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Compatibility with non-dict types in uns when reading from H5AD files. #41

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merged 5 commits into from
May 5, 2024
Merged

Compatibility with non-dict types in uns when reading from H5AD files. #41

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2d3dcc9
support non mapping types for uns/metadata when importing from h5ad/a…
jkanche May 5, 2024
4787173
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 5, 2024
ec896f7
Update docstring
jkanche May 5, 2024
988402e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 5, 2024
d3ae1e3
slightly better
jkanche May 5, 2024
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7 changes: 5 additions & 2 deletions src/singlecellexperiment/SingleCellExperiment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1015,7 +1015,9 @@ def from_anndata(cls, input: "anndata.AnnData") -> "SingleCellExperiment":
Input data.

Returns:
A ``SingleCellExperiment`` object.
A ``SingleCellExperiment`` object. If the input contains any data
in the ``uns`` attribute, the `metadata` slot of the ``SingleCellExperiment``
will contain a key ``uns``.
"""

layers = OrderedDict()
Expand All @@ -1028,12 +1030,13 @@ def from_anndata(cls, input: "anndata.AnnData") -> "SingleCellExperiment":
obsm = _to_normal_dict(input.obsm)
varp = _to_normal_dict(input.varp)
obsp = _to_normal_dict(input.obsp)
_metadata = {"uns": input.uns} if input.uns is not None else None

return cls(
assays=layers,
row_data=biocframe.BiocFrame.from_pandas(input.var),
column_data=biocframe.BiocFrame.from_pandas(input.obs),
metadata=input.uns,
metadata=_metadata,
reduced_dims=obsm,
row_pairs=varp,
column_pairs=obsp,
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8 changes: 8 additions & 0 deletions tests/test_sce_io.py
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Expand Up @@ -129,6 +129,14 @@ def test_SCE_randomAnnData():
assert tse is not None
assert isinstance(tse, SingleCellExperiment)

# to avoid unknown mapping types;
# ran into an issue with anndata.compat._overloaded_dict.OverloadedDict when loading a h5ad
adata.uns = {".internal": [f"obs_{i+1}" for i in range(n)]}
tse = singlecellexperiment.SingleCellExperiment.from_anndata(adata)

assert tse is not None
assert isinstance(tse, SingleCellExperiment)


def test_SCE_to_mudata():
tse = SingleCellExperiment(
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