Adjusted files with PEP8 compliance

README.md

@@ -169,7 +169,7 @@ Example run (You need to check at least one option with an ``X`` for the checkbo
    SCP
    GenerativeModeling
 
-2024-10-09 15:05:52,610 [INFO] Import module modules.applications.optimization.TSP.TSP
+2024-10-09 15:05:52,610 [INFO] Import module modules.applications.optimization.tsp.tsp
 [?] (Option for TSP) How many nodes does you graph need?:
  > [X] 3
    [ ] 4
@@ -187,13 +187,13 @@ Example run (You need to check at least one option with an ``X`` for the checkbo
    [ ] ReverseGreedyClassicalTSP
    [ ] RandomTSP
 
-2024-10-09 15:06:20,897 [INFO] Import module modules.solvers.GreedyClassicalTSP
+2024-10-09 15:06:20,897 [INFO] Import module modules.solvers.greedy_classical_tsp
 2024-10-09 15:06:20,933 [INFO] Skipping asking for submodule, since only 1 option (Local) is available.
 2024-10-09 15:06:20,933 [INFO] Import module modules.devices.Local
 2024-10-09 15:06:20,946 [INFO] Submodule configuration finished
 [?] How many repetitions do you want?: 1P
-2024-10-09 15:07:11,573 [INFO] Import module modules.applications.optimization.TSP.TSP
-2024-10-09 15:07:11,573 [INFO] Import module modules.solvers.GreedyClassicalTSP
+2024-10-09 15:07:11,573 [INFO] Import module modules.applications.optimization.tsp.tsp
+2024-10-09 15:07:11,573 [INFO] Import module modules.solvers.greedy_classical_tsp
 2024-10-09 15:07:11,574 [INFO] Import module modules.devices.Local
 2024-10-09 15:07:12,194 [INFO] [INFO] Created Benchmark run directory /Users/user1/quark/benchmark_runs/tsp-2024-10-09-15-07-11
 2024-10-09 15:07:12,194 [INFO] Codebase is based on revision 1d9d17aad7ddff623ff51f62ca3ec2756621c345 and has no uncommitted changes

docs/conf.py

@@ -45,8 +45,8 @@
 
 autosummary_generate = True  # Turn on sphinx.ext.autosummary
 autosummary_mock_imports = [
-    'modules.applications.optimization.PVC.createReferenceGraph',
-    'modules.applications.optimization.TSP.createReferenceGraph'
+    'modules.applications.optimization.pvc.createReferenceGraph',
+    'modules.applications.optimization.tsp.createReferenceGraph'
 ]
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).

docs/tutorial.rst

@@ -182,7 +182,7 @@ Example run (You need to check at least one option with an ``X`` for the checkbo
          SCP
          GenerativeModeling
 
-      2024-10-09 15:05:52,610 [INFO] Import module modules.applications.optimization.TSP.TSP
+      2024-10-09 15:05:52,610 [INFO] Import module modules.applications.optimization.tsp.tsp
       [?] (Option for TSP) How many nodes does you graph need?:
        > [X] 3
          [ ] 4
@@ -200,13 +200,13 @@ Example run (You need to check at least one option with an ``X`` for the checkbo
          [ ] ReverseGreedyClassicalTSP
          [ ] RandomTSP
 
-      2024-10-09 15:06:20,897 [INFO] Import module modules.solvers.GreedyClassicalTSP
+      2024-10-09 15:06:20,897 [INFO] Import module modules.solvers.greedy_classical_tsp
       2024-10-09 15:06:20,933 [INFO] Skipping asking for submodule, since only 1 option (Local) is available.
       2024-10-09 15:06:20,933 [INFO] Import module modules.devices.Local
       2024-10-09 15:06:20,946 [INFO] Submodule configuration finished
       [?] How many repetitions do you want?: 1P
-      2024-10-09 15:07:11,573 [INFO] Import module modules.applications.optimization.TSP.TSP
-      2024-10-09 15:07:11,573 [INFO] Import module modules.solvers.GreedyClassicalTSP
+      2024-10-09 15:07:11,573 [INFO] Import module modules.applications.optimization.tsp.tsp
+      2024-10-09 15:07:11,573 [INFO] Import module modules.solvers.greedy_classical_tsp
       2024-10-09 15:07:11,574 [INFO] Import module modules.devices.Local
       2024-10-09 15:07:12,194 [INFO] [INFO] Created Benchmark run directory /Users/user1/quark/benchmark_runs/tsp-2024-10-09-15-07-11
       2024-10-09 15:07:12,194 [INFO] Codebase is based on revision 1d9d17aad7ddff623ff51f62ca3ec2756621c345 and has no uncommitted changes
@@ -359,12 +359,12 @@ An example for this would be:
     [
       {
         "name": "TSP",
-        "module": "modules.applications.optimization.TSP.TSP",
+        "module": "modules.applications.optimization.tsp.tsp",
         "dir": "src",
         "submodules": [
           {
             "name": "GreedyClassicalTSP",
-            "module": "modules.solvers.GreedyClassicalTSP",
+            "module": "modules.solvers.greedy_classical_tsp",
             "submodules": []
           }
         ]

