Update linter, do lint fixes

.pre-commit-config.yaml

@@ -16,5 +16,5 @@ repos:
     rev: v0.5.1
     hooks:
       - id: ruff
-        args: [ --fix ]
+        args: [ '--fix', '--select', 'I']
       - id: ruff-format

docs/faqs.md

@@ -50,4 +50,4 @@ software.
 *Still have a question?*
 
 Get in touch by [sending us an email](mailto:[email protected])
-or [file a GitHub issue](https://github.com/HakaiInstitute/kelp-o-matic/issues)
+or [file a GitHub issue](https://github.com/HakaiInstitute/kelp-o-matic/issues)

kelp_o_matic/hann.py

@@ -1,12 +1,11 @@
 import math
 from abc import ABCMeta, abstractmethod
-from typing import Type, Annotated
+from typing import Annotated, Type
 
 import numpy as np
 import torch
 from rasterio.windows import Window
 
-
 # Implementation of paper:
 # https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229839#pone.0229839.ref007
 

kelp_o_matic/lib.py

@@ -1,16 +1,16 @@
 import warnings
 from pathlib import Path
-from typing import Union, Optional
+from typing import Optional, Union
 
 import rasterio
 
 from kelp_o_matic.managers import RichSegmentationManager
 from kelp_o_matic.models import (
+    KelpRGBIPresenceSegmentationModel,
+    KelpRGBISpeciesSegmentationModel,
     KelpRGBPresenceSegmentationModel,
     KelpRGBSpeciesSegmentationModel,
     MusselRGBPresenceSegmentationModel,
-    KelpRGBIPresenceSegmentationModel,
-    KelpRGBISpeciesSegmentationModel,
 )
 
 

kelp_o_matic/managers.py

@@ -8,7 +8,7 @@
 from rich.progress import Progress, SpinnerColumn, TimeElapsedColumn
 
 from kelp_o_matic.geotiff_io import GeotiffReader, GeotiffWriter
-from kelp_o_matic.hann import TorchMemoryRegister, BartlettHannKernel
+from kelp_o_matic.hann import BartlettHannKernel, TorchMemoryRegister
 from kelp_o_matic.models import _Model
 from kelp_o_matic.utils import all_same
 

kelp_o_matic/models.py

@@ -1,6 +1,6 @@
 import gc
-from abc import ABC, abstractmethod, ABCMeta
-from typing import Union, Type
+from abc import ABC, ABCMeta, abstractmethod
+from typing import Type, Union
 
 import numpy as np
 import torch

pyproject.toml

@@ -31,6 +31,9 @@ mkdocs = "^1.5.3"
 mkdocs-material = "^9.5.2"
 mkdocstrings-python = "^1.7.5"
 
+[tool.ruff.lint.isort]
+combine-as-imports = true
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"

tests/test_TorchMemoryRegister.py

@@ -5,7 +5,7 @@
 from rasterio.transform import from_origin
 from rasterio.windows import Window
 
-from kelp_o_matic.hann import TorchMemoryRegister, BartlettHannKernel, Kernel
+from kelp_o_matic.hann import BartlettHannKernel, Kernel, TorchMemoryRegister
 
 
 def create_dummy_tiff(