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{
stdenv,
lib,
buildPythonPackage,
fetchPypi,
cython,
ecos,
joblib,
numexpr,
numpy,
osqp,
pandas,
setuptools-scm,
scikit-learn,
scipy,
pytestCheckHook,
}:
buildPythonPackage rec {
pname = "scikit-survival";
version = "0.22.2";
pyproject = true;
src = fetchPypi {
inherit pname version;
hash = "sha256-DpyGdQwN4VgGYmdREJlPB6NWiVWu8Ur4ExbysxADMr8=";
};
nativeBuildInputs = [
cython
setuptools-scm
];
propagatedBuildInputs = [
ecos
joblib
numexpr
numpy
osqp
pandas
scikit-learn
scipy
];
pythonImportsCheck = [ "sksurv" ];
nativeCheckInputs = [ pytestCheckHook ];
# treat numpy versions as lower bounds, same as setuptools build
postPatch = ''
sed -i 's/numpy==/numpy>=/' pyproject.toml
'';
# Hack needed to make pytest + cython work
# https://github.com/NixOS/nixpkgs/pull/82410#issuecomment-827186298
preCheck = ''
export HOME=$(mktemp -d)
cp -r $TMP/$sourceRoot/tests $HOME
pushd $HOME
'';
postCheck = "popd";
# very long tests, unnecessary for a leaf package
disabledTests =
[
"test_coxph"
"test_datasets"
"test_ensemble_selection"
"test_minlip"
"test_pandas_inputs"
"test_survival_svm"
"test_tree"
]
++ lib.optional (stdenv.isDarwin && stdenv.isAarch64)
# floating point mismatch on aarch64
# 27079905.88052468 to far from 27079905.880496684
"test_coxnet";
meta = with lib; {
description = "Survival analysis built on top of scikit-learn";
homepage = "https://github.com/sebp/scikit-survival";
license = licenses.gpl3Only;
maintainers = with maintainers; [ GuillaumeDesforges ];
};
}
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