fix test errors after migration

GPy/__init__.py

@@ -1,6 +1,7 @@
 # Copyright (c) 2012, GPy authors (see AUTHORS.txt).
 # Licensed under the BSD 3-clause license (see LICENSE.txt)
 import warnings
+
 warnings.filterwarnings("ignore", category=DeprecationWarning)
 
 from . import core
@@ -18,30 +19,25 @@ from .util import normalizer
 
 # backwards compatibility
 import sys
-backwards_compatibility = ['lists_and_dicts', 'observable_array', 'index_operations']
+
+backwards_compatibility = ["lists_and_dicts", "observable_array", "index_operations"]
 for bc in backwards_compatibility:
-    sys.modules['GPy.core.parameterization.{!s}'.format(bc)] = getattr(core.parameterization, bc)
+    sys.modules["GPy.core.parameterization.{!s}".format(bc)] = getattr(
+        core.parameterization, bc
+    )
 
 # Direct imports for convenience:
 from .core import Model
 from .core.parameterization import priors
-from .core.parameterization import Param, Parameterized, ObsAr, transformations as constraints
+from .core.parameterization import (
+    Param,
+    Parameterized,
+    ObsAr,
+    transformations as constraints,
+)
 
 from .__version__ import __version__
 
-from numpy.testing import Tester
-
-with warnings.catch_warnings():
-    warnings.simplefilter('ignore')
-    try:
-        #Get rid of nose dependency by only ignoring if you have nose installed
-        from nose.tools import nottest
-        @nottest
-        def tests(verbose=10):
-            Tester(testing).test(verbose=verbose)
-    except:
-        def tests(verbose=10):
-            Tester(testing).test(verbose=verbose)
 
 def load(file_or_path):
     """
@@ -52,10 +48,12 @@ def load(file_or_path):
     # This is the pickling pain when changing _src -> src
     import sys
     import inspect
-    sys.modules['GPy.kern._src'] = kern.src
+
+    sys.modules["GPy.kern._src"] = kern.src
     for name, module in inspect.getmembers(kern.src):
-        if not name.startswith('_'):
+        if not name.startswith("_"):
-            sys.modules['GPy.kern._src.{}'.format(name)] = module
+            sys.modules["GPy.kern._src.{}".format(name)] = module
-    sys.modules['GPy.inference.optimization'] = inference.optimization
+    sys.modules["GPy.inference.optimization"] = inference.optimization
     import paramz
+
     return paramz.load(file_or_path)

GPy/old_tests/gp_transformation_tests.py

@@ -1,4 +1,3 @@
-from nose.tools import with_setup
 from GPy.models import GradientChecker
 from GPy.likelihoods.noise_models import gp_transformations
 import inspect

GPy/testing/move_files.py

@@ -0,0 +1,24 @@
+import os
+import subprocess
+
+
+python_files = [file for file in os.listdir() if file.endswith(".py")]
+
+python_test_files = [file for file in python_files if "test" in file]
+non_test_python_files = [file for file in python_files if "test" not in file]
+print("Python Test Files: ", python_test_files)
+
+print("Non-test Python Files:\n", non_test_python_files)
+
+for file in python_test_files:
+    if file.endswith("_tests.py"):
+        test_name = file.split("_tests.py")[0]
+    elif file.endswith("_test.py"):
+        test_name = file.split("_test.py")[0]
+    else:
+        raise ValueError(f"File is not named as expected: {file}")
+
+    to_file = "test_" + test_name + ".py"
+
+    # print(" ".join(["git", "mv", "-f", file, to_file]))
+    subprocess.run(["git", "mv", "-f", file, to_file])

GPy/testing/test_cython.py

@@ -24,7 +24,7 @@ These tests make sure that the pure python and cython codes work the same
 """
 
 
-@pytest.skipIf(
+@pytest.mark.skipif(
     not choleskies_cython_working,
     "Cython cholesky module has not been built on this machine",
 )
@@ -44,7 +44,7 @@ class CythonTestChols:
         assert np.allclose(A1, A2), "Flat mismatch!"
 
