diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 8ca1df32170a328272722d90706734af116b4525..b670494600dd5a55307cac2218c37790e5d8ac28 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -18,8 +18,10 @@
         "python.linting.pylintEnabled": false,
         "python.linting.flake8Enabled": true,
         "python.linting.flake8Args": [
-            "--select=ATL,ATL902,F,E101,E7,E9,W6",
-            "--ignore=ATL9,E701,E702,E704,E741"
+            "--isolated",
+            "--select ATL,F,E101,E7,E9,W6",
+            "--ignore E701,E702,E704,E741",
+            "--enable-extensions ATL902"
         ]
     },
 
diff --git a/.vscode/settings.json b/.vscode/settings.json
index 398fe985655b5416aeb95730effb322a95f9bc99..6d69fa0b822b58977876f4da269d4a8c72c4bdff 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -13,7 +13,9 @@
     "python.linting.flake8Enabled": true,
     "python.linting.flake8Path": "${workspaceFolder}/../build/ide_flake8",
     "python.linting.flake8Args": [
-        "--select=ATL,ATL902,F,E101,E7,E9,W6",
-        "--ignore=ATL9,E701,E702,E704,E741"
+        "--isolated",
+        "--select ATL,F,E101,E7,E9,W6",
+        "--ignore E701,E702,E704,E741",
+        "--enable-extensions ATL902"
     ]
 }
diff --git a/Projects/AthGeneration/CMakeLists.txt b/Projects/AthGeneration/CMakeLists.txt
index 8474b6549ff13f802553eddfc01473c897220945..af8450a0db944a13b95164aa09829eb4177c3ec5 100644
--- a/Projects/AthGeneration/CMakeLists.txt
+++ b/Projects/AthGeneration/CMakeLists.txt
@@ -11,8 +11,9 @@ unset( _version )
 set( HEPMC3_USE TRUE CACHE BOOL "Build with HepMC3" )
 
 # Configure flake8:
-set( ATLAS_FLAKE8 flake8_atlas --select ATL,ATL902,F,E101,E7,E9,W6
-                               --ignore ATL9,E701,E702,E704,E741
+set( ATLAS_FLAKE8 flake8_atlas --isolated --select ATL,F,E101,E7,E9,W6
+                               --ignore E701,E702,E704,E741
+                               --enable-extensions ATL902
    CACHE STRING "Default flake8 command" )
 set( ATLAS_PYTHON_CHECKER ${ATLAS_FLAKE8}
    CACHE STRING "Python checker command to run during Python module compilation" )
diff --git a/Projects/AthSimulation/CMakeLists.txt b/Projects/AthSimulation/CMakeLists.txt
index d4286dc7c5bc6c2f4b5ad99ed2367601c66aeffc..9dcf3fd443653e710a084a7565385a9b14297bc2 100644
--- a/Projects/AthSimulation/CMakeLists.txt
+++ b/Projects/AthSimulation/CMakeLists.txt
@@ -11,8 +11,9 @@ unset( _version )
 set( HEPMC3_USE TRUE CACHE BOOL "Build with HepMC3" )
 
 # Configure flake8:
-set( ATLAS_FLAKE8 flake8_atlas --select ATL,ATL902,F,E101,E7,E9,W6
-                               --ignore ATL9,E701,E702,E704,E741
+set( ATLAS_FLAKE8 flake8_atlas --isolated --select ATL,F,E101,E7,E9,W6
+                               --ignore E701,E702,E704,E741
+                               --enable-extensions ATL902
    CACHE STRING "Default flake8 command" )
 set( ATLAS_PYTHON_CHECKER ${ATLAS_FLAKE8}
    CACHE STRING "Python checker command to run during Python module compilation" )
diff --git a/Projects/Athena/CMakeLists.txt b/Projects/Athena/CMakeLists.txt
index fef7e1389937d9f1cf951f0b862114cfa2bc6d9c..cd16b00980666a9aba968cedb43e9bd8e05806de 100644
--- a/Projects/Athena/CMakeLists.txt
+++ b/Projects/Athena/CMakeLists.txt
@@ -56,8 +56,9 @@ mark_as_advanced( TDAQ-COMMON_ATROOT TDAQ_PROJECT_NAME
 set( HEPMC3_USE TRUE CACHE BOOL "Build with HepMC3" )
 
 # Configure flake8:
-set( ATLAS_FLAKE8 flake8_atlas --select ATL,ATL902,F,E101,E7,E9,W6
-                               --ignore ATL9,E701,E702,E704,E741
+set( ATLAS_FLAKE8 flake8_atlas --isolated --select ATL,F,E101,E7,E9,W6
+                               --ignore E701,E702,E704,E741
+                               --enable-extensions ATL902
    CACHE STRING "Default flake8 command" )
 set( ATLAS_PYTHON_CHECKER ${ATLAS_FLAKE8}
    CACHE STRING "Python checker command to run during Python module compilation" )