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{ lib
, buildPythonPackage
, fetchpatch
, cython
, numpy
, pytestCheckHook
, scipy
, scikit-learn
, fetchPypi
, joblib
, six
, pythonRelaxDepsHook
}:
buildPythonPackage rec {
pname = "hdbscan";
version = "0.8.33";
src = fetchPypi {
inherit pname version;
hash = "sha256-V/q8Xw5F9I0kB7NccxGSq8iWN2QR/n5LuDb/oD04+Q0=";
};
patches = [
# should be included in next release
(fetchpatch {
name = "joblib-1.2.0-compat.patch";
url = "https://github.com/scikit-learn-contrib/hdbscan/commit/d829c639923f6866e1917e46ddbde45b513913f3.patch";
excludes = [
"docs/basic_hdbscan.rst"
"docs/how_hdbscan_works.rst"
];
hash = "sha256-t0D4OsHEcMwmBZM8Mk1N0uAKi6ra+TOzEks9/efsvWI=";
})
];
pythonRemoveDeps = [ "cython" ];
nativeBuildInputs = [ pythonRelaxDepsHook cython ];
propagatedBuildInputs = [ numpy scipy scikit-learn joblib 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"
];
pythonImportsCheck = [ "hdbscan" ];
meta = with lib; {
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";
license = licenses.bsd3;
};
}
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