[pre-commit.ci] pre-commit autoupdate (#785)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/pre-commit/mirrors-mypy: v1.7.1 → v1.8.0](pre-commit/mirrors-mypy@v1.7.1...v1.8.0)
- [github.com/psf/black: 23.11.0 → 24.1.1](psf/black@23.11.0...24.1.1)
- [github.com/pre-commit/mirrors-prettier: v4.0.0-alpha.4 → v4.0.0-alpha.8](pre-commit/mirrors-prettier@v4.0.0-alpha.4...v4.0.0-alpha.8)
- [github.com/astral-sh/ruff-pre-commit: v0.1.7 → v0.1.14](astral-sh/ruff-pre-commit@v0.1.7...v0.1.14)

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

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

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: LLehner <64135338+LLehner@users.noreply.github.com>
Co-authored-by: Giovanni Palla <25887487+giovp@users.noreply.github.com>

.pre-commit-config.yaml

@@ -7,18 +7,18 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.7.1
+      rev: v1.8.0
       hooks:
           - id: mypy
             additional_dependencies: [numpy, pandas, types-requests]
             exclude: .scripts/ci/download_data.py|squidpy/datasets/_(dataset|image).py # See https://github.com/pre-commit/mirrors-mypy/issues/33
     - repo: https://github.com/psf/black
-      rev: 23.11.0
+      rev: 24.1.1
       hooks:
           - id: black
             additional_dependencies: [toml]
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v4.0.0-alpha.4
+      rev: v4.0.0-alpha.8
       hooks:
           - id: prettier
     - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -56,7 +56,7 @@ repos:
           - id: blacken-docs
     - repo: https://github.com/astral-sh/ruff-pre-commit
       # Ruff version.
-      rev: v0.1.7
+      rev: v0.1.14
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

src/squidpy/_constants/_constants.py

@@ -1,4 +1,5 @@
 """Constants that user deals with."""
+
 from enum import unique
 
 from squidpy._constants._utils import ModeEnum

src/squidpy/_constants/_pkg_constants.py

@@ -1,4 +1,5 @@
 """Internal constants not exposed to the user."""
+
 from __future__ import annotations
 
 from typing import Any, Callable, Mapping, Optional, Sequence, Union

src/squidpy/_utils.py

@@ -1,4 +1,5 @@
 """Spatial tools general utility functions."""
+
 from __future__ import annotations
 
 import functools

src/squidpy/gr/__init__.py

@@ -1,4 +1,5 @@
 """The graph module."""
+
 from squidpy.gr._build import spatial_neighbors
 from squidpy.gr._ligrec import ligrec
 from squidpy.gr._nhood import centrality_scores, interaction_matrix, nhood_enrichment

src/squidpy/gr/_build.py

@@ -1,4 +1,5 @@
 """Functions for building graphs from spatial coordinates."""
+
 from __future__ import annotations
 
 import warnings

src/squidpy/gr/_ligrec.py

@@ -1,4 +1,5 @@
 """Permutation test function as described in CellPhoneDB 2.0."""
+
 from __future__ import annotations
 
 from abc import ABC

src/squidpy/gr/_nhood.py

@@ -1,4 +1,5 @@
 """Functions for neighborhood enrichment analysis (permutation test, centralities measures etc.)."""
+
 from __future__ import annotations
 
 from functools import partial

src/squidpy/gr/_ppatterns.py

@@ -1,4 +1,5 @@
 """Functions for point patterns spatial statistics."""
+
 from __future__ import annotations
 
 from itertools import chain

src/squidpy/gr/_ripley.py

@@ -1,4 +1,5 @@
 """Functions for point patterns spatial statistics."""
+
 from __future__ import annotations
 
 from typing import (

src/squidpy/gr/_utils.py

@@ -1,4 +1,5 @@
 """Graph utilities."""
+
 from __future__ import annotations
 
 from contextlib import contextmanager

src/squidpy/im/__init__.py

@@ -1,4 +1,5 @@
 """The image module."""
+
 from squidpy.im._container import ImageContainer
 from squidpy.im._feature import calculate_image_features
 from squidpy.im._process import process

src/squidpy/im/_feature_mixin.py

@@ -74,18 +74,15 @@ def _get_channels(xr_img: NDArrayA | xr.DataArray, channels: Channel_t | None) -
 class HasGetItemProtocol(Protocol):
     """Protocol for FeatureMixin to have correct definition of ImageContainer."""
 
-    def __getitem__(self, key: str) -> xr.DataArray:
-        ...
+    def __getitem__(self, key: str) -> xr.DataArray: ...
 
     @property
     def data(self) -> xr.Dataset:  # noqa: D102
         ...
 
-    def _get_layer(self, layer: str | None) -> str:
-        ...
+    def _get_layer(self, layer: str | None) -> str: ...
 
-    def _get_library_id(self, library_id: str | None) -> str:
-        ...
+    def _get_library_id(self, library_id: str | None) -> str: ...
 
 
 class FeatureMixin:

src/squidpy/pl/__init__.py

@@ -1,4 +1,5 @@
 """The plotting module."""
+
 from squidpy.pl._graph import (
     centrality_scores,
     co_occurrence,

src/squidpy/pl/_color_utils.py

@@ -1,4 +1,5 @@
 """Utils for plotting functions."""
+
 from __future__ import annotations
 
 from typing import Any, Mapping, Optional, Sequence, Union

src/squidpy/pl/_graph.py

@@ -1,4 +1,5 @@
 """Plotting for graph functions."""
+
 from __future__ import annotations
 
 from pathlib import Path

src/squidpy/tl/__init__.py

@@ -1,2 +1,3 @@
 """The design matrix module."""
+
 from squidpy.tl._var_by_distance import var_by_distance