improve comments; remove old unused param in 10x reader

Author: LucaMarconato

src/spatialdata_io/readers/_utils/_read_10x_h5.py

@@ -69,7 +69,6 @@ def _read_10x_h5(
         - `['gene_ids']`: Gene IDs
         - `['feature_types']`: Feature types
     """
-    start = logger.info(f"reading {filename}")
     filename = Path(filename) if isinstance(filename, str) else filename
     is_present = filename.is_file()
     if not is_present:
@@ -78,7 +77,7 @@ def _read_10x_h5(
         v3 = "/matrix" in f
 
     if v3:
-        adata = _read_v3_10x_h5(filename, start=start)
+        adata = _read_v3_10x_h5(filename)
         if genome:
             if genome not in adata.var["genome"].values:
                 raise ValueError(
@@ -95,7 +94,7 @@ def _read_10x_h5(
     return adata
 
 
-def _read_v3_10x_h5(filename: str | Path, *, start: Any | None = None) -> AnnData:
+def _read_v3_10x_h5(filename: str | Path) -> AnnData:
     """Read hdf5 file from Cell Ranger v3 or later versions."""
     with h5py.File(str(filename), "r") as f:
         try:

src/spatialdata_io/readers/xenium.py

@@ -72,7 +72,7 @@ def xenium(
     image_models_kwargs: Mapping[str, Any] = MappingProxyType({}),
     labels_models_kwargs: Mapping[str, Any] = MappingProxyType({}),
 ) -> SpatialData:
-    """Read a *10X Genomics Xenium* dataset into a SpatialData object.
+    """Read a *10x Genomics Xenium* dataset into a SpatialData object.
 
     This function reads the following files:
 
@@ -87,7 +87,8 @@ def xenium(
 
     .. seealso::
 
-        - `10X Genomics Xenium file format  <https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/analysis/xoa-output-at-a-glance>`_.
+        - `10x Genomics Xenium file format <https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/analysis/xoa-output-at-a-glance>`_.
+        - `Release notes for the Xenium format <https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/release-notes/release-notes-for-xoa>`_.
 
     Parameters
     ----------
@@ -490,7 +491,7 @@ def _get_labels_and_indices_mapping(
                         f"{expected_label_index}."
                     )
             else:
-                labels_positional_indices = z["polygon_sets"][mask_index]["cell_index"][...]
+                labels_positional_indices = z["polygon_sets"][f"{mask_index}"]["cell_index"][...]
                 if not np.array_equal(labels_positional_indices, np.arange(len(labels_positional_indices))):
                     raise ValueError(
                         "The positional indices of the labels do not match the expected range. Please report this "