Fix precommit compliants

pyproject.toml

@@ -73,33 +73,15 @@ addopts = "--cov --cov-report term-missing --cov-report xml --cov-report lcov:lc
 line-length = 100
 # skip-string-normalization = true
 target-version = [
-    "py37",
     "py38",
     "py39",
     "py310",
     "py311",
 ]
 
 [tool.ruff]
-select = ["F",
-	  "E",
-	  "I",
-	  "W",
-	  "UP",
-	  "Q",
-	  # "SIM",
-	  # "PTH",
-	  #"RET",
-	 ]
-ignore = ["E722"]
-line-length = 120
-# Allow autofix for all enabled rules (when `--fix`) is provided.
-fixable = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "EM", "ERA", "EXE", "FBT", "ICN", "INP", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PTH", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "TRY", "UP", "YTT"]
-unfixable = []
 # Exclude a variety of commonly ignored directories.
 exclude = [
-    "dev*",
-    "ximage/test*",
     ".bzr",
     ".direnv",
     ".eggs",
@@ -117,10 +99,107 @@ exclude = [
     "_build",
     "buck-out",
     "build",
+    "docs",
     "dist",
     "node_modules",
     "venv",
 ]
 
+line-length = 120
+indent-width = 4
+
+[tool.ruff.format]
+
+# Enable reformatting of code snippets in docstrings.
+docstring-code-format = true
+
+[tool.ruff.lint]
+
+select = [
+    # pydocstyle
+    # "D",
+    # Pyflakes
+    "F",
+    # pycodestyle
+    "E",
+    "W",
+    # isort
+    "I",
+    # pyupgrade
+    "UP",
+    # flake8-quotes
+    "Q",
+    # flake8-bugbear
+    #"B",
+    # flake8-return
+    #"RET",
+    # flake8-unused-arguments
+    #"ARG",
+    # flake8-raise
+    #"RSE",
+    # flake8-pytest-style
+    #"PT",
+    # flake8-simplify
+    # "SIM",
+    # Perflint
+    #"PERF",
+    # pandas-vet
+    #"PD",
+    # pylint
+    #"PL",
+    # flake8-commas
+    #"COM",
+    # flake8-slots
+    #"SLOT",
+    # flake8-comprehensions
+    # "C4",
+    # Ruff custom rules
+    # "RUF"
+
+    #---------------------
+    #### Future rules ####
+    # flake8-use-pathlib
+    # "PTH",
+    # NumPy-specific rules  (for 2.0)
+    # "NPY",
+    # refurb
+    # "FURB", # require preview
+]
+ignore = [
+    "E722",
+    "PT011", # pytest raised error must be checked if match the expected error msg
+    "PERF203",
+
+    # Docstyle Rules
+    "D404", # Docstring can't start with "This"
+    "D401", # First sentence must be in imperative mood
+
+    # Complexity rules
+    "PLR0913",
+    "PLR2004",
+    "PLR0912",
+    "PLR0915",
+]
+
+# Allow autofix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.lint.per-file-ignores]
+
+# Ignore `E402` (import violations) in all Jupyter Notebooks.
+"*.ipynb" = ["E402"]
+
+# Rules to ignore in test files
+"test_*.py" = [
+    "ARG",  # avoid problems with fixtures
+    "D100", "D101","D102", "D103", "D104", "D105",  # Missing docstrings
+]
+"setup.py" = ["D100"]
+"*__init__.py" = ["D104"]
+
 [tool.codespell]
     ignore-words-list = 'nD'

ximage/tests/accessor/test_accessor_args.py

@@ -2,10 +2,8 @@
 
 from ximage.accessor.methods import XImage_Base_Accessor, XImage_DataArray_Accessor
 from ximage.labels.labels import label
-from ximage.patch.labels_patch import get_patches_from_labels
-from ximage.patch.labels_patch import get_patches_isel_dict_from_labels
 from ximage.labels.plot_labels import plot_labels
-
+from ximage.patch.labels_patch import get_patches_from_labels, get_patches_isel_dict_from_labels
 
 # Utils functions ##############################################################
 

ximage/tests/labels/test_labels.py

@@ -1,12 +1,10 @@
 import numpy as np
 import pytest
 import xarray as xr
-
 from pytest import apply_to_all_array_types
 
 from ximage.labels import labels
 
-
 # Tests for public functions ###################################################
 
 
@@ -305,8 +303,6 @@ def test_get_labels_stats():
         ]
     )
 
-    values_area = [5, 1, 3]
-
     # Test result returned in decreasing order
     label_indices, values_returned = labels._get_labels_stats(array, label_array)
     assert np.array_equal(label_indices, np.array([0, 2, 1]))
@@ -699,7 +695,11 @@ def test_xr_get_labels():
             [1, 1],
         ]
     )
-    sort_by = lambda array: np.mean(array)
+
+    def my_sort_function(array):
+        return np.mean(array)
+
+    sort_by = my_sort_function
     sort_decreasing = False
     labeled_comprehension_kwargs = {
         "out_dtype": np.float16,

ximage/tests/labels/test_plot_labels.py

@@ -1,7 +1,7 @@
-from matplotlib.image import AxesImage
 import matplotlib.pyplot as plt
 import numpy as np
 import xarray as xr
+from matplotlib.image import AxesImage
 
 from ximage.labels.plot_labels import plot_labels
 

ximage/tests/patch/test_checks_patch.py

@@ -2,7 +2,6 @@
 
 from ximage.patch import checks
 
-
 # Utils functions ##############################################################
 
 
@@ -105,7 +104,7 @@ def test_check_stride():
 
     # Check no partitioning method
     partitioning_method = None
-    assert checks.check_stride(None, dimension_names, shape, partitioning_method) == None
+    assert checks.check_stride(None, dimension_names, shape, partitioning_method) is None
 
     # Check default stride
     partitioning_method = "tiling"

ximage/tests/patch/test_labels_patch.py

@@ -1,12 +1,10 @@
 import numpy as np
 import pytest
 import xarray as xr
-
-from pytest import apply_to_all_array_types, SaneEqualityArray
+from pytest import SaneEqualityArray, apply_to_all_array_types
 
 from ximage.patch import labels_patch
 
-
 # Utils functions ##############################################################
 
 

ximage/tests/patch/test_slices.py

@@ -2,7 +2,6 @@
 
 from ximage.patch import slices
 
-
 # Tests for public functions ###################################################