feat: presets

[flying-sheep]

• Closes Scanpy 2.0 preview #4000, closes Remove default from sc.pp.scale’s zero_center (so it never accidentally densifies) #3730
• Tests included or not required because:

• Release notes not necessary because:

Self-documenting presets work!

E.g.:

• code:

  scanpy/src/scanpy/_settings.py

  Lines 90 to 96 in 3bae7ae

  	@_preset_property("flavor")
  	def highly_variable_genes() -> Mapping[Preset, HVGFlavor]:
  	"""Flavor for :func:`~scanpy.pp.highly_variable_genes`."""
  	return {
  	Preset.ScanpyV1: "seurat",
  	Preset.SeuratV5: "seurat_v3",
  	}

• docs: https://icb-scanpy--3653.com.readthedocs.build/en/3653/generated/scanpy.Preset.highly_variable_genes.html

[codecov]

Codecov Report

❌ Patch coverage is 93.26923% with 14 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.34%. Comparing base (b5efe54) to head (ab0e916).
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
src/scanpy/_settings/presets.py	91.08%	9 Missing ⚠️
src/scanpy/preprocessing/_scale.py	66.66%	2 Missing ⚠️
src/scanpy/tools/_leiden.py	75.00%	2 Missing ⚠️
src/scanpy/readwrite.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3653      +/-   ##
==========================================
+ Coverage   78.23%   78.34%   +0.11%     
==========================================
  Files         117      117              
  Lines       12661    12782     +121     
==========================================
+ Hits         9905    10014     +109     
- Misses       2756     2768      +12     

Flag	Coverage Δ
hatch-test.low-vers	77.64% <93.26%> (+0.11%)	⬆️
hatch-test.pre	77.30% <93.26%> (+0.12%)	⬆️

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

Files with missing lines	Coverage Δ
src/scanpy/__init__.py	100.00% <100.00%> (ø)
src/scanpy/_settings/__init__.py	86.54% <100.00%> (+0.50%)	⬆️
src/scanpy/_utils/__init__.py	75.28% <ø> (-0.11%)	⬇️
src/scanpy/experimental/pp/_normalization.py	94.25% <100.00%> (+0.06%)	⬆️
src/scanpy/plotting/_anndata.py	85.53% <100.00%> (ø)
src/scanpy/plotting/_baseplot_class.py	88.32% <100.00%> (ø)
src/scanpy/plotting/_dotplot.py	94.87% <100.00%> (ø)
src/scanpy/plotting/_matrixplot.py	96.51% <100.00%> (ø)
src/scanpy/plotting/_stacked_violin.py	85.85% <100.00%> (ø)
src/scanpy/plotting/_tools/__init__.py	76.17% <100.00%> (ø)
... and 15 more

[flying-sheep]

TODO: add jaccard to seurat preset #3828

[flying-sheep]

@ilan-gold I asked your review because of scope:

• I’ll add some tests, but how thoroughly should it be tested? certainly not all 2.0 preview things
• I filed anndata.acc based API #4007 for a AdRef based API, which would be relevant here too
• I filed Opinionated defaults for 2.0 #4008 to maybe do more opinionated changes to after implementing anndata.acc based API #4007
• anything that should be done now instead of later?

[ilan-gold]

This is a pretty harmless PR so nothing comes to mind as absolutely pressing. The architecture overall makes sense.

I would beef up the docs a bit to make it clear how to use this.

Why use ScanpyV2Preview instead of just ScanpyV2?

[flying-sheep]

Why use ScanpyV2Preview instead of just ScanpyV2?

Because when we release a new feature release before 2.0, I don’t want people to start relying on it keeping its behavior. I thought “preview” makes it clear that it’s not stable, but I’m open to suggestions.

[ilan-gold]

Modulo the repr (whcih I do think is worth discussion at the minmum if not a tweak), looks great!!!