[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

docs/conf.py

@@ -9,6 +9,7 @@
 from datetime import datetime
 from importlib.metadata import metadata
 from pathlib import Path
+
 import spatialdata_io.experimental
 
 _ = spatialdata_io.experimental

src/spatialdata_io/__main__.py

@@ -29,8 +29,7 @@
 
 @click.group()
 def cli() -> None:
-    """
-    Convert standard technology data formats to SpatialData object.
+    """Convert standard technology data formats to SpatialData object.
 
     Usage:
 

src/spatialdata_io/_docs.py

@@ -5,7 +5,7 @@
 from typing import Any
 
 
-def inject_docs(**kwargs: Any) -> Callable[..., Any]:  # noqa: D103
+def inject_docs(**kwargs: Any) -> Callable[..., Any]:
     # taken from scanpy
     def decorator(obj: Any) -> Any:
         obj.__doc__ = dedent(obj.__doc__).format(**kwargs)

src/spatialdata_io/_utils.py

@@ -11,8 +11,7 @@
 # these two functions should be removed and imported from spatialdata._utils once the multi_table branch, which
 # introduces them, is merged
 def deprecation_alias(**aliases: str) -> Callable[[Callable[..., RT]], Callable[..., RT]]:
-    """
-    Decorate a function to warn user of use of arguments set for deprecation.
+    """Decorate a function to warn user of use of arguments set for deprecation.
 
     Parameters
     ----------

src/spatialdata_io/converters/generic_to_zarr.py

@@ -21,8 +21,7 @@ def generic_to_zarr(
     data_axes: str | None = None,
     coordinate_system: str | None = None,
 ) -> None:
-    """
-    Read generic data from an input file and save it as a SpatialData zarr store.
+    """Read generic data from an input file and save it as a SpatialData zarr store.
 
     Parameters
     ----------

src/spatialdata_io/converters/legacy_anndata.py

@@ -22,8 +22,7 @@ def to_legacy_anndata(
     table_name: str | None = None,
     include_images: bool = False,
 ) -> AnnData:
-    """
-    Convert a SpatialData object to a (legacy) spatial AnnData object.
+    """Convert a SpatialData object to a (legacy) spatial AnnData object.
 
     This is useful for using packages expecting spatial information in AnnData, for example Scanpy and older versions
     of Squidpy. Using this format for any new package is not recommended.
@@ -219,8 +218,7 @@ def to_legacy_anndata(
 
 
 def from_legacy_anndata(adata: AnnData) -> SpatialData:
-    """
-    Convert (legacy) spatial AnnData object to SpatialData object.
+    """Convert (legacy) spatial AnnData object to SpatialData object.
 
     This is useful for parsing a (legacy) spatial AnnData object, for example the ones produced by Scanpy and older
     version of Squidpy.

src/spatialdata_io/readers/_utils/_read_10x_h5.py

@@ -44,8 +44,7 @@ def _read_10x_h5(
     genome: str | None = None,
     gex_only: bool = True,
 ) -> AnnData:
-    """
-    Read 10x-Genomics-formatted hdf5 file.
+    """Read 10x-Genomics-formatted hdf5 file.
 
     Parameters
     ----------

src/spatialdata_io/readers/codex.py

@@ -27,8 +27,7 @@ def codex(
     fcs: bool = True,
     imread_kwargs: Mapping[str, Any] = MappingProxyType({}),
 ) -> SpatialData:
-    """
-    Read *CODEX* formatted dataset.
+    """Read *CODEX* formatted dataset.
 
     This function reads the following files:
 

src/spatialdata_io/readers/cosmx.py

@@ -35,8 +35,7 @@ def cosmx(
     imread_kwargs: Mapping[str, Any] = MappingProxyType({}),
     image_models_kwargs: Mapping[str, Any] = MappingProxyType({}),
 ) -> SpatialData:
-    """
-    Read *Cosmx Nanostring* data.
+    """Read *Cosmx Nanostring* data.
 
     This function reads the following files:
 

src/spatialdata_io/readers/curio.py

@@ -19,8 +19,7 @@
 def curio(
     path: str | Path,
 ) -> SpatialData:
-    """
-    Read *Curio* formatted dataset.
+    """Read *Curio* formatted dataset.
 
     This function reads the following files:
 
@@ -73,7 +72,7 @@ def curio(
     categories = metrics[CurioKeys.CATEGORY].unique()
     for cat in categories:
         df = metrics.loc[metrics[CurioKeys.CATEGORY] == cat]
-        adata.uns[cat] = dict(zip(df.iloc[:, 0], df.iloc[:, 1]))
+        adata.uns[cat] = dict(zip(df.iloc[:, 0], df.iloc[:, 1], strict=False))
     adata.uns[CurioKeys.TOP_CLUSTER_DEFINING_FEATURES] = var_features_clusters
 
     # adding Moran's I information in adata.var, for the variable for which it is available