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]

❌ 1 Tests Failed:

Tests completed	Failed	Passed	Skipped
1872	1	1871	931

View the top 1 failed test(s) by shortest run time

tests/test_neighbors_key_added.py::test_neighbors_pca_keys_added_without_previous_pca_run

Stack Traces | 0.045s run time

adata = AnnData object with n_obs × n_vars = 700 × 765
    uns: 'pca'
    obsm: 'X_pca'
    varm: 'PCs'

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_neighbors_pca_keys_added_without_previous_pca_run#x1B[39;49;00m(adata: sc.AnnData) -> #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
        #x1B[94mdel#x1B[39;49;00m adata.uns[#x1B[33m"#x1B[39;49;00m#x1B[33mpca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
        #x1B[94mdel#x1B[39;49;00m adata.obsm[#x1B[33m"#x1B[39;49;00m#x1B[33mX_pca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
        #x1B[94mwith#x1B[39;49;00m pytest.warns(#x1B[90m#x1B[39;49;00m
            #x1B[96mUserWarning#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
            match=#x1B[33mr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33m.*Falling back to preprocessing with `sc.pp.pca` and default params#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
        ):#x1B[90m#x1B[39;49;00m
>           sc.pp.neighbors(adata, n_neighbors=n_neighbors, random_state=#x1B[94m0#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/test_neighbors_key_added.py#x1B[0m:60: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[.../scanpy/_utils/random.py#x1B[0m:204: in wrapper
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m func(*args, **kwargs)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/neighbors/__init__.py#x1B[0m:220: in neighbors
    #x1B[0mneighbors_.compute_neighbors(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/_utils/random.py#x1B[0m:204: in wrapper
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m func(*args, **kwargs)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/neighbors/__init__.py#x1B[0m:638: in compute_neighbors
    #x1B[0mx = _choose_representation(#x1B[96mself#x1B[39;49;00m._adata, use_rep=use_rep, n_pcs=n_pcs)#x1B[90m#x1B[39;49;00m
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/tools/_utils.py#x1B[0m:32: in _choose_representation
    #x1B[0mx = _get_pca_or_small_x(adata, n_pcs)#x1B[90m#x1B[39;49;00m
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/tools/_utils.py#x1B[0m:77: in _get_pca_or_small_x
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m adata.obsm[_pca_keys(adata)[#x1B[94m0#x1B[39;49;00m]]#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = AxisArrays with keys: X_pca
key = AnnData object with n_obs × n_vars = 700 × 765
    uns: 'pca'
    obsm: 'X_pca'
    varm: 'PCs'

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92m__getitem__#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m, key: #x1B[96mstr#x1B[39;49;00m) -> Value:#x1B[90m#x1B[39;49;00m
>       #x1B[94mreturn#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._data[key]#x1B[90m#x1B[39;49;00m
               ^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       TypeError: cannot use 'anndata._core.anndata.AnnData' as a dict key (unhashable type: 'AnnData')#x1B[0m

#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.few-extras/lib/python3.14.../anndata/_core/aligned_mapping.py#x1B[0m:216: TypeError

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