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{
lib,
buildPythonPackage,
fetchFromGitHub,
fetchpatch,
cython,
numpy,
scipy,
scikit-learn,
joblib,
six,
# test
pytestCheckHook,
}:
buildPythonPackage rec {
pname = "hdbscan";
version = "0.8.40";
format = "setuptools";
src = fetchFromGitHub {
owner = "scikit-learn-contrib";
repo = "hdbscan";
tag = "release-${version}";
hash = "sha256-xsBlmSQU47e+M+nRqUXdWKS7Rtj2QZ1UWLAvjSQOJ0Q=";
};
patches = [
(fetchpatch {
# Replace obsolete use of assert_raises with pytest.raises
name = "replace-assert_raises";
url = "https://github.com/scikit-learn-contrib/hdbscan/pull/667/commits/04d6a4dcdcd2bb2597419b8aa981d7620765809f.patch";
hash = "sha256-z/u5b2rNPKOCe+3/GVE8rMB5ajeU5PrvLVesjEgj9TA=";
})
];
pythonRemoveDeps = [ "cython" ];
nativeBuildInputs = [
cython
joblib
numpy
scikit-learn
scipy
six
];
preCheck = ''
cd hdbscan/tests
rm __init__.py
'';
nativeCheckInputs = [ pytestCheckHook ];
disabledTests = [
# known flaky tests: https://github.com/scikit-learn-contrib/hdbscan/issues/420
"test_mem_vec_diff_clusters"
"test_all_points_mem_vec_diff_clusters"
"test_approx_predict_diff_clusters"
# another flaky test https://github.com/scikit-learn-contrib/hdbscan/issues/421
"test_hdbscan_boruvka_balltree_matches"
# more flaky tests https://github.com/scikit-learn-contrib/hdbscan/issues/570
"test_hdbscan_boruvka_balltree"
"test_hdbscan_best_balltree_metric"
# "got an unexpected keyword argument"
"test_hdbscan_badargs"
];
disabledTestPaths = [
# joblib.externals.loky.process_executor.BrokenProcessPool:
"test_branches.py"
];
pythonImportsCheck = [ "hdbscan" ];
meta = {
description = "Hierarchical Density-Based Spatial Clustering of Applications with Noise, a clustering algorithm with a scikit-learn compatible API";
homepage = "https://github.com/scikit-learn-contrib/hdbscan";
changelog = "https://github.com/scikit-learn-contrib/hdbscan/releases/tag/release-${version}";
license = lib.licenses.bsd3;
maintainers = [ ];
};
}
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