Commit 4640bdd3 authored by Sarah Clark's avatar Sarah Clark
Browse files

python3Packages.hdbscan: fix build error

parent 87d5e58a

pkgs/development/python-modules/hdbscan/default.nix

+37 −11
Original line number Diff line number Diff line 
{

  lib,

  buildPythonPackage,

  fetchFromGitHub,

  fetchpatch,



  cython,

  numpy,

  pytestCheckHook,

  scipy,

  scikit-learn,

  fetchPypi,

  joblib,

  six,



  # test

  pytestCheckHook,

}:



buildPythonPackage rec {
@@ -16,27 +20,40 @@ buildPythonPackage rec { 
  version = "0.8.40";

  format = "setuptools";



  src = fetchPypi {

    inherit pname version;

    hash = "sha256-yeOD/xe+7gWRB1/2XVJL2ltaNd+wHSGCRae6MMjUihc=";

  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

  ];

  propagatedBuildInputs = [

    joblib

    numpy

    scipy

    scikit-learn

    joblib

    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"
@@ -47,13 +64,22 @@ buildPythonPackage rec { 
    # 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 = with lib; {

  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";

    license = licenses.bsd3;

    changelog = "https://github.com/scikit-learn-contrib/hdbscan/releases/tag/release-${version}";

    license = lib.licenses.bsd3;

    maintainers = [ ];

  };

}