Added logger to warning messages in surface functions. (#83)

* Added logger to warning messages with tests.

membrane_curvature/surface.py

@@ -17,6 +17,11 @@
 
 import numpy as np
 import warnings
+import MDAnalysis
+import logging
+
+MDAnalysis.start_logging()
+logger = logging.getLogger("MDAnalysis.MDAKit.membrane_curvature")
 
 
 def derive_surface(atoms, n_cells_x, n_cells_y, max_width_x, max_width_y):
@@ -88,17 +93,27 @@ def get_z_surface(coordinates, n_x_bins=10, n_y_bins=10, x_range=(0, 100), y_ran
     for l, m, z in zip(cell_x_floor, cell_y_floor, z_coords):
 
         try:
+            # negative coordinates
             if l < 0 or m < 0:
-                msg = ("Atom outside grid boundaries. Skipping atom.")
+                msg = ("Atom with negative coordinates falls "
+                       "outside grid boundaries. Element "
+                       "({},{}) in grid can't be assigned."
+                       " Skipping atom.").format(l, m)
                 warnings.warn(msg)
+                logger.warning(msg)
                 continue
 
             grid_z_coordinates[l, m] += z
             grid_norm_unit[l, m] += 1
 
+        # too large positive coordinates
         except IndexError:
-            msg = ("Atom outside grid boundaries. Skipping atom.")
+            msg = ("Atom coordinates exceed size of grid "
+                   "and element ({},{}) can't be assigned. "
+                   "Maximum (x,y) coordinates must be < ({}, {}). "
+                   "Skipping atom.").format(l, m, x_range[1], y_range[1])
             warnings.warn(msg)
+            logger.warning(msg)
 
     z_surface = normalized_grid(grid_z_coordinates, grid_norm_unit)
 

membrane_curvature/tests/test_membrane_curvature.py

@@ -569,3 +569,47 @@ def test_test_analysis_no_wrapping(self, universe):
         regex = (r"`wrap == False` may result in inaccurate calculation")
         with pytest.warns(UserWarning, match=regex):
             MembraneCurvature(universe, wrap=False)
+
+    @pytest.mark.parametrize('x_bin, y_bin, box_dim, dummy_array', [
+        # test too large x coordinates 2 bins
+        (2, 2, 200, np.array([[0., 0., 150.], [200., 0., 150.],
+                              [0., 100., 150.], [100., 100., 120.]])),
+        # test too large y coordinates 2 bins
+        (2, 2, 200, np.array([[0., 0., 150.], [100., 0., 150.],
+                              [0., 200., 150.], [100., 100., 150.]])),
+        # test too large y coordinates with 3 bins
+        (3, 3, 300, np.array([[0., 0., 150.], [100., 0., 150.], [200., 0., 150.],
+                              [0., 300., 150.], [100., 100., 120.], [200., 100., 120.],
+                              [0., 350., 120.], [100., 200., 120.], [200., 200., 120.]]))
+    ])
+    def test_positive_coordinates_exceed_grid(self, x_bin, y_bin, box_dim, dummy_array):
+        u = mda.Universe(dummy_array, n_atoms=len(dummy_array))
+        u.dimensions = [box_dim, box_dim, 300, 90., 90., 90.]
+        regex = (r"Atom coordinates exceed size of grid")
+        with pytest.warns(UserWarning, match=regex):
+            MembraneCurvature(u, select='all',
+                              n_x_bins=x_bin,
+                              n_y_bins=y_bin,
+                              wrap=False).run()
+
+    @pytest.mark.parametrize('x_bin, y_bin, box_dim, dummy_array', [
+        # test negative x coordinates 2 bins
+        (2, 2, 200, np.array([[-150., 0., 150.], [100., 0., 150.],
+                              [0., 100., 150.], [100., 100., 150.]])),
+        # test negative y coordinates 2 bins
+        (2, 2, 200, np.array([[0., 0., 150.], [200., 0., 150.],
+                              [0., -150., 150.], [100., 100., 120.]])),
+        # test negative x coordinates with 3 bins
+        (3, 3, 300, np.array([[0., 0., 150.], [-100., 0., 150.], [200., 0., 150.],
+                              [0., 100., 150.], [100., 100., 120.], [200., 100., 120.],
+                              [0., 200., 120.], [100., 200., 120.], [300., 200., 120.]]))
+    ])
+    def test_negative_coordinates_exceed_grid(self, x_bin, y_bin, box_dim, dummy_array):
+        u = mda.Universe(dummy_array, n_atoms=len(dummy_array))
+        u.dimensions = [box_dim, box_dim, 300,  90., 90., 90.]
+        regex = (r"Atom with negative coordinates falls")
+        with pytest.warns(UserWarning, match=regex):
+            MembraneCurvature(u, select='all',
+                              n_x_bins=x_bin,
+                              n_y_bins=y_bin,
+                              wrap=False).run()