pkgs/applications/science/misc/cwltool/default.nix

   1 { lib
   2 , fetchFromGitHub
   3 , git
   4 , nodejs
   5 , python3
   6 }:
   7
   8 python3.pkgs.buildPythonApplication rec {
   9   pname = "cwltool";
  10   version = "3.1.20240708091337";
  11   pyproject = true;
  12
  13   src = fetchFromGitHub {
  14     owner = "common-workflow-language";
  15     repo = "cwltool";
  16     rev = "refs/tags/${version}";
  17     hash = "sha256-Umxh8sRBy7fC6+GrcN1q4iO0KVpmUhGPtnqZZK/6c9M=";
  18   };
  19
  20   postPatch = ''
  21     substituteInPlace setup.py \
  22       --replace "ruamel.yaml >= 0.16, < 0.19" "ruamel.yaml" \
  23       --replace "prov == 1.5.1" "prov" \
  24       --replace '"schema-salad >= 8.4.20230426093816, < 9",' "" \
  25       --replace "PYTEST_RUNNER + " ""
  26     substituteInPlace pyproject.toml \
  27       --replace "ruamel.yaml>=0.16.0,<0.18" "ruamel.yaml" \
  28       --replace "mypy==1.10.0" "mypy==1.10.*"
  29   '';
  30
  31   nativeBuildInputs = [
  32     git
  33   ] ++ (with python3.pkgs; [
  34     setuptools
  35     setuptools-scm
  36   ]);
  37
  38   propagatedBuildInputs = with python3.pkgs; [
  39     argcomplete
  40     bagit
  41     coloredlogs
  42     cwl-utils
  43     mypy
  44     mypy-extensions
  45     prov
  46     psutil
  47     pydot
  48     rdflib
  49     requests
  50     ruamel-yaml
  51     schema-salad
  52     shellescape
  53     spython
  54     toml
  55     types-psutil
  56     types-requests
  57     typing-extensions
  58   ];
  59
  60   nativeCheckInputs = with python3.pkgs; [
  61     mock
  62     nodejs
  63     pytest-mock
  64     pytest-httpserver
  65     pytest-xdist
  66     pytestCheckHook
  67   ];
  68
  69   disabledTests = [
  70     "test_content_types"
  71     "test_env_filtering"
  72     "test_http_path_mapping"
  73     "test_modification_date"
  74   ];
  75
  76   disabledTestPaths = [
  77     "tests/test_udocker.py"
  78     "tests/test_provenance.py"
  79   ];
  80
  81   pythonImportsCheck = [
  82     "cwltool"
  83   ];
  84
  85   meta = with lib; {
  86     description = "Common Workflow Language reference implementation";
  87     mainProgram = "cwltool";
  88     homepage = "https://www.commonwl.org";
  89     changelog = "https://github.com/common-workflow-language/cwltool/releases/tag/${version}";
  90     license = with licenses; [ asl20 ];
  91     maintainers = with maintainers; [ veprbl ];
  92   };
  93 }