5 fix issue with geometry breaking from time to time

Tests/__init__.py

@@ -1,3 +1,29 @@
+import logging
 import os
+import warnings
 
-TEST_DIRECTORY = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+TEST_DIRECTORY = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+
+PROJECT_DIRECTORY = os.getenv('PROJECT_DIR', os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+
+# get the logger instance
+logger = logging.getLogger("pyVertexModel")
+
+formatter = logging.Formatter(
+    "%(levelname)s [%(asctime)s] pyVertexModel: %(message)s",
+    datefmt="%Y/%m/%d %I:%M:%S %p",
+)
+console_handler = logging.StreamHandler()
+console_handler.setFormatter(formatter)
+logger.addHandler(console_handler)
+
+logger.setLevel(logging.DEBUG)
+logger.propagate = False
+
+
+# Function to handle warnings
+def warning_handler(message, category, filename, lineno, file=None, line=None):
+    logger.warning(f'{filename}:{lineno}: {category.__name__}: {message}')
+
+# Set the warnings' showwarning function to the handler
+warnings.showwarning = warning_handler

Tests/test_geo.py

@@ -376,3 +376,57 @@ def test_get_node_neighbours_per_domain(self):
         # Check if node neighbours are the same
         assert_array1D(node_neighbours_test, np.concatenate(node_neighbours_expected))
 
+    def test_geometry_is_correct(self):
+        """
+        Test the function geometry_is_correct
+        :return:
+        """
+        # Load data
+        vModel_test = load_data('geometry_correct_1.pkl')
+
+        # Check if geometry is correct
+        self.assertTrue(vModel_test.geo.geometry_is_correct())
+
+        # Load data
+        vModel_test = load_data('geometry_correct_2.pkl')
+
+        # Check if geometry is correct
+        self.assertTrue(vModel_test.geo.geometry_is_correct())
+
+        # Load data
+        vModel_test = load_data('geometry_correct_3.pkl')
+
+        # Check if geometry is correct
+        self.assertTrue(vModel_test.geo.geometry_is_correct())
+
+    def test_geometry_is_incorrect(self):
+        """
+        Test the function geometry_is_correct
+        :return:
+        """
+        # Load data
+        vModel_test = load_data('vertices_going_wild_1.pkl')
+
+        # Check if geometry is correct
+        self.assertFalse(vModel_test.geo.geometry_is_correct())
+
+        # Another test with a different geometry
+        vModel_test = load_data('vertices_going_wild_2.pkl')
+
+        # Check if geometry is correct
+        self.assertFalse(vModel_test.geo.geometry_is_correct())
+
+        # Another test with a different geometry
+        vModel_test = load_data('vertices_going_wild_3.pkl')
+
+        # Check if geometry is correct
+        self.assertFalse(vModel_test.geo.geometry_is_correct())
+
+        # Another test with a different geometry
+        vModel_test = load_data('vertices_going_wild_4.pkl')
+
+        # Check if geometry is correct
+        self.assertFalse(vModel_test.geo.geometry_is_correct())
+
+
+

Tests/test_kg.py

@@ -9,7 +9,7 @@
 from pyVertexModel.Kg.kgTriEnergyBarrier import KgTriEnergyBarrier
 from pyVertexModel.Kg.kgViscosity import KgViscosity
 from pyVertexModel.Kg.kgVolume import KgVolume
-from pyVertexModel.algorithm.newtonRaphson import KgGlobal
+from pyVertexModel.algorithm.integrators import KgGlobal
 from pyVertexModel.geometry.geo import Geo
 
 
@@ -18,7 +18,7 @@ def test_kg_global_filename(filename):
     geo_n_test = Geo(mat_info['Geo_n'])
     geo_0_test = Geo(mat_info['Geo_0'])
     # Compute the global K, and g
-    g, K, E, _ = KgGlobal(geo_0_test, geo_n_test, geo_test, set_test)
+    g, K, E, _ = KgGlobal(geo_test, set_test, geo_n_test)
     # Get the expected results from the mat file
     g_expected = mat_info['g'][:, 0]
     k_expected = mat_info['K']
@@ -140,7 +140,7 @@ def test_KgGlobal(self):
         geo_n_test = Geo(mat_info['Geo_n'])
         geo_0_test = Geo(mat_info['Geo_0'])
 
-        g, K, E, _ = KgGlobal(geo_0_test, geo_n_test, geo_test, set_test)
+        g, K, E, _ = KgGlobal(geo_test, set_test, geo_n_test)
 
         g_expected = (mat_expected['gs_full'] + mat_expected['gv_full'] + mat_expected['gf_full'] +
                       mat_expected['gBA_full'] + mat_expected['gBAR_full'] + mat_expected['gC_full'] +

Tests/test_newtonRaphson.py

@@ -2,7 +2,7 @@
 
 from Tests.test_geo import check_if_cells_are_the_same
 from Tests.tests import load_data, Tests, assert_array1D, assert_matrix
-from pyVertexModel.algorithm.newtonRaphson import line_search, newton_raphson, newton_raphson_iteration, ml_divide, \
+from pyVertexModel.algorithm.integrators import line_search, newton_raphson, newton_raphson_iteration, ml_divide, \
     solve_remodeling_step
 from pyVertexModel.geometry.degreesOfFreedom import DegreesOfFreedom
 from pyVertexModel.geometry.geo import Geo
@@ -106,7 +106,7 @@ def test_newton_raphson_wingdisc(self):
         t_test = mat_info['t'][0][0]
 
         Set.iter = 1000000
-        geo_test, g_test, k_test, energy_test, set_test, gr_test, dyr_test, dy_test = (
+        geo_test, g_test, k_test, energy_test, set_test, gr_test, dyr_test, dy_test, _ = (
             newton_raphson(geo_0_test,
                            geo_n_test,
                            geo_test,
@@ -143,7 +143,7 @@ def test_newton_raphson(self):
         t_test = mat_info['t'][0][0]
 
         Set.iter = 1000000
-        geo_test, g_test, k_test, energy_test, set_test, gr_test, dyr_test, dy_test = (
+        geo_test, g_test, k_test, energy_test, set_test, gr_test, dyr_test, dy_test, _ = (
             newton_raphson(geo_0_test,
                            geo_n_test,
                            geo_test,
@@ -177,7 +177,7 @@ def test_line_search(self):
         g_test = mat_info['g'][:, 0]
         dy_test = mat_info['dy'][:, 0]
         set_test = Set(mat_info['Set'])
-        alpha = line_search(geo_0_test, geo_n_test, geo_test, dofs_test.Free, set_test, g_test, dy_test)
+        alpha = line_search(geo_test, dofs_test.Free, set_test, g_test, dy_test, geo_n_test)
 
         np.testing.assert_almost_equal(alpha, 1)
 
@@ -202,7 +202,7 @@ def test_line_search_cyst(self):
         g_test = mat_info['g'][:, 0]
         dy_test = mat_info['dy']
         set_test = Set(mat_info['Set'])
-        alpha = line_search(geo_0_test, geo_n_test, geo_test, dofs_test.Free, set_test, g_test, dy_test)
+        alpha = line_search(geo_test, dofs_test.Free, set_test, g_test, dy_test, geo_n_test)
 
         np.testing.assert_almost_equal(alpha, mat_info['alpha'][0][0])