feat: base without X_

[flying-sheep]

• Closes Don't prepend "X_" #3188
• Tests included or not required because:

• Release notes not necessary because:

TODO:

• scanpy/src/scanpy/plotting/_tools/scatterplots.py

  Line 858 in e6e9647

  if f"X_{basis}" not in adata.obsm:

• scanpy/src/scanpy/plotting/_utils.py

  Line 1034 in e6e9647

  elif f"X_{basis}" in adata.obsm:

• …

[codecov]

Codecov Report

❌ Patch coverage is 85.11905% with 25 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.89%. Comparing base (68eeb6a) to head (8dee00e).
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
src/scanpy/plotting/_tools/scatterplots.py	50.00%	7 Missing ⚠️
src/scanpy/tools/_ingest.py	64.28%	5 Missing ⚠️
src/scanpy/external/tl/_trimap.py	33.33%	4 Missing ⚠️
src/scanpy/external/exporting.py	50.00%	3 Missing ⚠️
src/scanpy/tools/_draw_graph.py	85.71%	3 Missing ⚠️
src/scanpy/_utils/__init__.py	92.30%	1 Missing ⚠️
src/scanpy/plotting/_utils.py	66.66%	1 Missing ⚠️
src/scanpy/tools/_utils.py	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4076      +/-   ##
==========================================
+ Coverage   79.72%   79.89%   +0.17%     
==========================================
  Files         120      120              
  Lines       12833    12900      +67     
==========================================
+ Hits        10231    10307      +76     
+ Misses       2602     2593       -9     

Flag	Coverage Δ
hatch-test.low-vers	78.95% <85.11%> (+0.16%)	⬆️
hatch-test.pre	79.76% <85.11%> (+0.19%)	⬆️

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

Files with missing lines	Coverage Δ
src/scanpy/_settings/presets.py	90.84% <100.00%> (+7.89%)	⬆️
src/scanpy/experimental/pp/_normalization.py	94.50% <100.00%> (+0.18%)	⬆️
src/scanpy/experimental/pp/_recipes.py	100.00% <100.00%> (ø)
src/scanpy/neighbors/__init__.py	82.23% <100.00%> (+0.18%)	⬆️
src/scanpy/plotting/_tools/__init__.py	76.17% <100.00%> (ø)
src/scanpy/plotting/_tools/paga.py	64.26% <100.00%> (ø)
src/scanpy/preprocessing/_pca/__init__.py	92.16% <100.00%> (+0.19%)	⬆️
src/scanpy/tools/_diffmap.py	82.60% <100.00%> (+0.79%)	⬆️
src/scanpy/tools/_dpt.py	66.37% <100.00%> (+0.75%)	⬆️
src/scanpy/tools/_embedding_density.py	62.29% <100.00%> (ø)
... and 10 more

[ilan-gold]

Are these the only two places that this is the case anymore i.e., prepend _X? It seems to have been done for PCA, but not UMAP:

scanpy/src/scanpy/tools/_umap.py

Line 147 in d96d91d

key_obsm, key_uns = ("X_umap", "umap") if key_added is None else [key_added] * 2

or am I misreading this?