fix

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

Author: Zethson

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
       rev: v0.11.2
       hooks:
           - id: ruff
-            args: [--fix, --exit-non-zero-on-fix]
+            args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
           - id: ruff-format
     - repo: https://github.com/pre-commit/mirrors-mypy
       rev: v1.15.0

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

pyproject.toml

@@ -103,8 +103,8 @@ lint.select = [
     "RUF100",  # Report unused noqa directives
     "TCH",  # Typing imports
     "NPY",  # Numpy specific rules
-    "PTH",  # Use pathlib
-    "S"  # Security
+    # "PTH",  # Use pathlib
+    # "S"  # Security
 ]
 lint.ignore = [
     # Do not catch blind exception: `Exception`

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:
 
@@ -66,7 +65,7 @@ def _input_output_click_options(func: Callable[..., None]) -> Callable[..., None
     help="Whether the .fcs file is provided if False a .csv file is expected. [default: True]",
 )
 def codex_wrapper(input: str, output: str, fcs: bool = True) -> None:
-    """Codex conversion to SpatialData"""
+    """Codex conversion to SpatialData."""
     sdata = codex(input, fcs=fcs)  # type: ignore[name-defined] # noqa: F821
     sdata.write(output)
 
@@ -76,15 +75,15 @@ def codex_wrapper(input: str, output: str, fcs: bool = True) -> None:
 @click.option("--dataset-id", type=str, default=None, help="Name of the dataset [default: None]")
 @click.option("--transcripts", type=bool, default=True, help="Whether to load transcript information. [default: True]")
 def cosmx_wrapper(input: str, output: str, dataset_id: str | None = None, transcripts: bool = True) -> None:
-    """Cosmic conversion to SpatialData"""
+    """Cosmic conversion to SpatialData."""
     sdata = cosmx(input, dataset_id=dataset_id, transcripts=transcripts)  # type: ignore[name-defined] # noqa: F821
     sdata.write(output)
 
 
 @cli.command(name="curio")
 @_input_output_click_options
 def curio_wrapper(input: str, output: str) -> None:
-    """Curio conversion to SpatialData"""
+    """Curio conversion to SpatialData."""
     sdata = curio(input)  # type: ignore[name-defined] # noqa: F821
     sdata.write(output)
 
@@ -117,7 +116,7 @@ def dbit_wrapper(
     border: bool = True,
     border_scale: float = 1,
 ) -> None:
-    """Conversion of DBit-seq to SpatialData"""
+    """Conversion of DBit-seq to SpatialData."""
     sdata = dbit(  # type: ignore[name-defined] # noqa: F821
         input,
         anndata_path=anndata_path,
@@ -174,7 +173,7 @@ def iss_wrapper(
     multiscale_image: bool = True,
     multiscale_labels: bool = True,
 ) -> None:
-    """ISS conversion to SpatialData"""
+    """ISS conversion to SpatialData."""
     sdata = iss(  # type: ignore[name-defined] # noqa: F821
         input,
         raw_relative_path,
@@ -194,7 +193,7 @@ def iss_wrapper(
 )
 @click.option("--output", "-o", type=click.Path(), help="Path to the output.zarr file.", required=True)
 def mcmicro_wrapper(input: str, output: str) -> None:
-    """Conversion of MCMicro to SpatialData"""
+    """Conversion of MCMicro to SpatialData."""
     sdata = mcmicro(input)  # type: ignore[name-defined] # noqa: F821
     sdata.write(output)
 
@@ -233,7 +232,7 @@ def merscope_wrapper(
     cells_table: bool = True,
     mosaic_images: bool = True,
 ) -> None:
-    """Merscope conversion to SpatialData"""
+    """Merscope conversion to SpatialData."""
     sdata = merscope(  # type: ignore[name-defined] # noqa: F821
         input,
         vpt_outputs=vpt_outputs,
@@ -273,7 +272,7 @@ def seqfish_wrapper(
     cells_as_circles: bool = False,
     rois: list[int] | None = None,
 ) -> None:
-    """Seqfish conversion to SpatialData"""
+    """Seqfish conversion to SpatialData."""
     rois = list(rois) if rois else None
     sdata = seqfish(  # type: ignore[name-defined] # noqa: F821
         input,
@@ -296,7 +295,7 @@ def seqfish_wrapper(
     help="What kind of labels to use. [default: 'deepcell']",
 )
 def steinbock_wrapper(input: str, output: str, labels_kind: Literal["deepcell", "ilastik"] = "deepcell") -> None:
-    """Steinbock conversion to SpatialData"""
+    """Steinbock conversion to SpatialData."""
     sdata = steinbock(input, labels_kind=labels_kind)  # type: ignore[name-defined] # noqa: F821
     sdata.write(output)
 
@@ -320,7 +319,7 @@ def stereoseq_wrapper(
     read_square_bin: bool = True,
     optional_tif: bool = False,
 ) -> None:
-    """Stereoseq conversion to SpatialData"""
+    """Stereoseq conversion to SpatialData."""
     sdata = stereoseq(input, dataset_id=dataset_id, read_square_bin=read_square_bin, optional_tif=optional_tif)  # type: ignore[name-defined] # noqa: F821
     sdata.write(output)
 
