Add spatialdata-io version and reader name to attrs

src/spatialdata_io/readers/_utils/_utils.py

@@ -17,6 +17,7 @@
     from collections.abc import Mapping
 
     from anndata import AnnData
+    from spatialdata import SpatialData
 
 PathLike = os.PathLike | str  # type:ignore[type-arg]
 
@@ -109,6 +110,15 @@ def parse_channels(path: Path) -> list[str]:
     return names
 
 
+def _set_reader_metadata(sdata: SpatialData, reader: str) -> SpatialData:
+    """Set spatialdata-io provenance metadata on a SpatialData object."""
+    from spatialdata_io import __version__
+
+    sdata.attrs["spatialdata_io_software_version"] = __version__
+    sdata.attrs["spatialdata_io_reader"] = reader
+    return sdata
+
+
 def parse_physical_size(path: Path | None = None, ome_pixels: Pixels | None = None) -> float:
     """Parse physical size from OME-TIFF to micrometer."""
     pixels = ome_pixels or from_tiff(path).images[0].pixels

src/spatialdata_io/readers/codex.py

@@ -16,6 +16,7 @@
 
 from spatialdata_io._constants._constants import CodexKeys
 from spatialdata_io._docs import inject_docs
+from spatialdata_io.readers._utils._utils import _set_reader_metadata
 
 if TYPE_CHECKING:
     from collections.abc import Mapping
@@ -89,7 +90,7 @@ def codex(
         logger.warning("Cannot find .tif file. Will build spatialdata with shapes and table only.")
         sdata = SpatialData(shapes={str(region): shapes}, table=table)
 
-    return sdata
+    return _set_reader_metadata(sdata, "codex")
 
 
 def _codex_df_to_anndata(df: pd.DataFrame) -> ad.AnnData:

src/spatialdata_io/readers/cosmx.py

@@ -21,6 +21,7 @@
 
 from spatialdata_io._constants._constants import CosmxKeys
 from spatialdata_io._docs import inject_docs
+from spatialdata_io.readers._utils._utils import _set_reader_metadata
 
 if TYPE_CHECKING:
     from collections.abc import Mapping
@@ -289,4 +290,5 @@ def cosmx(
     #             logg.warning(f"FOV `{str(fov)}` does not exist, skipping it.")
     #             continue
 
-    return SpatialData(images=images, labels=labels, points=points, tables={"table": table})
+    sdata = SpatialData(images=images, labels=labels, points=points, tables={"table": table})
+    return _set_reader_metadata(sdata, "cosmx")

src/spatialdata_io/readers/curio.py

@@ -11,6 +11,7 @@
 
 from spatialdata_io._constants._constants import CurioKeys
 from spatialdata_io._docs import inject_docs
+from spatialdata_io.readers._utils._utils import _set_reader_metadata
 
 __all__ = ["curio"]
 
@@ -97,4 +98,5 @@ def curio(
 
     shapes = ShapesModel.parse(xy, geometry=0, radius=10, index=adata.obs[CurioKeys.INSTANCE_KEY])
 
-    return SpatialData(table=table, shapes={CurioKeys.REGION.value: shapes})
+    sdata = SpatialData(table=table, shapes={CurioKeys.REGION.value: shapes})
+    return _set_reader_metadata(sdata, "curio")

src/spatialdata_io/readers/dbit.py

@@ -18,6 +18,7 @@
 
 from spatialdata_io._constants._constants import DbitKeys
 from spatialdata_io._docs import inject_docs
+from spatialdata_io.readers._utils._utils import _set_reader_metadata
 
 if TYPE_CHECKING:
     from numpy.typing import NDArray
@@ -363,4 +364,4 @@ def dbit(
     if hasimage:
         imgname = dataset_id + "_image"
         sdata.images[imgname] = image_sd
-    return sdata
+    return _set_reader_metadata(sdata, "dbit")

src/spatialdata_io/readers/iss.py

@@ -12,6 +12,7 @@
 from xarray import DataArray
 
 from spatialdata_io._docs import inject_docs
+from spatialdata_io.readers._utils._utils import _set_reader_metadata
 
 if TYPE_CHECKING:
     from collections.abc import Mapping
@@ -106,8 +107,9 @@ def iss(
         **image_models_kwargs,
     )
 
