Initial version

test/test_atoms.py

@@ -0,0 +1,7 @@
+from mdevaluate import atoms
+
+
+def test_compare_regex():
+    assert atoms.compare_regex(['OW', ], 'O')[0] == False
+    assert atoms.compare_regex(['WO', ], 'O')[0] == False
+    assert atoms.compare_regex(['O', ], 'O')[0] == True

test/test_checksum.py

@@ -0,0 +1,39 @@
+from mdevaluate import checksum
+
+import numpy as np
+
+
+def test_checksum():
+    salt = checksum.SALT
+    checksum.SALT = ''
+    assert checksum.checksum(1) == 304942582444936629325699363757435820077590259883
+    assert checksum.checksum('42') == checksum.checksum(42)
+    cs1 = checksum.checksum(999)
+    checksum.SALT = '999'
+    assert cs1 != checksum.checksum(999)
+
+    a = np.array([1, 2, 3])
+    assert checksum.checksum(a) == checksum.checksum(a.tobytes())
+
+    checksum.SALT = salt
+
+
+def test_version():
+
+    @checksum.version(1)
+    def f1():
+        pass
+
+    cs1 = checksum.checksum(f1)
+
+    @checksum.version(1)
+    def f1(x, y):
+        return x + y
+
+    assert cs1 == checksum.checksum(f1)
+
+    @checksum.version(2)
+    def f1(x, y):
+        pass
+
+    assert cs1 != checksum.checksum(f1)

test/test_coordinates.py

@@ -0,0 +1,31 @@
+import os
+import pytest
+
+import mdevaluate
+from mdevaluate import coordinates
+
+
+@pytest.fixture
+def trajectory(request):
+    return mdevaluate.open(os.path.join(os.path.dirname(__file__), 'data/water'))
+
+
+def test_coordinates_getitem(trajectory):
+    """
+    Tests for the Coordinates class.
+    """
+    assert isinstance(trajectory[0], coordinates.CoordinateFrame)
+    assert isinstance(trajectory[len(trajectory) - 1], coordinates.CoordinateFrame)
+    i = 0
+    dt = trajectory[1].time - trajectory[0].time
+    for f in trajectory:
+        assert f.step == i
+        assert round(f.time, 3) == round(i * dt, 3)
+        i += 1
+    sl = trajectory[0::10]
+    assert isinstance(sl, coordinates.Coordinates)
+    i = 0
+    for f in sl:
+        assert f.step == i
+        assert round(f.time, 3) == round(i * dt, 3)
+        i += 10

test/test_pbc.py

@@ -0,0 +1,14 @@
+from pytest import approx
+
+from mdevaluate import pbc
+import numpy as np
+
+
+def test_pbc_diff():
+    x = np.random.rand(10, 3)
+    y = np.random.rand(10, 3)
+    box = np.ones((3,))
+
+    assert (pbc.pbc_diff(x, x, box) == approx(0))
+    dxy = (pbc.pbc_diff(x, y, box)**2).sum(axis=1)**0.5
+    assert (dxy <= 0.75**0.5).all()

test/test_utils.py

@@ -0,0 +1,46 @@
+from copy import copy
+import pytest
+import numpy as np
+
+from mdevaluate import utils
+
+
+@pytest.fixture
+def logdata(request):
+    xdata = np.logspace(-1, 3, 50)
+    ydata = np.exp(- (xdata)**0.7)
+    return xdata, ydata
+
+
+def test_filon_fourier_transformation(logdata):
+    xdata, ydata = logdata
+
+    xdata_zero = copy(xdata)
+    xdata_zero[0] = 0
+    _, filon = utils.filon_fourier_transformation(xdata_zero, ydata)
+    assert not np.isnan(filon).any(), 'There are NaN values in the filon result!'
+
+    freqs = np.logspace(-4, 1)
+    filon_freqs, filon_imag = utils.filon_fourier_transformation(
+        xdata, xdata, frequencies=freqs, derivative='linear', imag=True
+        )
+
+    assert (freqs == filon_freqs).all()
+
+    freqs, filon_real = utils.filon_fourier_transformation(
+        xdata, xdata, frequencies=freqs, derivative='linear', imag=False
+        )
+    assert np.isclose(filon_imag.real, filon_real).all()
+
+
+def test_histogram():
+    data = np.random.rand(100)
+    bins = np.linspace(0, 1)
+    np_hist = np.histogram(data, bins=bins)[0]
+    ut_hist = utils.histogram(data, bins=bins)[0]
+    assert (np_hist == ut_hist).all()
+
+    bins = np.linspace(0.3, 1.5)
+    np_hist = np.histogram(data, bins=bins)[0]
+    ut_hist = utils.histogram(data, bins=bins)[0]
+    assert (np_hist == ut_hist).all()