test refactor: assert np.allclose to numpy.testing.assert_allclose

for much better error messages

pymatgen/analysis/chemenv/connectivity/tests/test_connected_components.py

@@ -7,6 +7,7 @@
 import networkx as nx
 import numpy as np
 import pytest
+from numpy.testing import assert_allclose
 
 from pymatgen.analysis.chemenv.connectivity.connected_components import ConnectedComponent
 from pymatgen.analysis.chemenv.connectivity.connectivity_finder import ConnectivityFinder
@@ -379,7 +380,7 @@ def test_periodicity(self):
         assert not cc.is_3d
         assert cc.is_periodic
         assert cc.periodicity == "2D"
-        assert np.allclose(cc.periodicity_vectors, [np.array([0, 1, 0]), np.array([1, 1, 0])])
+        assert_allclose(cc.periodicity_vectors, [np.array([0, 1, 0]), np.array([1, 1, 0])])
         assert isinstance(cc.periodicity_vectors, list)
         assert cc.periodicity_vectors[0].dtype is np.dtype(int)
 
@@ -449,7 +450,7 @@ def test_periodicity(self):
         assert cc.is_3d
         assert cc.is_periodic
         assert cc.periodicity == "3D"
-        assert np.allclose(
+        assert_allclose(
             cc.periodicity_vectors,
             [np.array([0, 1, 0]), np.array([1, 1, 0]), np.array([1, 1, 1])],
         )

pymatgen/analysis/chemenv/coordination_environments/tests/test_read_write.py

@@ -5,8 +5,7 @@
 import shutil
 import unittest
 
-import numpy as np
-from numpy.testing import assert_array_almost_equal
+from numpy.testing import assert_allclose, assert_array_almost_equal
 from pytest import approx
 
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
@@ -102,7 +101,7 @@ def test_structure_environments_neighbors_sets(self):
             [2.25, 0.99301365328679292],
         ]
 
-        assert np.allclose(nb_set.voronoi_grid_surface_points(), nb_set_surface_points)
+        assert_allclose(nb_set.voronoi_grid_surface_points(), nb_set_surface_points)
 
         neighb_sites = nb_set.neighb_sites
         coords = [

pymatgen/analysis/chemenv/utils/tests/test_coordination_geometry_utils.py

@@ -4,6 +4,7 @@
 import random
 
 import numpy as np
+from numpy.testing import assert_allclose
 from pytest import approx
 
 from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import Plane
@@ -24,7 +25,7 @@ def setUp(self):
     def test_factors_abcd_normal_vector(self):
         factors = self.plane.coefficients / self.expected_coefficients
         self.assert_all_close([factors[0]] * 4, list(factors))
-        assert np.allclose([2 / 3, 1 / 3, -2 / 3], self.plane.normal_vector)
+        assert_allclose([2 / 3, 1 / 3, -2 / 3], self.plane.normal_vector)
 
     def test_from_npoints_plane(self):
         best_fits = ["least_square_distance", "maximum_distance"]
@@ -94,12 +95,12 @@ def test_orthonormal_vectors(self):
         assert np.isclose(np.dot(ortho[0], ortho[1]), 0)
         assert np.isclose(np.dot(ortho[1], ortho[2]), 0)
         assert np.isclose(np.dot(ortho[2], ortho[0]), 0)
-        assert np.allclose(np.cross(ortho[0], ortho[1]), ortho[2])
-        assert np.allclose(np.cross(ortho[0], ortho[1]), self.plane.normal_vector)
-        assert np.allclose(np.cross(ortho[1], ortho[2]), ortho[0])
-        assert np.allclose(np.cross(ortho[2], ortho[0]), ortho[1])
+        assert_allclose(np.cross(ortho[0], ortho[1]), ortho[2])
+        assert_allclose(np.cross(ortho[0], ortho[1]), self.plane.normal_vector)
+        assert_allclose(np.cross(ortho[1], ortho[2]), ortho[0])
+        assert_allclose(np.cross(ortho[2], ortho[0]), ortho[1])
         assert not np.allclose(np.cross(ortho[1], ortho[0]), ortho[2])
-        assert np.allclose(np.cross(ortho[0], ortho[1]), self.plane.normal_vector)
+        assert_allclose(np.cross(ortho[0], ortho[1]), self.plane.normal_vector)
 
