python39Packages.gpy: unbreak on python3.9

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

@@ -1,5 +1,14 @@
-{ stdenv, buildPythonPackage, fetchPypi
-, numpy, scipy, six, paramz, nose, matplotlib, cython }:
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, numpy
+, scipy
+, six
+, paramz
+, matplotlib
+, cython
+, nose
+}:
 
 buildPythonPackage rec {
   pname = "GPy";
@@ -10,21 +19,35 @@ buildPythonPackage rec {
     sha256 = "04faf0c24eacc4dea60727c50a48a07ddf9b5751a3b73c382105e2a31657c7ed";
   };
 
-  # running tests produces "ImportError: cannot import name 'linalg_cython'"
-  # even though Cython has run
-  checkPhase = "nosetests -d";
-  doCheck = false;
-
+  buildInputs = [ cython ];
+  propagatedBuildInputs = [ numpy scipy six paramz matplotlib ];
   checkInputs = [ nose ];
 
-  buildInputs = [ cython ];
+  # $ nosetests GPy/testing/*.py
+  # => Ran 483 tests in 112.146s (on 8 cores)
+  # So instead, run shorter set of tests
+  checkPhase = ''
+    nosetests GPy/testing/linalg_test.py
+  '';
 
-  propagatedBuildInputs = [ numpy scipy six paramz matplotlib ];
+  # Rebuild cython-generated .c files since the included
+  # ones were built with an older version of cython that is
+  # incompatible with python3.9
+  preBuild = ''
+    for fn in $(find . -name '*.pyx'); do
+      echo $fn | sed 's/\.\.pyx$/\.c/' | xargs ${cython}/bin/cython -3
+    done
+  '';
+
+  pythonImportsCheck = [
+    "GPy"
+  ];
 
   meta = with stdenv.lib; {
     description = "Gaussian process framework in Python";
     homepage = "https://sheffieldml.github.io/GPy";
     license = licenses.bsd3;
     maintainers = with maintainers; [ bcdarwin ];
+    broken = stdenv.isDarwin;  # See inscrutable error message here: https://github.com/NixOS/nixpkgs/pull/107653#issuecomment-751527547
   };
 }