Migrate pre-commit to ruff

.pre-commit-config.yaml

@@ -1,41 +1,27 @@
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
-    hooks:
-      - id: check-docstring-first
-      - id: end-of-file-fixer
-      - id: trailing-whitespace
-        exclude: ^.napari-hub/*
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
-    hooks:
-      - id: isort
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.17.0
-    hooks:
-      - id: pyupgrade
-        args: [--py38-plus, --keep-runtime-typing]
-  - repo: https://github.com/myint/autoflake
-    rev: v2.3.1
-    hooks:
-      - id: autoflake
-        args: ["--in-place", "--remove-all-unused-imports"]
-  - repo: https://github.com/psf/black
-    rev: 24.8.0
-    hooks:
-      - id: black
-  - repo: https://github.com/PyCQA/flake8
-    rev: 7.1.1
-    hooks:
-      - id: flake8
-        additional_dependencies: [flake8-typing-imports>=1.9.0]
-  - repo: https://github.com/tlambert03/napari-plugin-checks
-    rev: v0.3.0
-    hooks:
-      - id: napari-plugin-checks
-  # https://mypy.readthedocs.io/en/stable/introduction.html
-  # you may wish to add this as well!
-  # - repo: https://github.com/pre-commit/mirrors-mypy
-  #   rev: v0.910-1
-  #   hooks:
-  #     - id: mypy
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.12.2
+  hooks:
+  - id: ruff-format
+    exclude: examples
+  - id: ruff
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  # .py files are skipped cause already checked by other hooks
+  hooks:
+  - id: check-yaml
+  - id: check-toml
+  - id: check-merge-conflict
+    exclude: .*\.py
+  - id: end-of-file-fixer
+    exclude: .*\.py
+  - id: trailing-whitespace
+    # trailing whitespace has meaning in markdown https://www.markdownguide.org/hacks/#indent-tab
+    exclude: .*\.py|.*\.md
+  - id: mixed-line-ending
+    exclude: .*\.py
+- repo: https://github.com/python-jsonschema/check-jsonschema
+  rev: 0.33.2
+  hooks:
+  - id: check-github-workflows

pyproject.toml

@@ -6,9 +6,82 @@ build-backend = "setuptools.build_meta"
 [tool.setuptools_scm]
 write_to = "src/PartSeg_smfish/_version.py"
 
-[tool.black]
+[tool.ruff]
 line-length = 79
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".mypy_cache",
+    ".pants.d",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+    "*vendored*",
+    "*_vendor*",
+]
 
-[tool.isort]
-profile = "black"
-line_length = 79
+fix = true
+
+[tool.ruff.format]
+quote-style = "double"
+
+[tool.ruff.lint]
+select = [
+    "E", "F", "W", #flake8
+    "UP", # pyupgrade
+    "I", # isort
+    "YTT", #flake8-2020
+    "TC", # flake8-type-checing
+    "BLE", # flake8-blind-exception
+    "B", # flake8-bugbear
+    "A", # flake8-builtins
+    "C4", # flake8-comprehensions
+    "ISC", # flake8-implicit-str-concat
+    "G", # flake8-logging-format
+    "PIE", # flake8-pie
+    "COM", # flake8-commas
+    "SIM", # flake8-simplify
+    "INP", # flake8-no-pep420
+    "PYI", # flake8-pyi
+    "Q", # flake8-quotes
+    "RSE", # flake8-raise
+    "RET", # flake8-return
+    "TID",  # flake8-tidy-imports # replace absolutify import
+    "TRY", # tryceratops
+    "ICN", # flake8-import-conventions
+    "RUF", # ruff specyfic rules
+    "NPY201", # checks compatibility with numpy version 2.0
+    "ASYNC", # flake8-async
+    "EXE", # flake8-executable
+    "FA", # flake8-future-annotations
+    "LOG", # flake8-logging
+    "SLOT", # flake8-slots
+    "PT", # flake8-pytest-style
+    "T20", # flake8-print
+]
+ignore = [
+    "COM812", # conflict with formatter
+]
+
+[tool.ruff.lint.pyupgrade]
+keep-runtime-typing = true
+
+
+[tool.ruff.lint.flake8-quotes]
+docstring-quotes = "double"
+inline-quotes = "double"
+multiline-quotes = "double"
+
+[tool.ruff.lint.isort]
+known-first-party=['PartSeg_smfish']
+combine-as-imports = true

src/PartSeg_smfish/__init__.py

@@ -9,8 +9,7 @@
 
 
 def register():
-    from PartSegCore.register import RegisterEnum
-    from PartSegCore.register import register as register_fun
+    from PartSegCore.register import RegisterEnum, register as register_fun
 
     from . import measurement, segmentation
 

src/PartSeg_smfish/_tests/test_segmentation.py

@@ -9,7 +9,7 @@
 )
 
 
-@pytest.mark.parametrize("mask", (True, False))
+@pytest.mark.parametrize("mask", [True, False])
 def test_gauss_estimate(mask):
     param = GaussBackgroundEstimateParameters(
         background_estimate_radius=5,
@@ -22,7 +22,7 @@ def test_gauss_estimate(mask):
     GaussBackgroundEstimate.spot_estimate(data, mask, (10, 10), param)
 
 
-@pytest.mark.parametrize("mask", (True, False))
+@pytest.mark.parametrize("mask", [True, False])
 def test_laplacian_estimate(mask):
     param = LaplacianBackgroundEstimateParameters(
         laplacian_radius=1.3,

src/PartSeg_smfish/copy_labels.py

@@ -44,7 +44,7 @@ def __init__(self, napari_viewer: Viewer):
         self.setLayout(layout)
 
         self.viewer.layers.selection.events.active.connect(
-            self.activate_widget
+            self.activate_widget,
         )
         self.copy_btn.clicked.connect(self.copy_action)
         self.check_all_btn.clicked.connect(self._check_all)
@@ -116,8 +116,21 @@ def copy_action(self):
             checked = {layer.selected_label}
         z_position = self.viewer.dims.current_step[layer.dtype.ndim - 3]
         for component_num in checked:
-            mask = layer.data[leading_zeros + (z_position,)] == component_num
+            mask = (
+                layer.data[
+                    (
+                        *leading_zeros,
+                        z_position,
+                    )
+                ]
+                == component_num
+            )
             start = max(0, self.lower.value())
             end = min(layer.data.shape[1] - 1, self.upper.value()) + 1
             for i in range(start, end):
-                layer.data[leading_zeros + (i,)][mask] = component_num
+                layer.data[
+                    (
+                        *leading_zeros,
+                        i,
+                    )
+                ][mask] = component_num