Full accessor support#158
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## main #158 +/- ##
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- Coverage 91.53% 91.09% -0.45%
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Files 10 11 +1
Lines 1619 1819 +200
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+ Hits 1482 1657 +175
- Misses 137 162 +25
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| del MuAcc.__dataclass_fields__["layers"] | ||
| del MuAcc.__dataclass_fields__["layer_cls"] | ||
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| A: MuAcc[AdRef] = MuAcc() |
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| A: MuAcc[AdRef] = MuAcc() | |
| M: MuAcc[AdRef] = MuAcc() |
or?
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I assumed A stands for accessor, not AnnData. But I'm fine with calling this M.
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I had genuinely never thought of that but it makes sense. I thought of it as accessor for AnnData. @flying-sheep thoughts here?
| def to_json(self, ref: R) -> list[str | int | None]: | ||
| """Serialize :class:`~anndata.acc.AdRef` to a JSON-compatible list.""" | ||
| if isinstance(ref.acc, ModMapAcc): | ||
| return [f"{ref.acc.dim}map", ref.idx] | ||
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| ret = super().to_json(ref) | ||
| if isinstance(ref.acc, _ModalityMixin): | ||
| ret = ["mod", ref.acc.mod, ret] | ||
| return ret | ||
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We have a JSON-schema for this - it may be worth doing this for MuData (in a way that builds on ours maybe?): https://anndata.scverse.org/en/latest/generated/anndata.acc.AdAcc.html#anndata.acc.AdAcc.from_json
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I've added a schema.
| del MuAcc.__dataclass_fields__["X"] | ||
| del MuAcc.__dataclass_fields__["layers"] | ||
| del MuAcc.__dataclass_fields__["layer_cls"] | ||
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I wonder if there is a better way to support this, maybe @flying-sheep has an idea. Bu this seems fine to me at first glance
Co-authored-by: Ilan Gold <ilanbassgold@gmail.com>
This reverts commit 36b3aea.
2 participants
Implement MuData acessors. These are similar to and build on AnnData accessors, but add an additional level for modalities. So it is now possible to e.g. do