Refactor test setup and fix Unicode issues in CLI tests:

- BaseTestCase: improved docstrings, simplified setup/teardown, pre-create logs folder, restore working directory after tests, ensure temp dir cleanup.
- TestEntropyManager: disable MDAnalysis and commands loggers to prevent logging noise during tests.
- TestLoggingConfig: use self.test_dir consistently instead of temp_dir.name for log file paths.
- TestMain: force UTF-8 mode for subprocess (-X utf8) and capture output with UTF-8 encoding to avoid UnicodeEncodeErrors on Windows.
- Inlcude `windows2025` within `project-ci.yaml` as the test cases now work on Windows

Author: harryswift01

.github/workflows/project-ci.yaml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-24.04]
+        os: [ubuntu-24.04, windows-2025]
         python-version: ["3.11", "3.12", "3.13"]
     steps:
       - name: Checkout repo

tests/test_CodeEntropy/test_base.py

@@ -1,43 +1,45 @@
-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.
+    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):
-        # Unique temporary test directory
+        """
+        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._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")
+        self.logs_path = os.path.join(self.test_dir, "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("")
+        self._orig_dir = os.getcwd()
+        os.chdir(self.test_dir)
 
     def tearDown(self):
-        # Shutdown logging and remove handlers (important for Windows)
-        logging.shutdown()
-        for handler in logging.root.handlers[:]:
-            logging.root.removeHandler(handler)
+        """
+        Clean up the test environment after each test method runs.
 
-        # Restore working directory
+        Actions performed:
+        1. Restores the original working directory.
+        2. Deletes the temporary test directory along with all its contents.
+        """
         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)
+            shutil.rmtree(self.test_dir, ignore_errors=True)

tests/test_CodeEntropy/test_entropy.py

@@ -1,3 +1,4 @@
+import logging
 import math
 import os
 import shutil
@@ -32,6 +33,10 @@ def setUp(self):
         super().setUp()
         self.test_data_dir = os.path.dirname(data.__file__)
 
+        # 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
         tprfile = os.path.join(self.test_data_dir, "md_A4_dna.tpr")

tests/test_CodeEntropy/test_logging_config.py

@@ -67,7 +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")
@@ -86,7 +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))
 

tests/test_CodeEntropy/test_main.py

@@ -102,6 +102,8 @@ def test_main_entry_point_runs(self):
         result = subprocess.run(
             [
                 sys.executable,
+                "-X",
+                "utf8",
                 "-m",
                 "CodeEntropy.main",
                 "--top_traj_file",
@@ -110,7 +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)