 
-@pytest.skipIf(
+@pytest.mark.skipif(
     not stationary_cython_working,
     "Cython stationary module has not been built on this machine",
 )
@@ -82,7 +82,7 @@ class TestStationary:
         assert np.allclose(g1, g2), "Gradient mismatch on rect lengthscale!"
 
 
-@pytest.skipIf(
+@pytest.mark.skipif(
     not choleskies_cython_working,
     "Cython cholesky module has not been built on this machine",
 )

GPy/testing/test_ep_likelihood.py

@@ -1,7 +1,6 @@
+import pytest
 import numpy as np
-import unittest
 import GPy
-from GPy.models import GradientChecker
 
 
 fixed_seed = 10
@@ -127,7 +126,7 @@ class TestObservationModels:
         GPy.util.classification.conf_matrix(probs_mean_ep_alt, self.binary_Y)
         GPy.util.classification.conf_matrix(probs_mean_ep_nested, self.binary_Y)
 
-    @pytest.skip(
+    @pytest.mark.skip(
         "Fails as a consequence of fixing the DSYR function. Needs to be reviewed!"
     )
     def test_ep_with_studentt(self):

GPy/testing/test_gpy_kernels_state_space.py

@@ -15,7 +15,6 @@ from .state_space_main_tests import (
     generate_brownian_data,
     generate_linear_plus_sin,
 )
-from nose import SkipTest
 
 # from state_space_main_tests import generate_x_points, generate_sine_data, \
 #    generate_linear_data, generate_brownian_data, generate_linear_plus_sin

GPy/testing/test_kernel.py

@@ -870,7 +870,7 @@ class TestKernelNonContinuous:
         )
 
 
-@pytest.skipIf(
+@pytest.mark.skipif(
     not cython_coregionalize_working,
     "Cython coregionalize module has not been built on this machine",
 )

GPy/testing/test_model.py

@@ -75,7 +75,7 @@ class TestMisc:
         Xp[:, 0] = Xp[:, 0] * 15 - 5
         Xp[:, 1] = Xp[:, 1] * 15
         _, var = m.predict(Xp)
-        assert np.all(var >= 0.0))
+        assert np.all(var >= 0.0)
 
     def test_raw_predict(self):
         self.setup()

GPy/testing/test_plotting.py

@@ -141,39 +141,42 @@ def _image_comparison(
             if ext == "npz":
 
                 def do_test():
-                    with pytest.skip
+                    with pytest.skip:
-                    if not os.path.exists(expected):
+                        if not os.path.exists(expected):
-                        import shutil
+                            import shutil
 
-                        shutil.copy2(actual, expected)
+                            shutil.copy2(actual, expected)
-                        # shutil.copy2(os.path.join(result_dir, "{}.{}".format(base, 'png')), os.path.join(baseline_dir, "{}.{}".format(base, 'png')))
+                            # shutil.copy2(os.path.join(result_dir, "{}.{}".format(base, 'png')), os.path.join(baseline_dir, "{}.{}".format(base, 'png')))
-                        raise IOError(
+                            raise IOError(
-                            "Baseline file {} not found, copying result {}".format(
+                                "Baseline file {} not found, copying result {}".format(
-                                expected, actual
+                                    expected, actual
+                                )
                             )
-                        )
+                        else:
-                    else:
+                            exp_dict = dict(np.load(expected).items())
-                        exp_dict = dict(np.load(expected).items())
+                            act_dict = dict(np.load(actual).items())
-                        act_dict = dict(np.load(actual).items())
+                            for name in act_dict:
-                        for name in act_dict:
+                                if name in exp_dict:
-                            if name in exp_dict:
+                                    try:
-                                try:
+                                        np.testing.assert_allclose(
-                                    np.testing.assert_allclose(
+                                            exp_dict[name],
-                                        exp_dict[name],
+                                            act_dict[name],
-                                        act_dict[name],
+                                            err_msg="Mismatch in {}.{}".format(
-                                        err_msg="Mismatch in {}.{}".format(base, name),
+                                                base, name
-                                        rtol=rtol,
+                                            ),
-                                        **kwargs
+                                            rtol=rtol,
-                                    )
+                                            **kwargs
-                                except AssertionError as e:
+                                        )
-                                    pass
+                                    except AssertionError as e:
+                                        pass
 
             else:
 
                 def do_test():
                     err = compare_images(expected, actual, tol, in_decorator=True)
                     if err:
-                        print("Error between {} and {} is {:.5f}, which is bigger then the tolerance of {:.5f}".format(
+                        print(
+                            "Error between {} and {} is {:.5f}, which is bigger then the tolerance of {:.5f}".format(
                                 actual, expected, err["rms"], tol
                             )
                         )
@@ -319,6 +322,7 @@ def test_figure():
         ):
             yield (do_test,)
 
