diff --git a/.github/workflows/project-ci.yaml b/.github/workflows/project-ci.yaml
index f03b22b..ea94844 100644
--- a/.github/workflows/project-ci.yaml
+++ b/.github/workflows/project-ci.yaml
@@ -9,12 +9,12 @@ on:
 
 jobs:
   tests:
-    runs-on: ubuntu-24.04
-    timeout-minutes: 30
+    name: Run tests
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
+        os: [ubuntu-24.04, windows-2025, macos-15]
         python-version: ["3.11", "3.12", "3.13"]
-    name: Run tests
     steps:
       - name: Checkout repo
         uses: actions/checkout@v5.0.0
@@ -36,7 +36,7 @@ jobs:
           github-token: ${{ secrets.GITHUB_TOKEN }}
 
   docs:
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
       - uses: actions/checkout@v5.0.0
diff --git a/.gitignore b/.gitignore
index f64f3de..a477332 100644
--- a/.gitignore
+++ b/.gitignore
@@ -110,6 +110,7 @@ ENV/
 *.csv
 Example_output/
 Example/data/*.csv
+*.lock
 
 # profraw files from LLVM? Unclear exactly what triggers this
 # There are reports this comes from LLVM profiling, but also Xcode 9.
diff --git a/docs/developer_guide.rst b/docs/developer_guide.rst
index 259d21b..7fe201a 100644
--- a/docs/developer_guide.rst
+++ b/docs/developer_guide.rst
@@ -19,7 +19,7 @@ Clone the repository::
 
 Install development dependencies::
 
-    pip install -e .[testing,docs,pre-commit]
+    pip install -e ".[testing,docs,pre-commit]"
 
 Running Tests
 -------------
diff --git a/docs/getting_started.rst b/docs/getting_started.rst
index c677653..2a440d3 100644
--- a/docs/getting_started.rst
+++ b/docs/getting_started.rst
@@ -57,9 +57,6 @@ The program assumes the following default unit
 
 Quick start guide
 --------------------
-.. Warning::
-
-    CodeEntropy has not been tested on Windows
 
 A quick and easy way to get started is to use the command-line tool which you can run in bash by simply typing ``CodeEntropy``
 
diff --git a/tests/test_CodeEntropy/test_arg_config_manager.py b/tests/test_CodeEntropy/test_arg_config_manager.py
index 6aa15a8..bf6d220 100644
--- a/tests/test_CodeEntropy/test_arg_config_manager.py
+++ b/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.
diff --git a/tests/test_CodeEntropy/test_base.py b/tests/test_CodeEntropy/test_base.py
new file mode 100644
index 0000000..2c4da9a
--- /dev/null
+++ b/tests/test_CodeEntropy/test_base.py
@@ -0,0 +1,45 @@
+import os
+import shutil
+import tempfile
+import unittest
+
+
+class BaseTestCase(unittest.TestCase):
+    """
+    Base test case class for cross-platform unit tests.
+
+    Provides:
+    1. A unique temporary directory for each test to avoid filesystem conflicts.
+    2. Automatic restoration of the working directory after each test.
+    3. Prepares a logs folder path for tests that need logging configuration.
+    """
+
+    def setUp(self):
+        """
+        Prepare the test environment before each test method runs.
+
+        Actions performed:
+        1. Creates a unique temporary directory for the test.
+        2. Creates a 'logs' subdirectory within the temp directory.
+        3. Changes the current working directory to the temporary directory.
+        """
+        # Create a unique temporary test directory
+        self.test_dir = tempfile.mkdtemp(prefix="CodeEntropy_")
+        self.logs_path = os.path.join(self.test_dir, "logs")
+        os.makedirs(self.logs_path, exist_ok=True)
+
+        self._orig_dir = os.getcwd()
+        os.chdir(self.test_dir)
+
+    def tearDown(self):
+        """
+        Clean up the test environment after each test method runs.
+
+        Actions performed:
+        1. Restores the original working directory.
+        2. Deletes the temporary test directory along with all its contents.
+        """
+        os.chdir(self._orig_dir)
+
+        if os.path.exists(self.test_dir):
+            shutil.rmtree(self.test_dir, ignore_errors=True)
diff --git a/tests/test_CodeEntropy/test_data_logger.py b/tests/test_CodeEntropy/test_data_logger.py
index db0db9d..9e679c8 100644
--- a/tests/test_CodeEntropy/test_data_logger.py
+++ b/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.
diff --git a/tests/test_CodeEntropy/test_entropy.py b/tests/test_CodeEntropy/test_entropy.py
index f7af3bb..60f74a2 100644
--- a/tests/test_CodeEntropy/test_entropy.py
+++ b/tests/test_CodeEntropy/test_entropy.py
@@ -1,3 +1,4 @@
+import logging
 import math
 import os
 import shutil
@@ -20,32 +21,21 @@
 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)
+        # Disable MDAnalysis and commands file logging entirely
+        logging.getLogger("MDAnalysis").handlers = [logging.NullHandler()]
+        logging.getLogger("commands").handlers = [logging.NullHandler()]
 
