Replace flake8, isort and pyupgrade by ruff, enable additional useful…

…l rules (napari#5513)

Co-authored-by: Lorenzo Gaifas <[email protected]>
Co-authored-by: Matthias Bussonnier <[email protected]>

.pre-commit-config.yaml

@@ -8,36 +8,17 @@ repos:
     rev: v2.1.3
     hooks:
     - id: pycln
--   repo: https://github.com/pycqa/isort
-    rev: 5.11.4
-    hooks:
-    - id: isort
-      exclude: _vendor|vendored|examples
 -   repo: https://github.com/psf/black
     rev: 22.12.0
     hooks:
     - id: black
       pass_filenames: true
       exclude: _vendor|vendored|examples
 -   repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.230
+    rev: v0.0.235
     hooks:
       - id: ruff
         exclude: _vendor|vendored
--   repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-    - id: flake8
-      additional_dependencies: [flake8-typing-imports]
-      pass_filenames: true
-      # this seems to need to be here in addition to setup.cfg
-      exclude: _vendor|vendored|__init__.py|examples
--   repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
-    hooks:
-    - id: pyupgrade
-      args: ["--py38-plus", "--keep-runtime-typing"]
-      exclude: _vendor|vendored|examples
 -   repo: https://github.com/seddonym/import-linter
     rev: v1.6.0
     hooks:

examples/3D_paths.py

@@ -12,8 +12,8 @@
 
 import numpy as np
 from skimage import data
-import napari
 
+import napari
 
 blobs = data.binary_blobs(
             length=128, blob_size_fraction=0.05, n_dim=3, volume_fraction=0.05

examples/3Dimage_plane_rendering.py

@@ -7,11 +7,12 @@
 
 .. tags:: visualization-advanced, gui, layers
 """
-import napari
 import numpy as np
-from napari.utils.translations import trans
 from skimage import data
 
+import napari
+from napari.utils.translations import trans
+
 viewer = napari.Viewer(ndisplay=3)
 
 # add a 3D image

examples/3d_kymograph_.py

@@ -7,10 +7,12 @@
 
 .. tags:: experimental
 """
+from itertools import product
+
 import numpy as np
-import napari
 from tqdm import tqdm
-from itertools import product
+
+import napari
 
 try:
     from omero.gateway import BlitzGateway
@@ -157,4 +159,4 @@ def IDR_fetch_image(image_id: int, progressbar: bool = True) -> np.ndarray:
 v.camera.angles = (-20, 23, -50)
 v.camera.zoom = 0.17
 
-napari.run()
+napari.run()

examples/add-points-3d.py

@@ -8,10 +8,10 @@
 .. tags:: visualization-nD
 """
 
-from skimage import data
 from scipy import ndimage as ndi
-import napari
+from skimage import data
 
+import napari
 
 blobs = data.binary_blobs(
         length=128, volume_fraction=0.1, n_dim=3

examples/add_3D_image.py

@@ -8,8 +8,8 @@
 """
 
 from skimage import data
-import napari
 
+import napari
 
 blobs = data.binary_blobs(length=64, volume_fraction=0.1, n_dim=3).astype(
     float

examples/add_grayscale_image.py

@@ -7,10 +7,10 @@
 .. tags:: visualization-basic
 """
 
-from skimage import data
-import napari
 import numpy as np
+from skimage import data
 
+import napari
 
 # simulating a grayscale image here for testing contrast limits adjustments
 image = data.astronaut().mean(-1) * 100 + 100

examples/add_image.py

@@ -8,6 +8,7 @@
 """
 
 from skimage import data
+
 import napari
 
 # create the viewer with an image

examples/add_image_transformed.py

@@ -8,6 +8,7 @@
 """
 
 from skimage import data
+
 import napari
 
 # create the viewer with an image and transform (rotate) it

examples/add_labels.py

@@ -10,11 +10,11 @@
 
 from skimage import data
 from skimage.filters import threshold_otsu
-from skimage.segmentation import clear_border
 from skimage.measure import label
-from skimage.morphology import closing, square, remove_small_objects
-import napari
+from skimage.morphology import closing, remove_small_objects, square
+from skimage.segmentation import clear_border
 
+import napari
 
 image = data.coins()[50:-50, 50:-50]
 

examples/add_labels_with_features.py

@@ -8,14 +8,14 @@
 """
 
 
+import numpy as np
 from skimage import data
 from skimage.filters import threshold_otsu
-from skimage.segmentation import clear_border
 from skimage.measure import label
-from skimage.morphology import closing, square, remove_small_objects
-import numpy as np
-import napari
+from skimage.morphology import closing, remove_small_objects, square
+from skimage.segmentation import clear_border
 
+import napari
 
 image = data.coins()[50:-50, 50:-50]
 

examples/add_multiscale_image.py

@@ -7,11 +7,11 @@
 .. tags:: visualization-advanced
 """
 
+import numpy as np
 from skimage import data
 from skimage.transform import pyramid_gaussian
-import napari
-import numpy as np
 
+import napari
 
 # create multiscale from astronaut image
 base = np.tile(data.astronaut(), (8, 8, 1))

examples/add_points.py

@@ -11,8 +11,8 @@
 import numpy as np
 from skimage import data
 from skimage.color import rgb2gray
-import napari
 
