(chore): Update to Ruff 0.9 and add EM lints

[flying-sheep]

All changes mechanic except for some minor error message changes

[codecov]

Codecov Report

Attention: Patch coverage is 16.66667% with 475 lines in your changes missing coverage. Please review.

Project coverage is 75.36%. Comparing base (66f1b61) to head (d6fb426).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/scanpy/plotting/_anndata.py	16.27%	36 Missing ⚠️
src/scanpy/_utils/__init__.py	26.31%	28 Missing ⚠️
src/scanpy/readwrite.py	25.71%	26 Missing ⚠️
src/scanpy/plotting/_tools/paga.py	0.00%	24 Missing ⚠️
src/scanpy/plotting/_tools/scatterplots.py	14.28%	24 Missing ⚠️
src/scanpy/plotting/_tools/__init__.py	8.33%	22 Missing ⚠️
src/scanpy/plotting/_utils.py	9.09%	20 Missing ⚠️
src/scanpy/tools/_marker_gene_overlap.py	0.00%	14 Missing ⚠️
src/scanpy/tools/_rank_genes_groups.py	12.50%	14 Missing ⚠️
src/scanpy/preprocessing/_simple.py	45.45%	12 Missing ⚠️
... and 55 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3437      +/-   ##
==========================================
- Coverage   76.67%   75.36%   -1.31%     
==========================================
  Files         112      112              
  Lines       12945    13219     +274     
==========================================
+ Hits         9925     9963      +38     
- Misses       3020     3256     +236     

Files with missing lines	Coverage Δ
src/scanpy/logging.py	97.39% <ø> (ø)
src/scanpy/plotting/_stacked_violin.py	86.40% <ø> (ø)
src/scanpy/tools/_score_genes.py	86.66% <100.00%> (+0.52%)	⬆️
src/scanpy/_utils/_doctests.py	90.00% <0.00%> (-4.74%)	⬇️
src/scanpy/experimental/pp/_normalization.py	94.04% <66.66%> (-1.02%)	⬇️
src/scanpy/external/pl.py	33.68% <0.00%> (-0.36%)	⬇️
src/scanpy/external/pp/_bbknn.py	53.84% <0.00%> (-4.49%)	⬇️
src/scanpy/external/pp/_dca.py	50.00% <0.00%> (-4.55%)	⬇️
src/scanpy/external/pp/_harmony_integrate.py	82.35% <0.00%> (-5.15%)	⬇️
src/scanpy/external/pp/_mnn_correct.py	22.22% <0.00%> (-1.31%)	⬇️
... and 58 more