python3Packages.hdbscan: unbreak

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

@@ -1,8 +1,9 @@
 { lib
 , buildPythonPackage
+, fetchpatch
 , cython
 , numpy
-, nose
+, pytestCheckHook
 , scipy
 , scikitlearn
 , fetchPypi
@@ -18,11 +19,22 @@ buildPythonPackage rec {
     inherit pname version;
     sha256 = "e3a418d0d36874f7b6a1bf0b7461f3857fc13a525fd48ba34caed2fe8973aa26";
   };
-
-  checkInputs = [ nose ];
+  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";
+    })
+  ];
 
   nativeBuildInputs = [ cython ];
   propagatedBuildInputs = [ numpy scipy scikitlearn joblib six ];
+  preCheck = ''
+    cd hdbscan/tests
+    rm __init__.py
+  '';
+  checkInputs = [ pytestCheckHook ];
 
   meta = with lib; {
     description = "Hierarchical Density-Based Spatial Clustering of Applications with Noise, a clustering algorithm with a scikit-learn compatible API";