     def test_execute_full_workflow(self):
         # Setup universe and args
@@ -56,7 +46,7 @@ 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 +143,7 @@ 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 +269,7 @@ 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 +476,7 @@ 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 +514,7 @@ 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 +629,7 @@ 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 +741,7 @@ 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 +1076,7 @@ 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 +1101,7 @@ 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 +1121,7 @@ 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 +1263,7 @@ 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 +1293,7 @@ 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 +1551,7 @@ 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 +1593,7 @@ 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 +1625,7 @@ 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 +1687,7 @@ 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()
diff --git a/tests/test_CodeEntropy/test_group_molecules.py b/tests/test_CodeEntropy/test_group_molecules.py
index 1914e5e..6f15805 100644
--- a/tests/test_CodeEntropy/test_group_molecules.py
+++ b/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'.
diff --git a/tests/test_CodeEntropy/test_levels.py b/tests/test_CodeEntropy/test_levels.py
index bf49ab2..4d0380f 100644
--- a/tests/test_CodeEntropy/test_levels.py
+++ b/tests/test_CodeEntropy/test_levels.py
@@ -1,38 +1,18 @@
-import os
-import shutil
-import tempfile
-import unittest
 from unittest.mock import MagicMock, patch
 
 import numpy as np
 
 from CodeEntropy.levels import LevelManager
-from CodeEntropy.main import main
+from tests.test_CodeEntropy.test_base import BaseTestCase
 
 
-class TestLevels(unittest.TestCase):
+class TestLevels(BaseTestCase):
     """
-    Unit tests for the functionality of Levels.
+    Unit tests for Levels.
     """
 
     def setUp(self):
-        """
-        Set up test environment.
-        """
-        self.test_dir = tempfile.mkdtemp(prefix="CodeEntropy_")
-        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)
+        super().setUp()
 
     def test_select_levels(self):
         """
diff --git a/tests/test_CodeEntropy/test_logging_config.py b/tests/test_CodeEntropy/test_logging_config.py
index 9640950..7a07b2a 100644
--- a/tests/test_CodeEntropy/test_logging_config.py
+++ b/tests/test_CodeEntropy/test_logging_config.py
@@ -1,26 +1,25 @@
 import logging
 import os
-import tempfile
 import unittest
 from unittest.mock import MagicMock
 
 from CodeEntropy.config.logging_config import LoggingConfig
+from tests.test_CodeEntropy.test_base import BaseTestCase
 
 
-class TestLoggingConfig(unittest.TestCase):
+class TestLoggingConfig(BaseTestCase):
+    """
+    Unit tests for LoggingConfig.
+    """
 
     def setUp(self):
-        # Use a temporary directory for logs
-        self.temp_dir = tempfile.TemporaryDirectory()
-        self.log_dir = os.path.join(self.temp_dir.name, "logs")
-        self.logging_config = LoggingConfig(folder=self.temp_dir.name)
+        super().setUp()
+        self.log_dir = self.logs_path
+        self.logging_config = LoggingConfig(folder=self.test_dir)
 
         self.mock_text = "Test console output"
         self.logging_config.console.export_text = MagicMock(return_value=self.mock_text)
 
-    def tearDown(self):
-        self.temp_dir.cleanup()
-
     def test_log_directory_created(self):
         """Check if the log directory is created upon init"""
         self.assertTrue(os.path.exists(self.log_dir))
@@ -68,7 +67,7 @@ def test_update_logging_level(self):
     def test_mdanalysis_and_command_loggers_exist(self):
         """Ensure specialized loggers are set up with correct configuration"""
         log_level = logging.DEBUG
-        self.logging_config = LoggingConfig(folder=self.temp_dir.name, level=log_level)
+        self.logging_config = LoggingConfig(folder=self.test_dir, level=log_level)
         self.logging_config.setup_logging()
 
         mda_logger = logging.getLogger("MDAnalysis")
@@ -87,7 +86,7 @@ def test_save_console_log_writes_file(self):
         filename = "test_log.txt"
         self.logging_config.save_console_log(filename)
 