src/BenchmarkManager.py → src/benchmark_manager.py

@@ -25,10 +25,10 @@
 
 import numpy as np
 
-from ConfigManager import ConfigManager
-from BenchmarkRecord import BenchmarkRecord, BenchmarkRecordStored
-from Plotter import Plotter
-from modules.Core import Core
+from config_manager import ConfigManager
+from benchmark_record import BenchmarkRecord, BenchmarkRecordStored
+from plotter import Plotter
+from modules.core import Core
 from utils import get_git_revision
 from utils_mpi import get_comm
 

src/BenchmarkRecord.py → src/benchmark_record.py

@@ -17,7 +17,7 @@
 import json
 from copy import deepcopy
 
-from Metrics import Metrics
+from metrics import Metrics
 
 
 class BenchmarkRecord:

src/ConfigManager.py → src/config_manager.py

@@ -23,8 +23,8 @@
 import yaml
 from typing_extensions import TypedDict, NotRequired, Self
 
-from modules.Core import Core
-from modules.applications import Application
+from modules.core import Core
+from modules.applications.application import Application
 from utils import _get_instance_with_sub_options, checkbox
 
 

src/demo/instruction_demo.py

@@ -1,8 +1,8 @@
 import logging
 
-from BenchmarkManager import Instruction
-from modules.Core import Core
-from modules.applications.Application import Application
+from benchmark_manager import Instruction
+from modules.core import Core
+from modules.applications.application import Application
 
 
 class InstructionDemo(Application):

src/Installer.py → src/installer.py

@@ -23,7 +23,7 @@
 from packaging import version
 import inquirer
 
-from modules.Core import Core
+from modules.core import Core
 from utils import _get_instance_with_sub_options, get_git_revision, checkbox
 
 
@@ -40,14 +40,14 @@ def __init__(self):
         self.python_version = "3.12.7"
         self.pip_version = "23.0"
         self.default_app_modules = [
-            {"name": "PVC", "class": "PVC", "module": "modules.applications.optimization.PVC.PVC"},
-            {"name": "SAT", "class": "SAT", "module": "modules.applications.optimization.SAT.SAT"},
-            {"name": "TSP", "class": "TSP", "module": "modules.applications.optimization.TSP.TSP"},
-            {"name": "ACL", "class": "ACL", "module": "modules.applications.optimization.ACL.ACL"},
-            {"name": "MIS", "class": "MIS", "module": "modules.applications.optimization.MIS.MIS"},
-            {"name": "SCP", "class": "SCP", "module": "modules.applications.optimization.SCP.SCP"},
+            {"name": "PVC", "class": "PVC", "module": "modules.applications.optimization.pvc.pvc"},
+            {"name": "SAT", "class": "SAT", "module": "modules.applications.optimization.sat.sat"},
+            {"name": "TSP", "class": "TSP", "module": "modules.applications.optimization.tsp.tsp"},
+            {"name": "ACL", "class": "ACL", "module": "modules.applications.optimization.acl.acl"},
+            {"name": "MIS", "class": "MIS", "module": "modules.applications.optimization.mis.mis"},
+            {"name": "SCP", "class": "SCP", "module": "modules.applications.optimization.scp.scp"},
             {"name": "GenerativeModeling", "class": "GenerativeModeling",
-             "module": "modules.applications.qml.generative_modeling.GenerativeModeling"}
+             "module": "modules.applications.qml.generative_modeling.generative_modeling"}
         ]
 
         self.core_requirements = [

src/main.py

@@ -20,7 +20,7 @@
 from collections.abc import Iterable
 import yaml
 
-from Installer import Installer
+from installer import Installer
 from utils import _expand_paths
 from utils_mpi import MPIStreamHandler, MPIFileHandler, get_comm
 
@@ -96,8 +96,8 @@ def start_benchmark_run(config_file: str = None, store_dir: str = None,
 
     benchmark_config = json.loads(benchmark_config["config"])
 
-    from BenchmarkManager import BenchmarkManager  # pylint: disable=C0415
-    from ConfigManager import ConfigManager  # pylint: disable=C0415
+    from benchmark_manager import BenchmarkManager  # pylint: disable=C0415
+    from config_manager import ConfigManager  # pylint: disable=C0415
 
     config_manager = ConfigManager()
     config_manager.set_config(benchmark_config)
@@ -146,15 +146,15 @@ def handle_benchmark_run(args: argparse.Namespace) -> None:
 
