Use numpy.testing.assert_allclose over assert np.allclose

[janosh]

Reason: significantly more helpful error messages on failed tests.

Example before with assert np.allclose:

tests/analysis/gb/test_grain.py:100: AssertionError

    def test_as_dict_and_from_dict(self):
        d1 = self.Cu_GB1.as_dict()
        d2 = self.Cu_GB2.as_dict()
        Cu_GB1_new = GrainBoundary.from_dict(d1)
        Cu_GB2_new = GrainBoundary.from_dict(d2)
        assert Cu_GB1_new.sigma == approx(self.Cu_GB1.sigma)
        assert Cu_GB1_new.rotation_angle == approx(self.Cu_GB1.rotation_angle)
        assert Cu_GB1_new.rotation_axis == self.Cu_GB1.rotation_axis
        assert Cu_GB1_new.gb_plane == self.Cu_GB1.gb_plane
        assert np.allclose(Cu_GB1_new.init_cell.lattice.matrix, self.Cu_GB1.init_cell.lattice.matrix)
>       assert np.allclose(
            Cu_GB1_new.oriented_unit_cell.lattice.matrix + 1e-3,
            self.Cu_GB1.oriented_unit_cell.lattice.matrix,
        )
E       assert False
E        +  where False = <function allclose at 0x1102feab0>((array([[-10.84922172,   0.        ,  10.84922172],\n       [-14.46562896,  10.84922172, -18.0820362 ],\n       [ -7.23281448,   3.61640724,  -7.23281448]]) + 0.001), array([[-10.84922172,   0.        ,  10.84922172],\n       [-14.46562896,  10.84922172, -18.0820362 ],\n       [ -7.23281448,   3.61640724,  -7.23281448]]))
E        +    where <function allclose at 0x1102feab0> = np.allclose
E        +    and   array([[-10.84922172,   0.        ,  10.84922172],\n       [-14.46562896,  10.84922172, -18.0820362 ],\n       [ -7.23281448,   3.61640724,  -7.23281448]]) = Lattice\n    abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.130102354156051 90.0 95.7391704...72\n      B : -14.46562896 10.84922172 -18.0820362\n      C : -7.23281448 3.61640724 -7.23281448\n    pbc : True True True.matrix
E        +      where Lattice\n    abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.130102354156051 90.0 95.7391704...72\n      B : -14.46562896 10.84922172 -18.0820362\n      C : -7.23281448 3.61640724 -7.23281448\n    pbc : True True True = Structure Summary\nLattice\n    abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.1301023541560...cSite: Cu (-16.27, 9.041, -10.85) [0.3889, 0.8333, 0.0]\nPeriodicSite: Cu (-12.66, 9.041, -14.47) [0.05556, 0.8333, 0.0].lattice
E        +        where Structure Summary\nLattice\n    abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.1301023541560...cSite: Cu (-16.27, 9.041, -10.85) [0.3889, 0.8333, 0.0]\nPeriodicSite: Cu (-12.66, 9.041, -14.47) [0.05556, 0.8333, 0.0] = Structure Summary\nLattice\n    abc : 15.343116497616757 25.571860829361263 87.14641575163476\n angles : 9.61799283329482...e: Cu (-45.26, 18.33, -34.41) [0.5261, 0.1568, 0.6344]\nPeriodicSite: Cu (-45.26, 20.14, -36.21) [0.508, 0.5483, 0.5413].oriented_unit_cell
E        +    and   array([[-10.84922172,   0.        ,  10.84922172],\n       [-14.46562896,  10.84922172, -18.0820362 ],\n       [ -7.23281448,   3.61640724,  -7.23281448]]) = Lattice\n    abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.130102354156051 90.0 95.7391704...72\n      B : -14.46562896 10.84922172 -18.0820362\n      C : -7.23281448 3.61640724 -7.23281448\n    pbc : True True True.matrix
E        +      where Lattice\n    abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.130102354156051 90.0 95.7391704...72\n      B : -14.46562896 10.84922172 -18.0820362\n      C : -7.23281448 3.61640724 -7.23281448\n    pbc : True True True = Structure Summary\nLattice\n    abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.1301023541560...cSite: Cu (-16.27, 9.041, -10.85) [0.3889, 0.8333, 0.0]\nPeriodicSite: Cu (-12.66, 9.041, -14.47) [0.05556, 0.8333, 0.0].lattice
E        +        where Structure Summary\nLattice\n    abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.1301023541560...cSite: Cu (-16.27, 9.041, -10.85) [0.3889, 0.8333, 0.0]\nPeriodicSite: Cu (-12.66, 9.041, -14.47) [0.05556, 0.8333, 0.0] = Structure Summary\nLattice\n    abc : 15.343116497616757 25.571860829361263 87.14641575163476\n angles : 9.61799283329482...e: Cu (-45.26, 18.33, -34.41) [0.5261, 0.1568, 0.6344]\nPeriodicSite: Cu (-45.26, 20.14, -36.21) [0.508, 0.5483, 0.5413].oriented_unit_cell
E        +          where Structure Summary\nLattice\n    abc : 15.343116497616757 25.571860829361263 87.14641575163476\n angles : 9.61799283329482...e: Cu (-45.26, 18.33, -34.41) [0.5261, 0.1568, 0.6344]\nPeriodicSite: Cu (-45.26, 20.14, -36.21) [0.508, 0.5483, 0.5413] = <tests.analysis.gb.test_grain.TestGrainBoundary testMethod=test_as_dict_and_from_dict>.Cu_GB1

After changing to numpy.testing.assert_allclose:

    def test_as_dict_and_from_dict(self):
        d1 = self.Cu_GB1.as_dict()
        d2 = self.Cu_GB2.as_dict()
        Cu_GB1_new = GrainBoundary.from_dict(d1)
        Cu_GB2_new = GrainBoundary.from_dict(d2)
        assert Cu_GB1_new.sigma == approx(self.Cu_GB1.sigma)
        assert Cu_GB1_new.rotation_angle == approx(self.Cu_GB1.rotation_angle)
        assert Cu_GB1_new.rotation_axis == self.Cu_GB1.rotation_axis
        assert Cu_GB1_new.gb_plane == self.Cu_GB1.gb_plane
        assert np.allclose(Cu_GB1_new.init_cell.lattice.matrix, self.Cu_GB1.init_cell.lattice.matrix)
>       assert_allclose(
            Cu_GB1_new.oriented_unit_cell.lattice.matrix + 1e-3,
            self.Cu_GB1.oriented_unit_cell.lattice.matrix,
        )

kwds = {'equal_nan': True, 'err_msg': '', 'header': 'Not equal to tolerance rtol=1e-07, atol=0', 'verbose': True}

E           AssertionError: 
E           Not equal to tolerance rtol=1e-07, atol=0
E           
E           Mismatched elements: 9 / 9 (100%)
E           Max absolute difference: 0.001
E           Max relative difference: 0.00027652
E            x: array([[-1.084822e+01,  1.000000e-03,  1.085022e+01],
E                  [-1.446463e+01,  1.085022e+01, -1.808104e+01],
E                  [-7.231814e+00,  3.617407e+00, -7.231814e+00]])
E            y: array([[-10.849222,   0.      ,  10.849222],
E                  [-14.465629,  10.849222, -18.082036],
E                  [ -7.232814,   3.616407,  -7.232814]])

aa84b65 fix return type doc str indentation
6f4bb28 don't use pytest.approx() with assert len(...)
b12e7eb use numpy.testing.assert_allclose over assert np.allclose
e025ffb np.allclose(np.array(...), ...) to np.allclose(..., ...)