[MAINT] switch to ruff, per napari/napari (#199)

Just to make life easier, switching this repo to also use ruff like
napari/napari, instead of flake8 and isort.
Also dropped some old Conda cruft from tox.ini which wasn't used.

After making the tooling changes, I also ran ruff and made various fixes
to get everything to pass.

.github/workflows/test_and_deploy.yml

@@ -25,7 +25,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        task: [flake8, black, isort]
+        task: [black, ruff]
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.8

.pre-commit-config.yaml

@@ -1,25 +1,13 @@
 repos:
--   repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-    - id: isort
-      exclude: _vendor|vendored|examples 
--   repo: https://github.com/python/black
+-   repo: https://github.com/psf/black-pre-commit-mirror
     rev: 23.12.1
     hooks:
     - id: black
       pass_filenames: true
       exclude: _vendor|vendored|examples
--   repo: https://github.com/PyCQA/flake8
-    rev: 3.8.4
-    hooks:
-    - id: flake8
-      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: v2.7.4
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.9
     hooks:
-    - id: pyupgrade
-      args: ["--py37-plus"]
-      exclude: _vendor|vendored|examples
+    - id: ruff
+      args: [ --fix ]
+      exclude: _vendor|vendored|examples

README.md

@@ -119,10 +119,9 @@ You can make sure your `[dev]` installation is working properly by running
 `pytest .` from within the repository.
 
 > [!NOTE]
-> We use [`pre-commit`](https://pre-commit.com) to sort imports with
-> [`isort`](https://github.com/timothycrosley/isort), format code with
-> [`black`](https://github.com/psf/black), and lint with
-> [`flake8`](https://github.com/PyCQA/flake8) automatically prior to each commit.
+> We use [`pre-commit`](https://pre-commit.com) to sort imports and lint with
+> [`ruff`](https://github.com/astral-sh/ruff) and format code with
+> [`black`](https://github.com/psf/black) automatically prior to each commit.
 > To minmize test errors when submitting pull requests, please install `pre-commit`
 > in your environment as follows:
 > ```sh

napari_animation/__init__.py

@@ -2,3 +2,5 @@
 from .animation import Animation
 from .key_frame import KeyFrame
 from .viewer_state import ViewerState
+
+__all__ = ["AnimationWidget", "Animation", "KeyFrame", "ViewerState"]

napari_animation/_qt/__init__.py

@@ -1 +1,3 @@
 from .animation_widget import AnimationWidget
+
+__all__ = ["AnimationWidget"]

napari_animation/_qt/animation_widget.py

@@ -10,7 +10,8 @@
     QWidget,
 )
 
-from ..animation import Animation
+from napari_animation.animation import Animation
+
 from .frame_widget import FrameWidget
 from .keyframelistcontrol_widget import KeyFrameListControlWidget
 from .keyframeslist_widget import KeyFramesListWidget

napari_animation/_qt/savedialog_widget.py

@@ -35,12 +35,12 @@ def getAnimationParameters(
         self,
         parent=None,
         caption="Select a file :",
-        dir=".",
+        directory=".",
         options=None,
     ):
         # Set dialog parameters
         self.setWindowTitle(caption)
-        self.setDirectory(dir)
+        self.setDirectory(directory)
         self.setNameFilter(self._qt_file_name_filters)
         self.setFileMode(QFileDialog.AnyFile)
         self.setAcceptMode(QFileDialog.AcceptSave)

napari_animation/_tests/conftest.py

@@ -18,7 +18,7 @@ def empty_animation(make_napari_viewer):
 
 @pytest.fixture
 def animation_with_key_frames(empty_animation):
-    for i in range(2):
+    for _i in range(2):
         empty_animation.capture_keyframe()
         empty_animation.viewer.camera.zoom *= 2
     return empty_animation

napari_animation/_tests/test_animation.py

@@ -139,7 +139,7 @@ def test_animation_file_metadata(animation_with_key_frames, tmp_path, ext):
 def test_layer_attribute_capture(layer_state, attribute):
     """Test that 'attribute' is captured in the layer state dictionary"""
     for layer_state_dict in layer_state.values():
-        assert attribute in layer_state_dict.keys()
+        assert attribute in layer_state_dict
 
 
 def test_end_state_reached(image_animation):

napari_animation/_tests/test_utils.py

@@ -5,7 +5,7 @@
 input_dict = [{"a": 1, "b": {"c": "d"}}]
 keys = [["b", "c"]]
 expected = ["d"]
-test_set = [param for param in zip(input_dict, keys, expected)]
+test_set = list(zip(input_dict, keys, expected))
 
 
 @pytest.mark.parametrize("input_dict,keys,expected", test_set)
@@ -16,12 +16,12 @@ def test_nested_get(input_dict, keys, expected):
 
 input_dict = [{"a": 1, "b": {"c": "d"}, "e": {}}]
 expected = [[["a"], ["b", "c"], ["e"]]]
-test_set = [param for param in zip(input_dict, expected)]
+test_set = list(zip(input_dict, expected))
 
 
 @pytest.mark.parametrize("input_dict,expected", test_set)
 def test_keys_to_list(input_dict, expected):
-    result = [keys for keys in keys_to_list(input_dict)]
+    result = list(keys_to_list(input_dict))
     for keys in result:
         assert isinstance(keys, list)
     assert result == expected

napari_animation/animation.py

@@ -142,7 +142,7 @@ def animate(
         filename,
         fps=20,
         quality=5,
-        format=None,
+        file_format=None,
         canvas_only=True,
         scale_factor=None,
     ):
@@ -158,7 +158,7 @@ def animate(
         quality: float
             number from 1 (lowest quality) to 9
             only applies to non-gif extensions
-        format: str
+        file_format: str
             The format to use to write the file. By default imageio selects the appropriate
             for you based on the filename.
         canvas_only : bool
@@ -202,14 +202,14 @@ def animate(
                         filename,
                         fps=fps,
                         quality=quality,
-                        format=format,
+                        format=file_format,
                         output_params=output_params,
                     )
                 else:
                     writer = imageio.get_writer(
                         filename,
                         duration=duration,
-                        format=format,
+                        format=file_format,
                     )
             except ValueError as err:
                 print(err)

napari_animation/frame_sequence.py

@@ -126,10 +126,10 @@ def __getitem__(self, key: int) -> ViewerState:
         if key not in self._cache:
             try:
                 kf0, kf1, frac = self._keyframe_index[key]
-            except KeyError:
+            except KeyError as err:
                 raise IndexError(
                     f"Frame index ({key}) out of range ({len(self)} frames)"
-                )
+                ) from err
             if frac == 0:
                 self._cache[key] = kf0.viewer_state
             else:
@@ -149,7 +149,7 @@ def iter_frames(
         scale_factor: float = None,
     ) -> Iterator[np.ndarray]:
         """Iterate over interpolated viewer states, and yield rendered frames."""
-        for i, state in enumerate(self):
+        for _i, state in enumerate(self):
             frame = state.render(viewer, canvas_only=canvas_only)
             if scale_factor not in (None, 1):
                 from scipy import ndimage as ndi

napari_animation/interpolation/__init__.py

@@ -1,3 +1,5 @@
 from .interpolation_constants import Interpolation
 from .typing import InterpolationMap
 from .viewer_state_interpolation import interpolate_viewer_state
+
+__all__ = ["Interpolation", "InterpolationMap", "interpolate_viewer_state"]

napari_animation/interpolation/utils.py

@@ -67,8 +67,8 @@ def keys_to_list(input_dict):
 
 def nested_assert_close(a, b):
     """Assert close on nested dicts."""
-    a_keys = [key for key in keys_to_list(a)]
-    b_keys = [key for key in keys_to_list(b)]
+    a_keys = list(keys_to_list(a))
+    b_keys = list(keys_to_list(b))
 
     assert a_keys == b_keys
 

napari_animation/interpolation/viewer_state_interpolation.py

@@ -43,7 +43,7 @@ def interpolate_viewer_state(
         v0 = nested_get(initial_state, keys)
         v1 = nested_get(final_state, keys)
 
-        all_keys_are_strings = all([isinstance(key, str) for key in keys])
+        all_keys_are_strings = all(isinstance(key, str) for key in keys)
         if interpolation_map is not None and all_keys_are_strings:
             attribute_name = ".".join(keys)
             interpolation_function = interpolation_map.get(

napari_animation/utils.py

@@ -43,6 +43,6 @@ def layer_attribute_changed(value, original_value):
             return True
         return any(
             layer_attribute_changed(value[key], original_value[key])
-            for key in value.keys()
+            for key in value
         )
     return not np.array_equal(value, original_value)

napari_animation/viewer_state.py

@@ -1,3 +1,4 @@
+import contextlib
 from dataclasses import dataclass
 
 import napari
@@ -59,10 +60,8 @@ def apply(self, viewer: napari.viewer.Viewer):
                 # Only setattr if value has changed to avoid expensive redraws
                 # dicts can hold arrays, e.g. `color`, requiring comparisons of key/value pairs
                 if layer_attribute_changed(value, original_value):
-                    try:
+                    with contextlib.suppress(AttributeError):
                         setattr(layer, attribute_name, value)
-                    except AttributeError:
-                        pass
 
     def render(
         self, viewer: napari.viewer.Viewer, canvas_only: bool = True

pyproject.toml

@@ -30,3 +30,28 @@ exclude = '''
   | 
 )
 '''
+
+# same as napari-cookiecutter
+[tool.ruff]
+line-length = 79
+select = [
+    "E", "F", "W", #flake8
+    "UP", # pyupgrade
+    "I", # isort
+    "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
+    "SIM", # flake8-simplify
+]
+ignore = [
+    "E501", # line too long. let black handle this
+    "UP006", "UP007", # type annotation. As using magicgui require runtime type annotation then we disable this.
+    "SIM117", # flake8-simplify - some of merged with statements are not looking great with black, reanble after drop python 3.9
+]
+
+target-version = "py38"
+fix = true

setup.cfg

@@ -47,8 +47,7 @@ testing =
 dev =
     pre-commit
     black
-    flake8
-    isort
+    ruff
     check-manifest
     %(testing)s
 
@@ -60,25 +59,6 @@ napari.manifest =
 [options.package_data]
 napari-animation = napari.yaml
 
-[isort]
-profile = black
-line_length = 79
-skip_glob = examples/
-multi_line_output=3
-
-
-[flake8]
-# Ignores - https://lintlyci.github.io/Flake8Rules
-# E203  Whitespace before ':'  (sometimes conflicts with black)
-# E501 line too long (84 > 79 characters)  (sometimes too annoying)
-# W503	Line break occurred before a binary operator
-# C901 McCabe complexity test. Would be nice to re-enable, but takes work
-ignore = E203,W503,E501,C901
-max-line-length = 79
-max-complexity = 18
-exclude = __init__.py,examples
-
-
 [coverage:report]
 exclude_lines =
     pragma: no cover

tox.ini

@@ -27,11 +27,6 @@ passenv =
     XAUTHORITY
     NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
     PYVISTA_OFF_SCREEN
-conda_deps =
-    # use conda to install numcodecs on mac py3.9
-    py39-macos: numcodecs
-conda_channels =
-    conda-forge
 deps = 
     pytest  # https://docs.pytest.org/en/latest/contents.html
     pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
@@ -47,16 +42,10 @@ deps =
 deps =
     napari[pyside2,testing]
 
-[testenv:isort]
+[testenv:ruff]
 skip_install = True
 deps = pre-commit
-commands = pre-commit run isort --all-files
-
-
-[testenv:flake8]
-skip_install = True
-deps = pre-commit
-commands = pre-commit run flake8 --all-files
+commands = pre-commit run ruff --all-files
 
 
 [testenv:black]