Use pytest for test_analysis and fix test

MDANSE/Tests/UnitTests/test_analysis.py

@@ -1,67 +1,64 @@
-import unittest
-
 import numpy as np
-
-from MDANSE.MolecularDynamics.Analysis import *
-
-
-class TestAnalysis(unittest.TestCase):
-    def test_mean_square_deviation_valid_no_masses_no_root(self):
-        coords1 = np.array([[1, 1, 1], [2, 1, 1], [3, 1, 1]])
-        coords2 = np.array([[0, 0, 0], [0, 0, 0], [0, 0, 0]])
-
-        msd = mean_square_deviation(coords1, coords2)
-        self.assertEqual(20 / 3, msd)
-
-    def test_mean_square_deviation_masses(self):
-        coords1 = np.array([[1, 1, 1], [2, 1, 1], [3, 1, 1]])
-        coords2 = np.array([[0, 0, 0], [0, 0, 0], [0, 0, 0]])
-        masses = np.array([3, 10, 1])
-
-        msd = mean_square_deviation(coords1, coords2, masses)
-        self.assertEqual(80 / 14, msd)
-
-    def test_mean_square_displacement_root(self):
-        coords1 = np.array([[1, 1, 1], [2, 1, 1], [8, 1, 1]])
-        coords2 = np.array([[0, 0, 0], [0, 0, 0], [0, 0, 0]])
-
-        msd = mean_square_deviation(coords1, coords2, root=True)
-        self.assertEqual(5, msd)
-
-    def test_mean_square_deviation_invalid(self):
-        coords1 = np.zeros((3, 3))
-        coords2 = np.zeros((4, 3))
-
-        with self.assertRaises(AnalysisError):
-            mean_square_deviation(coords1, coords2)
-
-    def test_mean_square_displacement(self):
-        coords = np.array([[1, 1, 1], [2, 1, 1], [3, 1, 1]])
-        msd = mean_square_displacement(coords, 1)
-        self.assertTrue(np.allclose([0.0, 1.0, 4.0], msd), f"\nactual = {msd}")
-
-    def test_mean_square_fluctuation_no_root(self):
-        coords = np.array([[1, 2, 1], [2, 1, 1], [10, 5, 5], [1, 1, 2]])
-        msf = mean_square_fluctuation(coords)
-        self.assertEqual(19.625, msf)
-
-    def test_mean_square_fluctuation_root(self):
-        coords = np.array([[1, 2, 1], [2, 1, 1], [10, 5, 5], [1, 1, 2]])
-        msf = mean_square_fluctuation(coords, True)
-        self.assertEqual(np.sqrt(19.625), msf)
-
-    def test_radius_of_gyration_no_masses_no_root(self):
-        coords = np.array([[1, 2, 1], [2, 1, 1], [10, 5, 5], [1, 1, 2]])
-        rog = radius_of_gyration(coords)
-        self.assertEqual(19.625, rog)
-
-    def test_radius_of_gyration_masses(self):
-        coords = np.array([[1, 2, 1], [2, 1, 1], [10, 5, 5], [1, 1, 2]])
-        masses = np.array([1, 1, 5, 1])
-        rog = radius_of_gyration(coords, masses)
-        self.assertEqual(24.15625, rog)
-
-    def test_radius_of_gyration_root(self):
-        coords = np.array([[1, 2, 1], [2, 1, 1], [10, 5, 5], [1, 1, 2]])
-        msf = mean_square_fluctuation(coords, True)
-        self.assertEqual(np.sqrt(19.625), msf)
+import pytest
+from MDANSE.MolecularDynamics.Analysis import (AnalysisError,
+                                               mean_square_deviation,
+                                               mean_square_displacement,
+                                               mean_square_fluctuation,
+                                               radius_of_gyration)
+
+COORDS = [
+    np.array([[0, 0, 0], [0, 0, 0], [0, 0, 0]], dtype=float),
+    np.array([[1, 1, 1], [2, 1, 1], [3, 1, 1]], dtype=float),
+    np.array([[1, 1, 1], [2, 1, 1], [8, 1, 1]], dtype=float),
+    np.array([[1, 2, 1], [2, 1, 1], [10, 5, 5], [1, 1, 2]], dtype=float),
+    np.array([[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0],
+              [0, 0, 1], [1, 0, 1], [1, 1, 1], [0, 1, 1]], dtype=float),
+    np.array([[1, 1, 1], [2, 1, 1], [2, 2, 1], [1, 2, 1],
+              [1, 1, 2], [2, 1, 2], [2, 2, 2], [1, 2, 2]], dtype=float),
+]
+
+@pytest.mark.parametrize("coords,masses,root,expected", [
+    ((COORDS[1], COORDS[0]), None, False, 20/3),
+    ((COORDS[1], COORDS[0]), [3, 10, 1], False, 80/14),
+    ((COORDS[2], COORDS[0]), None, True, 5),
+    ((COORDS[4], COORDS[5]), None, True, np.sqrt(3)),
+    ((COORDS[4], COORDS[5]), None, False, 3),
+    ])
+def test_mean_square_deviation(coords, masses, root, expected):
+    msd = mean_square_deviation(*coords, masses, root)
+    assert msd == expected
+
+@pytest.mark.parametrize("coords,masses,root,expected", [
+    ([np.zeros((3, 3)), np.zeros((3, 4))], None, False, AnalysisError),
+])
+def test_invalid(coords, masses, root, expected):
+    with pytest.raises(expected):
+        mean_square_deviation(*coords, masses, root)
+
+@pytest.mark.parametrize("coords, n_configs, expected", [
+    (COORDS[1], 1, [0., 1., 4.])
+])
+def test_mean_square_displacement(coords, n_configs, expected):
+    msd = mean_square_displacement(coords, n_configs)
+    assert np.allclose(msd, expected)
+
+@pytest.mark.parametrize("coords, root, expected", [
+    (COORDS[3], False, 19.625),
+    (COORDS[3], True, np.sqrt(19.625)),
+    (COORDS[4], False, 0.75),
+])
+def test_mean_square_fluctuation(coords, root, expected):
+    msf = mean_square_fluctuation(coords, root=root)
+    assert msf == expected
+
+@pytest.mark.parametrize("coords, masses, root, expected", [
+    (COORDS[3], None, False, 19.625),
+    (COORDS[3], [1, 1, 5, 1], False, 24.15625),
+    (COORDS[3], None, True, np.sqrt(19.625)),
+    (COORDS[3], [1, 1, 5, 1], True, np.sqrt(24.15625)),
+    (COORDS[4], None, True, np.sqrt(0.75)),
+    (COORDS[4], [1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0], True, np.sqrt(0.5))
+])
+def test_radius_of_gyration(coords, masses, root, expected):
+    rog = radius_of_gyration(coords, masses, root=root)
+    assert rog == expected