🧪 Bolt: Add missing unit tests for runner.run function

.gitignore

@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/

tests/test_runner.py

@@ -0,0 +1,81 @@
+import os
+import pytest
+from unittest.mock import patch, MagicMock
+
+import bionetgen.modelapi.runner as runner
+
+
+def test_runner_run_with_out():
+    with patch("bionetgen.modelapi.runner.BNGCLI") as mock_cli_class:
+        with patch("os.chdir") as mock_chdir:
+            mock_cli_inst = MagicMock()
+            mock_cli_class.return_value = mock_cli_inst
+            mock_cli_inst.result = "mock_result"
+
+            cur_dir = os.getcwd()
+            res = runner.run("test.bngl", out="out_dir")
+
+            mock_cli_class.assert_called_once_with(
+                "test.bngl",
+                "out_dir",
+                runner.conf["bngpath"],
+                suppress=False,
+                timeout=None,
+            )
+            mock_cli_inst.run.assert_called_once()
+            mock_chdir.assert_called_once_with(cur_dir)
+            assert res == "mock_result"
+
+
+def test_runner_run_without_out():
+    with patch("bionetgen.modelapi.runner.BNGCLI") as mock_cli_class:
+        with patch("bionetgen.modelapi.runner.TemporaryDirectory") as mock_tempdir:
+            with patch("os.chdir") as mock_chdir:
+                mock_tempdir.return_value.__enter__.return_value = "temp_dir"
+                mock_cli_inst = MagicMock()
+                mock_cli_class.return_value = mock_cli_inst
+                mock_cli_inst.result = "mock_result"
+
+                cur_dir = os.getcwd()
+                res = runner.run("test.bngl")
+
+                mock_cli_class.assert_called_once_with(
+                    "test.bngl",
+                    "temp_dir",
+                    runner.conf["bngpath"],
+                    suppress=False,
+                    timeout=None,
+                )
+                mock_cli_inst.run.assert_called_once()
+                mock_chdir.assert_called_once_with(cur_dir)
+                assert res == "mock_result"
+
+
+def test_runner_run_exception_with_out():
+    with patch("bionetgen.modelapi.runner.BNGCLI") as mock_cli_class:
+        with patch("os.chdir") as mock_chdir:
+            mock_cli_inst = MagicMock()
+            mock_cli_class.return_value = mock_cli_inst
+            mock_cli_inst.run.side_effect = RuntimeError("Run failed")
+
+            cur_dir = os.getcwd()
+            with pytest.raises(RuntimeError):
+                runner.run("test.bngl", out="out_dir")
+
+            mock_chdir.assert_called_once_with(cur_dir)
+
+
+def test_runner_run_exception_without_out():
+    with patch("bionetgen.modelapi.runner.BNGCLI") as mock_cli_class:
+        with patch("bionetgen.modelapi.runner.TemporaryDirectory") as mock_tempdir:
+            with patch("os.chdir") as mock_chdir:
+                mock_tempdir.return_value.__enter__.return_value = "temp_dir"
+                mock_cli_inst = MagicMock()
+                mock_cli_class.return_value = mock_cli_inst
+                mock_cli_inst.run.side_effect = RuntimeError("Run failed")
+
+                cur_dir = os.getcwd()
+                with pytest.raises(RuntimeError):
+                    runner.run("test.bngl")
+
+                mock_chdir.assert_called_once_with(cur_dir)