diff --git a/pkgs/development/python-modules/apptools/default.nix b/pkgs/development/python-modules/apptools/default.nix
index 60360301a09b..8540a8f39c4b 100644
--- a/pkgs/development/python-modules/apptools/default.nix
+++ b/pkgs/development/python-modules/apptools/default.nix
@@ -2,11 +2,13 @@
   lib,
   buildPythonPackage,
   configobj,
-  fetchPypi,
-  importlib-resources,
+  fetchFromGitHub,
+  numpy,
   pandas,
+  pyface,
   pytestCheckHook,
   pythonOlder,
+  setuptools,
   tables,
   traits,
   traitsui,
@@ -14,27 +16,37 @@
 
 buildPythonPackage rec {
   pname = "apptools";
-  version = "5.2.1";
-  format = "setuptools";
+  version = "5.3.0";
+  pyproject = true;
 
-  disabled = pythonOlder "3.7";
+  disabled = pythonOlder "3.8";
 
-  src = fetchPypi {
-    inherit pname version;
-    hash = "sha256-xiaPXfzzCIvK92oAA+ULd3TQG1JY1xmbQQtIUv8iRuM=";
+  src = fetchFromGitHub {
+    owner = "enthought";
+    repo = "apptools";
+    rev = "refs/tags/${version}";
+    hash = "sha256-qNtDHmvl5HbtdbjnugVM7CKVCW+ysAwRB9e2Ounh808=";
   };
 
-  propagatedBuildInputs = [
-    configobj
-    traits
-    traitsui
-  ] ++ lib.optionals (pythonOlder "3.9") [ importlib-resources ];
+  build-system = [ setuptools ];
 
-  nativeCheckInputs = [
-    tables
-    pandas
-    pytestCheckHook
-  ];
+  dependencies = [ traits ];
+
+  optional-dependencies = {
+    gui = [
+      pyface
+      traitsui
+    ];
+    h5 = [
+      numpy
+      pandas
+      tables
+    ];
+    persistence = [ numpy ];
+    preferences = [ configobj ];
+  };
+
+  nativeCheckInputs = [ pytestCheckHook ] ++ lib.flatten (lib.attrValues optional-dependencies);
 
   preCheck = ''
     export HOME=$TMP
diff --git a/pkgs/development/python-modules/envisage/default.nix b/pkgs/development/python-modules/envisage/default.nix
index 94964c9a581a..30b450719b5f 100644
--- a/pkgs/development/python-modules/envisage/default.nix
+++ b/pkgs/development/python-modules/envisage/default.nix
@@ -4,47 +4,42 @@
   buildPythonPackage,
   fetchPypi,
   ipython,
+  pyface,
   pytestCheckHook,
   pythonAtLeast,
   pythonOlder,
   setuptools,
   traits,
+  traitsui,
 }:
 
 buildPythonPackage rec {
   pname = "envisage";
   version = "7.0.3";
-  format = "pyproject";
+  pyproject = true;
 
-  disabled = pythonOlder "3.6";
+  disabled = pythonOlder "3.8";
 
   src = fetchPypi {
     inherit pname version;
     hash = "sha256-97GviL86j/8qmsbja7SN6pkp4/YSIEz+lK7WKwMWyeM=";
   };
 
-  # for the optional dependency ipykernel, only versions < 6 are
-  # supported, so it's not included in the tests, and not propagated
-  propagatedBuildInputs = [
-    traits
+  build-system = [ setuptools ];
+
+  dependencies = [
     apptools
+    pyface
     setuptools
-  ];
+    traits
+    traitsui
+  ] ++ apptools.optional-dependencies.preferences;
 
   preCheck = ''
     export HOME=$PWD/HOME
   '';
 
-  nativeCheckInputs = [
-    ipython
-    pytestCheckHook
-  ];
-
-  disabledTestPaths = lib.optionals (pythonAtLeast "3.10") [
-    # https://github.com/enthought/envisage/issues/455
-    "envisage/tests/test_egg_basket_plugin_manager.py"
-    "envisage/tests/test_egg_plugin_manager.py"
-  ];
+  nativeCheckInputs = [ pytestCheckHook ];
 
   pythonImportsCheck = [ "envisage" ];