diff --git a/pkgs/development/python-modules/qtconsole/default.nix b/pkgs/development/python-modules/qtconsole/default.nix
index 858785307a47..fcda25cc9ff2 100644
--- a/pkgs/development/python-modules/qtconsole/default.nix
+++ b/pkgs/development/python-modules/qtconsole/default.nix
@@ -21,14 +21,14 @@
 
 buildPythonPackage rec {
   pname = "qtconsole";
-  version = "5.6.0";
+  version = "5.6.1";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "jupyter";
     repo = "qtconsole";
     rev = "refs/tags/${version}";
-    hash = "sha256-V82tGAmpvfGeUoewtJXXsBBXx2HNcV9/IMJxJg3bJL8=";
+    hash = "sha256-esCt7UQ0va/FJ0gdSrcc/k/FgyBVqKy7ttrN6E6mx+E=";
   };
 
   build-system = [ setuptools ];
diff --git a/pkgs/development/python-modules/spyder-kernels/default.nix b/pkgs/development/python-modules/spyder-kernels/default.nix
index 46bf6bb70bb2..c0511c2fc6a7 100644
--- a/pkgs/development/python-modules/spyder-kernels/default.nix
+++ b/pkgs/development/python-modules/spyder-kernels/default.nix
@@ -18,14 +18,14 @@
 
 buildPythonPackage rec {
   pname = "spyder-kernels";
-  version = "3.0.0";
+  version = "3.0.1";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "spyder-ide";
     repo = "spyder-kernels";
     rev = "refs/tags/v${version}";
-    hash = "sha256-oyPgujvaj2tqouZKuMVDq3gxm0GNrKmeUWqUFUkEMB4=";
+    hash = "sha256-OWdm4ytF9evqMEOOASssMag6QuJq2MwqmIZ+4et5IoI=";
   };
 
   build-system = [ setuptools ];
diff --git a/pkgs/development/python-modules/spyder/default.nix b/pkgs/development/python-modules/spyder/default.nix
index 6c18f7e382e8..dfd9a79aeb38 100644
--- a/pkgs/development/python-modules/spyder/default.nix
+++ b/pkgs/development/python-modules/spyder/default.nix
@@ -3,6 +3,11 @@
   buildPythonPackage,
   fetchPypi,
 
+  # nativeBuildInputs
+
+  # build-system
+  setuptools,
+
   # dependencies
   aiohttp,
   asyncssh,
@@ -40,7 +45,6 @@
   rope,
   rtree,
   scipy,
-  setuptools,
   spyder-kernels,
   superqt,
   textdistance,
@@ -51,18 +55,21 @@
 
 buildPythonPackage rec {
   pname = "spyder";
-  version = "6.0.1";
+  version = "6.0.2";
   pyproject = true;
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-cJeC6ICRWIu+YU3m673ntHVEpNbCJeGZ3lrSK3fYsTA=";
+    hash = "sha256-mPUrAYFn3k5NQrsk7B2aPFnkAxKSKC4I97DnFPK1pvM=";
   };
 
   patches = [ ./dont-clear-pythonpath.patch ];
 
-  build-system = [
+  nativeBuildInputs = [
     pyqtwebengine.wrapQtAppsHook
+  ];
+
+  build-system = [
     setuptools
   ];