Separate optimized and original implementations

IlyaMuravjov · IlyaMuravjov · commit c66ad81688e6 · 2024-03-12T23:07:46.000+03:00
diff --git a/Dockerfile-all-tools b/Dockerfile-all-tools
@@ -80,3 +80,5 @@ RUN pip3 install pygraphblas==5.1.8.0
 RUN cd /py_algo && pip3 install -r requirements.txt
 RUN cd /py_algo/deps/CFPQ_Data && python3 setup.py install
 COPY . /py_algo
+
+# TODO add data downloading
diff --git a/cfpq_algo/all_pairs/all_cfl_pairs_reachability_impls.py b/cfpq_algo/all_pairs/all_cfl_pairs_reachability_impls.py
@@ -1,10 +1,10 @@
 from typing import List
 
-from src.problems.Base.template_cfg.matrix.incremental_all_pairs_cfl_reachability_algo import \
+from cfpq_algo.all_pairs.matrix.incremental_all_pairs_cfl_reachability_algo import \
     IncrementalAllPairsCFLReachabilityMatrixAlgo
-from src.problems.Base.template_cfg.matrix.non_incremental_all_pairs_cfl_reachability_algo import \
+from cfpq_algo.all_pairs.matrix.non_incremental_all_pairs_cfl_reachability_algo import \
     NonIncrementalAllPairsCFLReachabilityMatrixAlgo
-from src.problems.Base.template_cfg.template_cfg_all_pairs_reachability import AllPairsCflReachabilityAlgo
+from cfpq_algo.all_pairs.all_pairs_cfl_reachability_algo import AllPairsCflReachabilityAlgo
 
 ALL_PAIRS_CFL_REACHABILITY_ALGOS: List[AllPairsCflReachabilityAlgo] = [
     IncrementalAllPairsCFLReachabilityMatrixAlgo(),
diff --git a/cfpq_algo/all_pairs/all_pairs_cfl_reachability_algo.py b/cfpq_algo/all_pairs/all_pairs_cfl_reachability_algo.py
@@ -3,9 +3,9 @@
 
 from graphblas.core.matrix import Matrix
 
-from src.algo_setting.algo_setting import AlgoSetting
-from src.grammar.cnf_grammar_template import CnfGrammarTemplate
-from src.graph.label_decomposed_graph import LabelDecomposedGraph
+from cfpq_algo.setting.algo_setting import AlgoSetting
+from cfpq_model.cnf_grammar_template import CnfGrammarTemplate
+from cfpq_model.label_decomposed_graph import LabelDecomposedGraph
 
 
 class AllPairsCflReachabilityAlgoInstance(ABC):
diff --git a/cfpq_algo/all_pairs/matrix/abstract_all_pairs_cfl_reachability.py b/cfpq_algo/all_pairs/matrix/abstract_all_pairs_cfl_reachability.py
@@ -5,13 +5,13 @@
 from graphblas.core.operator import Semiring, Monoid
 from graphblas.semiring import any_pair
 
-from src.algo_setting.algo_setting import AlgoSetting
-from src.grammar.cnf_grammar_template import CnfGrammarTemplate
-from src.graph.label_decomposed_graph import OptimizedLabelDecomposedGraph, LabelDecomposedGraph
-from src.matrix.matrix_optimizer_setting import get_matrix_optimizer_settings
-from src.matrix.utils import complimentary_mask, identity_matrix
-from src.problems.Base.template_cfg.template_cfg_all_pairs_reachability import AllPairsCflReachabilityAlgoInstance
-from src.utils.subtractable_semiring import SubtractableSemiring
+from cfpq_algo.setting.algo_setting import AlgoSetting
+from cfpq_model.cnf_grammar_template import CnfGrammarTemplate
+from cfpq_model.label_decomposed_graph import OptimizedLabelDecomposedGraph, LabelDecomposedGraph
+from cfpq_algo.setting.matrix_optimizer_setting import get_matrix_optimizer_settings, create_matrix_optimizer
+from cfpq_matrix.utils import complimentary_mask, identity_matrix
+from cfpq_algo.all_pairs.all_pairs_cfl_reachability_algo import AllPairsCflReachabilityAlgoInstance
+from cfpq_model.subtractable_semiring import SubtractableSemiring
 