-        output_path = os.path.join(self.temp_dir.name, "logs", filename)
+        output_path = os.path.join(self.test_dir, "logs", filename)
         # Check file exists
         self.assertTrue(os.path.exists(output_path))
 
diff --git a/tests/test_CodeEntropy/test_main.py b/tests/test_CodeEntropy/test_main.py
index 1a60972..6db9dd8 100644
--- a/tests/test_CodeEntropy/test_main.py
+++ b/tests/test_CodeEntropy/test_main.py
@@ -2,33 +2,21 @@
 import shutil
 import subprocess
 import sys
-import tempfile
 import unittest
 from unittest.mock import MagicMock, patch
 
 from CodeEntropy.main import main
+from tests.test_CodeEntropy.test_base import BaseTestCase
 
 
-class TestMain(unittest.TestCase):
+class TestMain(BaseTestCase):
     """
     Unit tests for the main functionality of CodeEntropy.
     """
 
     def setUp(self):
-        """
-        Set up a temporary directory as the working directory before each test.
-        """
-        self.test_dir = tempfile.mkdtemp(prefix="CodeEntropy_")
-        self._orig_dir = os.getcwd()
-        os.chdir(self.test_dir)
-
-    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)
+        super().setUp()
+        self.code_entropy = main
 
     @patch("CodeEntropy.main.sys.exit")
     @patch("CodeEntropy.main.RunManager")
@@ -41,7 +29,7 @@ def test_main_successful_run(self, mock_RunManager, mock_exit):
         mock_RunManager.return_value = mock_run_manager_instance
 
         # Simulate that RunManager.create_job_folder returns a folder
-        mock_RunManager.create_job_folder.return_value = "dummy_folder"
+        mock_RunManager.create_job_folder.return_value = "mock_folder/job001"
 
         # Simulate the successful completion of the run_entropy_workflow method
         mock_run_manager_instance.run_entropy_workflow.return_value = None
@@ -71,7 +59,7 @@ def test_main_exception_triggers_exit(
         mock_RunManager.return_value = mock_run_manager_instance
 
         # Simulate that RunManager.create_job_folder returns a folder
-        mock_RunManager.create_job_folder.return_value = "dummy_folder"
+        mock_RunManager.create_job_folder.return_value = "mock_folder/job001"
 
         # Simulate an exception in the run_entropy_workflow method
         mock_run_manager_instance.run_entropy_workflow.side_effect = Exception(
@@ -114,6 +102,8 @@ def test_main_entry_point_runs(self):
         result = subprocess.run(
             [
                 sys.executable,
+                "-X",
+                "utf8",
                 "-m",
                 "CodeEntropy.main",
                 "--top_traj_file",
@@ -122,7 +112,7 @@ def test_main_entry_point_runs(self):
             ],
             cwd=self.test_dir,
             capture_output=True,
-            text=True,
+            encoding="utf-8",
         )
 
         self.assertEqual(result.returncode, 0)
diff --git a/tests/test_CodeEntropy/test_run.py b/tests/test_CodeEntropy/test_run.py
index 565e476..54def3e 100644
--- a/tests/test_CodeEntropy/test_run.py
+++ b/tests/test_CodeEntropy/test_run.py
@@ -1,6 +1,4 @@
 import os
-import shutil
-import tempfile
 import unittest
 from io import StringIO
 from unittest.mock import MagicMock, mock_open, patch
@@ -11,37 +9,24 @@
 from rich.console import Console
 
 from CodeEntropy.run import RunManager
+from tests.test_CodeEntropy.test_base import BaseTestCase
 