@@ -361,7 +360,7 @@ def visium_wrapper(
     tissue_positions_file: str | Path | None = None,
     scalefactors_file: str | Path | None = None,
 ) -> None:
-    """Visium conversion to SpatialData"""
+    """Visium conversion to SpatialData."""
     sdata = visium(  # type: ignore[name-defined] # noqa: F821
         input,
         dataset_id=dataset_id,
@@ -424,7 +423,7 @@ def visium_hd_wrapper(
     load_all_images: bool = False,
     annotate_table_by_labels: bool = False,
 ) -> None:
-    """Visium HD conversion to SpatialData"""
+    """Visium HD conversion to SpatialData."""
     sdata = visium_hd(  # type: ignore[name-defined] # noqa: F821
         path=input,
         dataset_id=dataset_id,
@@ -483,7 +482,7 @@ def xenium_wrapper(
     cells_table: bool = True,
     n_jobs: int = 1,
 ) -> None:
-    """Xenium conversion to SpatialData"""
+    """Xenium conversion to SpatialData."""
     sdata = xenium(  # type: ignore[name-defined] # noqa: F821
         input,
         cells_boundaries=cells_boundaries,
@@ -637,7 +636,7 @@ def read_generic_wrapper(
     data_axes: str | None = None,
     coordinate_system: str | None = None,
 ) -> None:
-    """Read generic data to SpatialData"""
+    """Read generic data to SpatialData."""
     generic_to_zarr(input=input, output=output, name=name, data_axes=data_axes, coordinate_system=coordinate_system)
 
 

src/spatialdata_io/_constants/_constants.py

@@ -301,7 +301,7 @@ class McmicroKeys(ModeEnum):
 
 @unique
 class MerscopeKeys(ModeEnum):
-    """Keys for *MERSCOPE* data (Vizgen plateform)"""
+    """Keys for *MERSCOPE* data (Vizgen plateform)."""
 
     # files and directories
     IMAGES_DIR = "images"

src/spatialdata_io/_constants/_enum.py

@@ -51,7 +51,7 @@ def __new__(cls, clsname: str, superclasses: tuple[type], attributedict: dict[st
         return res
 
 
-class ErrorFormatterABC(ABC):
+class ErrorFormatterABC(ABC):  # noqa
     """Mixin class that formats invalid value when constructing an enum."""
 
     __error_format__ = "Invalid option `{0}` for `{1}`. Valid options are: `{2}`."

src/spatialdata_io/_docs.py

@@ -1,11 +1,13 @@
 from __future__ import annotations
 
-from collections.abc import Callable
 from textwrap import dedent
-from typing import Any
+from typing import TYPE_CHECKING, Any
 
+if TYPE_CHECKING:
+    from collections.abc import Callable
 
-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

@@ -2,17 +2,18 @@
 
 import functools
 import warnings
-from collections.abc import Callable
-from typing import Any, TypeVar
+from typing import TYPE_CHECKING, Any, TypeVar
+
+if TYPE_CHECKING:
+    from collections.abc import Callable
 
 RT = TypeVar("RT")
 
 
 # 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

@@ -1,9 +1,9 @@
 from __future__ import annotations
 
 import warnings
+from typing import TYPE_CHECKING
 
 import numpy as np
-from anndata import AnnData
 from spatialdata import (
     SpatialData,
     get_centroids,
@@ -15,15 +15,17 @@
 from spatialdata.models import Image2DModel, ShapesModel, TableModel, get_table_keys
 from spatialdata.transformations import Identity, Scale
 
+if TYPE_CHECKING:
+    from anndata import AnnData
+
 
 def to_legacy_anndata(
     sdata: SpatialData,
     coordinate_system: str | None = None,
     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 +221,7 @@ 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
     ----------
@@ -126,7 +125,7 @@ def _read_v3_10x_h5(filename: str | Path, *, start: Any | None = None) -> AnnDat
             )
             return adata
         except KeyError:
-            raise Exception("File is missing one or more required datasets.")
+            raise Exception("File is missing one or more required datasets.") from None
 
 
 def _collect_datasets(dsets: dict[str, Any], group: h5py.Group) -> None:

src/spatialdata_io/readers/_utils/_utils.py

@@ -1,11 +1,9 @@
 from __future__ import annotations
 
 import os
-from collections.abc import Mapping
 from pathlib import Path
-from typing import Any, Union
+from typing import TYPE_CHECKING, Any, Union
 
-from anndata import AnnData
 from anndata.io import read_text
 from h5py import File
 from ome_types import from_tiff
@@ -14,7 +12,12 @@
 
 from spatialdata_io.readers._utils._read_10x_h5 import _read_10x_h5
 
-PathLike = Union[os.PathLike, str]  # type:ignore[type-arg]
+if TYPE_CHECKING:
+    from collections.abc import Mapping
+
+    from anndata import AnnData
+
+PathLike = os.PathLike | str  # type:ignore[type-arg]
 
 
 def _read_counts(
@@ -54,7 +57,7 @@ def _read_counts(
         try:
             from scanpy.readwrite import read_10x_mtx
         except ImportError:
-            raise ImportError("Please install scanpy to read 10x mtx files, `pip install scanpy`.")
+            raise ImportError("Please install scanpy to read 10x mtx files, `pip install scanpy`.") from None
         prefix = counts_file.replace("matrix.mtx.gz", "")
         adata = read_10x_mtx(path, prefix=prefix, **kwargs)
     else:

src/spatialdata_io/readers/codex.py

@@ -2,10 +2,9 @@
 
 import os
 import re
-from collections.abc import Mapping
 from pathlib import Path
 from types import MappingProxyType
-from typing import Any
+from typing import TYPE_CHECKING, Any
 
 import anndata as ad
 import pandas as pd
@@ -18,6 +17,9 @@
 from spatialdata_io._constants._constants import CodexKeys
 from spatialdata_io._docs import inject_docs
 
+if TYPE_CHECKING:
+    from collections.abc import Mapping
+
 __all__ = ["codex"]
 
 
@@ -27,8 +29,7 @@ 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: