diff --git a/.github/workflows/python-cleanliness.yml b/.github/workflows/python-cleanliness.yml
index 6a001b8fb6..5d5b39cbad 100644
--- a/.github/workflows/python-cleanliness.yml
+++ b/.github/workflows/python-cleanliness.yml
@@ -11,15 +11,17 @@ jobs:
     runs-on: ubuntu-22.04
 
     steps:
-      # git checkout the PR
       - uses: actions/checkout@v5
         with:
           submodules: 'recursive'
 
+      # Run flake8 but exclude git submodules and third-party libraries
+      - run: pipx run flake8 --show-source --exclude=MAVProxy/modules/mavproxy_cesium
+
       - name: Install dependencies
         run: |
-          python -m pip install -U flake8
+          python -m pip install --upgrade flake8
 
       - name: Check Python with Flake8
         run: |
-            scripts/run_flake8.py MAVProxy
+          scripts/run_flake8.py MAVProxy
diff --git a/MAVProxy/modules/lib/ANUGA/geo_reference.py b/MAVProxy/modules/lib/ANUGA/geo_reference.py
index d7027d0f9b..1f72803890 100644
--- a/MAVProxy/modules/lib/ANUGA/geo_reference.py
+++ b/MAVProxy/modules/lib/ANUGA/geo_reference.py
@@ -4,6 +4,7 @@
 
 """
 
+# flake8: noqa
 
 #FIXME: Ensure that all attributes of a georef are treated everywhere
 #and unit test
diff --git a/MAVProxy/modules/lib/ANUGA/lat_long_UTM_conversion.py b/MAVProxy/modules/lib/ANUGA/lat_long_UTM_conversion.py
index f751a3431f..3ba11376c0 100644
--- a/MAVProxy/modules/lib/ANUGA/lat_long_UTM_conversion.py
+++ b/MAVProxy/modules/lib/ANUGA/lat_long_UTM_conversion.py
@@ -5,6 +5,8 @@
 # see http://www.pygps.org
 #
 
+# flake8: noqa
+
 from math import pi, sin, cos, tan, sqrt
 
 #LatLong- UTM conversion..h
diff --git a/MAVProxy/modules/lib/ANUGA/redfearn.py b/MAVProxy/modules/lib/ANUGA/redfearn.py
index cdb5b0b416..434a8156d0 100644
--- a/MAVProxy/modules/lib/ANUGA/redfearn.py
+++ b/MAVProxy/modules/lib/ANUGA/redfearn.py
@@ -12,6 +12,8 @@
 http://www.icsm.gov.au/icsm/
 
 """
+# flake8: noqa
+
 from MAVProxy.modules.lib.ANUGA.geo_reference import Geo_reference, DEFAULT_ZONE
 
 
diff --git a/MAVProxy/modules/lib/LowPassFilter2p.py b/MAVProxy/modules/lib/LowPassFilter2p.py
index d2c656270b..44822a9d76 100644
--- a/MAVProxy/modules/lib/LowPassFilter2p.py
+++ b/MAVProxy/modules/lib/LowPassFilter2p.py
@@ -1,5 +1,7 @@
 #!/usr/bin/env python3
 
+# flake8: noqa
+
 from math import *
 
 class LowPassFilter2p:
diff --git a/MAVProxy/modules/lib/MacOS/__init__.py b/MAVProxy/modules/lib/MacOS/__init__.py
index 4f8c669301..079ab3dc99 100644
--- a/MAVProxy/modules/lib/MacOS/__init__.py
+++ b/MAVProxy/modules/lib/MacOS/__init__.py
@@ -1,2 +1 @@
 # version of matplotlib backends modified to work with MacOS
-
diff --git a/MAVProxy/modules/lib/MacOS/backend_agg.py b/MAVProxy/modules/lib/MacOS/backend_agg.py
index 2ed9c4b097..1d9ba629f0 100644
--- a/MAVProxy/modules/lib/MacOS/backend_agg.py
+++ b/MAVProxy/modules/lib/MacOS/backend_agg.py
@@ -19,6 +19,8 @@
   * integrate screen dpi w/ ppi and text
 
 """
+# flake8: noqa
+
 import threading
 import numpy as np
 
diff --git a/MAVProxy/modules/lib/MacOS/backend_wx.py b/MAVProxy/modules/lib/MacOS/backend_wx.py
index 561c0f9075..6e7047ceba 100644
--- a/MAVProxy/modules/lib/MacOS/backend_wx.py
+++ b/MAVProxy/modules/lib/MacOS/backend_wx.py
@@ -14,6 +14,8 @@
 
 """
 
+# flake8: noqa
+
 import sys
 import os
 import os.path
diff --git a/MAVProxy/modules/lib/MacOS/backend_wxagg.py b/MAVProxy/modules/lib/MacOS/backend_wxagg.py
index 1137cec50c..b4c91a0399 100644
--- a/MAVProxy/modules/lib/MacOS/backend_wxagg.py
+++ b/MAVProxy/modules/lib/MacOS/backend_wxagg.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 import matplotlib
 from matplotlib.figure import Figure
 
diff --git a/MAVProxy/modules/lib/MacOS/wxversion.py b/MAVProxy/modules/lib/MacOS/wxversion.py
index cef5886a9b..7237aa9d67 100644
--- a/MAVProxy/modules/lib/MacOS/wxversion.py
+++ b/MAVProxy/modules/lib/MacOS/wxversion.py
@@ -74,6 +74,8 @@
 
 """
 
+# flake8: noqa
+
 import re, sys, os, glob, fnmatch
 
 
diff --git a/MAVProxy/modules/lib/camera_projection.py b/MAVProxy/modules/lib/camera_projection.py
index 815aecb0b9..87e96b67fc 100755
--- a/MAVProxy/modules/lib/camera_projection.py
+++ b/MAVProxy/modules/lib/camera_projection.py
@@ -3,6 +3,8 @@
 class to project a camera view onto the map
 '''
 
+# flake8: noqa
+
 import json
 import math
 import time
diff --git a/MAVProxy/modules/lib/dumpstacks.py b/MAVProxy/modules/lib/dumpstacks.py
index 27278e1b74..d6251328d9 100644
--- a/MAVProxy/modules/lib/dumpstacks.py
+++ b/MAVProxy/modules/lib/dumpstacks.py
@@ -1,5 +1,4 @@
-
-
+# flake8: noqa
 
 import threading, sys, traceback
 
diff --git a/MAVProxy/modules/lib/geodesic_grid.py b/MAVProxy/modules/lib/geodesic_grid.py
index 5e51d9147b..52e72362e1 100644
--- a/MAVProxy/modules/lib/geodesic_grid.py
+++ b/MAVProxy/modules/lib/geodesic_grid.py
@@ -20,6 +20,8 @@
 as reference for defining the geodesic sections and implementing almost all
 functions. Those files should be consulted for implementation details.
 '''
+# flake8: noqa
+
 import math
 
 from pymavlink.rotmat import Matrix3, Vector3
diff --git a/MAVProxy/modules/lib/graph_ui.py b/MAVProxy/modules/lib/graph_ui.py
index e262dc4cce..7e259fc491 100644
--- a/MAVProxy/modules/lib/graph_ui.py
+++ b/MAVProxy/modules/lib/graph_ui.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 from MAVProxy.modules.lib import grapher
 from MAVProxy.modules.lib import multiproc
 
diff --git a/MAVProxy/modules/lib/graphdefinition.py b/MAVProxy/modules/lib/graphdefinition.py
index ffb8353678..d3d967dc1f 100644
--- a/MAVProxy/modules/lib/graphdefinition.py
+++ b/MAVProxy/modules/lib/graphdefinition.py
@@ -2,6 +2,8 @@
 GraphDefinition class
 '''
 
+# flake8: noqa
+
 class GraphDefinition(object):
     '''a pre-defined graph'''
     def __init__(self, name, expression, description, expressions, filename):
diff --git a/MAVProxy/modules/lib/grapher.py b/MAVProxy/modules/lib/grapher.py
index fe5884aba9..155f66001b 100755
--- a/MAVProxy/modules/lib/grapher.py
+++ b/MAVProxy/modules/lib/grapher.py
@@ -4,6 +4,8 @@
  core library for graphing in mavexplorer
 '''
 
+# flake8: noqa
+
 import ast
 import sys, struct, time, os, datetime, platform
 import math, re
diff --git a/MAVProxy/modules/lib/live_graph.py b/MAVProxy/modules/lib/live_graph.py
index d11a4107d5..4a6a5797e0 100755
--- a/MAVProxy/modules/lib/live_graph.py
+++ b/MAVProxy/modules/lib/live_graph.py
@@ -8,6 +8,8 @@
   http://eli.thegreenplace.net/files/prog_code/wx_mpl_dynamic_graph.py.txt
 """
 
+# flake8: noqa
+
 import platform
 from MAVProxy.modules.lib import mp_util
 from MAVProxy.modules.lib import multiproc
diff --git a/MAVProxy/modules/lib/live_graph_ui.py b/MAVProxy/modules/lib/live_graph_ui.py
index 574a28d4ab..6edfa9cffc 100644
--- a/MAVProxy/modules/lib/live_graph_ui.py
+++ b/MAVProxy/modules/lib/live_graph_ui.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 from MAVProxy.modules.lib.wx_loader import wx
 from MAVProxy.modules.lib import icon
 import time
diff --git a/MAVProxy/modules/lib/magfit.py b/MAVProxy/modules/lib/magfit.py
index 499809e74c..5f663ebd2a 100644
--- a/MAVProxy/modules/lib/magfit.py
+++ b/MAVProxy/modules/lib/magfit.py
@@ -4,6 +4,8 @@
 fit best estimate of magnetometer offsets, diagonals, off-diagonals, cmot and scaling using WMM target
 '''
 
+# flake8: noqa
+
 from MAVProxy.modules.lib import wx_processguard
 from MAVProxy.modules.lib.wx_loader import wx
 
diff --git a/MAVProxy/modules/lib/mav_fft.py b/MAVProxy/modules/lib/mav_fft.py
index 9a686fe59f..29237758a4 100644
--- a/MAVProxy/modules/lib/mav_fft.py
+++ b/MAVProxy/modules/lib/mav_fft.py
@@ -4,6 +4,8 @@
 extract ISBH and ISBD messages from AP_Logging files and produce FFT plots
 '''
 
+# flake8: noqa
+
 import numpy
 import os
 import pylab
diff --git a/MAVProxy/modules/lib/mp_checklist.py b/MAVProxy/modules/lib/mp_checklist.py
index 1be8dbf0dc..373f63870f 100755
--- a/MAVProxy/modules/lib/mp_checklist.py
+++ b/MAVProxy/modules/lib/mp_checklist.py
@@ -5,6 +5,8 @@
   Created by Stephen Dade (stephen_dade@hotmail.com)
 """
 
+# flake8: noqa
+
 import sys
 import os
 import time
diff --git a/MAVProxy/modules/lib/mp_elevation.py b/MAVProxy/modules/lib/mp_elevation.py
index 47af99b041..50cdcf5ed7 100755
--- a/MAVProxy/modules/lib/mp_elevation.py
+++ b/MAVProxy/modules/lib/mp_elevation.py
@@ -5,6 +5,8 @@
 Created by Stephen Dade (stephen_dade@hotmail.com)
 '''
 
+# flake8: noqa
+
 import os
 import sys
 import time
diff --git a/MAVProxy/modules/lib/mp_image.py b/MAVProxy/modules/lib/mp_image.py
index 13980d6e0b..35fee7f319 100755
--- a/MAVProxy/modules/lib/mp_image.py
+++ b/MAVProxy/modules/lib/mp_image.py
@@ -6,6 +6,8 @@
 June 2012
 '''
 
+# flake8: noqa
+
 import time
 from MAVProxy.modules.lib.wx_loader import wx
 import cv2
diff --git a/MAVProxy/modules/lib/mp_instructor.py b/MAVProxy/modules/lib/mp_instructor.py
index 02c4cb70af..ef7e7330bb 100755
--- a/MAVProxy/modules/lib/mp_instructor.py
+++ b/MAVProxy/modules/lib/mp_instructor.py
@@ -5,6 +5,8 @@
   André Kjellstrup @ NORCE
 """
 
+# flake8: noqa
+
 from MAVProxy.modules.lib import mp_util
 from MAVProxy.modules.lib import multiproc
 from MAVProxy.modules.lib.wx_loader import wx
diff --git a/MAVProxy/modules/lib/mp_menu.py b/MAVProxy/modules/lib/mp_menu.py
index 2ef3d40adb..cd8465b5f4 100644
--- a/MAVProxy/modules/lib/mp_menu.py
+++ b/MAVProxy/modules/lib/mp_menu.py
@@ -6,6 +6,8 @@
 November 2013
 '''
 
+# flake8: noqa
+
 from MAVProxy.modules.lib import mp_util
 from MAVProxy.modules.lib import multiproc
 import platform
diff --git a/MAVProxy/modules/lib/mp_module.py b/MAVProxy/modules/lib/mp_module.py
index 9c64bf7657..7778313e70 100644
--- a/MAVProxy/modules/lib/mp_module.py
+++ b/MAVProxy/modules/lib/mp_module.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 import time
 from pymavlink import mavutil
 import traceback
diff --git a/MAVProxy/modules/lib/mp_settings.py b/MAVProxy/modules/lib/mp_settings.py
index 6a6cab25d6..d4317f8e6d 100644
--- a/MAVProxy/modules/lib/mp_settings.py
+++ b/MAVProxy/modules/lib/mp_settings.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''settings object for MAVProxy modules'''
 
+# flake8: noqa
+
 import time
 import fnmatch
 
diff --git a/MAVProxy/modules/lib/mp_substitute.py b/MAVProxy/modules/lib/mp_substitute.py
index 1bcb2273a6..acd3caa09f 100644
--- a/MAVProxy/modules/lib/mp_substitute.py
+++ b/MAVProxy/modules/lib/mp_substitute.py
@@ -2,6 +2,8 @@
 variable substitution in strings using a dictionary
 '''
 
+# flake8: noqa
+
 import sys
 
 class MAVSubstituteError(Exception):
diff --git a/MAVProxy/modules/lib/mp_util.py b/MAVProxy/modules/lib/mp_util.py
index 86a44ff515..4ed4ee63b1 100644
--- a/MAVProxy/modules/lib/mp_util.py
+++ b/MAVProxy/modules/lib/mp_util.py
@@ -2,6 +2,8 @@
 # -*- coding: utf-8 -*-
 '''common mavproxy utility functions'''
 
+# flake8: noqa
+
 import gzip
 import math
 import os
diff --git a/MAVProxy/modules/lib/mp_widgets.py b/MAVProxy/modules/lib/mp_widgets.py
index 9115a572ef..26cbfc41d4 100644
--- a/MAVProxy/modules/lib/mp_widgets.py
+++ b/MAVProxy/modules/lib/mp_widgets.py
@@ -6,6 +6,8 @@
 June 2012
 '''
 
+# flake8: noqa
+
 from MAVProxy.modules.lib.wx_loader import wx
 import cv2
 import numpy as np
diff --git a/MAVProxy/modules/lib/msgstats.py b/MAVProxy/modules/lib/msgstats.py
index cab9cc37c5..941bcebf35 100644
--- a/MAVProxy/modules/lib/msgstats.py
+++ b/MAVProxy/modules/lib/msgstats.py
@@ -4,6 +4,8 @@
 show stats on messages in a log in MAVExplorer
 '''
 
+# flake8: noqa
+
 import fnmatch
 from MAVProxy.modules.lib.multiproc_util import MPDataLogChildTask
 
diff --git a/MAVProxy/modules/lib/multiproc.py b/MAVProxy/modules/lib/multiproc.py
index 524100e5b0..629a50905c 100644
--- a/MAVProxy/modules/lib/multiproc.py
+++ b/MAVProxy/modules/lib/multiproc.py
@@ -10,6 +10,8 @@
 make things work on MacOS
 '''
 
+# flake8: noqa
+
 class PipeQueue(object):
     '''simulate a queue using a pipe. This is used to avoid a problem with
     pipes on MacOS, while still keeping similar syntax'''
diff --git a/MAVProxy/modules/lib/multiproc_util.py b/MAVProxy/modules/lib/multiproc_util.py
index 734a1f59af..a1dfcef567 100644
--- a/MAVProxy/modules/lib/multiproc_util.py
+++ b/MAVProxy/modules/lib/multiproc_util.py
@@ -4,6 +4,8 @@
     custom pickle functions and class wrappers
 '''
 
+# flake8: noqa
+
 from MAVProxy.modules.lib import multiproc
 
 import copyreg
diff --git a/MAVProxy/modules/lib/ntrip.py b/MAVProxy/modules/lib/ntrip.py
index 66586c8cc8..b6216c7228 100755
--- a/MAVProxy/modules/lib/ntrip.py
+++ b/MAVProxy/modules/lib/ntrip.py
@@ -4,6 +4,8 @@
  based on client from http://github.com/jcmb/NTRIP
 """
 
+# flake8: noqa
+
 import socket
 import sys
 import datetime
diff --git a/MAVProxy/modules/lib/opengl.py b/MAVProxy/modules/lib/opengl.py
index dff71bee05..13ed81c68f 100644
--- a/MAVProxy/modules/lib/opengl.py
+++ b/MAVProxy/modules/lib/opengl.py
@@ -15,6 +15,8 @@
 '''
 Module with helpers for OpenGL rendering.
 '''
+# flake8: noqa
+
 import math
 
 from ctypes import *
diff --git a/MAVProxy/modules/lib/optparse_gui/__init__.py b/MAVProxy/modules/lib/optparse_gui/__init__.py
index 1aa76a716f..fc35c83186 100644
--- a/MAVProxy/modules/lib/optparse_gui/__init__.py
+++ b/MAVProxy/modules/lib/optparse_gui/__init__.py
@@ -5,6 +5,8 @@
 options/args, instead of parsing command line arguments
 '''
 
+# flake8: noqa
+
 import os
 import sys
 import re
diff --git a/MAVProxy/modules/lib/param_ftp.py b/MAVProxy/modules/lib/param_ftp.py
index 9e2cbfc9cd..431a3b392a 100755
--- a/MAVProxy/modules/lib/param_ftp.py
+++ b/MAVProxy/modules/lib/param_ftp.py
@@ -3,6 +3,8 @@
 decode ftp parameter protocol data
 '''
 
+# flake8: noqa
+
 import struct
 import sys
 
diff --git a/MAVProxy/modules/lib/param_help.py b/MAVProxy/modules/lib/param_help.py
index 0ba9842a64..d10ba98cfc 100644
--- a/MAVProxy/modules/lib/param_help.py
+++ b/MAVProxy/modules/lib/param_help.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 import time, os
 from pymavlink import mavutil, mavparm
 from MAVProxy.modules.lib import mp_util
diff --git a/MAVProxy/modules/lib/rline.py b/MAVProxy/modules/lib/rline.py
index 5062c82706..cbad6f3221 100644
--- a/MAVProxy/modules/lib/rline.py
+++ b/MAVProxy/modules/lib/rline.py
@@ -2,6 +2,8 @@
 readline handling for mavproxy
 '''
 
+# flake8: noqa
+
 import sys, glob, os, platform
 import re
 
diff --git a/MAVProxy/modules/lib/rtcm3.py b/MAVProxy/modules/lib/rtcm3.py
index 5bde1a57b2..f322e47bfd 100644
--- a/MAVProxy/modules/lib/rtcm3.py
+++ b/MAVProxy/modules/lib/rtcm3.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''Decode RTCM v3 messages'''
 
+# flake8: noqa
+
 RTCMv3_PREAMBLE = 0xD3
 POLYCRC24 = 0x1864CFB
 
diff --git a/MAVProxy/modules/lib/srtm.py b/MAVProxy/modules/lib/srtm.py
index 387a073309..e649d4ae29 100755
--- a/MAVProxy/modules/lib/srtm.py
+++ b/MAVProxy/modules/lib/srtm.py
@@ -1,5 +1,7 @@
 #!/usr/bin/env python3
 
+# flake8: noqa
+
 # Pylint: Disable name warnings
 # pylint: disable-msg=C0103
 
diff --git a/MAVProxy/modules/lib/textconsole.py b/MAVProxy/modules/lib/textconsole.py
index 31bc4fa2ea..72d09dd526 100644
--- a/MAVProxy/modules/lib/textconsole.py
+++ b/MAVProxy/modules/lib/textconsole.py
@@ -3,6 +3,8 @@
 """
   MAVProxy default console
 """
+# flake8: noqa
+
 import sys
 
 class SimpleConsole():
diff --git a/MAVProxy/modules/lib/wavefront.py b/MAVProxy/modules/lib/wavefront.py
index 1935c02b2a..fc57a75304 100644
--- a/MAVProxy/modules/lib/wavefront.py
+++ b/MAVProxy/modules/lib/wavefront.py
@@ -33,6 +33,8 @@
 Unsupported directives found while parsing are stored in the parser's
 ignored_directives attribute.
 '''
+# flake8: noqa
+
 import os
 try:
     import cPickle as pickle
diff --git a/MAVProxy/modules/lib/win_layout.py b/MAVProxy/modules/lib/win_layout.py
index 622c6b9c8c..16458824e9 100644
--- a/MAVProxy/modules/lib/win_layout.py
+++ b/MAVProxy/modules/lib/win_layout.py
@@ -1,5 +1,7 @@
 #!/usr/bin/env python3
 
+# flake8: noqa
+
 import os, wx, pickle
 from MAVProxy.modules.lib import mp_util
 
diff --git a/MAVProxy/modules/lib/wx_addlink.py b/MAVProxy/modules/lib/wx_addlink.py
index a68788b496..ee22fa0102 100644
--- a/MAVProxy/modules/lib/wx_addlink.py
+++ b/MAVProxy/modules/lib/wx_addlink.py
@@ -3,6 +3,8 @@
 GUI for adding new links to MAVProxy
 '''
 
+# flake8: noqa
+
 import wx
 from pymavlink import mavutil
 
diff --git a/MAVProxy/modules/lib/wx_loader.py b/MAVProxy/modules/lib/wx_loader.py
index e79912723d..16f8868545 100644
--- a/MAVProxy/modules/lib/wx_loader.py
+++ b/MAVProxy/modules/lib/wx_loader.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 from MAVProxy.modules.lib import wx_util
 
 if not wx_util.safe:
diff --git a/MAVProxy/modules/lib/wxconsole.py b/MAVProxy/modules/lib/wxconsole.py
index e172eaad51..9faa9a6419 100755
--- a/MAVProxy/modules/lib/wxconsole.py
+++ b/MAVProxy/modules/lib/wxconsole.py
@@ -3,6 +3,8 @@
 """
   MAVProxy message console, implemented in a child process
 """
+# flake8: noqa
+
 import threading
 import sys, time
 
diff --git a/MAVProxy/modules/lib/wxconsole_ui.py b/MAVProxy/modules/lib/wxconsole_ui.py
index 444578d135..65e88a9114 100644
--- a/MAVProxy/modules/lib/wxconsole_ui.py
+++ b/MAVProxy/modules/lib/wxconsole_ui.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 import errno
 import time
 import platform
diff --git a/MAVProxy/modules/lib/wxconsole_util.py b/MAVProxy/modules/lib/wxconsole_util.py
index 98a7dc9e19..171fee989d 100644
--- a/MAVProxy/modules/lib/wxconsole_util.py
+++ b/MAVProxy/modules/lib/wxconsole_util.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 class Text():
     '''text to write to console'''
     def __init__(self, text, fg='black', bg='white'):
diff --git a/MAVProxy/modules/lib/wxgrapheditor.py b/MAVProxy/modules/lib/wxgrapheditor.py
index 9845c9885b..d05c587dd2 100644
--- a/MAVProxy/modules/lib/wxgrapheditor.py
+++ b/MAVProxy/modules/lib/wxgrapheditor.py
@@ -1,6 +1,8 @@
 '''
 Graphical editing of graph definition
 '''
+# flake8: noqa
+ 
 from MAVProxy.modules.lib.wx_loader import wx
 from MAVProxy.modules.lib.graphdefinition import GraphDefinition
 
diff --git a/MAVProxy/modules/lib/wxhorizon.py b/MAVProxy/modules/lib/wxhorizon.py
index 0271144634..c84678660d 100755
--- a/MAVProxy/modules/lib/wxhorizon.py
+++ b/MAVProxy/modules/lib/wxhorizon.py
@@ -3,6 +3,8 @@
 """
   MAVProxy horizon indicator.
 """
+# flake8: noqa
+ 
 from MAVProxy.modules.lib import multiproc
 import time
 
diff --git a/MAVProxy/modules/lib/wxhorizon_ui.py b/MAVProxy/modules/lib/wxhorizon_ui.py
index 1489afb34d..cf8a015c13 100644
--- a/MAVProxy/modules/lib/wxhorizon_ui.py
+++ b/MAVProxy/modules/lib/wxhorizon_ui.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 import time
 from MAVProxy.modules.lib.wxhorizon_util import Attitude, VFR_HUD, Global_Position_INT, BatteryInfo, FlightState, WaypointInfo, FPS
 from MAVProxy.modules.lib.wx_loader import wx
diff --git a/MAVProxy/modules/lib/wxhorizon_util.py b/MAVProxy/modules/lib/wxhorizon_util.py
index 0e5f8a1155..fff3e892a2 100644
--- a/MAVProxy/modules/lib/wxhorizon_util.py
+++ b/MAVProxy/modules/lib/wxhorizon_util.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 class Attitude():
     '''The current Attitude Data'''
     def __init__(self, attitudeMsg):
diff --git a/MAVProxy/modules/lib/wxrc.py b/MAVProxy/modules/lib/wxrc.py
index df04fb97b4..d156a212d9 100644
--- a/MAVProxy/modules/lib/wxrc.py
+++ b/MAVProxy/modules/lib/wxrc.py
@@ -3,6 +3,8 @@
 """
   MAVProxy RC GUI
 """
+# flake8: noqa
+
 from MAVProxy.modules.lib import multiproc
 from MAVProxy.modules.lib.wx_loader import wx
 import wx.lib.agw.pygauge as PG
diff --git a/MAVProxy/modules/lib/wxsaildash.py b/MAVProxy/modules/lib/wxsaildash.py
index 22e3025f38..a6804681aa 100644
--- a/MAVProxy/modules/lib/wxsaildash.py
+++ b/MAVProxy/modules/lib/wxsaildash.py
@@ -4,6 +4,8 @@
   MAVProxy sailing dashboard
 """
 
+# flake8: noqa
+
 from MAVProxy.modules.lib import multiproc
 import time
 
diff --git a/MAVProxy/modules/lib/wxsaildash_ui.py b/MAVProxy/modules/lib/wxsaildash_ui.py
index 60649535d9..10698bd94b 100644
--- a/MAVProxy/modules/lib/wxsaildash_ui.py
+++ b/MAVProxy/modules/lib/wxsaildash_ui.py
@@ -2,6 +2,8 @@
   MAVProxy sailing dashboard gui elements
 """
 
+# flake8: noqa
+
 from MAVProxy.modules.lib.wx_loader import wx
 from MAVProxy.modules.lib.wxsaildash_util import WindReference, SpeedUnit, WindAngleAndSpeed, WaterSpeedAndHeading
 
diff --git a/MAVProxy/modules/lib/wxsaildash_util.py b/MAVProxy/modules/lib/wxsaildash_util.py
index ccd2af0a6d..42fbba4a9b 100644
--- a/MAVProxy/modules/lib/wxsaildash_util.py
+++ b/MAVProxy/modules/lib/wxsaildash_util.py
@@ -2,6 +2,8 @@
 MAVProxy sailing dashboard utility classes
 '''
 
+# flake8: noqa
+
 import enum
 
 class WindReference(enum.Enum):
diff --git a/MAVProxy/modules/lib/wxsettings.py b/MAVProxy/modules/lib/wxsettings.py
index 0ff0909d08..68016b6026 100644
--- a/MAVProxy/modules/lib/wxsettings.py
+++ b/MAVProxy/modules/lib/wxsettings.py
@@ -1,6 +1,8 @@
 '''
 Graphical editing of mp_settings object
 '''
+# flake8: noqa
+
 import os, sys
 from MAVProxy.modules.lib import multiproc
 import threading
diff --git a/MAVProxy/modules/lib/wxsettings_ui.py b/MAVProxy/modules/lib/wxsettings_ui.py
index 3748341060..ef2a576c3c 100644
--- a/MAVProxy/modules/lib/wxsettings_ui.py
+++ b/MAVProxy/modules/lib/wxsettings_ui.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 import sys
 from MAVProxy.modules.lib.wx_loader import wx
 
diff --git a/MAVProxy/modules/mavproxy_DGPS.py b/MAVProxy/modules/mavproxy_DGPS.py
index 1b0be88704..d4e7d4b487 100644
--- a/MAVProxy/modules/mavproxy_DGPS.py
+++ b/MAVProxy/modules/mavproxy_DGPS.py
@@ -3,6 +3,8 @@
 support for a GCS attached DGPS system
 '''
 
+# flake8: noqa
+
 import socket, errno
 from pymavlink import mavutil
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_GPSInject.py b/MAVProxy/modules/mavproxy_GPSInject.py
index 4651762082..975eab1048 100644
--- a/MAVProxy/modules/mavproxy_GPSInject.py
+++ b/MAVProxy/modules/mavproxy_GPSInject.py
@@ -3,6 +3,8 @@
 primarily used to inject uBlox AssistNow data
 """
 
+# flake8: noqa
+
 import random
 import time
 import os
diff --git a/MAVProxy/modules/mavproxy_GPSInput.py b/MAVProxy/modules/mavproxy_GPSInput.py
index e285f3810e..3d3d00d846 100644
--- a/MAVProxy/modules/mavproxy_GPSInput.py
+++ b/MAVProxy/modules/mavproxy_GPSInput.py
@@ -3,6 +3,8 @@
 support for GPS_INPUT message
 '''
 
+# flake8: noqa
+
 import socket, errno
 import json
 from pymavlink import mavutil
diff --git a/MAVProxy/modules/mavproxy_HIL.py b/MAVProxy/modules/mavproxy_HIL.py
index b4dd73dc17..be5c60326c 100644
--- a/MAVProxy/modules/mavproxy_HIL.py
+++ b/MAVProxy/modules/mavproxy_HIL.py
@@ -7,6 +7,8 @@
 This interfaces to Tools/autotest/jsbsim/runsim.py to run the JSBSim flight simulator
 '''
 
+# flake8: noqa
+
 import sys, os, time, socket, errno, struct, math
 from math import degrees, radians
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_OpenDroneID.py b/MAVProxy/modules/mavproxy_OpenDroneID.py
index 8df2b10438..2d469c1791 100644
--- a/MAVProxy/modules/mavproxy_OpenDroneID.py
+++ b/MAVProxy/modules/mavproxy_OpenDroneID.py
@@ -2,6 +2,8 @@
 Support for OpenDroneID
 '''
 
+# flake8: noqa
+
 from MAVProxy.modules.lib import mp_module
 from MAVProxy.modules.lib import mp_settings
 from pymavlink import mavutil
diff --git a/MAVProxy/modules/mavproxy_SIYI/__init__.py b/MAVProxy/modules/mavproxy_SIYI/__init__.py
index 01de3104d5..367bde499c 100644
--- a/MAVProxy/modules/mavproxy_SIYI/__init__.py
+++ b/MAVProxy/modules/mavproxy_SIYI/__init__.py
@@ -7,6 +7,8 @@
   circle hottest area?
 '''
 
+# flake8: noqa
+
 from MAVProxy.modules.lib import mp_module
 from MAVProxy.modules.lib import mp_settings
 from MAVProxy.modules.lib.mp_settings import MPSetting
diff --git a/MAVProxy/modules/mavproxy_SIYI/camera_view.py b/MAVProxy/modules/mavproxy_SIYI/camera_view.py
index d6abf347b5..ea31e66506 100644
--- a/MAVProxy/modules/mavproxy_SIYI/camera_view.py
+++ b/MAVProxy/modules/mavproxy_SIYI/camera_view.py
@@ -1,5 +1,7 @@
 #!/usr/bin/env python3
 
+# flake8: noqa
+
 from threading import Thread
 import cv2
 
diff --git a/MAVProxy/modules/mavproxy_SIYI/raw_thermal.py b/MAVProxy/modules/mavproxy_SIYI/raw_thermal.py
index 58d5b6d086..909d48b88a 100644
--- a/MAVProxy/modules/mavproxy_SIYI/raw_thermal.py
+++ b/MAVProxy/modules/mavproxy_SIYI/raw_thermal.py
@@ -1,5 +1,7 @@
 #!/usr/bin/env python3
 
+# flake8: noqa
+
 from threading import Thread
 import cv2
 import os
diff --git a/MAVProxy/modules/mavproxy_SIYI/tools/playback.py b/MAVProxy/modules/mavproxy_SIYI/tools/playback.py
index 1f0277a942..8fddb082ce 100755
--- a/MAVProxy/modules/mavproxy_SIYI/tools/playback.py
+++ b/MAVProxy/modules/mavproxy_SIYI/tools/playback.py
@@ -3,6 +3,8 @@
 playback videos with temperature data
 '''
 
+# flake8: noqa
+
 from MAVProxy.modules.lib.mp_image import MPImage
 from MAVProxy.modules.lib.mp_image import MPImageFrameCounter
 from MAVProxy.modules.lib.mp_image import MPImageOSD_HorizonLine
diff --git a/MAVProxy/modules/mavproxy_SIYI/tools/temp_dir.py b/MAVProxy/modules/mavproxy_SIYI/tools/temp_dir.py
index 0092e79033..7bba7721f8 100755
--- a/MAVProxy/modules/mavproxy_SIYI/tools/temp_dir.py
+++ b/MAVProxy/modules/mavproxy_SIYI/tools/temp_dir.py
@@ -2,6 +2,8 @@
 
 # save images in therm cap
 
+# flake8: noqa
+
 import sys
 import numpy as np
 import cv2
diff --git a/MAVProxy/modules/mavproxy_SIYI/tools/temp_view.py b/MAVProxy/modules/mavproxy_SIYI/tools/temp_view.py
index 5dbd36557f..351a135be7 100755
--- a/MAVProxy/modules/mavproxy_SIYI/tools/temp_view.py
+++ b/MAVProxy/modules/mavproxy_SIYI/tools/temp_view.py
@@ -1,5 +1,7 @@
 #!/usr/bin/env python3
 
+# flake8: noqa
+
 import sys
 import numpy as np
 import cv2
diff --git a/MAVProxy/modules/mavproxy_SecureCommand.py b/MAVProxy/modules/mavproxy_SecureCommand.py
index 35389af3cd..02451e460e 100644
--- a/MAVProxy/modules/mavproxy_SecureCommand.py
+++ b/MAVProxy/modules/mavproxy_SecureCommand.py
@@ -2,6 +2,8 @@
 Support for MAVLink SECURE_COMMAND
 '''
 
+# flake8: noqa
+
 from MAVProxy.modules.lib import mp_module
 from MAVProxy.modules.lib import mp_settings
 from pymavlink import mavutil
diff --git a/MAVProxy/modules/mavproxy_adsb.py b/MAVProxy/modules/mavproxy_adsb.py
index 30375ddf8a..b549a3abb0 100644
--- a/MAVProxy/modules/mavproxy_adsb.py
+++ b/MAVProxy/modules/mavproxy_adsb.py
@@ -4,6 +4,8 @@
 Dec 2015
 '''
 
+# flake8: noqa
+
 from math import *
 
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_ais.py b/MAVProxy/modules/mavproxy_ais.py
index be9877bb48..b72392e989 100644
--- a/MAVProxy/modules/mavproxy_ais.py
+++ b/MAVProxy/modules/mavproxy_ais.py
@@ -4,6 +4,8 @@
 June 2021
 '''
 
+# flake8: noqa
+
 from pymavlink import mavutil
 
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_antenna.py b/MAVProxy/modules/mavproxy_antenna.py
index 8635e9d9a5..af29522a57 100644
--- a/MAVProxy/modules/mavproxy_antenna.py
+++ b/MAVProxy/modules/mavproxy_antenna.py
@@ -5,6 +5,8 @@
 June 2012
 '''
 
+# flake8: noqa
+
 import sys, os, time
 from cuav.lib import cuav_util
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_arm.py b/MAVProxy/modules/mavproxy_arm.py
index dac121729d..b8109a07bd 100644
--- a/MAVProxy/modules/mavproxy_arm.py
+++ b/MAVProxy/modules/mavproxy_arm.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''arm/disarm command handling'''
 
+# flake8: noqa
+
 import time, os
 
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_asterix.py b/MAVProxy/modules/mavproxy_asterix.py
index eca56d3be6..4bce15c378 100644
--- a/MAVProxy/modules/mavproxy_asterix.py
+++ b/MAVProxy/modules/mavproxy_asterix.py
@@ -4,6 +4,8 @@
 This listens for SDPS on UDP and translates to ADSB_VEHICLE messages
 '''
 
+# flake8: noqa
+
 import pickle
 from math import *
 
diff --git a/MAVProxy/modules/mavproxy_auxopt.py b/MAVProxy/modules/mavproxy_auxopt.py
index 63b238335e..fee432b22f 100644
--- a/MAVProxy/modules/mavproxy_auxopt.py
+++ b/MAVProxy/modules/mavproxy_auxopt.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''auxopt command handling'''
 
+# flake8: noqa
+
 import time, os
 from MAVProxy.modules.lib import mp_module
 
diff --git a/MAVProxy/modules/mavproxy_battery.py b/MAVProxy/modules/mavproxy_battery.py
index 06625dd4cf..414c95892c 100644
--- a/MAVProxy/modules/mavproxy_battery.py
+++ b/MAVProxy/modules/mavproxy_battery.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''battery commands'''
 
+# flake8: noqa
+
 import time, math
 from pymavlink import mavutil
 
diff --git a/MAVProxy/modules/mavproxy_calibration.py b/MAVProxy/modules/mavproxy_calibration.py
index e93bc32630..11c1b6ccc5 100644
--- a/MAVProxy/modules/mavproxy_calibration.py
+++ b/MAVProxy/modules/mavproxy_calibration.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''calibration command handling'''
 
+# flake8: noqa
+
 import time, os
 from pymavlink import mavutil
 
diff --git a/MAVProxy/modules/mavproxy_cameraview.py b/MAVProxy/modules/mavproxy_cameraview.py
index 300969ca80..9c7bf4933a 100644
--- a/MAVProxy/modules/mavproxy_cameraview.py
+++ b/MAVProxy/modules/mavproxy_cameraview.py
@@ -5,6 +5,8 @@
 Feb 2014
 '''
 
+# flake8: noqa
+
 import math
 from MAVProxy.modules.mavproxy_map import mp_slipmap
 from MAVProxy.modules.lib import mp_util
diff --git a/MAVProxy/modules/mavproxy_checklist.py b/MAVProxy/modules/mavproxy_checklist.py
index d236422a44..d6efa7ad78 100755
--- a/MAVProxy/modules/mavproxy_checklist.py
+++ b/MAVProxy/modules/mavproxy_checklist.py
@@ -5,6 +5,8 @@
 July 2014
 '''
 
+# flake8: noqa
+
 import math, sys, os, time
 from MAVProxy.modules.lib import mp_checklist
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_cmdlong.py b/MAVProxy/modules/mavproxy_cmdlong.py
index 0ff00fbe52..f83ad85641 100644
--- a/MAVProxy/modules/mavproxy_cmdlong.py
+++ b/MAVProxy/modules/mavproxy_cmdlong.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''command long'''
 
+# flake8: noqa
+
 import time, os
 from numpy import equal
 from pymavlink import mavutil
diff --git a/MAVProxy/modules/mavproxy_console.py b/MAVProxy/modules/mavproxy_console.py
index f094540593..952bf6638c 100644
--- a/MAVProxy/modules/mavproxy_console.py
+++ b/MAVProxy/modules/mavproxy_console.py
@@ -4,6 +4,8 @@
   uses lib/console.py for display
 """
 
+# flake8: noqa
+
 import os, sys, math, time, re
 import traceback
 
diff --git a/MAVProxy/modules/mavproxy_dataflash_logger.py b/MAVProxy/modules/mavproxy_dataflash_logger.py
index cc29631309..c77d0a35f7 100644
--- a/MAVProxy/modules/mavproxy_dataflash_logger.py
+++ b/MAVProxy/modules/mavproxy_dataflash_logger.py
@@ -13,6 +13,8 @@
 libraries/DataFlash/DataFlash_MAVLink.*
 '''
 
+# flake8: noqa
+
 import os
 import os.path
 from pymavlink import mavutil
diff --git a/MAVProxy/modules/mavproxy_devop.py b/MAVProxy/modules/mavproxy_devop.py
index 5ad10e4edb..7d02b066b7 100644
--- a/MAVProxy/modules/mavproxy_devop.py
+++ b/MAVProxy/modules/mavproxy_devop.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''remote low level device operations'''
 
+# flake8: noqa
+
 import time, os, sys
 from pymavlink import mavutil
 
diff --git a/MAVProxy/modules/mavproxy_emuecu.py b/MAVProxy/modules/mavproxy_emuecu.py
index 1354076e22..f55f7d2c73 100644
--- a/MAVProxy/modules/mavproxy_emuecu.py
+++ b/MAVProxy/modules/mavproxy_emuecu.py
@@ -2,6 +2,8 @@
 control EMU ECU system
 """
 
+# flake8: noqa
+
 import time
 
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_example.py b/MAVProxy/modules/mavproxy_example.py
index 953bb672f9..aba3ddec40 100644
--- a/MAVProxy/modules/mavproxy_example.py
+++ b/MAVProxy/modules/mavproxy_example.py
@@ -12,6 +12,8 @@
 3. trim (or comment) out any functionality you do not need
 '''
 
+# flake8: noqa
+
 import os
 import os.path
 import sys
diff --git a/MAVProxy/modules/mavproxy_fakegps.py b/MAVProxy/modules/mavproxy_fakegps.py
index c59ae5b07a..112f894098 100644
--- a/MAVProxy/modules/mavproxy_fakegps.py
+++ b/MAVProxy/modules/mavproxy_fakegps.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''fake GPS input using GPS_INPUT packet'''
 
+# flake8: noqa
+
 import time
 from MAVProxy.modules.lib import mp_module
 from MAVProxy.modules.lib import mp_settings
diff --git a/MAVProxy/modules/mavproxy_fenceitem_protocol.py b/MAVProxy/modules/mavproxy_fenceitem_protocol.py
index 4f7516143e..d510579044 100644
--- a/MAVProxy/modules/mavproxy_fenceitem_protocol.py
+++ b/MAVProxy/modules/mavproxy_fenceitem_protocol.py
@@ -1,6 +1,8 @@
 """
     MAVProxy geofence module
 """
+# flake8: noqa
+
 import os, time, platform
 from pymavlink import mavwp, mavutil
 from MAVProxy.modules.lib import mp_util
diff --git a/MAVProxy/modules/mavproxy_firmware.py b/MAVProxy/modules/mavproxy_firmware.py
index 6f4e1b8171..f81b15d11e 100644
--- a/MAVProxy/modules/mavproxy_firmware.py
+++ b/MAVProxy/modules/mavproxy_firmware.py
@@ -2,6 +2,8 @@
 
 '''firmware handling'''
 
+# flake8: noqa
+
 import time, os, fnmatch
 import json
 import threading
diff --git a/MAVProxy/modules/mavproxy_followtest.py b/MAVProxy/modules/mavproxy_followtest.py
index 8f97532b0b..ad2e5b639b 100644
--- a/MAVProxy/modules/mavproxy_followtest.py
+++ b/MAVProxy/modules/mavproxy_followtest.py
@@ -5,6 +5,8 @@
  September 2016
 '''
 
+# flake8: noqa
+
 import sys, os, time, math
 from MAVProxy.modules.lib import mp_module
 from MAVProxy.modules.lib import mp_util
diff --git a/MAVProxy/modules/mavproxy_ftp.py b/MAVProxy/modules/mavproxy_ftp.py
index 7d3f66657c..5056a25d3d 100644
--- a/MAVProxy/modules/mavproxy_ftp.py
+++ b/MAVProxy/modules/mavproxy_ftp.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''mavlink file transfer support'''
 
+# flake8: noqa
+
 import io
 import time, os, sys
 import struct
diff --git a/MAVProxy/modules/mavproxy_gasheli.py b/MAVProxy/modules/mavproxy_gasheli.py
index efc6dffeba..fad49d6043 100644
--- a/MAVProxy/modules/mavproxy_gasheli.py
+++ b/MAVProxy/modules/mavproxy_gasheli.py
@@ -2,6 +2,8 @@
 helicopter monitoring and control module gas helicopters
 """
 
+# flake8: noqa
+
 import os, sys, math, time
 
 from pymavlink import mavutil
diff --git a/MAVProxy/modules/mavproxy_generator.py b/MAVProxy/modules/mavproxy_generator.py
index cd0881c7f0..02356647c1 100644
--- a/MAVProxy/modules/mavproxy_generator.py
+++ b/MAVProxy/modules/mavproxy_generator.py
@@ -4,6 +4,8 @@
 Peter Barker, Jun 2020
 '''
 
+# flake8: noqa
+
 import os
 import os.path
 import sys
diff --git a/MAVProxy/modules/mavproxy_genobstacles.py b/MAVProxy/modules/mavproxy_genobstacles.py
index 07fc41931a..1a6769d827 100644
--- a/MAVProxy/modules/mavproxy_genobstacles.py
+++ b/MAVProxy/modules/mavproxy_genobstacles.py
@@ -2,6 +2,8 @@
 generate dynamic obstacles for OBC 2018
 '''
 
+# flake8: noqa
+
 import time, pickle
 from math import *
 
diff --git a/MAVProxy/modules/mavproxy_gimbal.py b/MAVProxy/modules/mavproxy_gimbal.py
index 66a066a24a..776d962294 100644
--- a/MAVProxy/modules/mavproxy_gimbal.py
+++ b/MAVProxy/modules/mavproxy_gimbal.py
@@ -5,6 +5,8 @@
 January 2015
 '''
 
+# flake8: noqa
+
 import sys, os, time
 from MAVProxy.modules.lib import mp_module
 from MAVProxy.modules.lib import mp_util
diff --git a/MAVProxy/modules/mavproxy_gopro.py b/MAVProxy/modules/mavproxy_gopro.py
index 5deb859e00..4edd06411c 100644
--- a/MAVProxy/modules/mavproxy_gopro.py
+++ b/MAVProxy/modules/mavproxy_gopro.py
@@ -4,6 +4,8 @@
 To use this module connect to a Solo with a GoPro installed on the gimbal.
 '''
 
+# flake8: noqa
+
 import time, os
 
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_graph.py b/MAVProxy/modules/mavproxy_graph.py
index 5958542eab..4c57d777f3 100644
--- a/MAVProxy/modules/mavproxy_graph.py
+++ b/MAVProxy/modules/mavproxy_graph.py
@@ -4,6 +4,8 @@
   uses lib/live_graph.py for display
 """
 
+# flake8: noqa
+
 from pymavlink import mavutil
 import re, os, sys
 
diff --git a/MAVProxy/modules/mavproxy_heliplane.py b/MAVProxy/modules/mavproxy_heliplane.py
index 2f1451739e..a871230601 100644
--- a/MAVProxy/modules/mavproxy_heliplane.py
+++ b/MAVProxy/modules/mavproxy_heliplane.py
@@ -2,6 +2,8 @@
 monitoring of heliplane
 """
 
+# flake8: noqa
+
 import os, sys, math, time
 
 from pymavlink import mavutil
diff --git a/MAVProxy/modules/mavproxy_horizon.py b/MAVProxy/modules/mavproxy_horizon.py
index cb69d95672..01a568df0a 100644
--- a/MAVProxy/modules/mavproxy_horizon.py
+++ b/MAVProxy/modules/mavproxy_horizon.py
@@ -4,6 +4,8 @@
   uses lib/console.py for display
 """
 
+# flake8: noqa
+
 from MAVProxy.modules.lib import wxhorizon
 from MAVProxy.modules.lib import mp_module
 from MAVProxy.modules.lib.wxhorizon_util import Attitude, VFR_HUD, Global_Position_INT, BatteryInfo, FlightState, WaypointInfo, FPS
diff --git a/MAVProxy/modules/mavproxy_instructor.py b/MAVProxy/modules/mavproxy_instructor.py
index 1e71c5e102..5f238a5934 100755
--- a/MAVProxy/modules/mavproxy_instructor.py
+++ b/MAVProxy/modules/mavproxy_instructor.py
@@ -4,6 +4,8 @@
   André Kjellstrup @ NORCE
 """
 
+# flake8: noqa
+
 import math
 from MAVProxy.modules.lib import mp_instructor
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_joystick/__init__.py b/MAVProxy/modules/mavproxy_joystick/__init__.py
index 727b65559e..e1d54c8f50 100644
--- a/MAVProxy/modules/mavproxy_joystick/__init__.py
+++ b/MAVProxy/modules/mavproxy_joystick/__init__.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 import os
 import pygame
 import pkg_resources
diff --git a/MAVProxy/modules/mavproxy_joystick/controls.py b/MAVProxy/modules/mavproxy_joystick/controls.py
index b65bdec1f2..c53d026dad 100644
--- a/MAVProxy/modules/mavproxy_joystick/controls.py
+++ b/MAVProxy/modules/mavproxy_joystick/controls.py
@@ -1,6 +1,8 @@
 '''Joystick control classes'''
 
 
+# flake8: noqa
+
 def scale(val,
           inlow=-1, inhigh=1,
           outlow=1000, outhigh=2000):
diff --git a/MAVProxy/modules/mavproxy_joystick/findjoy.py b/MAVProxy/modules/mavproxy_joystick/findjoy.py
index bc3f0b12e6..064b4993ff 100644
--- a/MAVProxy/modules/mavproxy_joystick/findjoy.py
+++ b/MAVProxy/modules/mavproxy_joystick/findjoy.py
@@ -7,6 +7,8 @@
     python -m MAVProxy.modules.mavproxy_joystick.findjoy
 '''
 
+# flake8: noqa
+
 import argparse
 import collections
 import pygame
diff --git a/MAVProxy/modules/mavproxy_layout.py b/MAVProxy/modules/mavproxy_layout.py
index e52045fc44..68672e57cc 100644
--- a/MAVProxy/modules/mavproxy_layout.py
+++ b/MAVProxy/modules/mavproxy_layout.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''window layout command handling'''
 
+# flake8: noqa
+
 from MAVProxy.modules.lib import mp_module
 
 class LayoutModule(mp_module.MPModule):
diff --git a/MAVProxy/modules/mavproxy_magical/__init__.py b/MAVProxy/modules/mavproxy_magical/__init__.py
index a9f59b7c22..82e4723827 100644
--- a/MAVProxy/modules/mavproxy_magical/__init__.py
+++ b/MAVProxy/modules/mavproxy_magical/__init__.py
@@ -17,6 +17,8 @@
 module magcal_graph. Some people read it "magical_graph" at the time of
 release, thus the silly reason for the name of this module.
 """
+# flake8: noqa
+
 import sys
 
 from pymavlink import mavutil
diff --git a/MAVProxy/modules/mavproxy_magical/glrenderer.py b/MAVProxy/modules/mavproxy_magical/glrenderer.py
index 9136c02506..1c22b12da9 100644
--- a/MAVProxy/modules/mavproxy_magical/glrenderer.py
+++ b/MAVProxy/modules/mavproxy_magical/glrenderer.py
@@ -12,6 +12,9 @@
 #
 # You should have received a copy of the GNU General Public License along
 # with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# flake8: noqa
+
 from OpenGL.GL import *
 from pymavlink.rotmat import Vector3
 
diff --git a/MAVProxy/modules/mavproxy_magical/magical_ui.py b/MAVProxy/modules/mavproxy_magical/magical_ui.py
index 4f278d9675..8782b176c3 100644
--- a/MAVProxy/modules/mavproxy_magical/magical_ui.py
+++ b/MAVProxy/modules/mavproxy_magical/magical_ui.py
@@ -12,6 +12,9 @@
 #
 # You should have received a copy of the GNU General Public License along
 # with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# flake8: noqa
+
 import math
 import os
 import time
diff --git a/MAVProxy/modules/mavproxy_magical/wxgeodesicgrid.py b/MAVProxy/modules/mavproxy_magical/wxgeodesicgrid.py
index fef014a06f..f25267a7f8 100644
--- a/MAVProxy/modules/mavproxy_magical/wxgeodesicgrid.py
+++ b/MAVProxy/modules/mavproxy_magical/wxgeodesicgrid.py
@@ -13,6 +13,8 @@
 # You should have received a copy of the GNU General Public License along
 # with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+# flake8: noqa
+
 import math
 import os.path
 import time
diff --git a/MAVProxy/modules/mavproxy_magical/wxvehicle.py b/MAVProxy/modules/mavproxy_magical/wxvehicle.py
index 01530bd4b2..800e5d1feb 100644
--- a/MAVProxy/modules/mavproxy_magical/wxvehicle.py
+++ b/MAVProxy/modules/mavproxy_magical/wxvehicle.py
@@ -13,6 +13,8 @@
 # You should have received a copy of the GNU General Public License along
 # with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+# flake8: noqa
+
 import math
 import time
 
diff --git a/MAVProxy/modules/mavproxy_map/__init__.py b/MAVProxy/modules/mavproxy_map/__init__.py
index c0c3e9087b..697cad89aa 100644
--- a/MAVProxy/modules/mavproxy_map/__init__.py
+++ b/MAVProxy/modules/mavproxy_map/__init__.py
@@ -5,6 +5,8 @@
 June 2012
 '''
 
+# flake8: noqa
+
 import os
 import math
 import functools
diff --git a/MAVProxy/modules/mavproxy_map/mp_slipmap.py b/MAVProxy/modules/mavproxy_map/mp_slipmap.py
index 9329626a06..48fdf4942e 100755
--- a/MAVProxy/modules/mavproxy_map/mp_slipmap.py
+++ b/MAVProxy/modules/mavproxy_map/mp_slipmap.py
@@ -6,6 +6,8 @@
 June 2012
 '''
 
+# flake8: noqa
+
 import time
 import cv2
 
diff --git a/MAVProxy/modules/mavproxy_messagerate.py b/MAVProxy/modules/mavproxy_messagerate.py
index ca467d140b..fc29d68abf 100644
--- a/MAVProxy/modules/mavproxy_messagerate.py
+++ b/MAVProxy/modules/mavproxy_messagerate.py
@@ -6,6 +6,8 @@
 Simply display message rates
 '''
 
+# flake8: noqa
+
 import time
 
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_misseditor/__init__.py b/MAVProxy/modules/mavproxy_misseditor/__init__.py
index 4ef85de713..9087491d04 100644
--- a/MAVProxy/modules/mavproxy_misseditor/__init__.py
+++ b/MAVProxy/modules/mavproxy_misseditor/__init__.py
@@ -5,6 +5,8 @@
 June 2104
 '''
 
+# flake8: noqa
+
 from MAVProxy.modules.lib import mp_module
 
 class MissionEditorModule(mp_module.MPModule):
diff --git a/MAVProxy/modules/mavproxy_misseditor/button_renderer.py b/MAVProxy/modules/mavproxy_misseditor/button_renderer.py
index 09250cfc34..1ba583e8a5 100644
--- a/MAVProxy/modules/mavproxy_misseditor/button_renderer.py
+++ b/MAVProxy/modules/mavproxy_misseditor/button_renderer.py
@@ -6,6 +6,8 @@
 June 2014
 '''
 
+# flake8: noqa
+
 from ..lib.wx_loader import wx
 from wx import grid
 import copy
diff --git a/MAVProxy/modules/mavproxy_misseditor/me_defines.py b/MAVProxy/modules/mavproxy_misseditor/me_defines.py
index 5a62590fa3..9129130dcb 100644
--- a/MAVProxy/modules/mavproxy_misseditor/me_defines.py
+++ b/MAVProxy/modules/mavproxy_misseditor/me_defines.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 from pymavlink import mavutil
 import fnmatch
 
diff --git a/MAVProxy/modules/mavproxy_misseditor/me_event.py b/MAVProxy/modules/mavproxy_misseditor/me_event.py
index bd660443b6..660a938918 100644
--- a/MAVProxy/modules/mavproxy_misseditor/me_event.py
+++ b/MAVProxy/modules/mavproxy_misseditor/me_event.py
@@ -4,6 +4,8 @@
 Michael Day
 June 2014
 '''
+# flake8: noqa
+
 #MissionEditorEvents come FROM the GUI (with a few exceptions where the Mission Editor Module sends a message to itself, e.g., MEE_TIME_TO_QUIT)
 #MissionEditorGUIEvents go TO the GUI
 #enum for MissionEditorEvent types
diff --git a/MAVProxy/modules/mavproxy_misseditor/missionEditorFrame.py b/MAVProxy/modules/mavproxy_misseditor/missionEditorFrame.py
index 6a71ae71ec..3e2d076425 100755
--- a/MAVProxy/modules/mavproxy_misseditor/missionEditorFrame.py
+++ b/MAVProxy/modules/mavproxy_misseditor/missionEditorFrame.py
@@ -4,6 +4,8 @@
 # generated by wxGlade 0.6.8 on Wed Jun 11 13:41:49 2014
 #
 
+# flake8: noqa
+
 from ..lib.wx_loader import wx
 from wx import grid
 import traceback
diff --git a/MAVProxy/modules/mavproxy_misseditor/mission_editor.py b/MAVProxy/modules/mavproxy_misseditor/mission_editor.py
index 4bdb8e748c..cb1e5362e3 100644
--- a/MAVProxy/modules/mavproxy_misseditor/mission_editor.py
+++ b/MAVProxy/modules/mavproxy_misseditor/mission_editor.py
@@ -5,6 +5,8 @@
 June 2104
 '''
 
+# flake8: noqa
+
 from MAVProxy.modules.lib import mp_util
 from MAVProxy.modules.lib import multiproc
 from MAVProxy.modules.lib import win_layout
diff --git a/MAVProxy/modules/mavproxy_mmap/__init__.py b/MAVProxy/modules/mavproxy_mmap/__init__.py
index 8e86456899..256021cb46 100644
--- a/MAVProxy/modules/mavproxy_mmap/__init__.py
+++ b/MAVProxy/modules/mavproxy_mmap/__init__.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 import os
 import sys
 import webbrowser
diff --git a/MAVProxy/modules/mavproxy_mmap/mmap_server.py b/MAVProxy/modules/mavproxy_mmap/mmap_server.py
index 25e1bbc2d1..26ffe0d92e 100644
--- a/MAVProxy/modules/mavproxy_mmap/mmap_server.py
+++ b/MAVProxy/modules/mavproxy_mmap/mmap_server.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 import BaseHTTPServer
 import json
 import os.path
diff --git a/MAVProxy/modules/mavproxy_movinghome.py b/MAVProxy/modules/mavproxy_movinghome.py
index aedb6c6aaa..7f8ea41db9 100644
--- a/MAVProxy/modules/mavproxy_movinghome.py
+++ b/MAVProxy/modules/mavproxy_movinghome.py
@@ -8,6 +8,8 @@
 
 '''
 
+# flake8: noqa
+
 import os
 import os.path
 import sys
diff --git a/MAVProxy/modules/mavproxy_msg.py b/MAVProxy/modules/mavproxy_msg.py
index e9f301ae18..7916e75bd4 100644
--- a/MAVProxy/modules/mavproxy_msg.py
+++ b/MAVProxy/modules/mavproxy_msg.py
@@ -7,6 +7,8 @@
 
 '''
 
+# flake8: noqa
+
 from pymavlink import mavutil
 import time
 
diff --git a/MAVProxy/modules/mavproxy_nmeagps.py b/MAVProxy/modules/mavproxy_nmeagps.py
index c8022c0057..a72eff192a 100644
--- a/MAVProxy/modules/mavproxy_nmeagps.py
+++ b/MAVProxy/modules/mavproxy_nmeagps.py
@@ -4,6 +4,8 @@
 connect to a NMEA GPS on a serial port and provide this as location position
 '''
 
+# flake8: noqa
+
 import sys, os, serial, time
 from MAVProxy.modules.lib import mp_module
 from MAVProxy.modules.lib import mp_settings
diff --git a/MAVProxy/modules/mavproxy_nmeaout.py b/MAVProxy/modules/mavproxy_nmeaout.py
index 3437a999d5..0e804d2c11 100644
--- a/MAVProxy/modules/mavproxy_nmeaout.py
+++ b/MAVProxy/modules/mavproxy_nmeaout.py
@@ -13,6 +13,8 @@
 
 '''
 
+# flake8: noqa
+
 import sys, os, serial
 from MAVProxy.modules.lib import mp_module
 
diff --git a/MAVProxy/modules/mavproxy_nokov/__init__.py b/MAVProxy/modules/mavproxy_nokov/__init__.py
index c37baf7dc4..294429463d 100755
--- a/MAVProxy/modules/mavproxy_nokov/__init__.py
+++ b/MAVProxy/modules/mavproxy_nokov/__init__.py
@@ -3,6 +3,8 @@
 it works with nokov software
 """
 
+# flake8: noqa
+
 import time
 
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_nsh.py b/MAVProxy/modules/mavproxy_nsh.py
index d9e25179b1..bb9ed8a9c4 100644
--- a/MAVProxy/modules/mavproxy_nsh.py
+++ b/MAVProxy/modules/mavproxy_nsh.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''remote nsh console handling'''
 
+# flake8: noqa
+
 import time, os, fnmatch, sys, time
 from pymavlink import mavutil, mavwp
 from MAVProxy.modules.lib import mp_settings
diff --git a/MAVProxy/modules/mavproxy_ntrip.py b/MAVProxy/modules/mavproxy_ntrip.py
index cee5148874..a1871fd71b 100644
--- a/MAVProxy/modules/mavproxy_ntrip.py
+++ b/MAVProxy/modules/mavproxy_ntrip.py
@@ -2,6 +2,8 @@
 send NTRIP data to flight controller
 """
 
+# flake8: noqa
+
 import random
 import time
 
diff --git a/MAVProxy/modules/mavproxy_optitrack/DataDescriptions.py b/MAVProxy/modules/mavproxy_optitrack/DataDescriptions.py
index f56159825e..09655096fd 100644
--- a/MAVProxy/modules/mavproxy_optitrack/DataDescriptions.py
+++ b/MAVProxy/modules/mavproxy_optitrack/DataDescriptions.py
@@ -21,6 +21,8 @@
 # and receive data via a NatNet connection and decode it using the NatNetClient library.
 
