fix #382: handle 'layers' as h5py.Dataset in read_stereo_h5ad#447
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fix #382: handle 'layers' as h5py.Dataset in read_stereo_h5ad#447cursor[bot] wants to merge 1 commit into
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In _read_stereo_h5ad_from_group(), the 'layers' key handler unconditionally called f[k].keys(), which fails when 'layers' is stored as an h5py.Dataset rather than an h5py.Group. Added isinstance(f[k], h5py.Group) check before iterating sub-keys, falling back to h5ad.read_dataset() for the Dataset case. This matches the existing pattern used for 'exp_matrix' handling in the same function. Added tests covering both Group and Dataset code paths. Co-authored-by: wanruiwen-genomics-cn <wanruiwen-genomics-cn@users.noreply.github.com>
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Summary
In
_read_stereo_h5ad_from_group(), thelayerskey handler unconditionally calledf[k].keys()on line 318 ofstereo/io/reader.py. When a Stereopy-format H5AD file storeslayersas anh5py.Datasetrather than anh5py.Group, this raisesAttributeError: 'Dataset' object has no attribute 'keys'.The root cause is a missing type guard — the same pattern is already correctly handled for
exp_matrix(lines 303–307) andexp_matrix@raw(lines 327–330) in the same function.Changes
stereo/io/reader.py: Added anisinstance(f[k], h5py.Group)check before iterating overf['layers']sub-keys. Iflayersis aGroup, the existing per-key iteration is preserved. If it's aDataset, it is read directly viah5ad.read_dataset().tests/test_read_h5ad_layers.py: Added 3 pytest tests verifying both the Group and Dataset code paths, plus a regression test confirming the originalAttributeErrorno longer occurs.Verification
exp_matrixClassification
layersas a flat Dataset)Closes #382