cwltool: 3.1.20250110105449 -> 3.1.20250925164626 (#448423)

{

  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

    typing-extensions

  ];

  nativeCheckInputs = with py.pkgs; [

  nativeCheckInputs = with python3Packages; [

    mock

    nodejs

    pytest-mock

    pytestCheckHook

  ];

  pythonRelaxDeps = [ "prov" ];

  disabledTests = [

    "test_content_types"

    "test_env_filtering"