update pre-comit (#698)

scverse · Jun 4, 2023 · 4530150 · 4530150
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -23,10 +23,10 @@ jobs:
                 python: [3.9, "3.10"]
                 os: [ubuntu-latest]
                 include:
-                    - python: 3.8
-                      os: macos-latest
                     - python: 3.9
                       os: macos-latest
+                    - python: "3.10"
+                      os: macos-latest
         env:
             OS: ${{ matrix.os }}
             PYTHON: ${{ matrix.python }}

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.2.0
+      rev: v1.3.0
       hooks:
           - id: mypy
             additional_dependencies: [numpy, pandas, types-requests]
@@ -56,7 +56,7 @@ repos:
           - id: blacken-docs
     - repo: https://github.com/charliermarsh/ruff-pre-commit
       # Ruff version.
-      rev: v0.0.265
+      rev: v0.0.270
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

diff --git a/docs/source/_ext/typed_returns.py b/docs/source/_ext/typed_returns.py
@@ -15,9 +15,9 @@ def _process_return(lines: Iterable[str]) -> Iterator[str]:
             yield line
 
 
-def _parse_returns_section(self: NumpyDocstring, section: str) -> List[str]:
+def _parse_returns_section(self: NumpyDocstring, section: str) -> list[str]:
     lines_raw = list(_process_return(self._dedent(self._consume_to_next_section())))
-    lines: List[str] = self._format_block(":returns: ", lines_raw)
+    lines: list[str] = self._format_block(":returns: ", lines_raw)
     if lines and lines[-1]:
         lines.append("")
     return lines

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -1,6 +1,6 @@
 Installation
 ============
-Squidpy requires Python version >= 3.8 to run.
+Squidpy requires Python version >= 9 to run.
 
 PyPI
 ----

diff --git a/docs/source/utils.py b/docs/source/utils.py
@@ -55,7 +55,7 @@ def fetch_local(repo_path: Union[str, Path]) -> None:
 
 
 class MaybeMiniGallery(MiniGallery):
-    def run(self) -> List[str]:
+    def run(self) -> list[str]:
         config = self.state.document.settings.env.config
         backreferences_dir = config.sphinx_gallery_conf["backreferences_dir"]
         obj_list = self.arguments[0].split()
@@ -75,7 +75,7 @@ def run(self) -> List[str]:
             return []
 
 
-def _get_thumbnails(root: Union[str, Path]) -> Dict[str, str]:
+def _get_thumbnails(root: Union[str, Path]) -> dict[str, str]:
     res = {}
     root = Path(root)
     thumb_path = Path(__file__).parent.parent.parent / "docs" / "source"

diff --git a/pyproject.toml b/pyproject.toml
@@ -184,9 +184,7 @@ target-version = "py38"
     "squidpy/pl/_interactive/_widgets.py"= ["D"]
     ".scripts/ci/download_data.py"= ["D","B"]
     # "squidpy/*.py"= ["RST303"]
-[tool.ruff.pyupgrade]
-# Preserve types, even if a file imports `from __future__ import annotations`.
-keep-runtime-typing = true
+
 [tool.ruff.flake8-tidy-imports]
 # Disallow all relative imports.
 ban-relative-imports = "all"
diff --git a/requirements.txt b/requirements.txt
@@ -15,7 +15,7 @@ omnipath @ git+https://github.com/saezlab/omnipath@master
 pandas>=1.5.0
 Pillow>=8.0.0
 scanpy>=1.9.3
-scikit-image>=0.19
+scikit-image>=0.19,<=0.20 # due to https://github.com/scikit-image/scikit-image/issues/6850 breaks rescale ufunc
 scikit-learn>=0.24.0
 statsmodels>=0.12.0
 tifffile!=2022.4.22  # https://github.com/scverse/squidpy/issues/526

diff --git a/setup.py b/setup.py
@@ -55,7 +55,6 @@
         "Operating System :: MacOS :: MacOS X",
         "Typing :: Typed",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Environment :: Console",

diff --git a/squidpy/__init__.py b/squidpy/__init__.py
@@ -1,3 +1,5 @@
+from importlib.metadata import version
+
 from packaging.version import parse
 
 from squidpy import datasets, gr, im, pl, read, tl
@@ -11,11 +13,6 @@
 )
 __version__ = "1.2.3"
 
