Restructure setup() and teardown() to a unified format:

- move the `setup()` and `teardown()` functions to a `test_base.py` file to centrally manage the setup and teardown of files
- use `logging.shutdown()` to ensure logging handlers are correctly closed and shutdown after use to avoid file IO issues within tests
- ensure the correct format of `jobxxx` folders are being used within tests ti ensure consistency

Author: harryswift01

tests/test_CodeEntropy/test_arg_config_manager.py

@@ -1,27 +1,24 @@
 import argparse
 import logging
 import os
-import shutil
-import tempfile
 import unittest
 from unittest.mock import MagicMock, mock_open, patch
 
 import tests.data as data
 from CodeEntropy.config.arg_config_manager import ConfigManager
 from CodeEntropy.main import main
+from tests.test_CodeEntropy.test_base import BaseTestCase
 
 
-class test_arg_config_manager(unittest.TestCase):
+class TestArgConfigManager(BaseTestCase):
     """
     Unit tests for the ConfigManager.
     """
 
     def setUp(self):
-        """
-        Setup test data and output directories.
-        """
+        super().setUp()
+
         self.test_data_dir = os.path.dirname(data.__file__)
-        self.test_dir = tempfile.mkdtemp(prefix="CodeEntropy_")
         self.config_file = os.path.join(self.test_dir, "config.yaml")
 
         # Create a mock config file
@@ -30,18 +27,6 @@ def setUp(self):
             with open(self.config_file, "w") as f:
                 f.write(mock_file.return_value.read())
 
-        # Change to test directory
-        self._orig_dir = os.getcwd()
-        os.chdir(self.test_dir)
-
-    def tearDown(self):
-        """
-        Clean up after each test.
-        """
-        os.chdir(self._orig_dir)
-        if os.path.exists(self.test_dir):
-            shutil.rmtree(self.test_dir)
-
     def list_data_files(self):
         """
         List all files in the test data directory.

tests/test_CodeEntropy/test_base.py

@@ -0,0 +1,43 @@
+import logging
+import os
+import shutil
+import tempfile
+import unittest
+import uuid
+
+
+class BaseTestCase(unittest.TestCase):
+    """
+    Base class for tests with cross-platform setup and teardown.
+    Creates unique temporary directories and pre-creates expected log files.
+    """
+
+    def setUp(self):
+        # Unique temporary test directory
+        self.test_dir = tempfile.mkdtemp(prefix="CodeEntropy_")
+        self._orig_dir = os.getcwd()
+        os.chdir(self.test_dir)
+
+        # Unique job folder + logs
+        self.job_id = f"job_{uuid.uuid4().hex[:6]}"
+        self.job_path = os.path.join(self.test_dir, self.job_id)
+        self.logs_path = os.path.join(self.job_path, "logs")
+        os.makedirs(self.logs_path, exist_ok=True)
+
+        # Pre-create log files
+        for fname in ["mdanalysis.log", "program.log", "program.com"]:
+            with open(os.path.join(self.logs_path, fname), "w") as f:
+                f.write("")
+
+    def tearDown(self):
+        # Shutdown logging and remove handlers (important for Windows)
+        logging.shutdown()
+        for handler in logging.root.handlers[:]:
+            logging.root.removeHandler(handler)
+
+        # Restore working directory
+        os.chdir(self._orig_dir)
+
+        # Remove temp directory (fail loudly if locked)
+        if os.path.exists(self.test_dir):
+            shutil.rmtree(self.test_dir, ignore_errors=False)

tests/test_CodeEntropy/test_data_logger.py

@@ -1,7 +1,4 @@
 import json
-import os
-import shutil
-import tempfile
 import unittest
 
 import numpy as np
@@ -10,38 +7,20 @@
 from CodeEntropy.config.data_logger import DataLogger
 from CodeEntropy.config.logging_config import LoggingConfig
 from CodeEntropy.main import main
+from tests.test_CodeEntropy.test_base import BaseTestCase
 
 
-class TestDataLogger(unittest.TestCase):
+class TestDataLogger(BaseTestCase):
     """
-    Unit tests for the DataLogger class. These tests verify the
-    correct behavior of data logging, JSON export, and table
-    logging functionalities.
+    Unit tests for the DataLogger class.
     """
 
     def setUp(self):
-        """
-        Set up a temporary test environment before each test.
-        Creates a temporary directory and initializes a DataLogger instance.
-        """
-        self.test_dir = tempfile.mkdtemp(prefix="CodeEntropy_")
+        super().setUp()
         self.code_entropy = main
-
-        self._orig_dir = os.getcwd()
-        os.chdir(self.test_dir)
-
         self.logger = DataLogger()
         self.output_file = "test_output.json"
 
-    def tearDown(self):
-        """
-        Clean up the test environment after each test.
-        Removes the temporary directory and restores the original working directory.
-        """
-        os.chdir(self._orig_dir)
-        if os.path.exists(self.test_dir):
-            shutil.rmtree(self.test_dir)
-
     def test_init(self):
         """
         Test that the DataLogger initializes with empty molecule and residue data lists.

tests/test_CodeEntropy/test_entropy.py

@@ -20,32 +20,17 @@
 from CodeEntropy.levels import LevelManager
 from CodeEntropy.main import main
 from CodeEntropy.run import ConfigManager, RunManager
+from tests.test_CodeEntropy.test_base import BaseTestCase
 
