Improve Test Coverage for main.py

tests/test_CodeEntropy/test_main.py

@@ -1,3 +1,8 @@
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
 import unittest
 from unittest.mock import MagicMock, patch
 
@@ -9,6 +14,22 @@ class TestMain(unittest.TestCase):
     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)
+
     @patch("CodeEntropy.main.sys.exit")
     @patch("CodeEntropy.main.RunManager")
     def test_main_successful_run(self, mock_RunManager, mock_exit):
@@ -68,6 +89,51 @@ def test_main_exception_triggers_exit(
             "Fatal error during entropy calculation: Test exception", exc_info=True
         )
 
+    def test_main_entry_point_runs(self):
+        """
+        Test that the CLI entry point (main.py) runs successfully with minimal required
+        arguments.
+        """
+        # Prepare input files
+        data_dir = os.path.abspath(
+            os.path.join(os.path.dirname(__file__), "..", "data")
+        )
+        tpr_path = shutil.copy(os.path.join(data_dir, "md_A4_dna.tpr"), self.test_dir)
+        trr_path = shutil.copy(
+            os.path.join(data_dir, "md_A4_dna_xf.trr"), self.test_dir
+        )
+
+        config_path = os.path.join(self.test_dir, "config.yaml")
+        with open(config_path, "w") as f:
+            f.write("run1:\n" "  selection_string: resid 1\n")
+
+        result = subprocess.run(
+            [
+                sys.executable,
+                "-m",
+                "CodeEntropy.main",
+                "--top_traj_file",
+                tpr_path,
+                trr_path,
+            ],
+            cwd=self.test_dir,
+            capture_output=True,
+            text=True,
+        )
+
+        self.assertEqual(result.returncode, 0)
+
+        # Check for job folder and output file
+        job_dir = os.path.join(self.test_dir, "job001")
+        output_file = os.path.join(job_dir, "output_file.json")
+
+        self.assertTrue(os.path.exists(job_dir))
+        self.assertTrue(os.path.exists(output_file))
+
+        with open(output_file) as f:
+            content = f.read()
+            self.assertIn("DA", content)
+
 
 if __name__ == "__main__":
     unittest.main()