Merge branch 'fix/warning' of https://github.com/scverse/spatialdata-io into fix/warning

Author: Zethson

README.md

@@ -111,8 +111,7 @@ Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and univers
 [link-docs]: https://spatialdata.scverse.org/projects/io/en/latest/
 [link-api]: https://spatialdata.scverse.org/projects/io/en/latest/api.html
 [link-cli]: https://spatialdata.scverse.org/projects/io/en/latest/cli.html
-
-[//]: # (numfocus-fiscal-sponsor-attribution)
+[//]: # "numfocus-fiscal-sponsor-attribution"
 
 spatialdata-io is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
 If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

docs/extensions/typed_returns.py

@@ -11,7 +11,7 @@ def _process_return(lines):
         m = re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line)
         if m:
             # Once this is in scanpydoc, we can use the fancy hover stuff
-            yield f'-{m["param"]} (:class:`~{m["type"]}`)'
+            yield f"-{m['param']} (:class:`~{m['type']}`)"
         else:
             yield line
 

src/spatialdata_io/_constants/_enum.py

@@ -42,7 +42,7 @@ def wrapper(*args: Any, **kwargs: Any) -> "ErrorFormatterABC":
 class ABCEnumMeta(EnumMeta, ABCMeta):
     def __call__(cls, *args: Any, **kwargs: Any) -> Any:
         if getattr(cls, "__error_format__", None) is None:
-            raise TypeError(f"Can't instantiate class `{cls.__name__}` " f"without `__error_format__` class attribute.")
+            raise TypeError(f"Can't instantiate class `{cls.__name__}` without `__error_format__` class attribute.")
         return super().__call__(*args, **kwargs)
 
     def __new__(cls, clsname: str, superclasses: tuple[type], attributedict: dict[str, Any]) -> "ABCEnumMeta":
@@ -59,7 +59,9 @@ class ErrorFormatterABC(ABC):
     @classmethod
     def _format(cls, value: Enum) -> str:
         return cls.__error_format__.format(
-            value, cls.__name__, [m.value for m in cls.__members__.values()]  # type: ignore[attr-defined]
+            value,
+            cls.__name__,
+            [m.value for m in cls.__members__.values()],  # type: ignore[attr-defined]
         )
 
 

src/spatialdata_io/converters/legacy_anndata.py

@@ -113,9 +113,9 @@ def to_legacy_anndata(
         assert len(css) == 1, "The SpatialData object has more than one coordinate system. Please specify one."
         coordinate_system = css[0]
     else:
-        assert (
-            coordinate_system in css
-        ), f"The SpatialData object does not have the coordinate system {coordinate_system}."
+        assert coordinate_system in css, (
+            f"The SpatialData object does not have the coordinate system {coordinate_system}."
+        )
     sdata = sdata.filter_by_coordinate_system(coordinate_system)
 
     if table_name is None:
@@ -288,9 +288,9 @@ def from_legacy_anndata(adata: AnnData) -> SpatialData:
             # construct the spatialdata elements
             if hires is not None:
                 # prepare the hires image
-                assert (
-                    tissue_hires_scalef is not None
-                ), "tissue_hires_scalef is required when an the hires image is present"
+                assert tissue_hires_scalef is not None, (
+                    "tissue_hires_scalef is required when an the hires image is present"
+                )
                 hires_image = Image2DModel.parse(
                     hires, dims=("y", "x", "c"), transformations={f"{dataset_id}_downscaled_hires": Identity()}
                 )
@@ -301,9 +301,9 @@ def from_legacy_anndata(adata: AnnData) -> SpatialData:
                 shapes_transformations[f"{dataset_id}_downscaled_hires"] = scale_hires
             if lowres is not None:
                 # prepare the lowres image
-                assert (
-                    tissue_lowres_scalef is not None
-                ), "tissue_lowres_scalef is required when an the lowres image is present"
+                assert tissue_lowres_scalef is not None, (
+                    "tissue_lowres_scalef is required when an the lowres image is present"
+                )
                 lowres_image = Image2DModel.parse(
                     lowres, dims=("y", "x", "c"), transformations={f"{dataset_id}_downscaled_lowres": Identity()}
                 )

