Support non-standard metadata objects when reading from H5AD files. (#41

)

Fixes an issue where `uns` is not a dictionary. Update tests and documentation.

src/singlecellexperiment/SingleCellExperiment.py

@@ -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()
@@ -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,

tests/test_sce_io.py

@@ -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(