-try:
-    from importlib_metadata import version  # Python < 3.8
-except ImportError:
-    from importlib.metadata import version  # Python = 3.8
-
 
 try:
     __full_version__ = parse(version(__name__))

diff --git a/squidpy/_constants/_pkg_constants.py b/squidpy/_constants/_pkg_constants.py
@@ -21,12 +21,12 @@ def __get__(self, obj: Any, owner: Any) -> str:
 class Key:
     class img:
         @classmethod
-        def segment(cls, backend: Union[str, SegmentationBackend], layer_added: Optional[str] = None) -> str:
+        def segment(cls, backend: str | SegmentationBackend, layer_added: str | None = None) -> str:
             return f"segmented_{SegmentationBackend(backend).s}" if layer_added is None else layer_added
 
         @classmethod
         def process(
-            cls, method: Union[str, Processing, Callable[[Any], Any]], img_id: str, layer_added: Optional[str] = None
+            cls, method: str | Processing | Callable[[Any], Any], img_id: str, layer_added: str | None = None
         ) -> str:
             if layer_added is not None:
                 return layer_added
@@ -91,11 +91,11 @@ def size_key(cls) -> str:
             return "spot_diameter_fullres"
 
         @classmethod
-        def spatial_neighs(cls, value: Optional[str] = None) -> str:
+        def spatial_neighs(cls, value: str | None = None) -> str:
             return f"{Key.obsm.spatial}_neighbors" if value is None else f"{value}_neighbors"
 
         @classmethod
-        def ligrec(cls, cluster: str, value: Optional[str] = None) -> str:
+        def ligrec(cls, cluster: str, value: str | None = None) -> str:
             return f"{cluster}_ligrec" if value is None else value
 
         @classmethod
@@ -127,7 +127,7 @@ def spot_diameter(
             cls,
             adata: AnnData,
             spatial_key: str,
-            library_id: Optional[str] = None,
+            library_id: str | None = None,
             spot_diameter_key: str = "spot_diameter_fullres",
         ) -> float:
             try:
@@ -174,7 +174,7 @@ def _sort_haystack(
             adata: AnnData,
             spatial_key: str,
             library_id: Sequence[str] | str | None = None,
-            sub_key: Optional[str] = None,
+            sub_key: str | None = None,
         ) -> Sequence[str] | None:
             if spatial_key not in adata.uns:
                 raise KeyError(f"Spatial key {spatial_key!r} not found in `adata.uns`.")
@@ -195,9 +195,9 @@ def _sort_haystack(
 
     class obsp:
         @classmethod
-        def spatial_dist(cls, value: Optional[str] = None) -> str:
+        def spatial_dist(cls, value: str | None = None) -> str:
             return f"{Key.obsm.spatial}_distances" if value is None else f"{value}_distances"
 
         @classmethod
-        def spatial_conn(cls, value: Optional[str] = None) -> str:
+        def spatial_conn(cls, value: str | None = None) -> str:
             return f"{Key.obsm.spatial}_connectivities" if value is None else f"{value}_connectivities"
diff --git a/squidpy/_constants/_utils.py b/squidpy/_constants/_utils.py
@@ -1,10 +1,12 @@
+from __future__ import annotations
+
 from abc import ABC, ABCMeta
 from enum import Enum, EnumMeta
 from functools import wraps
-from typing import Any, Callable, Mapping, Tuple, Type
+from typing import Any, Callable, Mapping, Tuple
 
 
-def _pretty_raise_enum(cls: Type["ModeEnum"], fun: Callable[..., Any]) -> Callable[..., Any]:
+def _pretty_raise_enum(cls: type[ModeEnum], fun: Callable[..., Any]) -> Callable[..., Any]:
     @wraps(fun)
     def wrapper(*args: Any, **kwargs: Any) -> Any:
         try:
@@ -49,8 +51,8 @@ class ABCEnumMeta(EnumMeta, ABCMeta):
     """Metaclass which injects."""
 
