Merge branch 'develop'

Author: tayden

.pre-commit-config.yaml

@@ -1,23 +1,20 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
+exclude: ^.*\.lock$
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
-      - id: check-added-large-files
   - repo: https://github.com/python-poetry/poetry
-    rev:  1.4.0
+    rev:  1.8.0
     hooks:
       - id: poetry-check
       - id: poetry-lock
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.265
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.1
     hooks:
       - id: ruff
-        args: [ --fix ]
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      - id: black
+        args: [ '--fix', '--select', 'I']
+      - id: ruff-format

glint_mask_generator/__init__.py

@@ -5,11 +5,11 @@
 """
 
 from .maskers import (
+    CIRThresholdMasker,
     Masker,
-    RGBThresholdMasker,
-    P4MSThresholdMasker,
     MicasenseRedEdgeThresholdMasker,
-    CIRThresholdMasker,
+    P4MSThresholdMasker,
+    RGBThresholdMasker,
 )
 
 __all__ = [

glint_mask_generator/cli.py

@@ -4,6 +4,7 @@
 Date: 2020-05-30
 Description: Command line interface to the glint-mask-tools.
 """
+
 import os
 import sys
 from typing import List
@@ -12,11 +13,11 @@
 from tqdm import tqdm
 
 from .maskers import (
+    CIRThresholdMasker,
     Masker,
     MicasenseRedEdgeThresholdMasker,
     P4MSThresholdMasker,
     RGBThresholdMasker,
-    CIRThresholdMasker,
 )
 
 

glint_mask_generator/glint_algorithms.py

@@ -3,6 +3,7 @@
 Organization: Hakai Institute
 Date: 2020-09-18
 """
+
 import math
 from abc import ABC, abstractmethod
 from typing import Sequence

glint_mask_generator/image_loaders.py

@@ -3,11 +3,12 @@
 Organization: Hakai Institute
 Date: 2020-09-18
 """
+
 import re
 from abc import ABC, ABCMeta, abstractmethod
 from functools import singledispatchmethod
 from pathlib import Path
-from typing import Iterable, List, Union, TYPE_CHECKING
+from typing import TYPE_CHECKING, Iterable, List, Union
 
 import numpy as np
 from PIL import Image
@@ -72,9 +73,7 @@ def save_mask(mask: np.ndarray, out_path: str):
         mask_img = Image.fromarray(mask, mode="L")
         mask_img.save(str(out_path))
 
-    def apply_masker(
-        self, img_paths: Union[List[str], str], masker: "Masker"
-    ):  # noqa: F821
+    def apply_masker(self, img_paths: Union[List[str], str], masker: "Masker"):  # noqa: F821
         img = self.load_image(img_paths)
         img = self.preprocess_image(img)
         mask = masker.algorithm(img)
@@ -105,9 +104,7 @@ class CIRLoader(SingleFileImageLoader):
     _bit_depth = 8
     _crop_size = 256
 
-    def apply_masker(
-        self, img_paths: Union[List[str], str], masker: "Masker"
-    ):  # noqa: F821
+    def apply_masker(self, img_paths: Union[List[str], str], masker: "Masker"):  # noqa: F821
         """Compute the image mask by moving a window over the input.
         These CIR images are too large to be read into memory simultaneously so this
         image masking routine is special.

glint_mask_generator/maskers.py

@@ -3,6 +3,7 @@
 Organization: Hakai Institute
 Date: 2020-09-18
 """
+
 import concurrent.futures
 import os
 from typing import Callable, List, Optional, Sequence, Union

glint_mask_generator/utils.py

@@ -3,6 +3,7 @@
 Organization: Hakai Institute
 Date: 2020-09-18
 """
+
 from pathlib import Path
 from typing import Iterable
 

gui/__main__.py

@@ -3,14 +3,15 @@
 Organization: Hakai Institute
 Date: 2020-09-16
 """
+
 import os
 import sys
 from typing import List, Sequence
 
+from loguru import logger
 from PyQt6 import QtWidgets, uic
 from PyQt6.QtCore import QObject, QRunnable, QThreadPool, pyqtSignal, pyqtSlot
 from PyQt6.QtGui import QIcon
-from loguru import logger
 
 from glint_mask_generator import (
     CIRThresholdMasker,

poetry.lock

@@ -14,12 +14,12 @@ packages = [
 glint-mask = 'glint_mask_generator.cli:main'
 
 [tool.poetry.dependencies]
-python = ">=3.9,<3.12"
+python = ">=3.9,<3.13"
 numpy = "~=1.25.1"
 fire = "~=0.5.0"
-Pillow = ">=9.3,<10.4"
+Pillow = "~=10.4"
 scipy = "~=1.11.1"
-tqdm = ">=4.65,<4.67"
+tqdm = "~=4.65"
 loguru = "~=0.7.0"
 pyqt6 = "^6.4.0"
 
@@ -29,6 +29,8 @@ pyinstaller = "^5.6.2"
 pre-commit = "^3.3.3"
 ruff = "^0.8.1"
 
+[tool.ruff.lint.isort]
+combine-as-imports = true
 
 [build-system]
 requires = ["poetry-core"]