python312Packages.cwl-upgrader: 1.2.11 -> 1.2.12, cwltool: 3.1.20241024121129 -> 3.1.20241217163858 (#368861)

Author: veprbl

pkgs/by-name/cw/cwltool/package.nix

@@ -6,39 +6,50 @@
   python3,
 }:
 
-python3.pkgs.buildPythonApplication rec {
+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 {
   pname = "cwltool";
-  version = "3.1.20241024121129";
+  version = "3.1.20241217163858";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "common-workflow-language";
     repo = "cwltool";
     rev = "refs/tags/${version}";
-    hash = "sha256-MocgfELgis9b+byeDU7mDQcXnLhaWBtvGbqm7MtRdf8=";
+    hash = "sha256-46x/7ewnt1eTu+1GdmPUExpiFfYE3mN8N8VFMM4r1Vk=";
   };
 
   postPatch = ''
     substituteInPlace setup.py \
-      --replace-fail "ruamel.yaml >= 0.16, < 0.19" "ruamel.yaml" \
       --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 "ruamel.yaml>=0.16.0,<0.18" "ruamel.yaml" \
-      --replace-fail "mypy==1.13.0" "mypy"
   '';
 
-  nativeBuildInputs =
-    [
-      git
-    ]
-    ++ (with python3.pkgs; [
-      setuptools
-      setuptools-scm
-    ]);
+  build-system = with py.pkgs; [
+    setuptools
+    setuptools-scm
+  ];
+
+  nativeBuildInputs = [ git ];
 
-  dependencies = with python3.pkgs; [
+  dependencies = with py.pkgs; [
     argcomplete
     bagit
     coloredlogs
@@ -50,6 +61,7 @@ python3.pkgs.buildPythonApplication rec {
     pydot
     rdflib
     requests
+    rich-argparse
     ruamel-yaml
     schema-salad
     shellescape
@@ -60,7 +72,7 @@ python3.pkgs.buildPythonApplication rec {
     typing-extensions
   ];
 
-  nativeCheckInputs = with python3.pkgs; [
+  nativeCheckInputs = with py.pkgs; [
     mock
     nodejs
     pytest-mock
@@ -89,7 +101,7 @@ python3.pkgs.buildPythonApplication rec {
     description = "Common Workflow Language reference implementation";
     homepage = "https://www.commonwl.org";
     changelog = "https://github.com/common-workflow-language/cwltool/releases/tag/${version}";
-    license = with licenses; [ asl20 ];
+    license = licenses.asl20;
     maintainers = with maintainers; [ veprbl ];
     mainProgram = "cwltool";
   };

pkgs/development/python-modules/cwl-upgrader/default.nix

@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "cwl-upgrader";
-  version = "1.2.11";
+  version = "1.2.12";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -22,7 +22,7 @@ buildPythonPackage rec {
     owner = "common-workflow-language";
     repo = "cwl-upgrader";
     rev = "refs/tags/v${version}";
-    hash = "sha256-P8607Io/KIJqAnrValM+rRK59tQITcC/jyGwkge8qN0=";
+    hash = "sha256-cfEd1XAu31u+NO27d3RNA5lhCpRpYK8NeaCxhQ/1GNU=";
   };
 
   postPatch = ''