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{ lib
, buildPythonPackage
, fetchpatch
, cython
, numpy
, pytestCheckHook
, scipy
, scikit-learn
, fetchPypi
, joblib
, six
, pythonRelaxDepsHook
}:
buildPythonPackage rec {
pname = "hdbscan";
version = "0.8.27";
src = fetchPypi {
inherit pname version;
sha256 = "e3a418d0d36874f7b6a1bf0b7461f3857fc13a525fd48ba34caed2fe8973aa26";
};
patches = [
# This patch fixes compatibility with numpy 1.20. It will be in the next release
# after 0.8.27
(fetchpatch {
url = "https://github.com/scikit-learn-contrib/hdbscan/commit/5b67a4fba39c5aebe8187a6a418da677f89a63e0.patch";
sha256 = "07d7jdwk0b8kgaqkifd529sarji01j1jiih7cfccc5kxmlb5py9h";
})
];
pythonRemoveDeps = [ "cython" ];
nativeBuildInputs = [ pythonRelaxDepsHook cython ];
propagatedBuildInputs = [ numpy scipy scikit-learn joblib six ];
preCheck = ''
cd hdbscan/tests
rm __init__.py
'';
checkInputs = [ 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;
maintainers = with maintainers; [ ixxie ];
};
}
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