 
-class TestEntropyManager(unittest.TestCase):
+class TestEntropyManager(BaseTestCase):
     """
-    Unit tests for the functionality of EntropyManager.
+    Unit tests for EntropyManager.
     """
 
     def setUp(self):
-        """
-        Set up test environment.
-        """
-        self.test_dir = tempfile.mkdtemp(prefix="CodeEntropy_")
+        super().setUp()
         self.test_data_dir = os.path.dirname(data.__file__)
-        self.code_entropy = main
-
-        # Change to test directory
-        self._orig_dir = os.getcwd()
-        os.chdir(self.test_dir)
-
-    def tearDown(self):
-        """
-        Clean up after each test.
-        """
-        os.chdir(self._orig_dir)
-        if os.path.exists(self.test_dir):
-            shutil.rmtree(self.test_dir)
 
     def test_execute_full_workflow(self):
         # Setup universe and args
@@ -56,7 +41,7 @@ def test_execute_full_workflow(self):
         args = MagicMock(
             bin_width=0.1, temperature=300, selection_string="all", water_entropy=False
         )
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -153,7 +138,7 @@ def test_execute_triggers_handle_water_entropy_minimal(self):
         args = MagicMock(
             bin_width=0.1, temperature=300, selection_string="all", water_entropy=True
         )
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -279,7 +264,7 @@ def test_initialize_molecules(self):
         args = MagicMock(
             bin_width=0.1, temperature=300, selection_string="all", water_entropy=False
         )
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -486,7 +471,7 @@ def test_get_reduced_universe_reduced(self, mock_args):
         u = mda.Universe(tprfile, trrfile)
 
         config_manager = ConfigManager()
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
 
         parser = config_manager.setup_argparse()
         args = parser.parse_args()
@@ -524,7 +509,7 @@ def test_get_molecule_container(self, mock_args):
 
         # Setup managers
         config_manager = ConfigManager()
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
 
         parser = config_manager.setup_argparse()
         args = parser.parse_args()
@@ -639,7 +624,7 @@ def test_process_vibrational_only_levels(self):
 
         # Setup managers and arguments
         args = MagicMock(bin_width=0.1, temperature=300, selection_string="all")
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -751,7 +736,7 @@ def test_process_conformational_residue_level(self):
 
         # Setup managers and arguments
         args = MagicMock(bin_width=0.1, temperature=300, selection_string="all")
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -1086,7 +1071,7 @@ def test_vibrational_entropy_init(self):
         args.temperature = 300
         args.selection_string = "all"
 
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -1111,7 +1096,7 @@ def test_frequency_calculation_0(self):
         lambdas = [0]
         temp = 298
 
-        run_manager = RunManager("mock_folder")
+        run_manager = RunManager("mock_folder/job001")
 
         ve = VibrationalEntropy(
             run_manager, MagicMock(), MagicMock(), MagicMock(), MagicMock(), MagicMock()
@@ -1131,7 +1116,7 @@ def test_frequency_calculation_positive(self):
         temp = 298
 
         # Create a mock RunManager and set return value for get_KT2J
-        run_manager = RunManager("mock_folder")
+        run_manager = RunManager("mock_folder/job001")
 
         # Instantiate VibrationalEntropy with mocks
         ve = VibrationalEntropy(
@@ -1273,7 +1258,7 @@ def test_vibrational_entropy_polymer_force(self):
         temp = 298
         highest_level = "yes"
 
-        run_manager = RunManager("mock_folder")
+        run_manager = RunManager("mock_folder/job001")
         ve = VibrationalEntropy(
             run_manager, MagicMock(), MagicMock(), MagicMock(), MagicMock(), MagicMock()
         )
@@ -1303,7 +1288,7 @@ def test_vibrational_entropy_polymer_torque(self):
         temp = 298
         highest_level = "yes"
 
-        run_manager = RunManager("mock_folder")
+        run_manager = RunManager("mock_folder/job001")
         ve = VibrationalEntropy(
             run_manager, MagicMock(), MagicMock(), MagicMock(), MagicMock(), MagicMock()
         )
@@ -1561,7 +1546,7 @@ def test_confirmational_entropy_init(self):
         args.temperature = 300
         args.selection_string = "all"
 
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -1603,7 +1588,7 @@ def test_assign_conformation(self):
 
         # Setup managers and arguments
         args = MagicMock(bin_width=0.1, temperature=300, selection_string="all")
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -1635,7 +1620,7 @@ def test_conformational_entropy_calculation(self):
 
         # Setup managers and arguments
         args = MagicMock(bin_width=0.1, temperature=300, selection_string="all")
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -1697,7 +1682,7 @@ def test_orientational_entropy_init(self):
         args.temperature = 300
         args.selection_string = "all"
 
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()

tests/test_CodeEntropy/test_group_molecules.py

@@ -1,37 +1,21 @@
-import os
-import shutil
-import tempfile
 import unittest
 from unittest.mock import MagicMock
 
 import numpy as np
 
 from CodeEntropy.group_molecules import GroupMolecules
+from tests.test_CodeEntropy.test_base import BaseTestCase
 
 
-class TestMain(unittest.TestCase):
+class TestGroupMolecules(BaseTestCase):
     """
-    Unit tests for the functionality of GroupMolecules class.
+    Unit tests for GroupMolecules.
     """
 
     def setUp(self):
-        """
-        Set up a temporary directory as the working directory before each test.
-        Initialize GroupMolecules instance.
-        """
-        self.test_dir = tempfile.mkdtemp(prefix="CodeEntropy_")
-        self._orig_dir = os.getcwd()
-        os.chdir(self.test_dir)
+        super().setUp()
         self.group_molecules = GroupMolecules()
 
-    def tearDown(self):
-        """
-        Clean up by removing the temporary directory and restoring the original working
-        directory.
-        """
-        os.chdir(self._orig_dir)
-        shutil.rmtree(self.test_dir)
-
     def test_by_none_returns_individual_groups(self):
         """
         Test _by_none returns each molecule in its own group when grouping is 'each'.