Fix imports

src/quark/ConfigManager.py

@@ -23,9 +23,9 @@
 import yaml
 from typing_extensions import TypedDict, NotRequired, Self
 
-from modules.Core import Core
-from modules.applications import Application
-from utils import _get_instance_with_sub_options, checkbox
+from quark.modules.Core import Core
+from quark.modules.applications import Application
+from quark.utils import _get_instance_with_sub_options, checkbox
 
 
 class ConfigModule(TypedDict):

src/quark/Installer.py

@@ -23,8 +23,8 @@
 from packaging import version
 import inquirer
 
-from modules.Core import Core
-from utils import _get_instance_with_sub_options, get_git_revision, checkbox
+from quark.modules.Core import Core
+from quark.utils import _get_instance_with_sub_options, get_git_revision, checkbox
 
 
 class Installer:
@@ -34,7 +34,7 @@ class Installer:
     """
 
     def __init__(self):
-        self.quark_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", )
+        self.quark_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "..")
         self.settings_dir = f"{self.quark_dir}/.settings"
         self.envs_dir = f"{self.settings_dir}/envs"
         self.python_version = "3.12.7"

src/quark/__main__.py

@@ -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 quark.BenchmarkManager import BenchmarkManager  # pylint: disable=C0415
+    from quark.ConfigManager 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 quark.BenchmarkManager import BenchmarkManager  # pylint: disable=C0415
+    from quark.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 quark.ConfigManager import ConfigManager  # pylint: disable=C0415
         config_manager = ConfigManager()
         if args.modules:
             logging.info(f"Load application modules configuration from {args.modules}")

src/quark/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 quark.BenchmarkManager import Instruction
+from quark.modules.Core import Core
+from quark.modules.applications.Application import Application
 
 
 class InstructionDemo(Application):

src/quark/modules/Core.py

@@ -19,8 +19,8 @@
 from abc import ABC, abstractmethod
 from typing import final
 
-from utils import _get_instance_with_sub_options
-from Metrics import Metrics
+from quark.utils import _get_instance_with_sub_options
+from quark.Metrics import Metrics
 
 
 class Core(ABC):

src/quark/modules/applications/Application.py

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

src/quark/modules/applications/Mapping.py

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

src/quark/modules/applications/optimization/ACL/ACL.py

@@ -34,9 +34,9 @@
 import numpy as np
 import pulp
 
-from modules.applications.Application import Core
-from modules.applications.optimization.Optimization import Optimization
-from utils import start_time_measurement, end_time_measurement
+from quark.modules.applications.Application import Core
+from quark.modules.applications.optimization.Optimization import Optimization
+from quark.utils import start_time_measurement, end_time_measurement
 
 
 class ACL(Optimization):
@@ -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 quark.modules.solvers.MIPsolverACL import MIPaclp  # pylint: disable=C0415
             return MIPaclp()
         elif option == "QUBO":
-            from modules.applications.optimization.ACL.mappings.QUBO import Qubo  # pylint: disable=C0415
+            from quark.modules.applications.optimization.ACL.mappings.QUBO import Qubo  # pylint: disable=C0415
             return Qubo()
         else:
             raise NotImplementedError(f"Submodule Option {option} not implemented")

src/quark/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 start_time_measurement, end_time_measurement
+from quark.modules.applications.Mapping import Mapping
+from quark.modules.Core import Core
+from quark.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 quark.modules.solvers.QAOA import QAOA  # pylint: disable=C0415
             return QAOA()
         elif option == "QiskitQAOA":
-            from modules.solvers.QiskitQAOA import QiskitQAOA  # pylint: disable=C0415
+            from quark.modules.solvers.QiskitQAOA import QiskitQAOA  # pylint: disable=C0415
             return QiskitQAOA()
         else:
             raise NotImplementedError(f"Solver Option {option} not implemented")

src/quark/modules/applications/optimization/ACL/mappings/QUBO.py

@@ -23,8 +23,8 @@
     LinearEqualityToPenalty
 )
 