 
 class AbstractAllPairsCflReachabilityMatrixAlgoInstance(AllPairsCflReachabilityAlgoInstance, ABC):
@@ -26,8 +26,10 @@ def __init__(
             sub_op=lambda minuend, subtrahend: complimentary_mask(minuend, subtrahend)
         )
     ):
-        matrix_optimizers = get_matrix_optimizer_settings(settings)
-        self.graph = OptimizedLabelDecomposedGraph.from_unoptimized(graph, matrix_optimizers)
+        self.graph = OptimizedLabelDecomposedGraph.from_unoptimized(
+            graph,
+            matrix_optimizer = create_matrix_optimizer(settings)
+        )
         self.grammar = grammar
         self.settings = settings
         self.algebraic_structure = algebraic_structure
diff --git a/cfpq_algo/all_pairs/matrix/incremental_all_pairs_cfl_reachability_algo.py b/cfpq_algo/all_pairs/matrix/incremental_all_pairs_cfl_reachability_algo.py
@@ -1,11 +1,11 @@
 from typing import List
 
-from src.algo_setting.algo_setting import AlgoSetting
-from src.grammar.cnf_grammar_template import CnfGrammarTemplate
-from src.graph.label_decomposed_graph import OptimizedLabelDecomposedGraph, LabelDecomposedGraph
-from src.problems.Base.template_cfg.matrix.abstract_all_pairs_cfl_reachability import \
+from cfpq_algo.setting.algo_setting import AlgoSetting
+from cfpq_model.cnf_grammar_template import CnfGrammarTemplate
+from cfpq_model.label_decomposed_graph import LabelDecomposedGraph
+from cfpq_algo.all_pairs.matrix.abstract_all_pairs_cfl_reachability import \
     AbstractAllPairsCflReachabilityMatrixAlgoInstance
-from src.problems.Base.template_cfg.template_cfg_all_pairs_reachability import AllPairsCflReachabilityAlgoInstance, \
+from cfpq_algo.all_pairs.all_pairs_cfl_reachability_algo import AllPairsCflReachabilityAlgoInstance, \
     AllPairsCflReachabilityAlgo
 
 
diff --git a/cfpq_algo/all_pairs/matrix/non_incremental_all_pairs_cfl_reachability_algo.py b/cfpq_algo/all_pairs/matrix/non_incremental_all_pairs_cfl_reachability_algo.py
@@ -1,11 +1,11 @@
 from typing import List
 
-from src.algo_setting.algo_setting import AlgoSetting
-from src.grammar.cnf_grammar_template import CnfGrammarTemplate
-from src.graph.label_decomposed_graph import OptimizedLabelDecomposedGraph, LabelDecomposedGraph
-from src.problems.Base.template_cfg.matrix.abstract_all_pairs_cfl_reachability import \
+from cfpq_algo.setting.algo_setting import AlgoSetting
+from cfpq_model.cnf_grammar_template import CnfGrammarTemplate
+from cfpq_model.label_decomposed_graph import OptimizedLabelDecomposedGraph, LabelDecomposedGraph
+from cfpq_algo.all_pairs.matrix.abstract_all_pairs_cfl_reachability import \
     AbstractAllPairsCflReachabilityMatrixAlgoInstance
-from src.problems.Base.template_cfg.template_cfg_all_pairs_reachability import AllPairsCflReachabilityAlgoInstance, \
+from cfpq_algo.all_pairs.all_pairs_cfl_reachability_algo import AllPairsCflReachabilityAlgoInstance, \
     AllPairsCflReachabilityAlgo
 
 
diff --git a/cfpq_algo/setting/algo_setting.py b/cfpq_algo/setting/algo_setting.py
diff --git a/cfpq_algo/setting/algo_settings_manager.py b/cfpq_algo/setting/algo_settings_manager.py
@@ -2,9 +2,9 @@
 from argparse import ArgumentParser, Namespace
 from typing import List
 
