python312Packages.scikit-bio: add missing deps (#354208)

Author: pbsds

pkgs/development/python-modules/scikit-bio/default.nix

@@ -2,18 +2,22 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+
   setuptools,
   cython,
   oldest-supported-numpy,
+
   requests,
   decorator,
   natsort,
   numpy,
   pandas,
   scipy,
   h5py,
-  hdmedians,
   biom-format,
+  statsmodels,
+  patsy,
+
   python,
   pytestCheckHook,
 }:
@@ -44,15 +48,21 @@ buildPythonPackage rec {
     pandas
     scipy
     h5py
-    hdmedians
     biom-format
+    statsmodels
+    patsy
   ];
 
   nativeCheckInputs = [ pytestCheckHook ];
 
   # only the $out dir contains the built cython extensions, so we run the tests inside there
   pytestFlagsArray = [ "${placeholder "out"}/${python.sitePackages}/skbio" ];
 
+  disabledTestPaths = [
+    # don't know why, but this segfaults
+    "${placeholder "out"}/${python.sitePackages}/skbio/metadata/tests/test_intersection.py"
+  ];
+
   pythonImportsCheck = [ "skbio" ];
 
   meta = {