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{
gevent,
buildPythonPackage,
fetchFromGitHub,
hostname,
pytest,
pythonAtLeast,
lib,
stdenv,
}:
buildPythonPackage rec {
pname = "ruffus";
version = "2.8.4";
format = "setuptools";
src = fetchFromGitHub {
owner = "cgat-developers";
repo = "ruffus";
rev = "v${version}";
sha256 = "0fnzpchwwqsy5h18fs0n90s51w25n0dx0l74j0ka6lvhjl5sxn4c";
};
propagatedBuildInputs = [ gevent ];
nativeCheckInputs = [
hostname
pytest
];
# tests very flaky & hang often on darwin
doCheck = !stdenv.hostPlatform.isDarwin;
checkPhase =
# https://docs.python.org/3/whatsnew/3.13.html#re
lib.optionalString (pythonAtLeast "3.13") ''
substituteInPlace ruffus/test/test_ruffus_utility.py \
--replace-fail re.error re.PatternError
''
# test files do indeed need to be executed separately
+ ''
pushd ruffus/test
rm test_with_logger.py # spawns 500 processes
for f in test_*.py ; do
HOME=$TMPDIR pytest -v --disable-warnings $f
done
popd
'';
pythonImportsCheck = [ "ruffus" ];
meta = {
description = "Light-weight Python Computational Pipeline Management";
homepage = "http://www.ruffus.org.uk";
license = lib.licenses.mit;
maintainers = [ ];
};
}
|
