Updated PEP8 compliance

Co-authored-by: Greshma Shaji <[email protected]>
Co-authored-by: Marvin Erdmann <[email protected]>

README.md

@@ -136,7 +136,7 @@ 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
@@ -154,13 +154,13 @@ 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 BenchmarkRecord import BenchmarkRecord, BenchmarkRecordStored
-from ConfigManager import ConfigManager
-from modules.Core import Core
-from Plotter import Plotter
+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 @@
 from copy import deepcopy
 from typing import final
 
-from Metrics import Metrics
+from metrics import Metrics
 
 
 class BenchmarkRecord:

src/ConfigManager.py → src/config_manager.py

@@ -21,14 +21,14 @@
 import networkx as nx
 import numpy as np
 import yaml
-from typing_extensions import NotRequired, Self, TypedDict
+from typing_extensions import TypedDict, NotRequired, Self
 
-from modules.applications import Application
-from modules.Core import Core
+from modules.core import Core
+from modules.applications.application import Application
 from utils import _get_instance_with_sub_options, checkbox
 
 
-class ConfigModule(TypedDict):  # pylint: disable=R0903
+class ConfigModule(TypedDict):
     """
     Each instance consists of the name of the module, its config, and a list of its configured submodules, which are
     ConfigModule instances themselves. It can also contain the instance of the class associated to this module,
@@ -40,7 +40,7 @@ class ConfigModule(TypedDict):  # pylint: disable=R0903
     instance: NotRequired[Core]
 
 
-class BenchmarkConfig(TypedDict):  # pylint: disable=R0903
+class BenchmarkConfig(TypedDict):
     """
     Each instance consists of a ConfigModule associated with the application at the first level and the number of
     repetitions of the benchmark.

src/demo/instruction_demo.py

@@ -1,8 +1,8 @@
 import logging
 
-from BenchmarkManager import Instruction
-from modules.applications.Application import Application
-from modules.Core import Core
+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

@@ -12,19 +12,19 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 
-import inspect
-import json
 import logging
+import json
 import os
 import time
 from pathlib import Path
+import inspect
 
-import inquirer
 import yaml
 from packaging import version
+import inquirer
 
-from modules.Core import Core
-from utils import _get_instance_with_sub_options, checkbox, get_git_revision
+from modules.core import Core
+from utils import _get_instance_with_sub_options, get_git_revision, checkbox
 
 
 class Installer:
@@ -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 = [
@@ -96,26 +96,26 @@ def configure(self, env_name="default") -> None:
             self.save_env(module_db, env_name)
 
         requirements = self.collect_requirements(module_db["modules"])
-        # activate_requirements = checkbox("requirements", "Should we create an package file, if yes for "
-        #                                                  "which package manager?",
-        #                                  ["Conda", "PIP", "Print it here"])["requirements"]
-
-        # if "Conda" in activate_requirements:
-        #     self.create_conda_file(requirements, env_name)
-        # if "PIP" in activate_requirements:
-        self.create_req_file(requirements, env_name)
-        # if "Print it here" in activate_requirements:
-        #     logging.info("Please install:")
-        #     for p, v in requirements.items():
-        #         logging.info(f"  -  {p}{': ' + v[0] if v else ''}")
-
-        # activate_answer = inquirer.prompt([
-        #     inquirer.List("activate",
-        #                   message="Do you want to activate the QUARK module environment?",
-        #                   choices=["Yes", "No"])])["activate"]
-
-        # if activate_answer == "Yes":
-        self.set_active_env(env_name)
+        activate_requirements = checkbox("requirements", "Should we create an package file, if yes for "
+                                                         "which package manager?",
+                                         ["Conda", "PIP", "Print it here"])["requirements"]
+
+        if "Conda" in activate_requirements:
+            self.create_conda_file(requirements, env_name)
+        if "PIP" in activate_requirements:
+            self.create_req_file(requirements, env_name)
+        if "Print it here" in activate_requirements:
+            logging.info("Please install:")
+            for p, v in requirements.items():
+                logging.info(f"  -  {p}{': ' + v[0] if v else ''}")
+
+        activate_answer = inquirer.prompt([
+            inquirer.List("activate",
+                          message="Do you want to activate the QUARK module environment?",
+                          choices=["Yes", "No"])])["activate"]
+
+        if activate_answer == "Yes":
+            self.set_active_env(env_name)
 
     def check_for_configs(self) -> list:
         """

src/main.py

@@ -21,7 +21,7 @@
 
 import yaml
 
-from Installer import Installer
+from installer import Installer
 from utils import _expand_paths
 from utils_mpi import MPIFileHandler, MPIStreamHandler, get_comm
 
@@ -97,8 +97,8 @@ 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)
@@ -147,15 +147,15 @@ 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

@@ -13,8 +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

@@ -13,8 +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

@@ -26,17 +26,17 @@
 # The above copyright notice and this permission notice shall be included
 # in all copies or substantial portions of the Software.
 
-import logging
 import os
+import logging
 from typing import TypedDict
 
-import numpy as np
 import pandas as pd
+import numpy as np
 import pulp
 
-from modules.applications.Application import Core
-from modules.applications.optimization.Optimization import Optimization
-from utils import end_time_measurement, start_time_measurement
+from modules.applications.application import Core
+from modules.applications.optimization.optimization import Optimization
+from utils import start_time_measurement, end_time_measurement
 
 
 class ACL(Optimization):
@@ -84,12 +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

@@ -20,9 +20,9 @@
 from qiskit_optimization import QuadraticProgram
 from qiskit_optimization.converters import QuadraticProgramToQubo
 
-from modules.applications.Mapping import Mapping
-from modules.Core import Core
-from utils import end_time_measurement, start_time_measurement
+from modules.applications.mapping import Mapping
+from modules.core import Core
+from utils import start_time_measurement, end_time_measurement
 
 
 class Ising(Mapping):
@@ -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

@@ -12,18 +12,19 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 
-import logging
-import re
 from typing import TypedDict
+import re
+import logging
 
 import numpy as np
 from qiskit_optimization import QuadraticProgram
-from qiskit_optimization.converters import (InequalityToEquality,
-                                            IntegerToBinary,
-                                            LinearEqualityToPenalty)
+from qiskit_optimization.converters import (
+    InequalityToEquality, IntegerToBinary,
+    LinearEqualityToPenalty
+)
 
-from modules.applications.Mapping import Core, Mapping
-from utils import end_time_measurement, start_time_measurement
+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
 
@@ -268,7 +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")