 
-class TestRunManager(unittest.TestCase):
+class TestRunManager(BaseTestCase):
     """
     Unit tests for the RunManager class. These tests verify the
     correct behavior of run manager.
     """
 
     def setUp(self):
-        """
-        Set up a temporary directory as the working directory before each test.
-        """
-        self.test_dir = tempfile.mkdtemp(prefix="CodeEntropy_")
+        super().setUp()
         self.config_file = os.path.join(self.test_dir, "CITATION.cff")
-
-        # Create a mock config file
+        # Create mock config
         with patch("builtins.open", new_callable=mock_open) as mock_file:
             self.setup_citation_file(mock_file)
             with open(self.config_file, "w") as f:
                 f.write(mock_file.return_value.read())
-
-        self._orig_dir = os.getcwd()
-        os.chdir(self.test_dir)
-
-    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)
+        self.run_manager = RunManager(folder=self.test_dir)
 
     def setup_citation_file(self, mock_file):
         """
@@ -64,8 +49,9 @@ def test_create_job_folder_empty_directory(self, mock_listdir, mock_makedirs):
         mock_listdir.return_value = []
         new_folder_path = RunManager.create_job_folder()
         expected_path = os.path.join(self.test_dir, "job001")
-        self.assertEqual(new_folder_path, expected_path)
-        mock_makedirs.assert_called_once_with(expected_path, exist_ok=True)
+        self.assertEqual(
+            os.path.realpath(new_folder_path), os.path.realpath(expected_path)
+        )
 
     @patch("os.makedirs")
     @patch("os.listdir")
@@ -77,8 +63,23 @@ def test_create_job_folder_with_existing_folders(self, mock_listdir, mock_makedi
         mock_listdir.return_value = ["job001", "job002", "job003"]
         new_folder_path = RunManager.create_job_folder()
         expected_path = os.path.join(self.test_dir, "job004")
-        self.assertEqual(new_folder_path, expected_path)
-        mock_makedirs.assert_called_once_with(expected_path, exist_ok=True)
+
+        # Normalize paths cross-platform
+        normalized_new = os.path.normcase(
+            os.path.realpath(os.path.normpath(new_folder_path))
+        )
+        normalized_expected = os.path.normcase(
+            os.path.realpath(os.path.normpath(expected_path))
+        )
+
+        self.assertEqual(normalized_new, normalized_expected)
+
+        called_args, called_kwargs = mock_makedirs.call_args
+        normalized_called = os.path.normcase(
+            os.path.realpath(os.path.normpath(called_args[0]))
+        )
+        self.assertEqual(normalized_called, normalized_expected)
+        self.assertTrue(called_kwargs.get("exist_ok", False))
 
     @patch("os.makedirs")
     @patch("os.listdir")
@@ -90,10 +91,24 @@ def test_create_job_folder_with_non_matching_folders(
         folders.
         """
         mock_listdir.return_value = ["folderA", "another_one"]
+
         new_folder_path = RunManager.create_job_folder()
         expected_path = os.path.join(self.test_dir, "job001")
-        self.assertEqual(new_folder_path, expected_path)
-        mock_makedirs.assert_called_once_with(expected_path, exist_ok=True)
+
+        normalized_new = os.path.normcase(
+            os.path.realpath(os.path.normpath(new_folder_path))
+        )
+        normalized_expected = os.path.normcase(
+            os.path.realpath(os.path.normpath(expected_path))
+        )
+        self.assertEqual(normalized_new, normalized_expected)
+
+        called_args, called_kwargs = mock_makedirs.call_args
+        normalized_called = os.path.normcase(
+            os.path.realpath(os.path.normpath(called_args[0]))
+        )
+        self.assertEqual(normalized_called, normalized_expected)
+        self.assertTrue(called_kwargs.get("exist_ok", False))
 
     @patch("os.makedirs")
     @patch("os.listdir")
@@ -105,8 +120,21 @@ def test_create_job_folder_mixed_folder_names(self, mock_listdir, mock_makedirs)
         mock_listdir.return_value = ["job001", "abc", "job002", "random"]
         new_folder_path = RunManager.create_job_folder()
         expected_path = os.path.join(self.test_dir, "job003")
-        self.assertEqual(new_folder_path, expected_path)
-        mock_makedirs.assert_called_once_with(expected_path, exist_ok=True)
+
+        normalized_new = os.path.normcase(
+            os.path.realpath(os.path.normpath(new_folder_path))
+        )
+        normalized_expected = os.path.normcase(
+            os.path.realpath(os.path.normpath(expected_path))
+        )
+        self.assertEqual(normalized_new, normalized_expected)
+
+        called_args, called_kwargs = mock_makedirs.call_args
+        normalized_called = os.path.normcase(
+            os.path.realpath(os.path.normpath(called_args[0]))
+        )
+        self.assertEqual(normalized_called, normalized_expected)
+        self.assertTrue(called_kwargs.get("exist_ok", False))
 
