Closed
Description
Describe the issue:
Some SciPy tests involving masked arrays have been failing since ~7/15 (e.g. see CI in scipy/scipy#16610). It looks like some of the failures are resolved by gh-21977, but there are some that remain.
=================================== FAILURES ===================================
______________________ TestCorr.test_kendalltau_seasonal _______________________
../testenv/lib/python3.11/site-packages/scipy/stats/tests/test_mstats_basic.py:405: in test_kendalltau_seasonal
assert_almost_equal(output['global p-value (indep)'], 0.008, 3)
output = {'chi2 total': 0.9138890055275067, 'chi2 trend': 0.03518368100765739, 'global p-value (dep)': 0.9592698679548645, 'global p-value (indep)': 0.9415878180349753, ...}
self = <scipy.stats.tests.test_mstats_basic.TestCorr object at 0x7f75a3bf2650>
x = masked_array(
data=[[--, 4.0, 3.0, --],
[--, 3.0, 2.0, 6.0],
[4.0, 5.0, 5.0, 11.0],
[2.0, 3.... False, False, False],
[False, False, False, False],
[False, False, True, False]],
fill_value=1e+20)
/home/runner/.local/lib/python3.11/site-packages/numpy/ma/testutils.py:189: in assert_almost_equal
raise AssertionError(msg)
E AssertionError:
E Items are not equal:
E ACTUAL: 0.9415878180349753
E DESIRED: 0.008
actual = 0.9415878180349753
decimal = 3
desired = 0.008
err_msg = ''
msg = '\nItems are not equal:\n ACTUAL: 0.9415878180349753\n DESIRED: 0.008'
verbose = True
_______________________ TestTtest_rel.test_fully_masked ________________________
../testenv/lib/python3.11/site-packages/scipy/stats/tests/test_mstats_basic.py:1217: in test_fully_masked
assert_array_equal(p, (np.nan, np.nan))
outcome = masked_array(
data=[[--, -0.4495544480666782],
[--, 0.6433801600172545],
[--, 0.08038096427837299]],
mask=[[ True, False],
[ True, False],
[ True, False]],
fill_value=1e+20)
p = 1.0
pair = ([nan, nan], [1.0, 2.0])
self = <scipy.stats.tests.test_mstats_basic.TestTtest_rel object at 0x7f75a2eedb50>
t = masked
/home/runner/.local/lib/python3.11/site-packages/numpy/ma/testutils.py:225: in assert_array_equal
assert_array_compare(operator.__eq__, x, y,
err_msg = ''
verbose = True
x = 1.0
y = (nan, nan)
/home/runner/.local/lib/python3.11/site-packages/numpy/ma/testutils.py:213: in assert_array_compare
return np.testing.assert_array_compare(comparison,
comparison = <built-in function eq>
err_msg = ''
fill_value = True
header = 'Arrays are not equal'
m = False
verbose = True
x = masked_array(data=1.,
mask=False,
fill_value=1e+20)
y = masked_array(data=[nan, nan],
mask=False,
fill_value=1e+20)
/opt/hostedtoolcache/Python/3.11.0-beta.4/x64/lib/python3.11/contextlib.py:81: in inner
return func(*args, **kwds)
E AssertionError:
E Arrays are not equal
E
E x and y nan location mismatch:
E x: array(1.)
E y: array([nan, nan])
args = (<built-in function eq>, array(1.), array([nan, nan]))
func = <function assert_array_compare at 0x7f75b19c16c0>
kwds = {'err_msg': '', 'header': 'Arrays are not equal', 'verbose': True}
self = <contextlib._GeneratorContextManager object at 0x7f75b19a91d0>
_______________________ TestTtest_ind.test_fully_masked ________________________
../testenv/lib/python3.11/site-packages/scipy/stats/tests/test_mstats_basic.py:1316: in test_fully_masked
assert_array_equal(p, (np.nan, np.nan))
outcome = masked_array(
data=[[--, -0.4495544480666782],
[--, 0.6433801600172545],
[--, 0.08038096427837299]],
mask=[[ True, False],
[ True, False],
[ True, False]],
fill_value=1e+20)
p = 1.0
pair = (masked_array(data=[--, --, --],
mask=[ True, True, True],
fill_value=1e+20,
dtype=f...1600172545,
0.08038096427837299],
mask=[False, False, False],
fill_value=1e+20))
self = <scipy.stats.tests.test_mstats_basic.TestTtest_ind object at 0x7f75a3837150>
t = masked
/home/runner/.local/lib/python3.11/site-packages/numpy/ma/testutils.py:225: in assert_array_equal
assert_array_compare(operator.__eq__, x, y,
err_msg = ''
verbose = True
x = 1.0
y = (nan, nan)
/home/runner/.local/lib/python3.11/site-packages/numpy/ma/testutils.py:213: in assert_array_compare
return np.testing.assert_array_compare(comparison,
comparison = <built-in function eq>
err_msg = ''
fill_value = True
header = 'Arrays are not equal'
m = False
verbose = True
x = masked_array(data=1.,
mask=False,
fill_value=1e+20)
y = masked_array(data=[nan, nan],
mask=False,
fill_value=1e+20)
/opt/hostedtoolcache/Python/3.11.0-beta.4/x64/lib/python3.11/contextlib.py:81: in inner
return func(*args, **kwds)
E AssertionError:
E Arrays are not equal
E
E x and y nan location mismatch:
E x: array(1.)
