🤖 pre-commit autoupdate

.github/ISSUE_TEMPLATE/bug-report.md

@@ -27,9 +27,9 @@ If applicable, add screenshots to help explain your problem.
 
 **Desktop (please complete the following information):**
 
-- OS: \[e.g. Ubuntu\]
-- Hardware \[e.g. 8GB RAM\]
-- Version \[e.g. 1.0.0\]
+- OS: [e.g. Ubuntu]
+- Hardware [e.g. 8GB RAM]
+- Version [e.g. 1.0.0]
 
 **Additional context**
 Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -9,7 +9,7 @@ assignees: John-P
 ______________________________________________________________________
 
 **Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. I'm always frustrated when \[...\]
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
 
 **Describe the solution you'd like**
 A clear and concise description of what you want to happen.

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
   autoupdate_commit_msg: ':robot: pre-commit autoupdate'
 repos:
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.16
+    rev: 1.0.0
     hooks:
     - id: mdformat
       # Optionally add plugins
@@ -12,7 +12,7 @@ repos:
       - mdformat-black
       - mdformat-shfmt
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
       - id: check-added-large-files
         args: ['--maxkb=50000']
@@ -34,17 +34,17 @@ repos:
       - id: trailing-whitespace
         exclude: 'setup.cfg'
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 7.0.0
     hooks:
       - id: isort
-  - repo: https://github.com/psf/black
-    rev: 23.3.0 # Replace with any tag/version: https://github.com/psf/black/tags
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 25.11.0 # Replace with any tag/version: https://github.com/psf/black/tags
     hooks:
       - id: black
         language_version: python3
         additional_dependencies: ['click==8.0.4']  # Currently >8.0.4 breaks black
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 7.3.0
     hooks:
       - id: flake8
         additional_dependencies: [

tests/enums/test_color_space.py

@@ -1,4 +1,5 @@
 """Tests for the color space enum."""
+
 import pytest
 
 import wsic

tests/test_wsic.py

@@ -1,4 +1,5 @@
 """Tests for `wsic` package."""
+
 import sys
 import warnings
 from pathlib import Path
@@ -1230,12 +1231,14 @@ def test_convert(
             out_path,
             shape=reader.shape,
             codec=codec,
-            compression_level=4
-            if codec
-            in {
-                "blosc",
-            }
-            else 100,
+            compression_level=(
+                4
+                if codec
+                in {
+                    "blosc",
+                }
+                else 100
+            ),
         )
         writer.copy_from_reader(
             reader,

wsic/cli.py

@@ -1,4 +1,5 @@
 """Console script for wsic."""
+
 import sys
 from contextlib import suppress
 from pathlib import Path

wsic/enums.py

@@ -1,4 +1,5 @@
 """Enumerated types used by wsic."""
+
 from enum import Enum
 from numbers import Number
 from typing import Any, Dict, Optional, Tuple

wsic/magic.py

@@ -1,4 +1,5 @@
 """Detect file type by searching for signatures (magic numbers)."""
+
 import mmap
 import re
 from dataclasses import dataclass

wsic/metadata/__init__.py

@@ -1,4 +1,5 @@
 """Metadata parsing and generation."""
+
 from . import ngff
 
 __all__ = ["ngff"]

wsic/metadata/ngff.py

@@ -3,6 +3,7 @@
 Based on version 0.4 of the specification:
 https://ngff.openmicroscopy.org/0.4/
 """
+
 import sys
 from dataclasses import dataclass, field
 from numbers import Number

wsic/typedefs.py

@@ -1,4 +1,5 @@
 """Type definitions for wsic."""
+
 import re
 from pathlib import Path
 from typing import Union

wsic/validation.py

@@ -1,4 +1,5 @@
 """Functions used for data validation."""
+
 import warnings
 
 from wsic.utils import mpp2ppu

wsic/writers.py

@@ -31,7 +31,9 @@
 from wsic.enums import Codec, ColorSpace
 from wsic.metadata import ngff
 from wsic.readers import DICOMWSIReader, Reader, TIFFReader
-from wsic.tile_iterators import DaskTileIterator
+from wsic.tile_iterators import (
+    DaskTileIterator,
+)
 from wsic.tile_iterators import (
     PersistentMultiProcessTileIterator as MultiProcessTileIterator,
 )
@@ -1395,18 +1397,20 @@ def _write_ome_metadata(self, mpp: Tuple[float, ...]) -> None:
                     datasets=[
                         ngff.Dataset(
                             path=str(level),
-                            coordinateTransformations=[
-                                ngff.CoordinateTransformation(
-                                    "scale",
-                                    [
-                                        mpp[0] * downsample,
-                                        mpp[1] * downsample,
-                                        1,
-                                    ],
-                                )
-                            ]
-                            if mpp is not None
-                            else [ngff.CoordinateTransformation("identity")],
+                            coordinateTransformations=(
+                                [
+                                    ngff.CoordinateTransformation(
+                                        "scale",
+                                        [
+                                            mpp[0] * downsample,
+                                            mpp[1] * downsample,
+                                            1,
+                                        ],
+                                    )
+                                ]
+                                if mpp is not None
+                                else [ngff.CoordinateTransformation("identity")]
+                            ),
                         )
                         for level, downsample in enumerate(
                             [1] + self.pyramid_downsamples