     @patch("os.makedirs")
     @patch("os.listdir")
@@ -123,8 +151,20 @@ def test_create_job_folder_with_invalid_job_suffix(
         new_folder_path = RunManager.create_job_folder()
         expected_path = os.path.join(self.test_dir, "job003")
 
-        self.assertEqual(new_folder_path, expected_path)
-        mock_makedirs.assert_called_once_with(expected_path, exist_ok=True)
+        normalized_new = os.path.normcase(
+            os.path.realpath(os.path.normpath(new_folder_path))
+        )
+        normalized_expected = os.path.normcase(
+            os.path.realpath(os.path.normpath(expected_path))
+        )
+        self.assertEqual(normalized_new, normalized_expected)
+
+        called_args, called_kwargs = mock_makedirs.call_args
+        normalized_called = os.path.normcase(
+            os.path.realpath(os.path.normpath(called_args[0]))
+        )
+        self.assertEqual(normalized_called, normalized_expected)
+        self.assertTrue(called_kwargs.get("exist_ok", False))
 
     @patch("requests.get")
     def test_load_citation_data_success(self, mock_get):
@@ -255,7 +295,7 @@ def test_run_entropy_workflow(self):
         Test the run_entropy_workflow method to ensure it initializes and executes
         correctly with mocked dependencies.
         """
-        run_manager = RunManager("folder")
+        run_manager = RunManager("mock_folder/job001")
         run_manager._logging_config = MagicMock()
         run_manager._config_manager = MagicMock()
         run_manager.load_citation_data = MagicMock()
@@ -318,7 +358,7 @@ def test_run_configuration_warning(self):
         """
         Test that a warning is logged when the config entry is not a dictionary.
         """
-        run_manager = RunManager("folder")
+        run_manager = RunManager("mock_folder/job001")
         run_manager._logging_config = MagicMock()
         run_manager._config_manager = MagicMock()
         run_manager.load_citation_data = MagicMock()
@@ -367,7 +407,7 @@ def test_run_entropy_workflow_missing_traj_file(self):
         """
         Test that a ValueError is raised when 'top_traj_file' is missing.
         """
-        run_manager = RunManager("folder")
+        run_manager = RunManager("mock_folder/job001")
         run_manager._logging_config = MagicMock()
         run_manager._config_manager = MagicMock()
         run_manager.load_citation_data = MagicMock()
@@ -419,7 +459,7 @@ def test_run_entropy_workflow_missing_selection_string(self):
         """
         Test that a ValueError is raised when 'selection_string' is missing.
         """
-        run_manager = RunManager("folder")
+        run_manager = RunManager("mock_folder/job001")
         run_manager._logging_config = MagicMock()
         run_manager._config_manager = MagicMock()
         run_manager.load_citation_data = MagicMock()
@@ -504,7 +544,7 @@ def test_new_U_select_frame(self, MockMerge, MockAnalysisFromFunction):
         mock_merged_universe = MagicMock()
         MockMerge.return_value = mock_merged_universe
 
-        run_manager = RunManager("folder")
+        run_manager = RunManager("mock_folder/job001")
         result = run_manager.new_U_select_frame(mock_universe)
 
         mock_universe.select_atoms.assert_called_once_with("all", updating=True)
@@ -558,7 +598,7 @@ def test_new_U_select_atom(self, MockMerge, MockAnalysisFromFunction):
         mock_merged_universe = MagicMock()
         MockMerge.return_value = mock_merged_universe
 
-        run_manager = RunManager("folder")
+        run_manager = RunManager("mock_folder/job001")
         result = run_manager.new_U_select_atom(
             mock_universe, select_string="resid 1-10"
         )
@@ -591,7 +631,7 @@ def test_write_universe(self, mock_open, mock_pickle_dump):
         mock_file = MagicMock()
         mock_open.return_value = mock_file
 
-        run_manager = RunManager("folder")
+        run_manager = RunManager("mock_folder/job001")
         result = run_manager.write_universe(mock_universe, name="test_universe")
 
         mock_open.assert_called_once_with("test_universe.pkl", "wb")
@@ -616,7 +656,7 @@ def test_read_universe(self, mock_open, mock_pickle_load):
         # Path to the mock file
         path = "test_universe.pkl"
 
-        run_manager = RunManager("folder")
+        run_manager = RunManager("mock_folder/job001")
         result = run_manager.read_universe(path)
 
         mock_open.assert_called_once_with(path, "rb")