 
+# flake8: noqa
+
 import copy
 import hashlib
 import random
diff --git a/MAVProxy/modules/mavproxy_optitrack/MoCapData.py b/MAVProxy/modules/mavproxy_optitrack/MoCapData.py
index f29a2a0172..acd1ef7c6e 100644
--- a/MAVProxy/modules/mavproxy_optitrack/MoCapData.py
+++ b/MAVProxy/modules/mavproxy_optitrack/MoCapData.py
@@ -22,6 +22,8 @@
 
 #Utility functions
 
+# flake8: noqa
+
 import copy
 import hashlib
 import random
diff --git a/MAVProxy/modules/mavproxy_optitrack/NatNetClient.py b/MAVProxy/modules/mavproxy_optitrack/NatNetClient.py
index 60b1a5a3f4..53083593ab 100644
--- a/MAVProxy/modules/mavproxy_optitrack/NatNetClient.py
+++ b/MAVProxy/modules/mavproxy_optitrack/NatNetClient.py
@@ -14,6 +14,8 @@
 
 # OptiTrack NatNet direct depacketization library for Python 3.x
 
+# flake8: noqa
+
 import sys
 import socket
 import struct
diff --git a/MAVProxy/modules/mavproxy_optitrack/__init__.py b/MAVProxy/modules/mavproxy_optitrack/__init__.py
index ec7b8c6d36..1699e72b24 100644
--- a/MAVProxy/modules/mavproxy_optitrack/__init__.py
+++ b/MAVProxy/modules/mavproxy_optitrack/__init__.py
@@ -2,6 +2,8 @@
 # it works with optitrack motion capture cameras and optitrack motive tracker software (https://optitrack.com/software/motive/)
 # yuan-chu tai
 
+# flake8: noqa
+
 import time
 from pymavlink import mavutil
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_osd.py b/MAVProxy/modules/mavproxy_osd.py
index 76cb1eba76..2b1d0fc09d 100644
--- a/MAVProxy/modules/mavproxy_osd.py
+++ b/MAVProxy/modules/mavproxy_osd.py
@@ -5,6 +5,8 @@
 
 '''
 
+# flake8: noqa
+
 import os
 import os.path
 import sys
diff --git a/MAVProxy/modules/mavproxy_output.py b/MAVProxy/modules/mavproxy_output.py
index dfec9fb737..1570679753 100644
--- a/MAVProxy/modules/mavproxy_output.py
+++ b/MAVProxy/modules/mavproxy_output.py
@@ -6,6 +6,8 @@
     output remove 3      # to remove 3rd output
 '''
 
+# flake8: noqa
+
 from pymavlink import mavutil
 
 
diff --git a/MAVProxy/modules/mavproxy_paramedit/checklisteditor.py b/MAVProxy/modules/mavproxy_paramedit/checklisteditor.py
index 16fc9afea6..3d4b1842c8 100644
--- a/MAVProxy/modules/mavproxy_paramedit/checklisteditor.py
+++ b/MAVProxy/modules/mavproxy_paramedit/checklisteditor.py
@@ -1,4 +1,6 @@
 #!/usr/bin/env python3
+# flake8: noqa
+
 import wx
 import wx.grid as gridlib
 import math
diff --git a/MAVProxy/modules/mavproxy_paramedit/param_editor.py b/MAVProxy/modules/mavproxy_paramedit/param_editor.py
index d0f096ed28..cbcff57f2b 100644
--- a/MAVProxy/modules/mavproxy_paramedit/param_editor.py
+++ b/MAVProxy/modules/mavproxy_paramedit/param_editor.py
@@ -5,6 +5,8 @@
 June 2019
 '''
 
+# flake8: noqa
+
 import platform
 from MAVProxy.modules.lib import mp_util
 from MAVProxy.modules.lib import multiproc
diff --git a/MAVProxy/modules/mavproxy_paramedit/param_editor_frame.py b/MAVProxy/modules/mavproxy_paramedit/param_editor_frame.py
index a8ffe851c2..719bec84ed 100755
--- a/MAVProxy/modules/mavproxy_paramedit/param_editor_frame.py
+++ b/MAVProxy/modules/mavproxy_paramedit/param_editor_frame.py
@@ -3,6 +3,8 @@
 #
 # generated by wxGlade 0.7.1 on Wed May  8 16:56:24 2019
 #
+# flake8: noqa
+
 import wx
 import wx.grid
 import os
diff --git a/MAVProxy/modules/mavproxy_park.py b/MAVProxy/modules/mavproxy_park.py
index 0c621fe74b..2e8b3958bc 100644
--- a/MAVProxy/modules/mavproxy_park.py
+++ b/MAVProxy/modules/mavproxy_park.py
@@ -7,6 +7,8 @@
 in lateral or vertical direction from the "parked" point.
 """
 
+# flake8: noqa
+
 from pymavlink import mavutil
 import time
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_ppp.py b/MAVProxy/modules/mavproxy_ppp.py
index f71c7ee7b2..1e9999a9e1 100644
--- a/MAVProxy/modules/mavproxy_ppp.py
+++ b/MAVProxy/modules/mavproxy_ppp.py
@@ -5,6 +5,8 @@
 May 2012
 '''
 
+# flake8: noqa
+
 import time, os, fcntl, pty
 
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_proximity.py b/MAVProxy/modules/mavproxy_proximity.py
index 8fef9e43ad..bc7a5165d3 100644
--- a/MAVProxy/modules/mavproxy_proximity.py
+++ b/MAVProxy/modules/mavproxy_proximity.py
@@ -9,6 +9,8 @@
 
 '''
 
+# flake8: noqa
+
 import os
 import os.path
 import sys
diff --git a/MAVProxy/modules/mavproxy_rallypoint_protocol.py b/MAVProxy/modules/mavproxy_rallypoint_protocol.py
index aaa90f3589..0297888a59 100644
--- a/MAVProxy/modules/mavproxy_rallypoint_protocol.py
+++ b/MAVProxy/modules/mavproxy_rallypoint_protocol.py
@@ -2,6 +2,8 @@
     MAVProxy rally module
 """
 
+# flake8: noqa
+
 from pymavlink import mavwp
 from pymavlink import mavutil
 import time, os, platform
diff --git a/MAVProxy/modules/mavproxy_relay.py b/MAVProxy/modules/mavproxy_relay.py
index 6cea569cd9..35124e77dc 100644
--- a/MAVProxy/modules/mavproxy_relay.py
+++ b/MAVProxy/modules/mavproxy_relay.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''relay handling module'''
 
+# flake8: noqa
+
 import time
 from pymavlink import mavutil
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_restserver.py b/MAVProxy/modules/mavproxy_restserver.py
index f1747d4e7e..f5dc2909a7 100644
--- a/MAVProxy/modules/mavproxy_restserver.py
+++ b/MAVProxy/modules/mavproxy_restserver.py
@@ -6,6 +6,8 @@
 April 2018
 '''
 
+# flake8: noqa
+
 import time
 import json
 import socket
diff --git a/MAVProxy/modules/mavproxy_sail.py b/MAVProxy/modules/mavproxy_sail.py
index 9e99612948..a6c64da911 100644
--- a/MAVProxy/modules/mavproxy_sail.py
+++ b/MAVProxy/modules/mavproxy_sail.py
@@ -4,6 +4,8 @@
 November 2020
 '''
 
+# flake8: noqa
+
 from pymavlink import mavutil
 
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_sensors.py b/MAVProxy/modules/mavproxy_sensors.py
index 59f22c3ac3..a4b77982a5 100644
--- a/MAVProxy/modules/mavproxy_sensors.py
+++ b/MAVProxy/modules/mavproxy_sensors.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''monitor sensor consistancy'''
 
+# flake8: noqa
+
 import time, math
 from pymavlink import mavutil
 
diff --git a/MAVProxy/modules/mavproxy_serial.py b/MAVProxy/modules/mavproxy_serial.py
index 14c44c9d33..1f9142bbd8 100644
--- a/MAVProxy/modules/mavproxy_serial.py
+++ b/MAVProxy/modules/mavproxy_serial.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''serial_control MAVLink handling'''
 
+# flake8: noqa
+
 import time, os, fnmatch, sys
 from pymavlink import mavutil, mavwp
 from MAVProxy.modules.lib import mp_settings
diff --git a/MAVProxy/modules/mavproxy_setpos.py b/MAVProxy/modules/mavproxy_setpos.py
index 2a46d34bd2..ac1dbfc42d 100644
--- a/MAVProxy/modules/mavproxy_setpos.py
+++ b/MAVProxy/modules/mavproxy_setpos.py
@@ -2,6 +2,8 @@
 setpos command for SET_POSITION_TARGET_LOCAL_NED
 """
 
+# flake8: noqa
+
 import math
 import time
 
diff --git a/MAVProxy/modules/mavproxy_signing.py b/MAVProxy/modules/mavproxy_signing.py
index a3dbb9b375..fc1d60de15 100644
--- a/MAVProxy/modules/mavproxy_signing.py
+++ b/MAVProxy/modules/mavproxy_signing.py
@@ -3,6 +3,8 @@
 control MAVLink2 signing
 '''
 
+# flake8: noqa
+
 from pymavlink import mavutil
 import time, struct, math, sys
 import os
diff --git a/MAVProxy/modules/mavproxy_silvus.py b/MAVProxy/modules/mavproxy_silvus.py
index 40cfa42760..0770ecbba8 100644
--- a/MAVProxy/modules/mavproxy_silvus.py
+++ b/MAVProxy/modules/mavproxy_silvus.py
@@ -12,6 +12,8 @@
 thanks to Felix from Amber Technologies for the code this came from
 '''
 
+# flake8: noqa
+
 import time
 import datetime
 import socket
diff --git a/MAVProxy/modules/mavproxy_smartcamera/__init__.py b/MAVProxy/modules/mavproxy_smartcamera/__init__.py
index 460987ed4f..9e6ab91910 100644
--- a/MAVProxy/modules/mavproxy_smartcamera/__init__.py
+++ b/MAVProxy/modules/mavproxy_smartcamera/__init__.py
@@ -26,6 +26,8 @@
 # HEADER-FILES (Only those that are needed in this file)
 #****************************************************************************
 