-    return SpatialData(
+    sdata = SpatialData(
         images={f"{dataset_id}_raw_image": raw_image_parsed},
         labels={REGION: labels_image_parsed},
         table=table,
     )
+    return _set_reader_metadata(sdata, "iss")

src/spatialdata_io/readers/macsima.py

@@ -21,6 +21,7 @@
 
 from spatialdata_io._constants._enum import ModeEnum
 from spatialdata_io.readers._utils._utils import (
+    _set_reader_metadata,
     calc_scale_factors,
     parse_channels,
     parse_physical_size,
@@ -745,7 +746,7 @@ def create_sdata(
         sdata.images[f"{filtered_name}_nuclei_image"] = nuclei_image_element
         sdata.tables[f"{filtered_name}_nuclei_table"] = table_nuclei
 
-    return sdata
+    return _set_reader_metadata(sdata, "macsima")
 
 
 def create_table(mci: MultiChannelImage) -> ad.AnnData:

src/spatialdata_io/readers/mcmicro.py

@@ -17,6 +17,7 @@
 from yaml.loader import SafeLoader
 
 from spatialdata_io._constants._constants import McmicroKeys
+from spatialdata_io.readers._utils._utils import _set_reader_metadata
 
 if TYPE_CHECKING:
     from collections.abc import Mapping
@@ -189,7 +190,8 @@ def mcmicro(
 
     tables_dict = _get_tables(path, markers, tma)
 
-    return SpatialData(images=images, labels=labels, tables=tables_dict)
+    sdata = SpatialData(images=images, labels=labels, tables=tables_dict)
+    return _set_reader_metadata(sdata, "mcmicro")
 
 
 def _load_params(path: Path) -> Any:

src/spatialdata_io/readers/merscope.py

@@ -22,6 +22,7 @@
 
 from spatialdata_io._constants._constants import MerscopeKeys
 from spatialdata_io._docs import inject_docs
+from spatialdata_io.readers._utils._utils import _set_reader_metadata
 
 if TYPE_CHECKING:
     from collections.abc import Callable, Mapping
@@ -227,7 +228,8 @@ def merscope(
                 f"At least one of the following files does not exist: {count_path}, {obs_path}. The table is not loaded."
             )
 
-    return SpatialData(shapes=shapes, points=points, images=images, tables=tables)
+    sdata = SpatialData(shapes=shapes, points=points, images=images, tables=tables)
+    return _set_reader_metadata(sdata, "merscope")
 
 
 def _get_reader(backend: str | None) -> Callable:  # type: ignore[type-arg]

src/spatialdata_io/readers/seqfish.py

@@ -28,6 +28,7 @@
 
 from spatialdata_io._constants._constants import SeqfishKeys as SK
 from spatialdata_io._docs import inject_docs
+from spatialdata_io.readers._utils._utils import _set_reader_metadata
 
 if TYPE_CHECKING:
     from collections.abc import Mapping
@@ -270,7 +271,7 @@ def _get_scale_factors(raster_path: Path, raster_models_scale_factors: list[int]
 
     sdata = SpatialData(images=images, labels=labels, points=points, tables=tables, shapes=shapes)
 
