆️
hatch-test.pre	77.32% <100.00%> (+0.09%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
src/scanpy/preprocessing/_highly_variable_genes.py	95.10% <100.00%> (+0.06%)	⬆️

... and 1 file with indirect coverage changes

[scverse-benchmark]

Benchmark changes

Change	Before [4c7c5c0]	After [8b3f328]	Ratio	Benchmark (Parameter)
-	96.8±0.3ms	80.0±0.3ms	0.83	preprocessing_log.HVGSuite.time_highly_variable_genes('seurat_v3')

Comparison: https://github.com/scverse/scanpy/compare/4c7c5c0e8bacc958370fcb0988495a6bf8410add..8b3f328748a0f2cc350509b14adb85fc9b2aa7b5
Last changed: Fri, 30 Jan 2026 12:10:18 +0000

More details: https://github.com/scverse/scanpy/pull/3952/checks?check_run_id=61986886627

[Intron7]

@ilan-gold I tried my old kernel that failed two years ago. It works now as well and might even be a bit faster than the proposed kernels, likely due to better memory coalescing per thread. Numba must have done some work on the parallel execution engine.