-from modules.applications.Mapping import Mapping, Core
-from utils import start_time_measurement, end_time_measurement
+from quark.modules.applications.Mapping import Mapping, Core
+from quark.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 quark.modules.solvers.Annealer import Annealer  # pylint: disable=C0415
             return Annealer()
         else:
             raise NotImplementedError(f"Solver Option {option} not implemented")

src/quark/modules/applications/optimization/MIS/MIS.py

@@ -20,10 +20,10 @@
 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 utils import start_time_measurement, end_time_measurement
+from quark.modules.applications.Application import Core
+from quark.modules.applications.optimization.Optimization import Optimization
+from quark.modules.applications.optimization.MIS.data.graph_layouts import generate_hexagonal_graph
+from quark.utils import start_time_measurement, end_time_measurement
 
 # Define R_rydberg
 R_rydberg = 9.75
@@ -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 quark.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 quark.modules.applications.optimization.MIS.mappings.NeutralAtom import NeutralAtom  # pylint: disable=C0415
             return NeutralAtom()
         else:
             raise NotImplementedError(f"Mapping Option {option} not implemented")

src/quark/modules/applications/optimization/MIS/mappings/NeutralAtom.py

@@ -17,8 +17,8 @@
 import networkx as nx
 import pulser
 
-from modules.applications.Mapping import Mapping, Core
-from utils import start_time_measurement, end_time_measurement
+from quark.modules.applications.Mapping import Mapping, Core
+from quark.utils import start_time_measurement, end_time_measurement
 
 
 class NeutralAtom(Mapping):
@@ -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 quark.modules.solvers.NeutralAtomMIS import NeutralAtomMIS  # pylint: disable=C0415
             return NeutralAtomMIS()
         else:
             raise NotImplementedError(f"Solver Option {option} not implemented")

src/quark/modules/applications/optimization/MIS/mappings/QIRO.py

@@ -15,8 +15,8 @@
 from typing import TypedDict
 import networkx
 
-from modules.applications.Mapping import Core, Mapping
-from utils import start_time_measurement, end_time_measurement
+from quark.modules.applications.Mapping import Core, Mapping
+from quark.utils import start_time_measurement, end_time_measurement
 
 
 class QIRO(Mapping):
@@ -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 quark.modules.solvers.QrispQIRO import QIROSolver  # pylint: disable=C0415
             return QIROSolver()
         else:
             raise NotImplementedError(f"Solver Option {option} not implemented")

src/quark/modules/applications/optimization/Optimization.py

@@ -14,8 +14,8 @@
 from abc import ABC, abstractmethod
 import logging
 
-from modules.applications.Application import Application
-from utils import start_time_measurement, end_time_measurement
+from quark.modules.applications.Application import Application
+from quark.utils import start_time_measurement, end_time_measurement
 
 
 class Optimization(Application, ABC):

src/quark/modules/applications/optimization/PVC/PVC.py

@@ -24,9 +24,9 @@
 from matplotlib.patches import Patch
 import numpy as np
 
-from modules.applications.Application import Core
-from modules.applications.optimization.Optimization import Optimization
-from utils import start_time_measurement, end_time_measurement
+from quark.modules.applications.Application import Core
+from quark.modules.applications.optimization.Optimization import Optimization
+from quark.utils import start_time_measurement, end_time_measurement
 
 
 class PVC(Optimization):
@@ -84,19 +84,19 @@ def get_default_submodule(self, option: str) -> Core:
         :raises NotImplementedError: If the option is not recognized
         """
         if option == "Ising":
-            from modules.applications.optimization.PVC.mappings.ISING import Ising  # pylint: disable=C0415
+            from quark.modules.applications.optimization.PVC.mappings.ISING import Ising  # pylint: disable=C0415
             return Ising()
         elif option == "QUBO":
-            from modules.applications.optimization.PVC.mappings.QUBO import QUBO  # pylint: disable=C0415
+            from quark.modules.applications.optimization.PVC.mappings.QUBO import QUBO  # pylint: disable=C0415
             return QUBO()
         elif option == "GreedyClassicalPVC":
-            from modules.solvers.GreedyClassicalPVC import GreedyClassicalPVC  # pylint: disable=C0415
+            from quark.modules.solvers.GreedyClassicalPVC import GreedyClassicalPVC  # pylint: disable=C0415
             return GreedyClassicalPVC()
         elif option == "ReverseGreedyClassicalPVC":
-            from modules.solvers.ReverseGreedyClassicalPVC import ReverseGreedyClassicalPVC  # pylint: disable=C0415
+            from quark.modules.solvers.ReverseGreedyClassicalPVC import ReverseGreedyClassicalPVC  # pylint: disable=C0415
             return ReverseGreedyClassicalPVC()
         elif option == "RandomPVC":
-            from modules.solvers.RandomClassicalPVC import RandomPVC  # pylint: disable=C0415
+            from quark.modules.solvers.RandomClassicalPVC import RandomPVC  # pylint: disable=C0415
             return RandomPVC()
         else:
             raise NotImplementedError(f"Mapping Option {option} not implemented")

