cellbender: keep uns as CellBender's loader gives it

src/adata/conversion/cellbender.py

@@ -202,6 +202,10 @@ def place_global(key: str, path: str, item: h5py.Dataset) -> None:
         rows = index
     elif n_latent in (0, n_barcodes):
         rows = None
+        if index_path is not None:
+            # A filtered 0.3+ file still lists every analysed droplet, which
+            # places nothing here; CellBender's loader keeps it in uns.
+            other[_INDEX] = index_path
     else:
         raise ValueError(
             f"Cannot tell which barcode each of CellBender's {n_latent:,} latent "
@@ -641,10 +645,9 @@ def _write_uns(root: Any, handle: h5py.File, latents: _Latents) -> None:
     meta = write_mapping(root["uns"], "cellbender")
     write_scalar(meta, "version", latents.version)
     for key, path in latents.other.items():
+        # A setting stays the one-element array CellBender stores it as,
+        # as its own loader gives it.
         value = np.asarray(handle[path][...])
-        if value.ndim == 1 and value.size == 1:
-            # CellBender wraps each scalar setting in a one-element array.
-            value = value.reshape(())
         if value.ndim == 0:
             item = value.item()
             write_scalar(meta, key, item.decode("utf-8", "replace") if isinstance(item, bytes) else item)

tests/test_cellbender.py

@@ -128,7 +128,7 @@ def test_each_latent_lands_on_its_own_barcode(tmp_path, version, filtered, suffi
     np.testing.assert_allclose(got.var["ambient_expression"], truth.ambient)
     uns = got.uns["cellbender"]
     assert uns["version"] == version
-    assert float(uns["target_false_positive_rate"]) == 0.01
+    assert np.ravel(uns["target_false_positive_rate"]).tolist() == [0.01]
     if version == "0.3":
         assert "features_analyzed_inds" in uns, "metadata stays in uns"
         assert "features_analyzed_inds" not in got.var
@@ -164,6 +164,24 @@ def test_latents_land_right_when_read_in_many_blocks(tmp_path, filtered, monkeyp
         assert np.array_equal(got.layers["cellranger"].toarray(), _raw_counts()[rows])
 
 
+@pytest.mark.parametrize("filtered", [False, True], ids=["full", "filtered"])
+@pytest.mark.parametrize("version", ["0.3", "0.2"])
+def test_uns_holds_what_cellbender_stored_as_its_loader_gives_it(tmp_path, version, filtered):
+    """Checked against real CellBender 0.3.2 output, uns differed from
+    CellBender's own loader twice: one-element settings were unwrapped to
+    scalars, so `uns[...][0]` broke, and a filtered file's
+    barcode_indices_for_latents, which places no rows there, was dropped."""
+    truth = _cellbender(tmp_path, version=version, filtered=filtered)
+    out = tmp_path / "out.h5ad"
+    _ok(truth.path, "-o", out)
+    uns = _read(out).uns["cellbender"]
+    # A scalar in 0.2, a one-element array since.
+    assert np.shape(uns["target_false_positive_rate"]) == (() if version == "0.2" else (1,))
+    # 0.2 drops the index from filtered files; 0.3+ keeps every analysed droplet's.
+    kept = version != "0.2" and filtered
+    assert ("barcode_indices_for_latents" in uns) == kept
+
+
 def test_cellbender_0_2_on_cell_ranger_2_input(tmp_path):
     truth = _cellbender(tmp_path, version="0.2", cellranger_v2=True)
     out = tmp_path / "out.h5ad"