src/spatialdata_io/readers/_utils/_read_10x_h5.py

@@ -84,7 +84,7 @@ def _read_10x_h5(
             if genome not in adata.var["genome"].values:
                 raise ValueError(
                     f"Could not find data corresponding to genome `{genome}` in `{filename}`. "
-                    f'Available genomes are: {list(adata.var["genome"].unique())}.'
+                    f"Available genomes are: {list(adata.var['genome'].unique())}."
                 )
             adata = adata[:, adata.var["genome"] == genome]
         if gex_only:

src/spatialdata_io/readers/dbit.py

@@ -279,10 +279,16 @@ def dbit(
 
     # search for files paths. Gives priority to files matching the pattern found in path.
     anndata_path_checked = _check_path(
-        path=path, path_specific=anndata_path, pattern=patt_h5ad, key=DbitKeys.COUNTS_FILE  # type: ignore
+        path=path,
+        path_specific=anndata_path,
+        pattern=patt_h5ad,
+        key=DbitKeys.COUNTS_FILE,  # type: ignore
     )[0]
     barcode_position_checked = _check_path(
-        path=path, path_specific=barcode_position, pattern=patt_barcode, key=DbitKeys.BARCODE_POSITION  # type: ignore
+        path=path,
+        path_specific=barcode_position,
+        pattern=patt_barcode,
+        key=DbitKeys.BARCODE_POSITION,  # type: ignore
     )[0]
     image_path_checked, hasimage = _check_path(
         path=path,  # type: ignore

src/spatialdata_io/readers/merscope.py

@@ -58,9 +58,9 @@ def _get_file_paths(path: Path, vpt_outputs: Path | str | dict[str, Any] | None)
         ]
         valid_boundaries = [path for path in plausible_boundaries if path.exists()]
 
-        assert (
-            valid_boundaries
-        ), f"Boundary file not found - expected to find one of these files: {', '.join(map(str, plausible_boundaries))}"
+        assert valid_boundaries, (
+            f"Boundary file not found - expected to find one of these files: {', '.join(map(str, plausible_boundaries))}"
+        )
 
         return (
             vpt_outputs / MerscopeKeys.COUNTS_FILE,
@@ -160,9 +160,9 @@ def merscope(
         assert isinstance(image_models_kwargs, dict)
         image_models_kwargs["scale_factors"] = [2, 2, 2, 2]
 
-    assert (
-        backend is None or backend in SUPPORTED_BACKENDS
-    ), f"Backend '{backend} not supported. Should be one of: {', '.join(SUPPORTED_BACKENDS)}"
+    assert backend is None or backend in SUPPORTED_BACKENDS, (
+        f"Backend '{backend} not supported. Should be one of: {', '.join(SUPPORTED_BACKENDS)}"
+    )
 
     path = Path(path).absolute()
     count_path, obs_path, boundaries_path = _get_file_paths(path, vpt_outputs)

src/spatialdata_io/readers/seqfish.py

@@ -200,7 +200,6 @@ def get_transcript_file(roi: str) -> str:
     points = {}
     if load_points:
         for x in rois_str:
-
             # prepare data
             name = f"{os.path.splitext(get_transcript_file(x))[0]}"
             p = pd.read_csv(path / get_transcript_file(x), delimiter=",")

src/spatialdata_io/readers/steinbock.py

@@ -58,8 +58,7 @@ def steinbock(
     labels = {}
     if len(set(samples).difference(set(samples_labels))):
         logger.warning(
-            f"Samples {set(samples).difference(set(samples_labels))} have images but no labels. "
-            "They will be ignored."
+            f"Samples {set(samples).difference(set(samples_labels))} have images but no labels. They will be ignored."
         )
     for sample in samples:
         images[f"{sample}_image"] = _get_images(

src/spatialdata_io/readers/visium_hd.py

@@ -479,9 +479,9 @@ def _load_image(
         if data.shape[-1] == 3:  # HE image in RGB format
             data = data.transpose(2, 0, 1)
         else:
-            assert data.shape[0] == min(
-                data.shape
-            ), "When the image is not in RGB, the first dimension should be the number of channels."
+            assert data.shape[0] == min(data.shape), (
+                "When the image is not in RGB, the first dimension should be the number of channels."
+            )
 
         image = DataArray(data, dims=("c", "y", "x"))
         parsed = Image2DModel.parse(image, scale_factors=scale_factors, rgb=None, **image_models_kwargs)