[pre-commit.ci] pre-commit autoupdate (#371)

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

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](pre-commit/pre-commit-hooks@v4.4.0...v4.5.0)
- [github.com/astral-sh/ruff-pre-commit: v0.0.285 → v0.2.0](astral-sh/ruff-pre-commit@v0.0.285...v0.2.0)
- [github.com/psf/black: 23.7.0 → 24.1.1](psf/black@23.7.0...24.1.1)

* [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>

Author: pre-commit-ci[bot]

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
+      rev: v4.5.0
       hooks:
           - id: check-docstring-first
           - id: check-executables-have-shebangs
@@ -16,10 +16,10 @@ repos:
           - id: requirements-txt-fixer
           - id: trailing-whitespace
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.0.285
+      rev: v0.2.0
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 23.7.0
+      rev: 24.1.1
       hooks:
           - id: black

cellfinder/core/classify/cube_generator.py

@@ -197,9 +197,7 @@ def __len__(self) -> int:
         """
         return len(self.batches)
 
-    def __getitem__(
-        self, index: int
-    ) -> Union[
+    def __getitem__(self, index: int) -> Union[
         np.ndarray,
         Tuple[np.ndarray, List[Dict[str, float]]],
         Tuple[np.ndarray, Dict],
@@ -389,9 +387,7 @@ def __len__(self) -> int:
         """
         return int(np.ceil(len(self.signal_list) / self.batch_size))
 
-    def __getitem__(
-        self, index: int
-    ) -> Union[
+    def __getitem__(self, index: int) -> Union[
         np.ndarray,
         Tuple[np.ndarray, List[Dict[str, float]]],
         Tuple[np.ndarray, Dict],

cellfinder/core/detect/filters/volume/ball_filter.py

@@ -327,6 +327,6 @@ def _walk(
                     THRESHOLD_VALUE,
                     kernel,
                 ):
-                    volume[
-                        ball_centre_x, ball_centre_y, middle_z
-                    ] = SOMA_CENTRE_VALUE
+                    volume[ball_centre_x, ball_centre_y, middle_z] = (
+                        SOMA_CENTRE_VALUE
+                    )

cellfinder/core/main.py

@@ -2,6 +2,7 @@
 N.B imports are within functions to prevent tensorflow being imported before
 it's warnings are silenced
 """
+
 import os
 from typing import Callable, List, Optional, Tuple
 

cellfinder/core/tools/prep.py

@@ -3,6 +3,7 @@
 ==================
 Functions to prepare files and directories needed for other functions
 """
+
 import os
 from pathlib import Path
 from typing import Optional

cellfinder/napari/curation.py

@@ -253,9 +253,9 @@ def set_training_data_non_cell(self):
             self.training_data_non_cell_layer = self.viewer.layers[
                 self.training_data_non_cell_choice.currentText()
             ]
-            self.training_data_non_cell_layer.metadata[
-                "point_type"
-            ] = Cell.UNKNOWN
+            self.training_data_non_cell_layer.metadata["point_type"] = (
+                Cell.UNKNOWN
+            )
             self.training_data_non_cell_layer.metadata["training_data"] = True
 
     def add_training_data(self):

examples/show_detection_sample.py

@@ -7,6 +7,7 @@
 - loads the cellfinder-napari cell detection plugin
 - opens the napari viewer
 """
+
 import napari
 
 from cellfinder.napari.sample_data import load_sample