diff --git a/.gitignore b/.gitignore
index 39aa9026..f9bf9c80 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/
diff --git a/tests/test_runner.py b/tests/test_runner.py
new file mode 100644
index 00000000..fa052b84
--- /dev/null
+++ b/tests/test_runner.py
@@ -0,0 +1,116 @@
+import os
+import unittest
+from unittest.mock import patch, MagicMock
+
+# Assuming the runner can be imported like this
+from bionetgen.modelapi.runner import run
+
+
+class TestRunner(unittest.TestCase):
+    @patch("bionetgen.modelapi.runner.BNGCLI")
+    @patch("bionetgen.modelapi.runner.TemporaryDirectory")
+    @patch("bionetgen.modelapi.runner.os.chdir")
+    def test_run_with_no_out(self, mock_chdir, mock_temp_dir, mock_bngcli):
+        # Setup mocks
+        mock_temp_dir.return_value.__enter__.return_value = "/tmp/mocked"
+        mock_cli_instance = MagicMock()
+        mock_cli_instance.result = "mocked_result"
+        mock_bngcli.return_value = mock_cli_instance
+
+        # Execute
+        result = run("mock_input.bngl")
+
+        # Verify
+        mock_temp_dir.assert_called_once()
+        mock_bngcli.assert_called_once_with(
+            "mock_input.bngl",
+            "/tmp/mocked",
+            unittest.mock.ANY,
+            suppress=False,
+            timeout=None,
+        )
+        mock_cli_instance.run.assert_called_once()
+        self.assertEqual(
+            mock_chdir.call_count, 1
+        )  # should return to original directory
+        self.assertEqual(result, "mocked_result")
+
+    @patch("bionetgen.modelapi.runner.BNGCLI")
+    @patch("bionetgen.modelapi.runner.os.chdir")
+    def test_run_with_out(self, mock_chdir, mock_bngcli):
+        # Setup mocks
+        mock_cli_instance = MagicMock()
+        mock_cli_instance.result = "mocked_result"
+        mock_bngcli.return_value = mock_cli_instance
+
+        # Execute
+        result = run("mock_input.bngl", out="/custom/out")
+
+        # Verify
+        mock_bngcli.assert_called_once_with(
+            "mock_input.bngl",
+            "/custom/out",
+            unittest.mock.ANY,
+            suppress=False,
+            timeout=None,
+        )
+        mock_cli_instance.run.assert_called_once()
+        self.assertEqual(mock_chdir.call_count, 1)
+        self.assertEqual(result, "mocked_result")
+
+    @patch("bionetgen.modelapi.runner.BNGCLI")
+    @patch("bionetgen.modelapi.runner.TemporaryDirectory")
+    @patch("bionetgen.modelapi.runner.os.chdir")
+    def test_run_with_no_out_exception(self, mock_chdir, mock_temp_dir, mock_bngcli):
+        # Setup mocks
+        mock_temp_dir.return_value.__enter__.return_value = "/tmp/mocked"
+        mock_cli_instance = MagicMock()
+        mock_cli_instance.run.side_effect = Exception("Test exception")
+        mock_bngcli.return_value = mock_cli_instance
+
+        # Execute and Verify
+        with self.assertRaises(Exception) as context:
+            run("mock_input.bngl")
+
+        self.assertTrue("Test exception" in str(context.exception))
+        mock_temp_dir.assert_called_once()
+        mock_bngcli.assert_called_once_with(
+            "mock_input.bngl",
+            "/tmp/mocked",
+            unittest.mock.ANY,
+            suppress=False,
+            timeout=None,
+        )
+        mock_cli_instance.run.assert_called_once()
+        self.assertEqual(
+            mock_chdir.call_count, 1
+        )  # Exception handling restores directory
+
+    @patch("bionetgen.modelapi.runner.BNGCLI")
+    @patch("bionetgen.modelapi.runner.os.chdir")
+    def test_run_with_out_exception(self, mock_chdir, mock_bngcli):
+        # Setup mocks
+        mock_cli_instance = MagicMock()
+        mock_cli_instance.run.side_effect = Exception("Test exception")
+        mock_bngcli.return_value = mock_cli_instance
+
+        # Execute and Verify
+        with self.assertRaises(Exception) as context:
+            run("mock_input.bngl", out="/custom/out")
+
+        self.assertTrue("Test exception" in str(context.exception))
+        mock_bngcli.assert_called_once_with(
+            "mock_input.bngl",
+            "/custom/out",
+            unittest.mock.ANY,
+            suppress=False,
+            timeout=None,
+        )
+        mock_cli_instance.run.assert_called_once()
+        self.assertEqual(
+            mock_chdir.call_count, 1
+        )  # Exception handling restores directory
+
+
+if __name__ == "__main__":
+    unittest.main()