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xenium code cleanup
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src/spatialdata_io/readers/xenium.py

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -221,7 +221,7 @@ def xenium(
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222222
if version is not None and version >= packaging.version.parse("2.0.0") and table is not None:
223223
assert cells_zarr is not None
224-
cell_summary_table = _get_cells_metadata_table_from_zarr(cells_zarr, specs, cells_zarr_cell_id_str)
224+
cell_summary_table = _get_cells_metadata_table_from_zarr(cells_zarr, cells_zarr_cell_id_str)
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try:
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_assert_arrays_equal_sampled(
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cell_summary_table[XeniumKeys.CELL_ID].values, table.obs[XeniumKeys.CELL_ID].values
@@ -515,7 +515,7 @@ def _get_labels_and_indices_mapping(
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mask_index: int,
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labels_name: str,
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cells_zarr: zarr.Group,
518-
cell_id_str: ArrayLike,
518+
cell_id_str: ArrayLike | None,
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labels_models_kwargs: Mapping[str, Any] = MappingProxyType({}),
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) -> tuple[GeoDataFrame, pd.DataFrame | None]:
521521
if mask_index not in [0, 1]:
@@ -572,7 +572,6 @@ def _get_labels_and_indices_mapping(
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@inject_docs(xx=XeniumKeys)
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def _get_cells_metadata_table_from_zarr(
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cells_zarr: zarr.Group,
575-
specs: dict[str, Any],
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cell_id_str: ArrayLike,
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) -> AnnData:
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"""Read cells metadata from ``{xx.CELLS_ZARR}``.

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