Catch all warnings

[flying-sheep]

• Closes Scanpy’s tests should prevent DeprecationWarnings and FutureWarnings #3558
• Tests included or not required because:

• Release notes not necessary because:

TODO:

• does this make sense?

  scanpy/tests/test_highly_variable_genes.py

  Lines 698 to 702 in 02ecd49

  	with (
  	pytest.warns(UserWarning, match="n_top_genes.*normalized dispersions")
  	if flavor == "cell_ranger"
  	else nullcontext()
  	):

[codecov]

Codecov Report

❌ Patch coverage is 84.50704% with 11 lines in your changes missing coverage. Please review.
✅ Project coverage is 75.96%. Comparing base (0b82c93) to head (4b6ec91).
⚠️ Report is 45 commits behind head on main.

Files with missing lines	Patch %	Lines
src/scanpy/tools/_leiden.py	20.00%	4 Missing ⚠️
src/scanpy/tools/_tsne.py	0.00%	3 Missing ⚠️
src/scanpy/tools/_sim.py	92.30%	2 Missing ⚠️
src/scanpy/_utils/__init__.py	66.66%	1 Missing ⚠️
src/scanpy/readwrite.py	91.66%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3724      +/-   ##
==========================================
- Coverage   76.02%   75.96%   -0.06%     
==========================================
  Files         117      117              
  Lines       12546    12549       +3     
==========================================
- Hits         9538     9533       -5     
- Misses       3008     3016       +8     

Files with missing lines	Coverage Δ
src/scanpy/datasets/_datasets.py	100.00% <100.00%> (ø)
src/scanpy/datasets/_utils.py	100.00% <ø> (ø)
src/scanpy/logging.py	97.34% <100.00%> (+0.02%)	⬆️
src/scanpy/plotting/_tools/__init__.py	75.88% <100.00%> (ø)
src/scanpy/plotting/_tools/paga.py	66.60% <100.00%> (-0.19%)	⬇️
src/scanpy/plotting/_tools/scatterplots.py	83.01% <100.00%> (-0.04%)	⬇️
src/scanpy/preprocessing/_highly_variable_genes.py	93.72% <100.00%> (+0.02%)	⬆️
src/scanpy/preprocessing/_pca/__init__.py	88.77% <ø> (+0.33%)	⬆️
src/scanpy/preprocessing/_simple.py	90.69% <ø> (ø)
src/scanpy/tools/_ingest.py	75.54% <ø> (ø)
... and 7 more

... and 1 file with indirect coverage changes

[ilan-gold]

I need to make another pass at this to be sure I understand what is going on. Here's my understanding, this PR seems to do a few things:

1. Remove all warnings in pyproject.toml that don't apply anymore (presumably?)
2. Catch all warnings explicitly that weren't caught before (I can see this locally)
3. Clean up some anndata<0.9 straggling functions/compat

Is this right?

I still get locally SparseEfficiencyWarning and NumbaPerformanceWarning. Do you see this as well?