     def __new__(  # noqa: D102
-        cls, clsname: str, bases: Tuple[EnumMeta, ...], namespace: Mapping[str, Any]
-    ) -> "ABCEnumMeta":
+        cls, clsname: str, bases: tuple[EnumMeta, ...], namespace: Mapping[str, Any]
+    ) -> ABCEnumMeta:
         res = super().__new__(cls, clsname, bases, namespace)  # type: ignore[arg-type]
         res.__new__ = _pretty_raise_enum(res, res.__new__)  # type: ignore[method-assign,arg-type]
         return res

diff --git a/squidpy/datasets/_dataset.pyi b/squidpy/datasets/_dataset.pyi
@@ -5,7 +5,7 @@ from anndata import AnnData
 from squidpy.datasets._utils import PathLike
 
 class Dataset(Protocol):
-    def __call__(self, path: Union[PathLike, None] = ..., **kwargs: Any) -> AnnData: ...
+    def __call__(self, path: PathLike | None = ..., **kwargs: Any) -> AnnData: ...
 
 four_i: Dataset
 imc: Dataset

diff --git a/squidpy/datasets/_image.pyi b/squidpy/datasets/_image.pyi
@@ -4,7 +4,7 @@ from squidpy.datasets._utils import PathLike
 from squidpy.im._container import ImageContainer
 
 class ImageDataset(Protocol):
-    def __call__(self, path: Union[PathLike, None] = ..., **kwargs: Any) -> ImageContainer: ...
+    def __call__(self, path: PathLike | None = ..., **kwargs: Any) -> ImageContainer: ...
 
 visium_fluo_image_crop: ImageDataset
 visium_hne_image_crop: ImageDataset

diff --git a/squidpy/datasets/_utils.py b/squidpy/datasets/_utils.py
@@ -24,7 +24,7 @@ class Metadata(ABC):
 
     doc_header: Optional[str] = field(default=None, repr=False)
     path: Optional[PathLike] = field(default=None, repr=False)
-    shape: Optional[Tuple[int, int]] = field(default=None, repr=False)
+    shape: Optional[tuple[int, int]] = field(default=None, repr=False)
     library_id: Optional[Union[str, Sequence[str]]] = field(default=None, repr=False)
 
     _DOC_FMT = ""
@@ -48,7 +48,7 @@ def _download(self, fpath: PathLike, backup_url: str, **kwargs: Any) -> Any:
     def _create_signature(self) -> Signature:
         pass
 
-    def _create_function(self, name: str, glob_ns: Dict[str, Any]) -> None:
+    def _create_function(self, name: str, glob_ns: dict[str, Any]) -> None:
         if name in globals():
             raise KeyError(f"Function name `{name}` is already present in `{sorted(globals().keys())}`.")
 

diff --git a/squidpy/gr/_build.py b/squidpy/gr/_build.py
@@ -145,7 +145,7 @@ def spatial_neighbors(
     )
 
     if library_key is not None:
-        mats: List[Tuple[spmatrix, spmatrix]] = []
+        mats: list[tuple[spmatrix, spmatrix]] = []
         ixs = []  # type: ignore[var-annotated]
         for lib in libs:
             ixs.extend(np.where(adata.obs[library_key] == lib)[0])

diff --git a/squidpy/gr/_ligrec.py b/squidpy/gr/_ligrec.py
@@ -6,16 +6,7 @@
 from functools import partial
 from itertools import product
 from types import MappingProxyType
-from typing import (
-    TYPE_CHECKING,
-    Any,
-    Iterable,
-    Literal,
-    Mapping,
-    Sequence,
-    Tuple,
-    Union,
-)
+from typing import TYPE_CHECKING, Any, Iterable, Literal, Mapping, Sequence, Union
 
 import numpy as np
 import pandas as pd
@@ -40,9 +31,9 @@
 __all__ = ["ligrec", "PermutationTest"]
 
 StrSeq = Sequence[str]
-SeqTuple = Sequence[Tuple[str, str]]
-Interaction_t = Union[pd.DataFrame, Mapping[str, StrSeq], StrSeq, Tuple[StrSeq, StrSeq], SeqTuple]
-Cluster_t = Union[StrSeq, Tuple[StrSeq, StrSeq], SeqTuple]
+SeqTuple = Sequence[tuple[str, str]]
+Interaction_t = Union[pd.DataFrame, Mapping[str, StrSeq], StrSeq, tuple[StrSeq, StrSeq], SeqTuple]
+Cluster_t = Union[StrSeq, tuple[StrSeq, StrSeq], SeqTuple]
 
 SOURCE = "source"
 TARGET = "target"

diff --git a/squidpy/gr/_ppatterns.py b/squidpy/gr/_ppatterns.py
@@ -461,8 +461,8 @@ def _p_value_calc(
     score: NDArrayA,
     sims: NDArrayA | None,
     weights: spmatrix | NDArrayA,
-    params: Dict[str, Any],
-) -> Dict[str, Any]:
+    params: dict[str, Any],
+) -> dict[str, Any]:
     """
     Handle p-value calculation for spatial autocorrelation function.
 
