got rid of some warning

Author: simongravelle

integration_tests/test_monte_carlo_move.py

@@ -1,5 +1,6 @@
 import sys
 import os
+import time
 import unittest
 import numpy as np
 from pint import UnitRegistry
@@ -41,16 +42,19 @@ def setUp(self):
             cut_off = rc,
             thermo_outputs = "Epot-press",
             desired_temperature = T,
-            neighbor = 20,
+            neighbor = 50,
             displace_mc = displace_mc,
         )
 
     def test_monte_carlo_run(self):
         """Test if the Monte Carlo simulation runs without errors."""
         try:
             # Run the Monte Carlo simulation (this should not raise an exception)
+            ti = time.time()
             self.mc.run()
             # If it runs successfully, assert True
+            tf = time.time()
+            print("Duration:", np.round(tf-ti, 2), "s")
             self.assertTrue(True)
         except Exception as e:
             # If any exception occurs, fail the test and print the error

molecular_simulation_code/measurements_utilities.py

@@ -1,6 +1,6 @@
 from numba import njit
 import numpy as np
-from typing import List
+from numba.typed import List
 
 from distances_utilities import compute_vector_matrix
 from forces_utilities import compute_force_matrix

molecular_simulation_code/simulation_handler.py

@@ -1,4 +1,5 @@
 import numpy as np
+from numba.typed import List
 
 from contacts_utilities import contact_matrix, compute_neighbor_lists
 
@@ -18,7 +19,12 @@ def update_neighbor_lists(self, force_update=False):
                                     box=self.box_mda)
 
             # Compute the neighbor lists from the contact matrix
-            self.neighbor_lists = compute_neighbor_lists(matrix)
+            python_neighbor_lists = compute_neighbor_lists(matrix)
+
+            # Convert Python list to numba.typed.List
+            self.neighbor_lists = List()
+            for neighbors in python_neighbor_lists:
+                self.neighbor_lists.append(neighbors)
 
     def update_cross_coefficients(self, force_update=False):
         """Update the Lennard-Jones cross-coefficients for all atom pairs."""

molecular_simulation_code/simulation_logger.py

@@ -9,8 +9,10 @@ def setup_logger(folder_name, overwrite=False):
     logger.setLevel(logging.INFO)
     logger.propagate = False  # Disable propagation to prevent double logging
 
-    # Clear any existing handlers if this function is called again
+    # Close and clear existing handlers, if any
     if logger.hasHandlers():
+        for handler in logger.handlers:
+            handler.close()  # Ensure handlers are properly closed
         logger.handlers.clear()
 
     # Create handlers for console and file