+import napari
 
 # add the image
 viewer = napari.view_image(rgb2gray(data.astronaut()))

examples/add_points_on_nD_shapes.py

@@ -7,9 +7,10 @@
 .. tags:: visualization-nD
 """
 
-import napari
 import numpy as np
 
+import napari
+
 # Create rectangles in 4D
 data = [
         [

examples/add_points_with_features.py

@@ -11,8 +11,8 @@
 import numpy as np
 from skimage import data
 from skimage.color import rgb2gray
-import napari
 
+import napari
 
 # add the image
 viewer = napari.view_image(rgb2gray(data.astronaut()))

examples/add_points_with_multicolor_text.py

@@ -9,6 +9,7 @@
 """
 
 import numpy as np
+
 import napari
 
 # add the image with three points

examples/add_points_with_text.py

@@ -9,8 +9,8 @@
 """
 
 import numpy as np
-import napari
 
+import napari
 
 # add the image
 viewer = napari.view_image(np.zeros((400, 400)))

examples/add_shapes.py

@@ -11,8 +11,8 @@
 
 import numpy as np
 from skimage import data
-import napari
 
+import napari
 
 # add the image
 viewer = napari.view_image(data.camera(), name='photographer')

examples/add_shapes_with_features.py

@@ -11,8 +11,8 @@
 
 import numpy as np
 from skimage import data
-import napari
 
+import napari
 
 # add the image
 viewer = napari.view_image(data.camera(), name='photographer')

examples/add_shapes_with_text.py

@@ -11,8 +11,8 @@
 
 import numpy as np
 from skimage import data
-import napari
 
+import napari
 
 # add the image
 viewer = napari.view_image(data.camera(), name='photographer')

examples/add_surface_2D.py

@@ -8,8 +8,8 @@
 """
 
 import numpy as np
-import napari
 
+import napari
 
 data = np.array([[0, 0], [0, 20], [10, 0], [10, 10]])
 faces = np.array([[0, 1, 2], [1, 2, 3]])

examples/add_vectors.py

@@ -11,10 +11,10 @@
 .. tags:: visualization-basic
 """
 
-import napari
-from skimage import data
 import numpy as np
+from skimage import data
 
+import napari
 
 # create the viewer and window
 viewer = napari.Viewer()

examples/add_vectors_color_by_angle.py

@@ -8,10 +8,10 @@
 .. tags:: visualization-advanced
 """
 
-import napari
-from skimage import data
 import numpy as np
+from skimage import data
 
+import napari
 
 # create the viewer and window
 viewer = napari.Viewer()

examples/add_vectors_image.py

@@ -11,9 +11,9 @@
 .. tags:: visualization-basic
 """
 
-import napari
 import numpy as np
 
+import napari
 
 # create the viewer and window
 viewer = napari.Viewer()

examples/affine_transforms.py

@@ -7,9 +7,10 @@
 .. tags:: visualization-advanced
 """
 import numpy as np
-import napari
 import scipy.ndimage as ndi
 
+import napari
+
 # Create a random image
 image = np.random.random((5, 5))
 

examples/annotate-2d.py

@@ -10,8 +10,8 @@
 
 import numpy as np
 from skimage import data
-import napari
 
+import napari
 
 print("click to add points; close the window when finished.")
 

examples/annotate_segmentation_with_text.py

@@ -10,9 +10,10 @@
 import numpy as np
 from skimage import data
 from skimage.filters import threshold_otsu
-from skimage.segmentation import clear_border
 from skimage.measure import label, regionprops_table
-from skimage.morphology import closing, square, remove_small_objects
+from skimage.morphology import closing, remove_small_objects, square
+from skimage.segmentation import clear_border
+
 import napari
 
 

examples/bbox_annotator.py

@@ -5,12 +5,12 @@
 .. tags:: gui
 """
 
-from magicgui.widgets import ComboBox, Container
-import napari
 import numpy as np
 import pandas as pd
+from magicgui.widgets import ComboBox, Container
 from skimage import data
 
+import napari
 
 # set up the categorical annotation values and text display properties
 box_annotations = ['person', 'sky', 'camera']

examples/clipboard_.py

@@ -7,15 +7,16 @@
 .. tags:: gui
 """
 
+from qtpy.QtWidgets import QPushButton, QVBoxLayout, QWidget
 from skimage import data
-from qtpy.QtWidgets import QVBoxLayout, QPushButton, QWidget
+
 import napari
 
 # create the viewer with an image
 viewer = napari.view_image(data.moon())
 
 class Grabber(QWidget):
-    def __init__(self):
+    def __init__(self) -> None:
         super().__init__()
 
         self.copy_canvas_btn = QPushButton("Copy Canvas to Clipboard", self)

examples/clipping_planes_interactive_.py

@@ -7,12 +7,13 @@
 
 .. tags:: experimental
 """
-import napari
 import numpy as np
-from skimage import data
 from scipy import ndimage
+from skimage import data
 from vispy.geometry import create_sphere
 
+import napari
+
 viewer = napari.Viewer(ndisplay=3)
 
 # VOLUME and LABELS