E y: array([nan, nan])
args = (<built-in function eq>, array(1.), array([nan, nan]))
func = <function assert_array_compare at 0x7f75b19c16c0>
kwds = {'err_msg': '', 'header': 'Arrays are not equal', 'verbose': True}
self = <contextlib._GeneratorContextManager object at 0x7f75b19a91d0>
______________________ TestTtest_1samp.test_fully_masked _______________________
../testenv/lib/python3.11/site-packages/scipy/stats/tests/test_mstats_basic.py:1403: in test_fully_masked
assert_array_equal(p, expected)
expected = (nan, nan)
outcome = masked_array(data=[--, --, --],
mask=[ True, True, True],
fill_value=1e+20,
dtype=float64)
p = 1.0
pair = ((nan, nan), 0.0)
self = <scipy.stats.tests.test_mstats_basic.TestTtest_1samp object at 0x7f75a35bfa50>
sup = <numpy.testing._private.utils.suppress_warnings object at 0x7f75996c5150>
t = masked
/home/runner/.local/lib/python3.11/site-packages/numpy/ma/testutils.py:225: in assert_array_equal
assert_array_compare(operator.__eq__, x, y,
err_msg = ''
verbose = True
x = 1.0
y = (nan, nan)
/home/runner/.local/lib/python3.11/site-packages/numpy/ma/testutils.py:213: in assert_array_compare
return np.testing.assert_array_compare(comparison,
comparison = <built-in function eq>
err_msg = ''
fill_value = True
header = 'Arrays are not equal'
m = False
verbose = True
x = masked_array(data=1.,
mask=False,
fill_value=1e+20)
y = masked_array(data=[nan, nan],
mask=False,
fill_value=1e+20)
/opt/hostedtoolcache/Python/3.11.0-beta.4/x64/lib/python3.11/contextlib.py:81: in inner
return func(*args, **kwds)
E AssertionError:
E Arrays are not equal
E
E x and y nan location mismatch:
E x: array(1.)
E y: array([nan, nan])
args = (<built-in function eq>, array(1.), array([nan, nan]))
func = <function assert_array_compare at 0x7f75b19c16c0>
kwds = {'err_msg': '', 'header': 'Arrays are not equal', 'verbose': True}
self = <contextlib._GeneratorContextManager object at 0x7f75b19a91d0>
_________________________ test_chisquare_masked_arrays _________________________
../testenv/lib/python3.11/site-packages/scipy/stats/tests/test_stats.py:3579: in test_chisquare_masked_arrays
mat.assert_array_almost_equal(g, expected_g, decimal=15)
chi2 = <scipy.stats._continuous_distns.chi2_gen object at 0x7f75ad58ae50>
chisq = masked_array(data=[24.0, 0.5],
mask=[False, False],
fill_value=1e+20)
expected_chisq = array([24. , 0.5])
expected_g = array([22.18070978, 0.50534308])
g = array([nan, nan])
mask = array([[0, 1],
[0, 1],
[0, 0],
[0, 0],
[1, 0]])
mobs = masked_array(
data=[[8, --],
[8, --],
[16, 3],
[32, 4],
[--, 5]],
mask=[[False, T...,
[False, True],
[False, False],
[False, False],
[ True, False]],
fill_value=999999)
obs = array([[ 8, -1],
[ 8, -1],
[16, 3],
[32, 4],
[-1, 5]])
p = array([nan, nan])
/home/runner/.local/lib/python3.11/site-packages/numpy/ma/testutils.py:265: in assert_array_almost_equal
assert_array_compare(compare, x, y, err_msg=err_msg, verbose=verbose,
compare = <function assert_array_almost_equal.<locals>.compare at 0x7f758bbc84a0>
decimal = 15
err_msg = ''
verbose = True
x = array([nan, nan])
y = array([22.18070978, 0.50534308])
/home/runner/.local/lib/python3.11/site-packages/numpy/ma/testutils.py:213: in assert_array_compare
return np.testing.assert_array_compare(comparison,
comparison = <function assert_array_almost_equal.<locals>.compare at 0x7f758bbc84a0>
err_msg = ''
fill_value = True
header = 'Arrays are not almost equal'
m = False
verbose = True
x = masked_array(data=[nan, nan],
mask=False,
fill_value=1e+20)
y = masked_array(data=[22.18070978, 0.50534308],
mask=False,
fill_value=1e+20)
/opt/hostedtoolcache/Python/3.11.0-beta.4/x64/lib/python3.11/contextlib.py:81: in inner
return func(*args, **kwds)
E AssertionError:
E Arrays are not almost equal
