diff --git a/pkgs/by-name/cw/cwltool/package.nix b/pkgs/by-name/cw/cwltool/package.nix
index df62af94dcd7..847d3484f7cf 100644
--- a/pkgs/by-name/cw/cwltool/package.nix
+++ b/pkgs/by-name/cw/cwltool/package.nix
@@ -1,62 +1,39 @@
 {
   lib,
   fetchFromGitHub,
-  git,
   nodejs,
-  python3,
+  python3Packages,
 }:
 
-let
-  py = python3.override {
-    packageOverrides = final: prev: {
-      # Requires "pydot >= 1.4.1, <3",
-      pydot = prev.pydot.overridePythonAttrs (old: rec {
-        version = "2.0.0";
-        src = old.src.override {
-          inherit version;
-          hash = "sha256-YCRq8hUSP6Bi8hzXkb5n3aI6bygN8J9okZ5jeh5PMjU=";
-        };
-        doCheck = false;
-      });
-    };
-  };
-in
-with py.pkgs;
-
-py.pkgs.buildPythonApplication rec {
+python3Packages.buildPythonApplication rec {
   pname = "cwltool";
-  version = "3.1.20250110105449";
+  version = "3.1.20250925164626";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "common-workflow-language";
     repo = "cwltool";
     tag = version;
-    hash = "sha256-V0CQiNkIw81s6e9224qcfbsOqBvMo34q+lRURpRetKs=";
+    hash = "sha256-esY/p7wm0HvLiX+jZENBye4NblYveYAXevYRQxk+u44=";
   };
 
   postPatch = ''
     substituteInPlace setup.py \
-      --replace-fail "prov == 1.5.1" "prov" \
-      --replace-fail '"schema-salad >= 8.7, < 9",' '"schema-salad",' \
       --replace-fail "PYTEST_RUNNER + " ""
     substituteInPlace pyproject.toml \
-      --replace-fail "mypy==1.14.1" "mypy"
+      --replace-fail "mypy==1.18.2" "mypy"
   '';
 
-  build-system = with py.pkgs; [
+  build-system = with python3Packages; [
     setuptools
     setuptools-scm
   ];
 
-  nativeBuildInputs = [ git ];
-
-  dependencies = with py.pkgs; [
+  dependencies = with python3Packages; [
     argcomplete
     bagit
     coloredlogs
     cwl-utils
-    mypy
     mypy-extensions
     prov
     psutil
@@ -74,7 +51,7 @@ py.pkgs.buildPythonApplication rec {
     typing-extensions
   ];
 
-  nativeCheckInputs = with py.pkgs; [
+  nativeCheckInputs = with python3Packages; [
     mock
     nodejs
     pytest-mock
@@ -83,6 +60,8 @@ py.pkgs.buildPythonApplication rec {
     pytestCheckHook
   ];
 
+  pythonRelaxDeps = [ "prov" ];
+
   disabledTests = [
     "test_content_types"
     "test_env_filtering"