@@ -515,7 +515,7 @@ def _p_value_calc(
     return results
 
 
-def _analytic_pval(score: NDArrayA, g: spmatrix | NDArrayA, params: Dict[str, Any]) -> tuple[NDArrayA, float]:
+def _analytic_pval(score: NDArrayA, g: spmatrix | NDArrayA, params: dict[str, Any]) -> tuple[NDArrayA, float]:
     """
     Analytic p-value computation.
 

diff --git a/squidpy/im/_container.py b/squidpy/im/_container.py
@@ -578,7 +578,12 @@ def _post_process(
     ) -> xr.Dataset:
         def _rescale(arr: xr.DataArray) -> xr.DataArray:
             scaling_fn = partial(
-                rescale, scale=[scale, scale, 1], preserve_range=True, order=1, channel_axis=-1, cval=cval
+                rescale,
+                preserve_range=True,
+                scale=[scale, scale, 1],
+                order=1,
+                channel_axis=-1,
+                cval=cval,
             )
             dtype = arr.dtype
 

diff --git a/squidpy/im/_feature_mixin.py b/squidpy/im/_feature_mixin.py
@@ -23,7 +23,7 @@
 from squidpy.gr._utils import _assert_non_empty_sequence
 from squidpy.im._coords import _NULL_PADDING, CropCoords
 
-Feature_t = Dict[str, Any]
+Feature_t = dict[str, Any]
 Channel_t = Union[int, Sequence[int]]
 
 
@@ -378,7 +378,7 @@ def convert_to_full_image_coordinates(x: NDArrayA, y: NDArrayA) -> NDArrayA:
         else:
             channels = ()
 
-        features: Dict[str, Any] = {}
+        features: dict[str, Any] = {}
         label_arr = self[label_layer].sel(z=library_id)
         label_arr_0 = label_arr[..., 0].values
         # calculate features that do not depend on the intensity image

diff --git a/squidpy/pl/_color_utils.py b/squidpy/pl/_color_utils.py
@@ -32,7 +32,7 @@ def _maybe_set_colors(
 
 def _get_palette(
     adata: AnnData,
-    cluster_key: Optional[str],
+    cluster_key: str | None,
     categories: Sequence[Any],
     palette: Palette_t = None,
     alpha: float = 1.0,

diff --git a/squidpy/pl/_interactive/_widgets.py b/squidpy/pl/_interactive/_widgets.py
@@ -301,20 +301,20 @@ def onCmapChanged(self, value: str) -> None:
         self._colorbar.cmap = self._create_colormap(value)
         self._colorbar._colorbar._update()
 
-    def setClim(self, value: Tuple[float, float]) -> None:
+    def setClim(self, value: tuple[float, float]) -> None:
         if value == self._clim:
             return
 
         self._clim = value
         self.climChanged.emit(*value)
 
-    def getClim(self) -> Tuple[float, float]:
+    def getClim(self) -> tuple[float, float]:
         return self._clim
 
-    def getOclim(self) -> Tuple[float, float]:
+    def getOclim(self) -> tuple[float, float]:
         return self._oclim
 
-    def setOclim(self, value: Tuple[float, float]) -> None:
+    def setOclim(self, value: tuple[float, float]) -> None:
         # original color limit used for 0-1 normalization
         self._oclim = value
 
@@ -354,7 +354,7 @@ def __init__(self, *args: Any, layer: Points, colorbar: CBarWidget, **kwargs: An
 
         self.valueChanged.connect(self._onValueChange)
 
-    def _onValueChange(self, percentile: Tuple[float, float]) -> None:
+    def _onValueChange(self, percentile: tuple[float, float]) -> None:
         # TODO(michalk8): use constants
         v = self._layer.metadata["data"]
         clipped = np.clip(v, *np.percentile(v, percentile))