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{ lib
, fetchFromGitHub
, git
, nodejs
, python3
}:
python3.pkgs.buildPythonApplication rec {
pname = "cwltool";
version = "3.1.20240112164112";
pyproject = true;
src = fetchFromGitHub {
owner = "common-workflow-language";
repo = "cwltool";
rev = "refs/tags/${version}";
hash = "sha256-Y0DORypXlTDv04qh796oXPSTxCXGb7rLQ8Su+/As7Lo=";
};
postPatch = ''
substituteInPlace setup.py \
--replace "ruamel.yaml >= 0.16, < 0.19" "ruamel.yaml" \
--replace "prov == 1.5.1" "prov" \
--replace '"schema-salad >= 8.4.20230426093816, < 9",' "" \
--replace "PYTEST_RUNNER + " ""
substituteInPlace pyproject.toml \
--replace "mypy==1.8.0" "mypy" \
--replace "ruamel.yaml>=0.16.0,<0.18" "ruamel.yaml"
'';
nativeBuildInputs = [
git
] ++ (with python3.pkgs; [
setuptools
setuptools-scm
]);
propagatedBuildInputs = with python3.pkgs; [
argcomplete
bagit
coloredlogs
cwl-utils
mypy
mypy-extensions
prov
psutil
pydot
rdflib
requests
ruamel-yaml
schema-salad
shellescape
spython
toml
types-psutil
types-requests
typing-extensions
];
nativeCheckInputs = with python3.pkgs; [
mock
nodejs
pytest-mock
pytest-httpserver
pytest-xdist
pytestCheckHook
];
disabledTests = [
"test_content_types"
"test_env_filtering"
"test_http_path_mapping"
"test_modification_date"
];
disabledTestPaths = [
"tests/test_udocker.py"
"tests/test_provenance.py"
];
pythonImportsCheck = [
"cwltool"
];
meta = with lib; {
description = "Common Workflow Language reference implementation";
homepage = "https://www.commonwl.org";
changelog = "https://github.com/common-workflow-language/cwltool/releases/tag/${version}";
license = with licenses; [ asl20 ];
maintainers = with maintainers; [ veprbl ];
};
}
|