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|
{ lib
, fetchFromGitHub
, python3
, rsync
}:
python3.pkgs.buildPythonApplication rec {
pname = "toil";
version = "5.7.1";
format = "setuptools";
src = fetchFromGitHub {
owner = "DataBiosphere";
repo = pname;
rev = "refs/tags/releases/${version}";
hash = "sha256-m+XvNyzd0ly2YqKhgxezgGaCXLs3CmupJMnp5RIZqNI=";
};
postPatch = ''
substituteInPlace requirements.txt \
--replace "docker>=3.7.2, <6" "docker"
'';
propagatedBuildInputs = with python3.pkgs; [
addict
dill
docker
enlighten
psutil
py-tes
pypubsub
python-dateutil
pytz
pyyaml
requests
typing-extensions
];
nativeCheckInputs = [
rsync
] ++ (with python3.pkgs; [
boto
botocore
flask
mypy-boto3-s3
pytestCheckHook
stubserver
]);
pytestFlagsArray = [
"src/toil/test"
];
pythonImportsCheck = [
"toil"
];
disabledTestPaths = [
# Tests are reaching their timeout
"src/toil/test/docs/scriptsTest.py"
"src/toil/test/jobStores/jobStoreTest.py"
"src/toil/test/provisioners/aws/awsProvisionerTest.py"
"src/toil/test/src"
"src/toil/test/wdl"
"src/toil/test/utils/utilsTest.py"
];
disabledTests = [
# Tests fail starting with 5.7.1
"testServices"
"testConcurrencyWithDisk"
"testJobConcurrency"
"testNestedResourcesDoNotBlock"
"test_omp_threads"
"testFileSingle"
"testFileSingle10000"
"testFileSingleCheckpoints"
"testFileSingleNonCaching"
"testFetchJobStoreFiles"
"testFetchJobStoreFilesWSymlinks"
"testJobStoreContents"
"test_cwl_on_arm"
"test_cwl_toil_kill"
];
meta = with lib; {
description = "Workflow engine written in pure Python";
homepage = "https://toil.ucsc-cgl.org/";
license = with licenses; [ asl20 ];
maintainers = with maintainers; [ veprbl ];
};
}
|