[Debichem-devel] Bug#1058454: prody: autopkgtest regression on i386

[Graham Inggs]

Source: prody
Version: 2.3.1+dfsg-3
Severity: serious
Tags: sid trixie
User: debian-ci at lists.debian.org
Usertags: regression

Hi Maintainer

The autopkgtest of prody 2.3.1+dfsg-3 is failing when tested with
numpy 1:1.24.2-2 [1].  I've copied what I hope is the relevant part of
the log below.

Regards
Graham


[1] https://ci.debian.net/packages/p/prody/testing/i386/


345s =================================== FAILURES
===================================
345s ______________________ TestANMResults.testHessianSymmetry
______________________
345s
345s self = <prody.tests.dynamics.test_enms.TestANMResults
testMethod=testHessianSymmetry>
345s
345s def testHessianSymmetry(self):
345s hessian = anm._getHessian()
345s > assert_equal(hessian, hessian.T, 'hessian is not symmetric')
345s
345s tests/dynamics/test_enms.py:123:
345s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _ _ _
345s
345s args = (<built-in function eq>, array([[ 6.9137506 , 0.02186812,
0.9401404 , ..., 0. ,
345s 0. , 0. ...33, 2.28102867],
345s [ 0. , 0. , 0. , ..., 0.89212883,
345s 2.28102867, 2.72983555]]))
345s kwds = {'err_msg': 'hessian is not symmetric', 'header': 'Arrays
are not equal', 'strict': False, 'verbose': True}
345s
345s @wraps(func)
345s def inner(*args, **kwds):
345s with self._recreate_cm():
345s > return func(*args, **kwds)
345s E AssertionError:
345s E Arrays are not equal
345s E hessian is not symmetric
345s E Mismatched elements: 6 / 51984 (0.0115%)
345s E Max absolute difference: 4.4408921e-16
345s E Max relative difference: 7.83963072e-16
345s E x: array([[ 6.913751, 0.021868, 0.94014 , ..., 0. , 0. ,
345s E 0. ],
345s E [ 0.021868, 9.066915, -0.076779, ..., 0. , 0. ,...
345s E y: array([[ 6.913751, 0.021868, 0.94014 , ..., 0. , 0. ,
345s E 0. ],
345s E [ 0.021868, 9.066915, -0.076779, ..., 0. , 0. ,...
345s
345s /usr/lib/python3.11/contextlib.py:81: AssertionError
345s _____________________ TestEXANMResults.testHessianSymmetry
_____________________
345s
345s self = <prody.tests.dynamics.test_enms.TestEXANMResults
testMethod=testHessianSymmetry>
345s
345s def testHessianSymmetry(self):
345s hessian = exanm._getHessian()
345s > assert_equal(hessian, hessian.T, 'hessian is not symmetric')
345s
345s tests/dynamics/test_enms.py:174:
345s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _ _ _
345s
345s args = (<built-in function eq>, array([[ 8.02436812, 0.27315085,
4.13687748, ..., 0. ,
345s 0. , 0. ...01, -3.66113893],
345s [ 0. , 0. , 0. , ..., 1.48069236,
345s -3.66113893, 28.20730453]]))
345s kwds = {'err_msg': 'hessian is not symmetric', 'header': 'Arrays
are not equal', 'strict': False, 'verbose': True}
345s
345s @wraps(func)
345s def inner(*args, **kwds):
345s with self._recreate_cm():
345s > return func(*args, **kwds)
345s E AssertionError:
345s E Arrays are not equal
345s E hessian is not symmetric
345s E Mismatched elements: 148 / 13089924 (0.00113%)
345s E Max absolute difference: 8.8817842e-16
345s E Max relative difference: 2.78880522e-16
345s E x: array([[ 8.024368, 0.273151, 4.136877, ..., 0. , 0. ,
345s E 0. ],
345s E [ 0.273151, 3.353604, -0.105517, ..., 0. , 0. ,...
345s E y: array([[ 8.024368, 0.273151, 4.136877, ..., 0. , 0. ,
345s E 0. ],
345s E [ 0.273151, 3.353604, -0.105517, ..., 0. , 0. ,...
345s
345s /usr/lib/python3.11/contextlib.py:81: AssertionError
345s ______________________ TestANM.testBuildMatrixCoordsArray
______________________
345s
345s self = <prody.tests.dynamics.test_enms.TestANM
testMethod=testBuildMatrixCoordsArray>
345s
345s def testBuildMatrixCoordsArray(self):
345s """Test output when *coords* is an array."""
345s
345s self.buildMatrix(COORDS)
345s > assert_equal(self.getMatrix(), self.getExpected(),
345s 'failed to get correct matrix')
345s
345s tests/dynamics/test_enms.py:288:
345s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _ _ _
345s
345s args = (<built-in function eq>, array([[ 6.9137506 , 0.02186812,
0.9401404 , ..., 0. ,
345s 0. , 0. ...33, 2.28102867],
345s [ 0. , 0. , 0. , ..., 0.89212883,
345s 2.28102867, 2.72983555]]))
345s kwds = {'err_msg': 'failed to get correct matrix', 'header':
'Arrays are not equal', 'strict': False, 'verbose': True}
345s
345s @wraps(func)
345s def inner(*args, **kwds):
345s with self._recreate_cm():
345s > return func(*args, **kwds)
345s E AssertionError:
345s E Arrays are not equal
345s E failed to get correct matrix
345s E Mismatched elements: 1 / 51984 (0.00192%)
345s E Max absolute difference: 1.77635684e-15
345s E Max relative difference: 1.43455679e-16
345s E x: array([[ 6.913751, 0.021868, 0.94014 , ..., 0. , 0. ,
345s E 0. ],
345s E [ 0.021868, 9.066915, -0.076779, ..., 0. , 0. ,...
345s E y: array([[ 6.913751, 0.021868, 0.94014 , ..., 0. , 0. ,
345s E 0. ],
345s E [ 0.021868, 9.066915, -0.076779, ..., 0. , 0. ,...
345s
345s /usr/lib/python3.11/contextlib.py:81: AssertionError