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{
lib,
stdenv,
buildPythonPackage,
fetchFromGitHub,
eigen,
# build-system
cython,
numpy,
packaging,
scikit-learn,
setuptools,
setuptools-scm,
# dependencies
ecos,
joblib,
numexpr,
osqp,
pandas,
scipy,
# tests
pytestCheckHook,
}:
buildPythonPackage rec {
pname = "scikit-survival";
version = "0.26.0";
pyproject = true;
src = fetchFromGitHub {
owner = "sebp";
repo = "scikit-survival";
tag = "v${version}";
hash = "sha256-xtrGFNRHF8bL8Q82gIQLayuCSDFMrBBkQ63F+Nmbdes=";
};
postPatch = ''
ln -s ${lib.getInclude eigen}/include/eigen3/Eigen \
sksurv/linear_model/src/eigen
'';
build-system = [
cython
numpy
packaging
scikit-learn
setuptools
setuptools-scm
];
pythonRelaxDeps = [
"osqp"
];
dependencies = [
ecos
joblib
numexpr
numpy
osqp
pandas
scikit-learn
scipy
];
pythonImportsCheck = [ "sksurv" ];
nativeCheckInputs = [ pytestCheckHook ];
# Hack needed to make pytest + cython work
# https://github.com/NixOS/nixpkgs/pull/82410#issuecomment-827186298
preCheck = ''
rm -rf sksurv
'';
disabledTests = [
# very long tests, unnecessary for a leaf package
"test_coxph"
"test_datasets"
"test_ensemble_selection"
"test_minlip"
"test_pandas_inputs"
"test_survival_svm"
"test_tree"
]
++ lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64) [
# floating point mismatch on aarch64
# 27079905.88052468 to far from 27079905.880496684
"test_coxnet"
];
meta = {
description = "Survival analysis built on top of scikit-learn";
homepage = "https://github.com/sebp/scikit-survival";
changelog = "https://github.com/sebp/scikit-survival/releases/tag/v${version}";
license = lib.licenses.gpl3Plus;
maintainers = [ ];
};
}
|