     :param args: Namespace with the arguments given by the user
     """
-    from BenchmarkManager import BenchmarkManager  # pylint: disable=C0415
-    from Plotter import Plotter  # pylint: disable=C0415
+    from benchmark_manager import BenchmarkManager  # pylint: disable=C0415
+    from plotter import Plotter  # pylint: disable=C0415
 
     benchmark_manager = BenchmarkManager(fail_fast=args.failfast)
 
     if args.summarize:
         benchmark_manager.summarize_results(args.summarize)
     else:
-        from ConfigManager import ConfigManager  # pylint: disable=C0415
+        from config_manager import ConfigManager  # pylint: disable=C0415
         config_manager = ConfigManager()
         if args.modules:
             logging.info(f"Load application modules configuration from {args.modules}")

src/modules/applications/Application.py → src/modules/applications/application.py

@@ -13,7 +13,7 @@
 #  limitations under the License.
 
 from abc import ABC, abstractmethod
-from modules.Core import Core
+from modules.core import Core
 
 
 class Application(Core, ABC):

src/modules/applications/Mapping.py → src/modules/applications/mapping.py

@@ -13,7 +13,7 @@
 #  limitations under the License.
 
 from abc import ABC, abstractmethod
-from modules.Core import Core
+from modules.core import Core
 
 
 class Mapping(Core, ABC):

src/modules/applications/optimization/ACL/ACL.py → src/modules/applications/optimization/acl/acl.py

@@ -34,8 +34,8 @@
 import numpy as np
 import pulp
 
-from modules.applications.Application import Core
-from modules.applications.optimization.Optimization import Optimization
+from modules.applications.application import Core
+from modules.applications.optimization.optimization import Optimization
 from utils import start_time_measurement, end_time_measurement
 
 
@@ -84,10 +84,10 @@ def get_default_submodule(self, option: str) -> Core:
         :raises NotImplementedError: If the option is not recognized
         """
         if option == "MIPsolverACL":
-            from modules.solvers.MIPsolverACL import MIPaclp  # pylint: disable=C0415
+            from modules.solvers.mip_solver_acl import MIPaclp  # pylint: disable=C0415
             return MIPaclp()
         elif option == "QUBO":
-            from modules.applications.optimization.ACL.mappings.QUBO import Qubo  # pylint: disable=C0415
+            from modules.applications.optimization.acl.mappings.qubo import Qubo  # pylint: disable=C0415
             return Qubo()
         else:
             raise NotImplementedError(f"Submodule Option {option} not implemented")

src/modules/applications/optimization/ACL/mappings/ISING.py → src/modules/applications/optimization/acl/mappings/ising.py

@@ -20,8 +20,8 @@
 from qiskit_optimization import QuadraticProgram
 from qiskit_optimization.converters import QuadraticProgramToQubo
 
-from modules.applications.Mapping import Mapping
-from modules.Core import Core
+from modules.applications.mapping import Mapping
+from modules.core import Core
 from utils import start_time_measurement, end_time_measurement
 
 
@@ -200,10 +200,10 @@ def get_default_submodule(self, option: str) -> Core:
         :raises NotImplementedError: If the option is not recognized
         """
         if option == "QAOA":
-            from modules.solvers.QAOA import QAOA  # pylint: disable=C0415
+            from modules.solvers.qaoa import QAOA  # pylint: disable=C0415
             return QAOA()
         elif option == "QiskitQAOA":
-            from modules.solvers.QiskitQAOA import QiskitQAOA  # pylint: disable=C0415
+            from modules.solvers.qiskit_qaoa import QiskitQAOA  # pylint: disable=C0415
             return QiskitQAOA()
         else:
             raise NotImplementedError(f"Solver Option {option} not implemented")

src/modules/applications/optimization/ACL/mappings/QUBO.py → src/modules/applications/optimization/acl/mappings/qubo.py

@@ -23,7 +23,7 @@
     LinearEqualityToPenalty
 )
 
-from modules.applications.Mapping import Mapping, Core
+from modules.applications.mapping import Mapping, Core
 from utils import start_time_measurement, end_time_measurement
 
 # TODO Large chunks of this code is duplicated in ACL.mappings.ISING -> unify
@@ -269,7 +269,7 @@ def get_default_submodule(self, option: str) -> Core:
         :raises NotImplementedError: If the option is not recognized
         """
         if option == "Annealer":
-            from modules.solvers.Annealer import Annealer  # pylint: disable=C0415
+            from modules.solvers.annealer import Annealer  # pylint: disable=C0415
             return Annealer()
         else:
             raise NotImplementedError(f"Solver Option {option} not implemented")

src/modules/applications/optimization/MIS/mappings/NeutralAtom.py → src/modules/applications/optimization/mis/mappings/neutral_atom.py