+
 @pytest.mark.skipif(
     matplotlib is None or baseline_dir is None, reason="Matplotlib not installed"
 )
@@ -363,6 +367,7 @@ def test_kernel():
         ):
             yield (do_test,)
 
+
 @pytest.mark.skipif(
     matplotlib is None or baseline_dir is None, reason="Matplotlib not installed"
 )
@@ -406,6 +411,7 @@ def test_plot():
     ):
         yield (do_test,)
 
+
 @pytest.mark.skipif(
     matplotlib is None or baseline_dir is None, reason="Matplotlib not installed"
 )
@@ -441,6 +447,7 @@ def test_twod():
     ):
         yield (do_test,)
 
+
 @pytest.mark.skipif(
     matplotlib is None or baseline_dir is None, reason="Matplotlib not installed"
 )
@@ -477,6 +484,7 @@ def test_threed():
     ):
         yield (do_test,)
 
+
 @pytest.mark.skipif(
     matplotlib is None or baseline_dir is None, reason="Matplotlib not installed"
 )
@@ -502,6 +510,7 @@ def test_sparse():
     ):
         yield (do_test,)
 
+
 @pytest.mark.skipif(
     matplotlib is None or baseline_dir is None, reason="Matplotlib not installed"
 )
@@ -534,6 +543,7 @@ def test_classification():
     ):
         yield (do_test,)
 
+
 @pytest.mark.skipif(
     matplotlib is None or baseline_dir is None, reason="Matplotlib not installed"
 )
@@ -564,6 +574,7 @@ def test_sparse_classification():
     ):
         yield (do_test,)
 
+
 @pytest.mark.skipif(
     matplotlib is None or baseline_dir is None, reason="Matplotlib not installed"
 )
@@ -621,6 +632,7 @@ def test_gplvm():
     ):
         yield (do_test,)
 
+
 @pytest.mark.skipif(
     matplotlib is None or baseline_dir is None, reason="Matplotlib not installed"
 )

GPy/testing/test_serialization.py

@@ -377,7 +377,9 @@ class TestSerialization:
         m2_r = GPy.models.GPClassification.load_model(
             "temp_test_gp_classifier_without_data.json.zip", (X, Y)
         )
-        assert type(m) == type(m2_r), "Incorrect model type. Expected: {} Actual: {}".format(type(m), type(m2_r)),
+        assert type(m) == type(
+            m2_r
+        ), "Incorrect model type. Expected: {} Actual: {}".format(type(m), type(m2_r))
         os.remove("temp_test_gp_classifier_with_data.json.zip")
         os.remove("temp_test_gp_classifier_without_data.json.zip")
 
@@ -415,11 +417,15 @@ class TestSerialization:
         m1_r = GPy.models.SparseGPClassification.load_model(
             "temp_test_sparse_gp_classifier_with_data.json.zip"
         )
-        assert type(m) == type(m1_r), "Incorrect model type. Expected: {} Actual: {}".format(type(m), type(m1_r))
+        assert type(m) == type(
+            m1_r
+        ), "Incorrect model type. Expected: {} Actual: {}".format(type(m), type(m1_r))
         m2_r = GPy.models.SparseGPClassification.load_model(
             "temp_test_sparse_gp_classifier_without_data.json.zip", (X, Y)
         )
-        assert type(m) == type(m2_r), "Incorrect model type. Expected: {} Actual: {}".format(type(m), type(m2_r)),
+        assert type(m) == type(
+            m2_r
+        ), "Incorrect model type. Expected: {} Actual: {}".format(type(m), type(m2_r))
         os.remove("temp_test_sparse_gp_classifier_with_data.json.zip")
         os.remove("temp_test_sparse_gp_classifier_without_data.json.zip")