-from src.algo_setting.algo_setting import AlgoSetting
-from src.algo_setting.preprocessor_setting import IndexExplodingPreProcessorSetting
-from src.matrix.matrix_optimizer_setting import OptimizeEmptyMatrixSetting, LazyAddMatrixSetting, \
+from cfpq_algo.setting.algo_setting import AlgoSetting
+from cfpq_algo.setting.preprocessor_setting import IndexExplodingPreProcessorSetting
+from cfpq_algo.setting.matrix_optimizer_setting import OptimizeEmptyMatrixSetting, LazyAddMatrixSetting, \
     OptimizeFormatMatrixSetting
 
 
diff --git a/cfpq_algo/setting/matrix_optimizer_setting.py b/cfpq_algo/setting/matrix_optimizer_setting.py
@@ -1,15 +1,20 @@
 from abc import ABC, abstractmethod
 from argparse import Namespace, ArgumentParser
-from typing import List
+from typing import List, Callable
 
 from graphblas.core.matrix import Matrix
 
-from src.algo_setting.algo_setting import AlgoSetting
-from src.matrix.optimized_matrix import OptimizedMatrix
-from src.matrix.format_optimized_matrix import FormatOptimizedMatrix
-from src.matrix.lazy_add_optimized_matrix import LazyAddOptimizedMatrix
-from src.matrix.matrix_to_optimized_adapter import MatrixToOptimizedAdapter
-from src.matrix.empty_optimized_matrix import EmptyOptimizedMatrix
+from cfpq_algo.setting.algo_setting import AlgoSetting
+from cfpq_matrix.optimized_matrix import OptimizedMatrix
+from cfpq_matrix.format_optimized_matrix import FormatOptimizedMatrix
+from cfpq_matrix.lazy_add_optimized_matrix import LazyAddOptimizedMatrix
+from cfpq_matrix.matrix_to_optimized_adapter import MatrixToOptimizedAdapter
+from cfpq_matrix.empty_optimized_matrix import EmptyOptimizedMatrix
+
+
+def create_matrix_optimizer(algo_settings: List[AlgoSetting]) -> Callable[[Matrix], OptimizedMatrix]:
+    optimizer_settings = get_matrix_optimizer_settings(algo_settings)
+    return lambda matrix: optimize_matrix(matrix, optimizer_settings)
 
 
 class MatrixOptimizerSetting(AlgoSetting, ABC):
diff --git a/cfpq_algo/setting/preprocessor_setting.py b/cfpq_algo/setting/preprocessor_setting.py
@@ -2,10 +2,10 @@
 from argparse import Namespace, ArgumentParser
 from typing import List
 
-from src.algo_setting.algo_setting import AlgoSetting
-from src.grammar.cnf_grammar_template import CnfGrammarTemplate, Symbol
-from src.graph.label_decomposed_graph import LabelDecomposedGraph
-from src.problems.Base.template_cfg.utils import explode_indices
+from cfpq_algo.setting.algo_setting import AlgoSetting
+from cfpq_model.cnf_grammar_template import CnfGrammarTemplate
+from cfpq_model.label_decomposed_graph import LabelDecomposedGraph
+from cfpq_model.utils import explode_indices
 
 
 class PreProcessorSetting(AlgoSetting, ABC):
diff --git a/cfpq_cli/run_all_pairs_cflr.py b/cfpq_cli/run_all_pairs_cflr.py
@@ -4,15 +4,15 @@
 from time import time
 from typing import Optional, List
 
-from src.algo_setting.algo_setting import AlgoSetting
-from src.algo_setting.algo_settings_manager import AlgoSettingsManager
-from src.algo_setting.preprocessor_setting import preprocess_graph_and_grammar
-from src.grammar.cnf_grammar_template import CnfGrammarTemplate
-from src.graph.label_decomposed_graph import LabelDecomposedGraph
-from src.problems.Base.template_cfg.template_cfg_all_pairs_reachability_impls import \
+from cfpq_algo.setting.algo_setting import AlgoSetting
+from cfpq_algo.setting.algo_settings_manager import AlgoSettingsManager
+from cfpq_algo.setting.preprocessor_setting import preprocess_graph_and_grammar
+from cfpq_model.cnf_grammar_template import CnfGrammarTemplate
+from cfpq_model.label_decomposed_graph import LabelDecomposedGraph
+from cfpq_algo.all_pairs.all_cfl_pairs_reachability_impls import \
     ALL_PAIRS_CFL_REACHABILITY_ALGO_NAMES, \
     get_all_pairs_cfl_reachability_algo
-from src.utils.time_limit import time_limit, TimeoutException
+from cfpq_cli.time_limit import time_limit, TimeoutException
 
