[Debichem-devel] Bug#994785: python-ase: autopkgtest regression on arm64/ppc64el: TestSlab.test_vibration_on_surface

[Paul Gevers]

Source: python-ase
Version: 3.22.0-1
X-Debbugs-CC: debian-ci at lists.debian.org
Severity: serious
User: debian-ci at lists.debian.org
Usertags: regression

Dear maintainer(s),

With a recent upload of python-ase the autopkgtest of python-ase fails
in testing when that autopkgtest is run with the binary packages of
python-ase from unstable. It passes when run with only packages from
testing. In tabular form:

                       pass            fail
python-ase             from testing    3.22.0-1
all others             from testing    from testing

I copied some of the output at the bottom of this report.

Currently this regression is blocking the migration to testing [1]. Can
you please investigate the situation and fix it?

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[0] You can see what packages were added from the second line of the log
file quoted below. The migration software adds source package from
unstable to the list if they are needed to install packages from
python-ase/3.22.0-1. I.e. due to versioned dependencies or breaks/conflicts.
[1] https://qa.debian.org/excuses.php?package=python-ase

https://ci.debian.net/data/autopkgtest/testing/arm64/p/python-ase/15401492/log.gz

=================================== FAILURES
===================================
______________________ TestSlab.test_vibration_on_surface
______________________

self = <ase.test.vibrations.test_vib.TestSlab object at 0xffff796eaf70>
testdir =
PosixPath('/tmp/pytest-of-debci/pytest-0/test_vibration_on_surface0')

    def test_vibration_on_surface(self, testdir):
        from ase.build import fcc111, add_adsorbate
        ag_slab = fcc111('Ag', (4, 4, 2), a=2)
        n2 = Atoms('N2', positions=[[0., 0., 0.],
                                    [0., np.sqrt(2), np.sqrt(2)]])
        add_adsorbate(ag_slab, n2, height=1, position='fcc')

        # Add an interaction between the N atoms
        hessian_bottom_corner = np.zeros((2, 3, 2, 3))
        hessian_bottom_corner[-1, :, -2] = [1, 1, 1]
        hessian_bottom_corner[-2, :, -1] = [1, 1, 1]

        hessian = np.zeros((34, 3, 34, 3))
        hessian[32:, :, 32:, :] = hessian_bottom_corner

        ag_slab.calc = ForceConstantCalculator(hessian.reshape((34 * 3,
                                                                34 * 3)),
                                               ref=ag_slab.copy(),
                                               f0=np.zeros((34, 3)))

        # Check that Vibrations with restricted indices returns correct
Hessian
        vibs = Vibrations(ag_slab, indices=[-2, -1])
        vibs.run()
        vibs.read()

        assert_array_almost_equal(vibs.get_vibrations().get_hessian(),
                                  hessian_bottom_corner)

        # These should blow up if the vectors don't match number of atoms
        vibs.summary()
        vibs.write_jmol()

        for i in range(6):
            # Frozen atoms should have zero displacement
            assert_array_almost_equal(vibs.get_mode(i)[0], [0., 0., 0.])

            # The N atoms should have finite displacement
>           assert np.all(vibs.get_mode(i)[-2:, :])
E           assert False
E            +  where False = <function all at 0xffff83033d30>(array([[
0.00000000e+00, -2.21811191e-17,  2.25296944e-17],\n
[-1.88935009e-01,  1.88935009e-01,  1.69152862e-18]]))
E            +    where <function all at 0xffff83033d30> = np.all

/usr/lib/python3/dist-packages/ase/test/vibrations/test_vib.py:527:
AssertionError
----------------------------- Captured stdout call
-----------------------------
---------------------
  #    meV     cm^-1
---------------------
  0   29.9i    241.3i
  1    0.0       0.0
  2    0.0       0.0
  3    0.0       0.0
  4    0.0       0.0
  5   29.9     241.3
---------------------
Zero-point energy: 0.015 eV
--------------------------- Captured stdout teardown
---------------------------
Testdir: /tmp/pytest-of-debci/pytest-0/test_vibration_on_surface0
Global seed for "test/vibrations/test_vib.py:test_vibration_on_surface"
was: 16

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