     def test_plane_comparison(self):
         plane_test_1 = Plane.from_coefficients(4, 2, -4, 3)
@@ -164,14 +165,14 @@ def test_indices_separate(self):
         assert len(sep[0]) == 0
         assert len(sep[1]) == 3
         assert len(sep[2]) == 5
-        assert np.allclose(sep[1], [1, 2, 4])
-        assert np.allclose(sep[2], [0, 3, 5, 6, 7])
+        assert_allclose(sep[1], [1, 2, 4])
+        assert_allclose(sep[2], [0, 3, 5, 6, 7])
         sep = self.plane.indices_separate(plist, 10)
         assert len(sep[0]) == 0
         assert len(sep[1]) == 6
         assert len(sep[2]) == 2
-        assert np.allclose(sep[1], [0, 1, 2, 3, 4, 6])
-        assert np.allclose(sep[2], [5, 7])
+        assert_allclose(sep[1], [0, 1, 2, 3, 4, 6])
+        assert_allclose(sep[2], [5, 7])
         sep = self.plane.indices_separate(plist, 100000)
         assert len(sep[0]) == 0
         assert len(sep[1]) == 8
@@ -313,7 +314,7 @@ def test_projections(self):
         projected_points = self.plane.projectionpoints(expected_projected_points)
         projected_2d = self.plane.project_and_to2dim(expected_projected_points, "mean")
         for ii, pp in enumerate(expected_projected_points):
-            assert np.allclose(pp, projected_points[ii])
+            assert_allclose(pp, projected_points[ii])
         for i1, i2 in itertools.combinations(list(range(len(expected_projected_points))), 2):
             assert np.isclose(
                 np.linalg.norm(expected_projected_points[i1] - expected_projected_points[i2]),
@@ -333,15 +334,15 @@ def test_projections(self):
         projected_2d = self.plane.project_and_to2dim(points_to_project, "mean")
         projected_2d_bis = self.plane.project_and_to2dim(points_to_project, meanpoint)
         for ii, pp in enumerate(projected_2d):
-            assert np.allclose(pp, projected_2d_bis[ii])
+            assert_allclose(pp, projected_2d_bis[ii])
         for i1, i2 in itertools.combinations(list(range(len(projected_points))), 2):
             assert np.isclose(
                 np.linalg.norm(projected_points[i1] - projected_points[i2]),
                 np.linalg.norm(projected_2d[i1] - projected_2d[i2]),
             )
         for pp in points_to_project:
             projected_2d = self.plane.project_and_to2dim([pp], pp)
-            assert np.allclose(projected_2d[0], 0)
+            assert_allclose(projected_2d[0], 0)
         # Check some specific projections
         points = [
             np.zeros(3, np.float_),
@@ -359,7 +360,7 @@ def test_projections(self):
             np.array([-1.55555556, 0.72222222, -0.44444444]),
         ]
         for ii, pp in enumerate(projected_points):
-            assert np.allclose(pp, expected_projected_points[ii])
+            assert_allclose(pp, expected_projected_points[ii])
             assert self.plane.is_in_plane(pp, 0.0000001)
         projected_2d_points_000 = self.plane.project_and_to2dim(points, [0, 0, 0])
         projected_2d_points_mean = self.plane.project_and_to2dim(points, "mean")

pymatgen/analysis/chemenv/utils/tests/test_graph_utils.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
-import numpy as np
 import pytest
+from numpy.testing import assert_allclose
 