-    return sdata
+    return _set_reader_metadata(sdata, "seqfish")
 
 
 def _is_ome_tiff_multiscale(ome_tiff_file: Path) -> bool:

src/spatialdata_io/readers/steinbock.py

@@ -13,6 +13,7 @@
 from spatialdata.transformations.transformations import Identity
 
 from spatialdata_io._constants._constants import SteinbockKeys
+from spatialdata_io.readers._utils._utils import _set_reader_metadata
 
 if TYPE_CHECKING:
     from collections.abc import Mapping
@@ -101,7 +102,8 @@ def steinbock(
         raise ValueError("Samples in table and images are inconsistent, please check.")
     table = TableModel.parse(adata, region=regions.unique().tolist(), region_key="region", instance_key="cell_id")
 
-    return SpatialData(images=images, labels=labels, tables={"table": table})
+    sdata = SpatialData(images=images, labels=labels, tables={"table": table})
+    return _set_reader_metadata(sdata, "steinbock")
 
 
 def _get_images(

src/spatialdata_io/readers/stereoseq.py

@@ -20,7 +20,7 @@
 
 from spatialdata_io._constants._constants import StereoseqKeys as SK
 from spatialdata_io._docs import inject_docs
-from spatialdata_io.readers._utils._utils import _initialize_raster_models_kwargs
+from spatialdata_io.readers._utils._utils import _initialize_raster_models_kwargs, _set_reader_metadata
 
 if TYPE_CHECKING:
     from collections.abc import Mapping
@@ -339,4 +339,4 @@ def stereoseq(
         images[Path(cell_mask_name).stem] = masks
 
     sdata = SpatialData(images=images, tables=tables, shapes=shapes, points=points)
-    return sdata
+    return _set_reader_metadata(sdata, "stereoseq")

src/spatialdata_io/readers/visium.py

@@ -19,7 +19,7 @@
 
 from spatialdata_io._constants._constants import VisiumKeys
 from spatialdata_io._docs import inject_docs
-from spatialdata_io.readers._utils._utils import _read_counts
+from spatialdata_io.readers._utils._utils import _read_counts, _set_reader_metadata
 
 if TYPE_CHECKING:
     from collections.abc import Mapping
@@ -253,7 +253,8 @@ def visium(
             rgb=None,
         )
 
-    return SpatialData(images=images, shapes=shapes, tables={"table": table})
+    sdata = SpatialData(images=images, shapes=shapes, tables={"table": table})
+    return _set_reader_metadata(sdata, "visium")
 
 
 def _read_image(image_file: Path, imread_kwargs: dict[str, Any]) -> Any:

src/spatialdata_io/readers/visium_hd.py

@@ -31,6 +31,7 @@
 
 from spatialdata_io._constants._constants import VisiumHDKeys
 from spatialdata_io._docs import inject_docs
+from spatialdata_io.readers._utils._utils import _set_reader_metadata
 
 if TYPE_CHECKING:
     from collections.abc import Mapping
@@ -576,7 +577,7 @@ def _get_bins(path_bins: Path) -> list[str]:
                 sdata=sdata, table_name=bin_size_str, rasterized_labels_name=labels_name
             )
 
-    return sdata
+    return _set_reader_metadata(sdata, "visium_hd")
 
 
 def _infer_dataset_id(path: Path) -> str:

src/spatialdata_io/readers/xenium.py

@@ -39,7 +39,7 @@
 from spatialdata_io._docs import inject_docs
 from spatialdata_io._utils import deprecation_alias, zarr_open
 from spatialdata_io.readers._utils._read_10x_h5 import _read_10x_h5
-from spatialdata_io.readers._utils._utils import _initialize_raster_models_kwargs
+from spatialdata_io.readers._utils._utils import _initialize_raster_models_kwargs, _set_reader_metadata
 
 if TYPE_CHECKING:
     from collections.abc import Mapping
@@ -400,7 +400,7 @@ def filter(self, record: logging.LogRecord) -> bool:
         for key, value in extra_images.items():
             sdata.images[key] = value
 
-    return sdata
+    return _set_reader_metadata(sdata, "xenium")
 
 
 def _decode_cell_id_column(cell_id_column: pd.Series) -> pd.Series: