diff --git a/.flake8 b/.flake8
deleted file mode 100644
index 7cf3dea6f..000000000
--- a/.flake8
+++ /dev/null
@@ -1,3 +0,0 @@
-[flake8]
-exclude = .*/
-ignore = E203, E741, W503, W504
diff --git a/labelme/__init__.py b/labelme/__init__.py
index a544e969a..2ab8c3ca4 100644
--- a/labelme/__init__.py
+++ b/labelme/__init__.py
@@ -1,11 +1,7 @@
-# flake8: noqa
-
-import logging
 import sys
 
 from qtpy import QT_VERSION
 
-
 __appname__ = "labelme"
 
 # Semantic Versioning 2.0.0: https://semver.org/
@@ -17,12 +13,24 @@
 
 QT4 = QT_VERSION[0] == "4"
 QT5 = QT_VERSION[0] == "5"
-del QT_VERSION
 
 PY2 = sys.version[0] == "2"
 PY3 = sys.version[0] == "3"
-del sys
 
-from labelme.label_file import LabelFile
+# These need to be later than the above definitions due to
+# circular import dependencies.
+
 from labelme import testing
 from labelme import utils
+from labelme.label_file import LabelFile
+
+__all__ = [
+    "__appname__",
+    "LabelFile",
+    "PY2",
+    "PY3",
+    "QT4",
+    "QT5",
+    "testing",
+    "utils",
+]
diff --git a/labelme/cli/__init__.py b/labelme/cli/__init__.py
index 75751a56e..d44a080ba 100644
--- a/labelme/cli/__init__.py
+++ b/labelme/cli/__init__.py
@@ -1,6 +1,11 @@
-# flake8: noqa
-
 from . import draw_json
 from . import draw_label_png
 from . import export_json
 from . import on_docker
+
+__all__ = [
+    'draw_json',
+    'draw_label_png',
+    'export_json',
+    'on_docker',
+]
diff --git a/labelme/utils/__init__.py b/labelme/utils/__init__.py
index 7fa2154fe..7388cde14 100644
--- a/labelme/utils/__init__.py
+++ b/labelme/utils/__init__.py
@@ -1,7 +1,4 @@
-# flake8: noqa
-
 from ._io import lblsave
-
 from .image import apply_exif_orientation
 from .image import img_arr_to_b64
 from .image import img_arr_to_data
@@ -11,19 +8,44 @@
 from .image import img_data_to_png_data
 from .image import img_pil_to_data
 from .image import img_qt_to_arr
-
+from .qt import addActions
+from .qt import distance
+from .qt import distancetoline
+from .qt import fmtShortcut
+from .qt import labelValidator
+from .qt import newAction
+from .qt import newButton
+from .qt import newIcon
+from .qt import struct
 from .shape import labelme_shapes_to_label
 from .shape import masks_to_bboxes
 from .shape import polygons_to_mask
 from .shape import shape_to_mask
 from .shape import shapes_to_label
 
-from .qt import newIcon
-from .qt import newButton
-from .qt import newAction
-from .qt import addActions
-from .qt import labelValidator
-from .qt import struct
-from .qt import distance
-from .qt import distancetoline
-from .qt import fmtShortcut
+__all__ = [
+    "addActions",
+    "apply_exif_orientation",
+    "distance",
+    "distancetoline",
+    "fmtShortcut",
+    "img_arr_to_b64",
+    "img_arr_to_data",
+    "img_b64_to_arr",
+    "img_data_to_arr",
+    "img_data_to_pil",
+    "img_data_to_png_data",
+    "img_pil_to_data",
+    "img_qt_to_arr",
+    "labelValidator",
+    "labelme_shapes_to_label",
+    "lblsave",
+    "masks_to_bboxes",
+    "newAction",
+    "newButton",
+    "newIcon",
+    "polygons_to_mask",
+    "shape_to_mask",
+    "shapes_to_label",
+    "struct",
+]
diff --git a/labelme/widgets/__init__.py b/labelme/widgets/__init__.py
index 6283ef1e8..d2136f0b4 100644
--- a/labelme/widgets/__init__.py
+++ b/labelme/widgets/__init__.py
@@ -1,23 +1,27 @@
-# flake8: noqa
-
 from .ai_prompt_widget import AiPromptWidget
-
 from .brightness_contrast_dialog import BrightnessContrastDialog
-
 from .canvas import Canvas
-
 from .color_dialog import ColorDialog
-
 from .file_dialog_preview import FileDialogPreview
-
 from .label_dialog import LabelDialog
 from .label_dialog import LabelQLineEdit
-
 from .label_list_widget import LabelListWidget
 from .label_list_widget import LabelListWidgetItem
-
 from .tool_bar import ToolBar
-
 from .unique_label_qlist_widget import UniqueLabelQListWidget
-
 from .zoom_widget import ZoomWidget
+
+__all__ = [
+    "AiPromptWidget",
+    "BrightnessContrastDialog",
+    "Canvas",
+    "ColorDialog",
+    "FileDialogPreview",
+    "LabelDialog",
+    "LabelQLineEdit",
+    "LabelListWidget",
+    "LabelListWidgetItem",
+    "ToolBar",
+    "UniqueLabelQListWidget",
+    "ZoomWidget",
+]
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 994f110c6..a2c8bf63b 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,5 +1,5 @@
 github2pypi==1.0.0
 pytest
 pytest-qt
-ruff==0.1.9
+ruff==0.5.7
 twine
diff --git a/ruff.toml b/ruff.toml
index 205cc1d18..e524c154e 100644
--- a/ruff.toml
+++ b/ruff.toml
@@ -31,3 +31,8 @@ line-ending = "auto"
 
 [lint.isort]
 force-single-line = true
+
+[lint.per-file-ignores]
+"**/__init__.py" = [
+  "E402", # module level import not at top of file
+]