feat: accessors #2290
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feat: accessors #2290
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ilan-gold
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Jan 27, 2026
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ilan-gold
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Mentioned on slack, but I think the landing page needs to make clear A.obsm["pca"](adata) is possible!
I have to run now but I have a broader question - is there a desire to do some form of validation as well? Like A.obs["x"].validate(adata) or similar. And relatedly asserting types might be in-scope like A.obsm["X_pca"].is(np.ndarray).validate(adata) or similar
Super nice! Very exciting
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| @dataclass(frozen=True) | ||
| class RefAcc[R: AdRef[I], I](abc.ABC): # type: ignore | ||
| """Abstract base class for reference accessors. |
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I think a terminology page where you explain these concepts (either centralized on acc or within each class) would be good explaining full name i.e., "reference" for Ref and its meanings (and hten how they are composed)
| object.__setattr__(self, "obsp", GraphMapAcc("obs", ref_class=self.ref_class)) | ||
| object.__setattr__(self, "varp", GraphMapAcc("var", ref_class=self.ref_class)) | ||
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| def to_json(self, ref: R) -> list[str | int | None]: |
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Why have a to_json method? Genuinely wondering about the use-case here.
| You can refer to columns or the index in the way you would access them | ||
| in a :class:`~pandas.DataFrame`: | ||
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| >>> from anndata.acc import A |
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I would add a line
Suggested change
| >>> from anndata.acc import A | |
| >>> from anndata.acc import A, MetaAcc | |
| >>> isinstance(A.obs, MetaAcc) |
I think it's implicit in the description, but I would find this helpful (in all of the classes)
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User API design
AdPathinstances by descending into a central accessor constantA:anndata/tests/test_accessors.py
Lines 25 to 42 in 61fc920
AdPathinstance, e.g. to figure out which axes the resulting vector spans:anndata/tests/test_accessors.py
Lines 101 to 107 in 61fc920
AdPathinstance to extract a vector (see 1. for examples)subclassing
… is a direct goal of this, as people should be able to use
AdPathsubclasses. This means thatAdPathAPI is minimal and inspection can be done through.acc(could be even more minimal by just putting it all into a container?):anndata/src/anndata/acc/__init__.py
Lines 56 to 57 in 61fc920
anndata/src/anndata/acc/__init__.py
Lines 63 to 64 in 61fc920
AdAccconstant that produces your ownAdPathsubclass:anndata/src/anndata/acc/__init__.py
Line 415 in 61fc920
VecAcc.__getitem__to get anAdPathor a list of them. In that process,__getitem__callsprocess_idxwhich verifies and simplifies the indexaxes,__repr__, andidx_reprget called too to validate things workAdPathcan be used, which basically just delegates toVecAcc’saxes,__repr__,idx_repr, and__call__So in the end everything except for
__call__is validated, i.e.VecAcc.__getitem__raises exceptions on misuseanndata/src/anndata/acc/__init__.py
Lines 101 to 119 in 61fc920
TODO:
Especially since we already call these accessors! Instance namespaces (
adata.custom) #1869__dir__)