From 7691ceea31a8eda11a419be8c5d03e8071a1ea6a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 5 Feb 2024 19:08:03 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v4.5.0)
- [github.com/astral-sh/ruff-pre-commit: v0.0.285 → v0.2.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.285...v0.2.0)
- [github.com/psf/black: 23.7.0 → 24.1.1](https://github.com/psf/black/compare/23.7.0...24.1.1)
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 783a3d64..3117de90 100644
--- a/.pre-commit-config.yaml
+++ b/.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

From 78aeabb8fc1fe146f8c4057a269e616b1b9f9755 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 5 Feb 2024 19:09:45 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 cellfinder/core/classify/cube_generator.py           | 8 ++------
 cellfinder/core/detect/filters/volume/ball_filter.py | 6 +++---
 cellfinder/core/main.py                              | 1 +
 cellfinder/core/tools/prep.py                        | 1 +
 cellfinder/napari/curation.py                        | 6 +++---
 examples/show_detection_sample.py                    | 1 +
 6 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/cellfinder/core/classify/cube_generator.py b/cellfinder/core/classify/cube_generator.py
index f4c67515..56f226cd 100644
--- a/cellfinder/core/classify/cube_generator.py
+++ b/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],
diff --git a/cellfinder/core/detect/filters/volume/ball_filter.py b/cellfinder/core/detect/filters/volume/ball_filter.py
index 87dee650..13aed04c 100644
--- a/cellfinder/core/detect/filters/volume/ball_filter.py
+++ b/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
+                    )
diff --git a/cellfinder/core/main.py b/cellfinder/core/main.py
index bc2f0cf3..cb78cca4 100644
--- a/cellfinder/core/main.py
+++ b/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
 
diff --git a/cellfinder/core/tools/prep.py b/cellfinder/core/tools/prep.py
index 0e7e7217..e513917d 100644
--- a/cellfinder/core/tools/prep.py
+++ b/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
diff --git a/cellfinder/napari/curation.py b/cellfinder/napari/curation.py
index 34d60380..37b9eba3 100644
--- a/cellfinder/napari/curation.py
+++ b/cellfinder/napari/curation.py
@@ -246,9 +246,9 @@ 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):
diff --git a/examples/show_detection_sample.py b/examples/show_detection_sample.py
index 3a44f7d1..2831fca5 100644
--- a/examples/show_detection_sample.py
+++ b/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