feat: make use_rep accept anndata.acc - #4315
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flying-sheep
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Aug 21, 2026
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| # `A.to_json` only serializes vectors, so we add a dummy index | ||
| return [json.dumps(A.to_json(rep[:, :] if isinstance(rep, LayerAcc) else rep[0]))] |
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[:,:] works, but [0] is bad … maybe we should implement this in anndata first …
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flying-sheep
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Aug 21, 2026
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| [data] = rep # a 1-element list/array (see `_rep_to_json`) | ||
| return _resolve_rep(A.from_json(json.loads(data)).acc) |
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we should make this forward compatible and both handle from_json already returning a RepAcc and rep being a heterogeneous list.
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Aug 21, 2026
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| Use the indicated representation: | ||
| a :class:`~anndata.acc.LayerAcc` (e.g. `A.X`, `A.layers[...]`) or | ||
| :class:`~anndata.acc.MultiAcc` (e.g. `A.obsm[...]`, `A.varm[...]`). | ||
| A :class:`str` is :meth:`~anndata.acc.AdAcc.resolve`\ d to one of those | ||
| if :attr:`scanpy.settings.preset` is :attr:`~scanpy.Preset.ScanpyV2Preview`, | ||
| otherwise interpreted as `'X'` or a key of `.obsm`. | ||
| If `None`, the representation is chosen automatically: | ||
| For `.n_vars` < :attr:`~scanpy.settings.N_PCS` (default: 50), `.X` is used, otherwise 'X_pca' is used. | ||
| If 'X_pca' is not present, it’s computed with default parameters or `n_pcs` if present.\ | ||
| """ | ||
| For `.n_vars` < :attr:`~scanpy.settings.N_PCS` (default: 50), `.X` is used, otherwise the PCA | ||
| representation (`.obsm['X_pca']`, or `.obsm['pca']` if it was computed under | ||
| :attr:`~scanpy.Preset.ScanpyV2Preview`). | ||
| If it is not present, it’s computed with default parameters or `n_pcs` if present.""" |
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plenty complicated 😢
flying-sheep
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use_rep accepts anndata.accuse_rep accept anndata.acc
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #4315 +/- ##
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+ Coverage 80.08% 80.10% +0.02%
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Files 133 133
Lines 13424 13475 +51
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+ Hits 10750 10794 +44
- Misses 2674 2681 +7
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use_repacceptanndata.accacessors #4314