@@ -17,7 +17,7 @@
 import networkx as nx
 import pulser
 
-from modules.applications.Mapping import Mapping, Core
+from modules.applications.mapping import Mapping, Core
 from utils import start_time_measurement, end_time_measurement
 
 
@@ -85,7 +85,7 @@ def get_default_submodule(self, option: str) -> Core:
         :raises NotImplementedError: If the option is not recognized
         """
         if option == "NeutralAtomMIS":
-            from modules.solvers.NeutralAtomMIS import NeutralAtomMIS  # pylint: disable=C0415
+            from modules.solvers.neutral_atom_mis import NeutralAtomMIS  # pylint: disable=C0415
             return NeutralAtomMIS()
         else:
             raise NotImplementedError(f"Solver Option {option} not implemented")

src/modules/applications/optimization/MIS/mappings/QIRO.py → src/modules/applications/optimization/mis/mappings/qiro.py

@@ -15,7 +15,7 @@
 from typing import TypedDict
 import networkx
 
-from modules.applications.Mapping import Core, Mapping
+from modules.applications.mapping import Core, Mapping
 from utils import start_time_measurement, end_time_measurement
 
 
@@ -90,7 +90,7 @@ def get_default_submodule(self, option: str) -> Core:
         :raises NotImplementedError: If the option is not recognized
         """
         if option == "QrispQIRO":
-            from modules.solvers.QrispQIRO import QIROSolver  # pylint: disable=C0415
+            from modules.solvers.qrisp_qiro import QIROSolver  # pylint: disable=C0415
             return QIROSolver()
         else:
             raise NotImplementedError(f"Solver Option {option} not implemented")

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

@@ -20,9 +20,9 @@
 import matplotlib.pyplot as plt
 from matplotlib.lines import Line2D
 
-from modules.applications.Application import Core
-from modules.applications.optimization.Optimization import Optimization
-from modules.applications.optimization.MIS.data.graph_layouts import generate_hexagonal_graph
+from modules.applications.application import Core
+from modules.applications.optimization.optimization import Optimization
+from modules.applications.optimization.mis.data.graph_layouts import generate_hexagonal_graph
 from utils import start_time_measurement, end_time_measurement
 
 # Define R_rydberg
@@ -82,10 +82,10 @@ def get_default_submodule(self, option: str) -> Core:
         :raises NotImplementedError: If the option is not recognized
         """
         if option == "QIRO":
-            from modules.applications.optimization.MIS.mappings.QIRO import QIRO  # pylint: disable=C0415
+            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/Optimization.py → src/modules/applications/optimization/optimization.py

@@ -14,7 +14,7 @@
 from abc import ABC, abstractmethod
 import logging
 
-from modules.applications.Application import Application
+from modules.applications.application import Application
 from utils import start_time_measurement, end_time_measurement
 
 

src/modules/applications/optimization/PVC/mappings/ISING.py → src/modules/applications/optimization/pvc/mappings/ising.py

@@ -19,8 +19,8 @@
 import numpy as np
 from dimod import qubo_to_ising
 
-from modules.applications.Mapping import Mapping, Core
-from modules.applications.optimization.PVC.mappings.QUBO import QUBO
+from modules.applications.mapping import Mapping, Core
+from modules.applications.optimization.pvc.mappings.qubo import QUBO
 from utils import start_time_measurement, end_time_measurement
 
 
@@ -150,10 +150,10 @@ def get_default_submodule(self, option: str) -> Core:
         :raises NotImplementedError: If the option is not recognized
         """
         if option == "QAOA":
-            from modules.solvers.QAOA import QAOA  # pylint: disable=C0415
+            from modules.solvers.qaoa import QAOA  # pylint: disable=C0415
             return QAOA()
         if option == "PennylaneQAOA":
-            from modules.solvers.PennylaneQAOA import PennylaneQAOA  # pylint: disable=C0415
+            from modules.solvers.pennylane_qaoa import PennylaneQAOA  # pylint: disable=C0415
             return PennylaneQAOA()
         else:
             raise NotImplementedError(f"Solver Option {option} not implemented")

src/modules/applications/optimization/PVC/mappings/QUBO.py → src/modules/applications/optimization/pvc/mappings/qubo.py

@@ -19,7 +19,7 @@
 
 import networkx as nx
 
-from modules.applications.Mapping import Mapping, Core
+from modules.applications.mapping import Mapping, Core
 from utils import start_time_measurement, end_time_measurement
 
 
@@ -195,7 +195,7 @@ def get_default_submodule(self, option: str) -> Core:
         :raises NotImplementedError: If the option is not recognized
         """
         if option == "Annealer":
-            from modules.solvers.Annealer import Annealer  # pylint: disable=C0415
+            from modules.solvers.annealer import Annealer  # pylint: disable=C0415
             return Annealer()
         else:
             raise NotImplementedError(f"Solver Option {option} not implemented")