Package: src:python-skbio
Version: 0.5.5-2
Severity: serious
Tags: sid bullseye
User: debian-pyt...@lists.debian.org
Usertags: python3.8
python-skbio ftbfs in unstable, two failing tests:
======================================================================
ERROR: test_munging_invalid_type_to_self_type
(skbio.sequence.tests.test_sequence.TestDistance)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_skbio/build/skbio/sequence/tests/test_sequence.py",
line 2369, in test_munging_invalid_type_to_self_type
Sequence("ACGT").distance(42)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_skbio/build/skbio/sequence/_sequence.py",
line 1539, in distance
other = self._munge_to_self_type(other, 'distance')
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_skbio/build/skbio/sequence/_sequence.py",
line 2161, in _munge_to_self_type
return self.__class__(other)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_skbio/build/skbio/sequence/_sequence.py",
line 622, in __init__
s = np.frombuffer(sequence, dtype=np.uint8)
TypeError: a bytes-like object is required, not 'int'
======================================================================
ERROR: test_init_invalid_sequence
(skbio.sequence.tests.test_sequence.TestSequence)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_skbio/build/skbio/sequence/tests/test_sequence.py",
line 465, in test_init_invalid_sequence
Sequence(('a', 'b', 'c'))
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_skbio/build/skbio/sequence/_sequence.py",
line 622, in __init__
s = np.frombuffer(sequence, dtype=np.uint8)
TypeError: a bytes-like object is required, not 'tuple'
======================================================================
FAIL: test_no_variation_pearson
(skbio.stats.distance.tests.test_mantel.MantelTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/tests/test_mantel.py",
line 250, in test_no_variation_pearson
npt.assert_equal(obs, (0.0, 1.0, 3))
File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line
355, in assert_equal
assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k, err_msg), verbose)
File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line
427, in assert_equal
raise AssertionError(msg)
AssertionError:
Items are not equal:
item=0
ACTUAL: nan
DESIRED: 0.0
======================================================================
FAIL: test_one_sided_less (skbio.stats.distance.tests.test_mantel.MantelTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/tests/test_mantel.py",
line 189, in test_one_sided_less
self.assertEqual(obs, (1, 1, 3))
AssertionError: Tuples differ: (0.9999999999999998, 1.0, 3) != (1, 1, 3)
First differing element 0:
0.9999999999999998
1
- (0.9999999999999998, 1.0, 3)
+ (1, 1, 3)
======================================================================
FAIL: Test against a reference implementation from R's ape package
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_skbio/build/skbio/stats/ordination/tests/test_principal_coordinate_analysis.py",
line 250, in test_pcoa_biplot_from_ape
assert_ordination_results_equal(obs, exp, ignore_directionality=True,
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_skbio/build/skbio/util/_testing.py",
line 126, in assert_ordination_results_equal
_assert_frame_equal(left.features, right.features,
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_skbio/build/skbio/util/_testing.py",
line 171, in _assert_frame_equal
npt.assert_almost_equal(left_values, right_values, decimal=decimal)
File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line
584, in assert_almost_equal
return assert_array_almost_equal(actual, desired, decimal, err_msg)
File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line
1027, in assert_array_almost_equal
assert_array_compare(compare, x, y, err_msg=err_msg, verbose=verbose,
File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line
769, in assert_array_compare
flagged = func_assert_same_pos(x, y, func=isnan, hasval='nan')
File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line
745, in func_assert_same_pos
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
x and y nan location mismatch:
x: array([[-2.5170346e-02, -3.8742000e-02, 3.7030794e-02, -1.8248587e-02,
-1.2974103e-03, 8.1410679e-04, -1.7370121e-02, 3.6121106e-02,
nan],...
y: array([[-2.5170346e-02, -3.8742000e-02, 3.7030794e-02, -1.8248587e-02,
-1.2974103e-03, 8.1410679e-04, -1.7370121e-02, 3.6121106e-02,
0.0000000e+00],...
======================================================================
FAIL: test__identify_sample_groups_not_strict
(skbio.stats.tests.test_power.PowerAnalysisTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_skbio/build/skbio/stats/tests/test_power.py",
line 496, in test__identify_sample_groups_not_strict
npt.assert_array_equal(known_pairs[k][i], test_pairs[k][i])
File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line
917, in assert_array_equal
assert_array_compare(operator.__eq__, x, y, err_msg=err_msg,
File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line
841, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Arrays are not equal
Mismatch: 100%
x: array(['MM', 'WM'], dtype=object)
y: array(['WM', 'MM'], dtype=object)
----------------------------------------------------------------------
Ran 2340 tests in 55.022s
FAILED (SKIP=30, errors=2, failures=4)
E: pybuild pybuild:341: test: plugin distutils failed with: exit code=1: cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_skbio/build; python3.8 -m nose -v
dh_auto_test: pybuild --test --test-nose -i python{version} -p "3.8 3.7"
returned exit code 13
make: *** [debian/rules:13: build] Error 255
