Merge pull request #277654 from bcdarwin/update-gpy

{ lib, stdenv

{ lib

, stdenv

, buildPythonPackage

, fetchPypi

, fetchFromGitHub

, pythonOlder

, pytestCheckHook

, setuptools

, numpy

, scipy

, six

, paramz

, matplotlib

, cython

, nose

}:

buildPythonPackage rec {

  pname = "GPy";

  version = "1.10.0";

  version = "1.13.0";

  pyproject = true;

  src = fetchPypi {

    inherit pname version;

    sha256 = "a2b793ef8d0ac71739e7ba1c203bc8a5afa191058b42caa617e0e29aa52aa6fb";

  disabled = pythonOlder "3.9";

  # 1.13.0 not on PyPI yet

  src = fetchFromGitHub {

    owner = "SheffieldML";

    repo = "GPy";

    rev = "refs/tags/v.${version}";

    hash = "sha256-2HKKKBD/JFSeLQGvvgObxqxv9IHEKFnpaejdKbYZbmY=";

  };

  nativeBuildInputs = [ setuptools ];

  buildInputs = [ cython ];

  propagatedBuildInputs = [ numpy scipy six paramz matplotlib ];

  nativeCheckInputs = [ nose ];

  # $ 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

  ];

  nativeCheckInputs = [ pytestCheckHook ];

  # Rebuild cython-generated .c files since the included

  # ones were built with an older version of cython that is

  # incompatible with python3.9

  # Rebuild cython-generated .c files to ensure compatibility

  preBuild = ''

    for fn in $(find . -name '*.pyx'); do

      echo $fn | sed 's/\.\.pyx$/\.c/' | xargs ${cython}/bin/cython -3

    done

  '';

  pythonImportsCheck = [

    "GPy"

  ];

  pythonImportsCheck = [ "GPy" ];

  meta = with lib; {

    description = "Gaussian process framework in Python";

    homepage = "https://sheffieldml.github.io/GPy";

    changelog = "https://github.com/SheffieldML/GPy/releases/tag/v.${version}";

    license = licenses.bsd3;

    maintainers = with maintainers; [ bcdarwin ];

    broken = stdenv.isDarwin; # See inscrutable error message here: https://github.com/NixOS/nixpkgs/pull/107653#issuecomment-751527547