 from pymatgen.analysis.chemenv.connectivity.environment_nodes import EnvironmentNode
 from pymatgen.analysis.chemenv.utils.graph_utils import MultiGraphCycle, SimpleGraphCycle, get_delta
@@ -73,9 +73,9 @@ def test_get_delta(self):
         n1 = FakeNode(3)
         n2 = FakeNode(7)
         edge_data = {"start": 3, "end": 7, "delta": [2, 6, 4]}
-        assert np.allclose(get_delta(n1, n2, edge_data), [2, 6, 4])
+        assert_allclose(get_delta(n1, n2, edge_data), [2, 6, 4])
         edge_data = {"start": 7, "end": 3, "delta": [2, 6, 4]}
-        assert np.allclose(get_delta(n1, n2, edge_data), [-2, -6, -4])
+        assert_allclose(get_delta(n1, n2, edge_data), [-2, -6, -4])
         edge_data = {"start": 6, "end": 3, "delta": [2, 6, 4]}
         err_msg = "Trying to find a delta between two nodes with an edge that seems not to link these nodes."
         with pytest.raises(ValueError, match=err_msg):

pymatgen/analysis/interfaces/coherent_interfaces.py

@@ -6,6 +6,7 @@
 from typing import TYPE_CHECKING, Iterator, Sequence
 
 import numpy as np
+from numpy.testing import assert_allclose
 from scipy.linalg import polar
 
 from pymatgen.analysis.elasticity.strain import Deformation
@@ -87,13 +88,13 @@ def _find_matches(self) -> None:
         for match in self.zsl_matches:
             xform = get_2d_transform(film_vectors, match.film_vectors)
             strain, rot = polar(xform)
-            assert np.allclose(
+            assert_allclose(
                 strain, np.round(strain)
             ), "Film lattice vectors changed during ZSL match, check your ZSL Generator parameters"
 
             xform = get_2d_transform(substrate_vectors, match.substrate_vectors)
             strain, rot = polar(xform)
-            assert np.allclose(
+            assert_allclose(
                 strain, strain.astype(int)
             ), "Substrate lattice vectors changed during ZSL match, check your ZSL Generator parameters"
 
@@ -195,10 +196,10 @@ def get_interfaces(
             ).astype(int)
             film_sl_slab = film_slab.copy()
             film_sl_slab.make_supercell(super_film_transform)
-            assert np.allclose(
+            assert_allclose(
                 film_sl_slab.lattice.matrix[2], film_slab.lattice.matrix[2]
             ), "2D transformation affected C-axis for Film transformation"
-            assert np.allclose(
+            assert_allclose(
                 film_sl_slab.lattice.matrix[:2], match.film_sl_vectors
             ), "Transformation didn't make proper supercell for film"
 
@@ -208,10 +209,10 @@ def get_interfaces(
             ).astype(int)
             sub_sl_slab = sub_slab.copy()
             sub_sl_slab.make_supercell(super_sub_transform)
-            assert np.allclose(
+            assert_allclose(
                 sub_sl_slab.lattice.matrix[2], sub_slab.lattice.matrix[2]
             ), "2D transformation affected C-axis for Film transformation"
-            assert np.allclose(
+            assert_allclose(
                 sub_sl_slab.lattice.matrix[:2], match.substrate_sl_vectors
             ), "Transformation didn't make proper supercell for substrate"
 

pymatgen/analysis/magnetism/tests/test_analyzer.py

@@ -5,9 +5,9 @@
 import warnings
 from shutil import which
 
-import numpy as np
 import pytest
 from monty.serialization import loadfn
+from numpy.testing import assert_allclose
 from pytest import approx
 
 from pymatgen.analysis.magnetism import (
@@ -226,13 +226,13 @@ def test_round_magmoms(self):
         struct.add_site_property("magmom", [-5.0143, -5.02, 0.147, 0.146])
 
         msa = CollinearMagneticStructureAnalyzer(struct, round_magmoms=0.001, make_primitive=False)
-        assert np.allclose(msa.magmoms, [5.0171, 5.0171, -0.1465, -0.1465])
+        assert_allclose(msa.magmoms, [5.0171, 5.0171, -0.1465, -0.1465])
         assert msa.magnetic_species_and_magmoms["Ni"] == approx(5.0171)
         assert msa.magnetic_species_and_magmoms["O"] == approx(0.1465)
 