+# flake8: noqa
+
 # System Header files and Module Headers
 import time, math, sched, threading
 
diff --git a/MAVProxy/modules/mavproxy_smartcamera/sc_ExifWriter.py b/MAVProxy/modules/mavproxy_smartcamera/sc_ExifWriter.py
index 149b467657..af72089862 100755
--- a/MAVProxy/modules/mavproxy_smartcamera/sc_ExifWriter.py
+++ b/MAVProxy/modules/mavproxy_smartcamera/sc_ExifWriter.py
@@ -37,6 +37,8 @@
 # HEADER-FILES (Only those that are needed in this file)
 #****************************************************************************
 
+# flake8: noqa
+
 # System Header files and Module Headers
 
 # Module Dependent Headers
diff --git a/MAVProxy/modules/mavproxy_smartcamera/sc_SonyQX1.py b/MAVProxy/modules/mavproxy_smartcamera/sc_SonyQX1.py
index 242cebbab5..41eb26ac28 100644
--- a/MAVProxy/modules/mavproxy_smartcamera/sc_SonyQX1.py
+++ b/MAVProxy/modules/mavproxy_smartcamera/sc_SonyQX1.py
@@ -24,6 +24,8 @@
 # HEADER-FILES (Only those that are needed in this file)
 #****************************************************************************
 
+# flake8: noqa
+
 # System Header files and Module Headers
 import os, sys, time, math, cv2, struct, fcntl
 from datetime import datetime
diff --git a/MAVProxy/modules/mavproxy_smartcamera/sc_config.py b/MAVProxy/modules/mavproxy_smartcamera/sc_config.py
index a41c016c1a..727b1b1ae7 100644
--- a/MAVProxy/modules/mavproxy_smartcamera/sc_config.py
+++ b/MAVProxy/modules/mavproxy_smartcamera/sc_config.py
@@ -8,6 +8,8 @@
 
 """
 
+# flake8: noqa
+
 from os.path import expanduser
 import ConfigParser
 
diff --git a/MAVProxy/modules/mavproxy_smartcamera/sc_main.py b/MAVProxy/modules/mavproxy_smartcamera/sc_main.py
index b610f5f959..e16753d0dc 100644
--- a/MAVProxy/modules/mavproxy_smartcamera/sc_main.py
+++ b/MAVProxy/modules/mavproxy_smartcamera/sc_main.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 import time
 import math
 import cv2
diff --git a/MAVProxy/modules/mavproxy_smartcamera/sc_video.py b/MAVProxy/modules/mavproxy_smartcamera/sc_video.py
index 9148bcd6be..ae77a2a260 100644
--- a/MAVProxy/modules/mavproxy_smartcamera/sc_video.py
+++ b/MAVProxy/modules/mavproxy_smartcamera/sc_video.py
@@ -8,6 +8,8 @@
 Image size is held in the smart_camera.cnf
 """
 
+# flake8: noqa
+
 import sys
 from os.path import expanduser
 import time
diff --git a/MAVProxy/modules/mavproxy_smartcamera/sc_webcam.py b/MAVProxy/modules/mavproxy_smartcamera/sc_webcam.py
index a907440ff5..d4e721f06d 100644
--- a/MAVProxy/modules/mavproxy_smartcamera/sc_webcam.py
+++ b/MAVProxy/modules/mavproxy_smartcamera/sc_webcam.py
@@ -8,6 +8,8 @@
 Image size is held in the smart_camera.cnf
 """
 
+# flake8: noqa
+
 import sys
 import time
 import math
diff --git a/MAVProxy/modules/mavproxy_smartcamera/ssdp.py b/MAVProxy/modules/mavproxy_smartcamera/ssdp.py
index c912a22bcd..23b741f746 100644
--- a/MAVProxy/modules/mavproxy_smartcamera/ssdp.py
+++ b/MAVProxy/modules/mavproxy_smartcamera/ssdp.py
@@ -15,6 +15,8 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 
+# flake8: noqa
+
 import socket
 import httplib
 import StringIO
diff --git a/MAVProxy/modules/mavproxy_speech.py b/MAVProxy/modules/mavproxy_speech.py
index a8a2ce4bc8..18d161b819 100644
--- a/MAVProxy/modules/mavproxy_speech.py
+++ b/MAVProxy/modules/mavproxy_speech.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''tune command handling'''
 
+# flake8: noqa
+
 import time, os
 from MAVProxy.modules.lib import mp_module
 from MAVProxy.modules.lib import multiproc
diff --git a/MAVProxy/modules/mavproxy_swarm.py b/MAVProxy/modules/mavproxy_swarm.py
index c0074999dd..92fbcee10d 100644
--- a/MAVProxy/modules/mavproxy_swarm.py
+++ b/MAVProxy/modules/mavproxy_swarm.py
@@ -6,6 +6,8 @@
 
 '''
 
+# flake8: noqa
+
 import sys
 import time
 import wx.lib.scrolledpanel as scrolled
diff --git a/MAVProxy/modules/mavproxy_system_time.py b/MAVProxy/modules/mavproxy_system_time.py
index 9b8d47c81f..023a92beda 100644
--- a/MAVProxy/modules/mavproxy_system_time.py
+++ b/MAVProxy/modules/mavproxy_system_time.py
@@ -7,6 +7,8 @@
 
 '''
 
+# flake8: noqa
+
 import time
 
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_terrain.py b/MAVProxy/modules/mavproxy_terrain.py
index 9a31d6de65..00e8f12f00 100644
--- a/MAVProxy/modules/mavproxy_terrain.py
+++ b/MAVProxy/modules/mavproxy_terrain.py
@@ -2,6 +2,8 @@
   MAVProxy terrain handling module
 """
 
+# flake8: noqa
+
 import time
 
 from MAVProxy.modules.lib import mp_elevation
diff --git a/MAVProxy/modules/mavproxy_test.py b/MAVProxy/modules/mavproxy_test.py
index 8a12f4585d..e3d7afff79 100644
--- a/MAVProxy/modules/mavproxy_test.py
+++ b/MAVProxy/modules/mavproxy_test.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''test flight for DCM noise'''
 
+# flake8: noqa
+
 import time, math
 
 def enum(**enums):
diff --git a/MAVProxy/modules/mavproxy_tracker.py b/MAVProxy/modules/mavproxy_tracker.py
index 3b110fd667..e5e5b7ff6a 100644
--- a/MAVProxy/modules/mavproxy_tracker.py
+++ b/MAVProxy/modules/mavproxy_tracker.py
@@ -8,6 +8,8 @@
 June 2012
 '''
 
+# flake8: noqa
+
 import sys, os, time
 from MAVProxy.modules.lib import mp_settings
 from MAVProxy.modules import mavproxy_map
diff --git a/MAVProxy/modules/mavproxy_tuneopt.py b/MAVProxy/modules/mavproxy_tuneopt.py
index 2fd7190881..65fed18b53 100644
--- a/MAVProxy/modules/mavproxy_tuneopt.py
+++ b/MAVProxy/modules/mavproxy_tuneopt.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 '''tune command handling'''
 
+# flake8: noqa
+
 import time, os
 
 from MAVProxy.modules.lib import mp_module
diff --git a/MAVProxy/modules/mavproxy_ublox/__init__.py b/MAVProxy/modules/mavproxy_ublox/__init__.py
index 21fd022546..2c8eb2e93f 100644
--- a/MAVProxy/modules/mavproxy_ublox/__init__.py
+++ b/MAVProxy/modules/mavproxy_ublox/__init__.py
@@ -8,6 +8,8 @@
 To use the uBlox API you will need to create a file containing your API token in ~/.mavproxy/ublox/api_token
 '''
 
+# flake8: noqa
+
 import os
 import struct
 import time
diff --git a/MAVProxy/modules/mavproxy_ucenter.py b/MAVProxy/modules/mavproxy_ucenter.py
index dbd76a5b28..d99ab319cb 100644
--- a/MAVProxy/modules/mavproxy_ucenter.py
+++ b/MAVProxy/modules/mavproxy_ucenter.py
@@ -3,6 +3,8 @@
 via MAVLink serial-control
 '''
 
+# flake8: noqa
+
 from MAVProxy.modules.lib import mp_module
 from MAVProxy.modules.lib import mp_settings
 from pymavlink import mavutil
diff --git a/MAVProxy/modules/mavproxy_useralerts.py b/MAVProxy/modules/mavproxy_useralerts.py
index 11ce3b591b..faa2790a4e 100644
--- a/MAVProxy/modules/mavproxy_useralerts.py
+++ b/MAVProxy/modules/mavproxy_useralerts.py
@@ -4,6 +4,8 @@
 https://ardupilot.org/dev/docs/user-alerts-developer.html '''
 
 
+# flake8: noqa
+
 import sys
 import json
 import string
diff --git a/MAVProxy/modules/mavproxy_vicon.py b/MAVProxy/modules/mavproxy_vicon.py
index 2839770954..8c103d7100 100644
--- a/MAVProxy/modules/mavproxy_vicon.py
+++ b/MAVProxy/modules/mavproxy_vicon.py
@@ -2,6 +2,8 @@
 use vicon data to provide VISION_POSITION_ESTIMATE and GPS_INPUT data
 """
 
+# flake8: noqa
+
 import math
 import threading
 import time
diff --git a/MAVProxy/modules/mavproxy_warning.py b/MAVProxy/modules/mavproxy_warning.py
index 1a58a897bf..c51b737bf6 100644
--- a/MAVProxy/modules/mavproxy_warning.py
+++ b/MAVProxy/modules/mavproxy_warning.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python
 '''module to display and announce warnings about system failures'''
 
+# flake8: noqa
+
 import time
 from MAVProxy.modules.lib import mp_module
 from MAVProxy.modules.lib import mp_settings
diff --git a/MAVProxy/tools/MAVExplorer.py b/MAVProxy/tools/MAVExplorer.py
index 138062f18e..5ec0bfa112 100755
--- a/MAVProxy/tools/MAVExplorer.py
+++ b/MAVProxy/tools/MAVExplorer.py
@@ -5,6 +5,8 @@
 Andrew Tridgell December 2014
 '''
 
+# flake8: noqa
+
 import copy
 import sys
 import time
diff --git a/setup.py b/setup.py
index ee7364a0a9..565848a792 100755
--- a/setup.py
+++ b/setup.py
@@ -1,3 +1,5 @@
+# flake8: noqa
+
 from setuptools import setup
 import os, platform, sys
 
diff --git a/windows/returnVersion.py b/windows/returnVersion.py
index 39794e4532..a7371f2b7f 100644
--- a/windows/returnVersion.py
+++ b/windows/returnVersion.py
@@ -7,6 +7,6 @@
 with open("../setup.py") as f:
     searchlines = f.readlines()
     for i, line in enumerate(searchlines):
-        if "version = " in line: 
+        if "version = " in line:
             print(line[11:len(line)-2])
             break