src/quark/modules/applications/optimization/PVC/mappings/ISING.py

@@ -19,9 +19,9 @@
 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 utils import start_time_measurement, end_time_measurement
+from quark.modules.applications.Mapping import Mapping, Core
+from quark.modules.applications.optimization.PVC.mappings.QUBO import QUBO
+from quark.utils import start_time_measurement, end_time_measurement
 
 
 class Ising(Mapping):
@@ -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 quark.modules.solvers.QAOA import QAOA  # pylint: disable=C0415
             return QAOA()
         if option == "PennylaneQAOA":
-            from modules.solvers.PennylaneQAOA import PennylaneQAOA  # pylint: disable=C0415
+            from quark.modules.solvers.PennylaneQAOA import PennylaneQAOA  # pylint: disable=C0415
             return PennylaneQAOA()
         else:
             raise NotImplementedError(f"Solver Option {option} not implemented")

src/quark/modules/applications/optimization/PVC/mappings/QUBO.py

@@ -19,8 +19,8 @@
 
 import networkx as nx
 
-from modules.applications.Mapping import Mapping, Core
-from utils import start_time_measurement, end_time_measurement
+from quark.modules.applications.Mapping import Mapping, Core
+from quark.utils import start_time_measurement, end_time_measurement
 
 
 class QUBO(Mapping):
@@ -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 quark.modules.solvers.Annealer import Annealer  # pylint: disable=C0415
             return Annealer()
         else:
             raise NotImplementedError(f"Solver Option {option} not implemented")

src/quark/modules/applications/optimization/SAT/SAT.py

@@ -20,9 +20,9 @@
 from nnf import Var, And, Or
 from nnf.dimacs import dump
 
-from modules.Core import Core
-from modules.applications.optimization.Optimization import Optimization
-from utils import start_time_measurement, end_time_measurement
+from quark.modules.Core import Core
+from quark.modules.applications.optimization.Optimization import Optimization
+from quark.utils import start_time_measurement, end_time_measurement
 
 
 class SAT(Optimization):
@@ -88,23 +88,23 @@ def get_default_submodule(self, option: str) -> Core:
         :raises NotImplementedError: If the option is not recognized
         """
         if option == "QubovertQUBO":
-            from modules.applications.optimization.SAT.mappings.QubovertQUBO import \
+            from quark.modules.applications.optimization.SAT.mappings.QubovertQUBO import \
                 QubovertQUBO  # pylint: disable=C0415
             return QubovertQUBO()
         elif option == "Direct":
-            from modules.applications.optimization.SAT.mappings.Direct import Direct  # pylint: disable=C0415
+            from quark.modules.applications.optimization.SAT.mappings.Direct import Direct  # pylint: disable=C0415
             return Direct()
         elif option == "ChoiQUBO":
-            from modules.applications.optimization.SAT.mappings.ChoiQUBO import ChoiQUBO  # pylint: disable=C0415
+            from quark.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 quark.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
+            from quark.modules.applications.optimization.SAT.mappings.DinneenQUBO import DinneenQUBO  # pylint: disable=C0415
             return DinneenQUBO()
         elif option == "DinneenIsing":
-            from modules.applications.optimization.SAT.mappings.DinneenISING import \
+            from quark.modules.applications.optimization.SAT.mappings.DinneenISING import \
                 DinneenIsing  # pylint: disable=C0415
             return DinneenIsing()
         else: