Backport PR #1825 on branch 0.11.x ((chore): Update to Ruff 0.9 and add EM lints)

[flying-sheep]

No description provided.

[codecov]

Codecov Report

Attention: Patch coverage is 37.96992% with 165 lines in your changes missing coverage. Please review.

Project coverage is 83.60%. Comparing base (422fb77) to head (f9f06db).
Report is 1 commits behind head on 0.11.x.

Files with missing lines	Patch %	Lines
src/anndata/_core/anndata.py	32.30%	44 Missing ⚠️
src/anndata/experimental/merge.py	16.66%	20 Missing ⚠️
src/anndata/_core/merge.py	33.33%	16 Missing ⚠️
src/anndata/_core/sparse_dataset.py	50.00%	12 Missing ⚠️
src/anndata/tests/helpers.py	0.00%	11 Missing ⚠️
...anndata/experimental/multi_files/_anncollection.py	0.00%	8 Missing ⚠️
src/anndata/utils.py	42.85%	8 Missing ⚠️
src/anndata/_core/file_backing.py	0.00%	6 Missing ⚠️
src/anndata/_core/index.py	66.66%	6 Missing ⚠️
src/anndata/_io/read.py	40.00%	6 Missing ⚠️
... and 10 more

Additional details and impacted files

@@            Coverage Diff             @@
##           0.11.x    #1828      +/-   ##
==========================================
- Coverage   87.07%   83.60%   -3.47%     
==========================================
  Files          40       40              
  Lines        6110     6239     +129     
==========================================
- Hits         5320     5216     -104     
- Misses        790     1023     +233     

Files with missing lines	Coverage Δ
src/anndata/_core/aligned_mapping.py	93.44% <100.00%> (+0.02%)	⬆️
src/anndata/_io/specs/lazy_methods.py	97.80% <100.00%> (+0.04%)	⬆️
src/anndata/_io/write.py	77.01% <100.00%> (+0.26%)	⬆️
src/anndata/_settings.py	94.11% <100.00%> (ø)
src/anndata/io.py	100.00% <ø> (ø)
src/anndata/__init__.py	90.62% <0.00%> (-2.93%)	⬇️
src/anndata/_core/aligned_df.py	95.65% <0.00%> (-2.13%)	⬇️
src/anndata/_core/views.py	85.02% <50.00%> (-6.09%)	⬇️
src/anndata/_io/h5ad.py	92.68% <80.00%> (-0.32%)	⬇️
src/anndata/_io/specs/methods.py	88.10% <80.00%> (-0.51%)	⬇️
... and 15 more