         struct.add_site_property("magmom", [-5.0143, 4.5, 0.147, 0.146])
         msa = CollinearMagneticStructureAnalyzer(struct, round_magmoms=0.001, make_primitive=False)
-        assert np.allclose(msa.magmoms, [5.0143, -4.5, -0.1465, -0.1465])
+        assert_allclose(msa.magmoms, [5.0143, -4.5, -0.1465, -0.1465])
         assert msa.magnetic_species_and_magmoms["Ni"][0] == approx(4.5)
         assert msa.magnetic_species_and_magmoms["Ni"][1] == approx(5.0143)
         assert msa.magnetic_species_and_magmoms["O"] == approx(0.1465)

pymatgen/analysis/tests/test_interface_reactions.py

@@ -5,6 +5,7 @@
 import numpy as np
 import pytest
 from matplotlib.figure import Figure as mpl_figure
+from numpy.testing import assert_allclose
 from pandas import DataFrame
 from plotly.graph_objects import Figure as plotly_figure
 from scipy.spatial import ConvexHull
@@ -241,13 +242,13 @@ def test_convert(self):
         test_array = [(0.5, 1, 3), (0.4, 2, 3), (0, 1, 9), (1, 2, 7)]
         result = [InterfacialReactivity._convert(x, f1, f2) for x, f1, f2 in test_array]
         answer = [0.75, 0.5, 0, 1]
-        assert np.allclose(result, answer), f"_convert: conversion gets error! {answer} expected, but gets {result}"
+        assert_allclose(result, answer), f"_convert: conversion gets error! {answer} expected, but gets {result}"
 
     def test_reverse_convert(self):
         test_array = [(0.5, 1, 3), (0.4, 2, 3), (0, 1, 9), (1, 2, 7)]
         result = [InterfacialReactivity._reverse_convert(x, f1, f2) for x, f1, f2 in test_array]
         answer = [0.25, 0.3076923, 0, 1]
-        assert np.allclose(result, answer), f"_convert: conversion gets error! {answer} expected, but gets {result}"
+        assert_allclose(result, answer), f"_convert: conversion gets error! {answer} expected, but gets {result}"
 
     def test_products_property(self):
         test1 = sorted(self.ir[0].products) == sorted(["MnO2", "O2", "Mn"])
@@ -409,7 +410,7 @@ def test_minimum(self):
             (0.3333333, -4.0),
         ]
         for i, j in zip(self.ir, answer):
-            assert np.allclose(i.minimum, j), (
+            assert_allclose(i.minimum, j), (
                 f"minimum: the system with {i.c1_original.reduced_formula} and {i.c2_original.reduced_formula} "
                 f"gets error!{j} expected, but gets {i.minimum}"
             )
@@ -435,7 +436,7 @@ def energy_lst(lst):
             assert name_lst(i) == name_lst(
                 j
             ), f"get_no_mixing_energy: names get error, {name_lst(j)} expected but gets {name_lst(i)}"
-            assert np.allclose(energy_lst(i), energy_lst(j)), (
+            assert_allclose(energy_lst(i), energy_lst(j)), (
                 "get_no_mixing_energy: "
                 "no_mixing energies get error, "
                 f"{energy_lst(j)} expected but gets {energy_lst(i)}"

pymatgen/analysis/tests/test_phase_diagram.py

@@ -10,6 +10,7 @@
 import numpy as np
 import pytest
 from monty.serialization import dumpfn, loadfn
+from numpy.testing import assert_allclose
 from pytest import approx
 
 from pymatgen.analysis.phase_diagram import (
@@ -950,9 +951,9 @@ def test_unique_lines(self):
     def test_triangular_coord(self):
         coord = [0.5, 0.5]
         coord = triangular_coord(coord)
-        assert np.allclose(coord, [0.75, 0.4330127])
+        assert_allclose(coord, [0.75, 0.4330127])
 
     def test_tet_coord(self):
         coord = [0.5, 0.5, 0.5]
         coord = tet_coord(coord)
-        assert np.allclose(coord, [1.0, 0.57735027, 0.40824829])
+        assert_allclose(coord, [1.0, 0.57735027, 0.40824829])