E
E x and y nan location mismatch:
E x: array([nan, nan])
E y: array([22.18071 , 0.505343])
args = (<function assert_array_almost_equal.<locals>.compare at 0x7f758bbc84a0>, array([nan, nan]), array([22.18070978, 0.50534308]))
func = <function assert_array_compare at 0x7f75b19c16c0>
kwds = {'err_msg': '', 'header': 'Arrays are not almost equal', 'verbose': True}
self = <contextlib._GeneratorContextManager object at 0x7f75b19a91d0>
============================= slowest 10 durations =============================
16.80s call build/testenv/lib/python3.11/site-packages/scipy/stats/tests/test_continuous_basic.py::test_kappa4_array_gh13582
12.20s call build/testenv/lib/python3.11/site-packages/scipy/stats/tests/test_continuous_basic.py::test_cont_basic[500-200-skewnorm-arg91]
9.72s call build/testenv/lib/python3.11/site-packages/scipy/optimize/tests/test_direct.py::TestDIRECT::test_segmentation_fault[False]
7.68s call build/testenv/lib/python3.11/site-packages/scipy/sparse/linalg/_isolve/tests/test_iterative.py::test_precond_inverse[case1]
7.33s call build/testenv/lib/python3.11/site-packages/scipy/_lib/tests/test_import_cycles.py::test_modules_importable
5.79s call build/testenv/lib/python3.11/site-packages/scipy/optimize/tests/test_lsq_linear.py::TestTRF::test_large_rank_deficient
5.76s call build/testenv/lib/python3.11/site-packages/scipy/optimize/tests/test_lsq_linear.py::TestBVLS::test_large_rank_deficient
4.71s call build/testenv/lib/python3.11/site-packages/scipy/stats/tests/test_continuous_basic.py::test_cont_basic[500-200-truncweibull_min-arg100]
3.93s call build/testenv/lib/python3.11/site-packages/scipy/optimize/tests/test_optimize.py::TestOptimizeSimple::test_minimize_callback_copies_array[fmin]
3.68s call build/testenv/lib/python3.11/site-packages/scipy/optimize/_trustregion_constr/tests/test_report.py::test_gh12922
=========================== short test summary info ============================
FAILED ../testenv/lib/python3.11/site-packages/scipy/stats/tests/test_mstats_basic.py::TestCorr::test_kendalltau_seasonal
FAILED ../testenv/lib/python3.11/site-packages/scipy/stats/tests/test_mstats_basic.py::TestTtest_rel::test_fully_masked
FAILED ../testenv/lib/python3.11/site-packages/scipy/stats/tests/test_mstats_basic.py::TestTtest_ind::test_fully_masked
FAILED ../testenv/lib/python3.11/site-packages/scipy/stats/tests/test_mstats_basic.py::TestTtest_1samp::test_fully_masked
FAILED ../testenv/lib/python3.11/site-packages/scipy/stats/tests/test_stats.py::test_chisquare_masked_arrays
= 5 failed, 36748 passed, 2162 skipped, [1211](https://github.com/scipy/scipy/runs/7379137176?check_suite_focus=true#step:7:1212)4 deselected, 139 xfailed, 7 xpassed in 538.49s (0:08:58) =I am having trouble creating a MWE involving only NumPy because I haven't been successful at building NumPy main. I hope someone with (any relatively modern version of) SciPy and NumPy main can help me find one.
This test below passes in NumPy 1.21.2, but I believe it will fail with NumPy main. Can someone confirm and tell me what the value of res is in NumPy main?
Reproduce the code example:
import numpy as np
from numpy import ma
from scipy.stats import mstats
outcome = ma.masked_array(np.random.randn(3, 2), mask=[[1, 0], [1, 0], [1, 0]])
res = mstats.ttest_rel(outcome[:, 0], outcome[:, 1])
# I don't think it is good practice to compare a masked element to a NaN,
# but this is what was in the SciPy test.
np.testing.assert_array_equal(res, (np.nan, np.nan))
# In any case, if this no longer passes, why not?
# What is the value of `res` using NumPy main?
print(res)Error message:
-NumPy/Python version information:
1.21.2 3.9.7 (default, Sep 16 2021, 16:59:28) [MSC v.1916 64 bit (AMD64)]