apunkt/GPy
1
0
Fork 0
mirror of https://github.com/SheffieldML/GPy.git synced 2026-06-05 14:55:15 +02:00
Code Issues Projects Releases Packages Wiki Activity Actions

fix test errors after migration

Browse source
This commit is contained in:
Martin Bubel 2023-10-16 08:30:53 +02:00
parent cec7e999bb
commit d77f140fec
10 changed files with 95 additions and 58 deletions
Download patch file Download diff file Expand all files Collapse all files

38
GPy/__init__.py
View file

@ -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('_'):
sys.modules['GPy.kern._src.{}'.format(name)] = module
sys.modules['GPy.inference.optimization'] = inference.optimization
if not name.startswith("_"):
sys.modules["GPy.kern._src.{}".format(name)] = module
sys.modules["GPy.inference.optimization"] = inference.optimization
import paramz
return paramz.load(file_or_path)

1
GPy/old_tests/gp_transformation_tests.py
View file

@ -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

24
GPy/testing/move_files.py Normal file
View file

@ -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])

6
GPy/testing/test_cython.py
View file

@ -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",
)

5
GPy/testing/test_ep_likelihood.py
View file

@ -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):

1
GPy/testing/test_gpy_kernels_state_space.py
View file

@ -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

2
GPy/testing/test_kernel.py
View file

@ -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",
)

2
GPy/testing/test_model.py
View file

@ -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()

62
GPy/testing/test_plotting.py
View file

@ -141,39 +141,42 @@ def _image_comparison(
if ext == "npz":
def do_test():
with pytest.skip
if not os.path.exists(expected):
import shutil
with pytest.skip:
if not os.path.exists(expected):
import shutil
shutil.copy2(actual, expected)
# shutil.copy2(os.path.join(result_dir, "{}.{}".format(base, 'png')), os.path.join(baseline_dir, "{}.{}".format(base, 'png')))
raise IOError(
"Baseline file {} not found, copying result {}".format(
expected, actual
shutil.copy2(actual, expected)
# shutil.copy2(os.path.join(result_dir, "{}.{}".format(base, 'png')), os.path.join(baseline_dir, "{}.{}".format(base, 'png')))
raise IOError(
"Baseline file {} not found, copying result {}".format(
expected, actual
)
)
)
else:
exp_dict = dict(np.load(expected).items())
act_dict = dict(np.load(actual).items())
for name in act_dict:
if name in exp_dict:
try:
np.testing.assert_allclose(
exp_dict[name],
act_dict[name],
err_msg="Mismatch in {}.{}".format(base, name),
rtol=rtol,
**kwargs
)
except AssertionError as e:
pass
else:
exp_dict = dict(np.load(expected).items())
act_dict = dict(np.load(actual).items())
for name in act_dict:
if name in exp_dict:
try:
np.testing.assert_allclose(
exp_dict[name],
act_dict[name],
err_msg="Mismatch in {}.{}".format(
base, name
),
rtol=rtol,
**kwargs
)
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"
)

12
GPy/testing/test_serialization.py
View file

@ -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")