Increase code coverage

pyMBE.py

@@ -1924,9 +1924,6 @@ def generate_random_points_in_a_sphere(self, center, radius, n_samples, on_surfa
 
         Returns:
             samples(`list`): Coordinates of the sample points inside the hypersphere.
-
-        Note:
-            - Algorithm from: https://baezortega.github.io/2018/10/14/hypersphere-sampling/
         """
         # initial values
         center=np.array(center)

testsuite/calculate_net_charge_unit_test.py

@@ -72,6 +72,7 @@
                         espresso_system=espresso_system,
                         use_default_bond=True,)
 
+# Check the case where the returned charge has a dimension
 charge_map=pmb.calculate_net_charge(molecule_name=molecule_name,
                                     espresso_system=espresso_system)
 
@@ -91,6 +92,19 @@
                                                 8: 0.0*pmb.units.Quantity(1,'reduced_charge'), 
                                                 9: 0.0*pmb.units.Quantity(1,'reduced_charge')})
 
+# Check the case where the returned charge is dimensionless
+charge_map=pmb.calculate_net_charge(molecule_name=molecule_name,
+                                    espresso_system=espresso_system,
+                                    dimensionless=True)
+
+# Check mean charge
+np.testing.assert_equal(charge_map["mean"], 2.0)
+# Check molecule charge map
+np.testing.assert_equal(charge_map["molecules"],{0: 2.0, 1: 2.0})
+# Check residue charge map
+np.testing.assert_equal(charge_map["residues"],{0: 1.0, 1: 1.0, 2: 0.0, 3: 0.0, 4: 0.0, 5: 1.0, 6: 1.0, 7: 0.0, 8: 0.0, 9: 0.0})
+
+
 print("*** Unit test passed ***")
 print("*** Unit test: check that calculate_net_charge raises a ValueError if one provides the name of an object that is not a molecule ***")
 input_parameters={"molecule_name":"R1", 

testsuite/generate_coordinates_tests.py

@@ -111,4 +111,21 @@ def test_arrays_less_equal(arr1, arr2, rtol=1e-7, atol=1e-7):
 test_arrays_less_equal(np.linalg.norm(samples-np.asarray(center), axis=1), outer_radius)
 test_arrays_less_equal(inner_radius, np.linalg.norm(samples-np.asarray(center), axis=1))
 print("*** Unit test passed ***")
+print("*** Check that the function raises a ValueError if the user provides a negative radius ***")
+np.testing.assert_raises(ValueError, 
+                         pmb.generate_coordinates_outside_sphere,
+                         center=center,
+                         radius=-1.0,
+                         max_dist=5.0,
+                         n_samples=1)
+print("*** Unit test passed ***")
+print("*** Check that the function raises a ValueError if the user provides a larger inner radius than outer radius ***")
+np.testing.assert_raises(ValueError, 
+                         pmb.generate_coordinates_outside_sphere,
+                         center=center,
+                         radius=10.0,
+                         max_dist=5.0,
+                         n_samples=1)
+print("*** Unit test passed ***")
+
 print("*** All unit tests passed ***\n")