Merge branch 'dev' of github.com:bjmorgan/pyscses into dev

pyscses/grid.py

@@ -24,6 +24,7 @@ def phi_at_x(phi: np.ndarray,
 
     Returns:
         float: The electrostatic potential at the x coordinate with position [index].
+
     """
     index = index_of_grid_at_x(coordinates, x)
     return phi[index]
@@ -41,30 +42,32 @@ def energy_at_x(energy: np.ndarray,
 
     Returns:
         energy[index] (float): The segregation energy at the x coordinate with position [index].
-    """
 
+    """
     index = index_of_grid_at_x(coordinates, x)
     return energy[index]
 
 def index_of_grid_at_x(coordinates: np.ndarray,
                        x: float) -> int:
-    """
-    Assigns each site x coordinate to a position on a regularly or irregularly spaced grid.
-    Returns the index of the grid point clostest to the value x
+    """Assigns each site x coordinate to a position on a regularly or irregularly spaced grid.
+
+    Returns the index of the grid point closest to the value x
 
     Args:
-        coordinates (np.array): 1D grid of ordered numbers over a region.
-        x (float): Site x coordinate
+        coordinates (np.array): arraylike ordered list of x coordinates.
+        x (float): x coordinate.
 
     Returns:
-        int: Index of grid position closest to the site x coordinate.
+        int: Index of the coordinates array at the position closest to the input x coordinate.
+
     """
     return closest_index(coordinates, x)
 
 def closest_index(myList: Union[list[float], np.ndarray],
                   myNumber: float) -> int:
-    """
-    Assumes myList is sorted. Returns index of closest value to myNumber.
+    """Returns index of closest value to myNumber.
+
+    Assumes myList is sorted.
     If two numbers are equally close, return the index of the smallest number.
 
     Args:
@@ -73,6 +76,7 @@ def closest_index(myList: Union[list[float], np.ndarray],
 
     Returns:
         pos (int): Index of position of number in myList which is closest to myNumber.
+
     """
     myList = list(myList)
     pos = bisect_left(myList, myNumber)

tests/test_grid.py

@@ -1,13 +1,78 @@
 import unittest
 from pyscses.grid import Grid, delta_x_from_grid
+from pyscses.grid import (closest_index,
+    index_of_grid_at_x,
+    energy_at_x,
+    phi_at_x,
+    delta_x_from_grid)
 from pyscses.grid_point import GridPoint
 from pyscses.set_of_sites import SetOfSites
 from pyscses.site import Site
 from pyscses.defect_species import DefectSpecies
 from unittest.mock import Mock, MagicMock, patch, call
 import numpy as np
 
-class TestGrid( unittest.TestCase ):
+class TestGridFunctions(unittest.TestCase):
+
+    def test_closest_index(self):
+        a = [1,3,5,7,9]
+        self.assertEqual(closest_index(a, 3.1), 1)
+        self.assertEqual(closest_index(a, 4.1), 2)
+        self.assertEqual(closest_index(a, 4.0), 1)
+        self.assertEqual(closest_index(a, 0.1), 0)
+        self.assertEqual(closest_index(a, 9.5), 4)
+
+    def test_index_of_grid_at_x(self):
+        coordinates = np.array([-2.0, -1.0, 0.0, 1.0, 2.0])
+        with patch('pyscses.grid.closest_index') as mock_closest_index:
+            mock_closest_index.side_effect = [0, 2, 3]
+            self.assertEqual(index_of_grid_at_x(coordinates=coordinates,
+                                                x=-1.5), 0)
+            self.assertEqual(index_of_grid_at_x(coordinates=coordinates,
+                                                x=0.1), 2)
+            self.assertEqual(index_of_grid_at_x(coordinates=coordinates,
+                                                x=1.5), 3)
+
+
+    def test_energy_at_x(self):
+        energy = np.array([0.1, 0.2, 0.3, 0.4, 0.5])
+        coordinates = np.array([-2.0, -1.0, 0.0, 1.0, 2.0])
+        with patch('pyscses.grid.index_of_grid_at_x') as mock_index_of_grid_at_x:
+            mock_index_of_grid_at_x.side_effect = [0, 2, 3]
+            self.assertEqual(energy_at_x(energy=energy,
+                                         coordinates=coordinates,
+                                         x=-1.5), 0.1)
+            self.assertEqual(energy_at_x(energy=energy,
+                                         coordinates=coordinates,
+                                         x=-0.1), 0.3)
+            self.assertEqual(energy_at_x(energy=energy,
+                                         coordinates=coordinates,
+                                         x=0.6), 0.4)
+
+    def test_phi_at_x(self):
+        energy = np.array([0.1, 0.2, 0.3, 0.4, 0.5])
+        coordinates = np.array([-2.0, -1.0, 0.0, 1.0, 2.0])
+        with patch('pyscses.grid.index_of_grid_at_x') as mock_index_of_grid_at_x:
+            mock_index_of_grid_at_x.side_effect = [0, 2, 3]
+            self.assertEqual(phi_at_x(phi=energy,
+                                      coordinates=coordinates,
+                                      x=-1.5), 0.1)
+            self.assertEqual(phi_at_x(phi=energy,
+                                      coordinates=coordinates,
+                                      x=-0.1), 0.3)
+            self.assertEqual(phi_at_x(phi=energy,
+                                      coordinates=coordinates,
+                                      x=0.6), 0.4)
+
+    def test_delta_x_from_grid(self):
+        coordinates = np.array([0.0, 1.0, 3.0, 6.0, 10.0])
+        limits = (1.0, 4.0)
+        expected_delta_x = np.array([1.0, 1.5, 2.5, 3.5, 4.0])
+        np.testing.assert_array_equal(delta_x_from_grid(coordinates=coordinates,
+            limits=limits), expected_delta_x)
+
+
+class TestGrid(unittest.TestCase):
     @patch('pyscses.grid.index_of_grid_at_x')
     @patch('pyscses.grid.GridPoint')
     def test_grid_instance_is_initialised( self, mock_GridPoint, mock_index ):