adjusted file names and imports

.settings/module_db.json

@@ -2123,7 +2123,7 @@
           "name": "NeutralAtom",
           "class": "NeutralAtom",
           "args": {},
-          "module": "modules.applications.optimization.mis.mappings.neutralatom",
+          "module": "modules.applications.optimization.mis.mappings.neutral_atom",
           "requirements": [
             {
               "name": "pulser",

src/demo/instruction_demo.py

@@ -1,6 +1,6 @@
 import logging
 
-from BenchmarkManager import Instruction
+from benchmark_manager import Instruction
 from modules.core import Core
 from modules.applications.application import Application
 

src/modules/applications/optimization/mis/mis.py

@@ -85,7 +85,7 @@ def get_default_submodule(self, option: str) -> Core:
             from modules.applications.optimization.mis.mappings.qiro import QIRO  # pylint: disable=C0415
             return QIRO()
         elif option == "NeutralAtom":
-            from modules.applications.optimization.mis.mappings.neutralatom import NeutralAtom  # pylint: disable=C0415
+            from modules.applications.optimization.mis.mappings.neutral_atom import NeutralAtom  # pylint: disable=C0415
             return NeutralAtom()
         else:
             raise NotImplementedError(f"Mapping Option {option} not implemented")

src/modules/applications/optimization/sat/sat.py

@@ -98,7 +98,7 @@ def get_default_submodule(self, option: str) -> Core:
             from modules.applications.optimization.sat.mappings.choiqubo import ChoiQUBO  # pylint: disable=C0415
             return ChoiQUBO()
         elif option == "ChoiIsing":
-            from modules.applications.optimization.sat.mappings.choiIsing import ChoiIsing  # pylint: disable=C0415
+            from modules.applications.optimization.sat.mappings.choiising import ChoiIsing  # pylint: disable=C0415
             return ChoiIsing()
         elif option == "DinneenQUBO":
             from modules.applications.optimization.sat.mappings.dinneenqubo import DinneenQUBO  # pylint: disable=C0415

tests/modules/applications/optimization/mis/mappings/test_neutral_atom.py

@@ -9,7 +9,7 @@ class TestNeutralAtom(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         cls.neutral_atom_instance = NeutralAtom()
-        with open("tests/modules/applications/optimization/MIS/mappings/MIS_test_graph.pkl", "rb") as file:
+        with open("tests/modules/applications/optimization/mis/mappings/mis_test_graph.pkl", "rb") as file:
             cls.graph = pickle.load(file)
             cls.config = {}
 

tests/modules/applications/optimization/pvc/mappings/test_ising.py

@@ -11,7 +11,7 @@ class TestIsing(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         cls.ising_instance = Ising()
-        with open("tests/modules/applications/optimization/PVC/mappings/pvc_graph_1_seam.gpickle", "rb") as file:
+        with open("tests/modules/applications/optimization/pvc/mappings/pvc_graph_1_seam.gpickle", "rb") as file:
             cls.graph = pickle.load(file)
 
     def test_get_requirements(self):

tests/modules/applications/optimization/pvc/mappings/test_qubo.py

@@ -9,7 +9,7 @@ class TestQUBO(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         cls.qubo_instance = QUBO()
-        with open("tests/modules/applications/optimization/PVC/mappings/pvc_graph_1_seam.gpickle", "rb") as file:
+        with open("tests/modules/applications/optimization/pvc/mappings/pvc_graph_1_seam.gpickle", "rb") as file:
             cls.graph = pickle.load(file)
 
     def test_get_requirements(self):

tests/test_benchmark_manager.py

@@ -122,9 +122,9 @@ def test_save_as_json(self, mock_json_dump, mock_open_file):
         mock_open_file.assert_called_once_with(f"{self.benchmark_manager.store_dir}/results.json", 'w')
         mock_json_dump.assert_called_once_with(mock_results, mock_open_file(), indent=2)
 
-    @patch("src.BenchmarkManager.Plotter.visualize_results")
-    @patch("src.BenchmarkManager.BenchmarkManager._save_as_json")
-    @patch("src.BenchmarkManager.ConfigManager")
+    @patch("src.benchmark_manager.Plotter.visualize_results")
+    @patch("src.benchmark_manager.BenchmarkManager._save_as_json")
+    @patch("src.benchmark_manager.ConfigManager")
     def test_summarize_results(self, mock_config_manager, mock_save_json, mock_visualize):
         self.benchmark_manager.summarize_results(["/mock/dir1", "/mock/dir2"])
         mock_save_json.assert_called()
@@ -137,8 +137,8 @@ def test_load_results(self, mock_open_file, mock_glob):
         self.assertEqual(len(results), 4, "Expected to load results from both directories.")
         self.assertEqual(results[0]["result"], "mock", "Expected the first result to match mock.")
 
-    @patch("src.BenchmarkManager.preprocess")
-    @patch("src.BenchmarkManager.postprocess")
+    @patch("src.benchmark_manager.preprocess")
+    @patch("src.benchmark_manager.postprocess")
     def test_traverse_config(self, mock_postprocess, mock_preprocess):
         # Mock the preprocess function to return expected values
         mock_preprocess.return_value = (Instruction.PROCEED, "processed_input", 0.1)

tests/test_config_manager.py

@@ -10,8 +10,8 @@ class TestConfigManager(unittest.TestCase):
     def setUp(self):
         self.config_manager = ConfigManager()
 
-    @patch("src.ConfigManager.inquirer.prompt")
-    @patch("src.ConfigManager.checkbox")
+    @patch("src.config_manager.inquirer.prompt")
+    @patch("src.config_manager.checkbox")
     def test_query_module(self, mock_checkbox, mock_prompt):
         # Mock responses for checkbox and prompt
         mock_checkbox.return_value = {"param1": [1, 2]}  # Simulates a user selecting 1 and 2
@@ -96,7 +96,7 @@ def test_translate_legacy_config_helper(self):
         self.assertEqual(result[0]["name"], "SolverA")
         self.assertEqual(len(result[0]["submodules"]), 1)
 
-    @patch("src.ConfigManager._get_instance_with_sub_options")
+    @patch("src.config_manager._get_instance_with_sub_options")
     def test_load_config(self, mock_get_instance):
         mock_app_instance = MagicMock()
         mock_get_instance.return_value = mock_app_instance
@@ -218,8 +218,8 @@ def test_create_tree_figure(self):
             self.config_manager.create_tree_figure("/mock/store/dir")
             mock_savefig.assert_called_once_with("/mock/store/dir/BenchmarkGraph.png", format="PNG")
 
-    @patch("src.ConfigManager.inquirer.prompt")
-    @patch("src.ConfigManager.checkbox")
+    @patch("src.config_manager.inquirer.prompt")
+    @patch("src.config_manager.checkbox")
     def test_query_for_config(self, mock_checkbox, mock_prompt):
         mock_checkbox.return_value = {"param1": [1, 2, "Custom Input"]}
         mock_prompt.side_effect = [{"custom_input": "custom_value"}]