 
 def run_all_pairs_cflr(
@@ -67,7 +67,8 @@ def main(raw_args: List[str]):
                              'Indexed symbol names should end with `_i`. '
                              'The final two lines define the starting non-terminal as: '
                              '`Count:\\n <START_NON_TERMINAL>`.')
-    parser.add_argument('--time-limit', dest='time_limit', default=None, help='Sets a time limit in seconds.')
+    parser.add_argument('--time-limit', dest='time_limit', default=None, type=int,
+                        help='Sets a time limit in seconds.')
     parser.add_argument('--out', dest='out', default=None,
                         help='Specifies the output file for saving vertex pairs. '
                              'The line format is: `[START_VERTEX]\t[END_VERTEX]`. '
diff --git a/cfpq_cli/time_limit.py b/cfpq_cli/time_limit.py
diff --git a/cfpq_eval/eval_all_pairs_cflr.py b/cfpq_eval/eval_all_pairs_cflr.py
@@ -10,8 +10,8 @@
 
 import pandas as pd
 
-from cli.runners.all_pairs_cflr_tool_runner import IncompatibleCflrToolError
-from cli.runners.all_pairs_cflr_tool_runner_facade import run_appropriate_all_pairs_cflr_tool
+from cfpq_eval.runners.all_pairs_cflr_tool_runner import IncompatibleCflrToolError
+from cfpq_eval.runners.all_pairs_cflr_tool_runner_facade import run_appropriate_all_pairs_cflr_tool
 
 DISPLAY_STD_THRESHOLD = 0.1
 
diff --git a/cfpq_eval/runners/all_pairs_cflr_tool_runner.py b/cfpq_eval/runners/all_pairs_cflr_tool_runner.py
diff --git a/cfpq_eval/runners/all_pairs_cflr_tool_runner_facade.py b/cfpq_eval/runners/all_pairs_cflr_tool_runner_facade.py
@@ -1,12 +1,12 @@
 from pathlib import Path
 from typing import Optional
 
-from cli.runners.all_pairs_cflr_tool_runner import CflrToolRunResult
-from cli.runners.gigascale_algo_all_pairs_cflr_tool_runner import GigascaleAllPairsCflrToolRunner
-from cli.runners.graspan_algo_all_pairs_cflr_tool_runner import GraspanAllPairsCflrToolRunner
-from cli.runners.pearl_algo_all_pairs_cflr_tool_runner import PearlAllPairsCflrToolRunner
-from cli.runners.pocr_algo_all_pairs_cflr_tool_runner import PocrAllPairsCflrToolRunner
-from cli.runners.py_algo_all_pairs_cflr_tool_runner import PyAlgoAllPairsCflrToolRunner
+from cfpq_eval.runners.all_pairs_cflr_tool_runner import CflrToolRunResult
+from cfpq_eval.runners.gigascale_algo_all_pairs_cflr_tool_runner import GigascaleAllPairsCflrToolRunner
+from cfpq_eval.runners.graspan_algo_all_pairs_cflr_tool_runner import GraspanAllPairsCflrToolRunner
+from cfpq_eval.runners.pearl_algo_all_pairs_cflr_tool_runner import PearlAllPairsCflrToolRunner
+from cfpq_eval.runners.pocr_algo_all_pairs_cflr_tool_runner import PocrAllPairsCflrToolRunner
+from cfpq_eval.runners.py_algo_all_pairs_cflr_tool_runner import PyAlgoAllPairsCflrToolRunner
 
 
 def run_appropriate_all_pairs_cflr_tool(
diff --git a/cfpq_eval/runners/gigascale_algo_all_pairs_cflr_tool_runner.py b/cfpq_eval/runners/gigascale_algo_all_pairs_cflr_tool_runner.py
@@ -5,7 +5,7 @@
 from pathlib import Path
 from typing import Optional
 
-from cli.runners.all_pairs_cflr_tool_runner import AbstractAllPairsCflrToolRunner, CflrToolRunResult, \
+from cfpq_eval.runners.all_pairs_cflr_tool_runner import AbstractAllPairsCflrToolRunner, CflrToolRunResult, \
     IncompatibleCflrToolError
 
 
diff --git a/cfpq_eval/runners/graspan_algo_all_pairs_cflr_tool_runner.py b/cfpq_eval/runners/graspan_algo_all_pairs_cflr_tool_runner.py
@@ -6,10 +6,10 @@
 
 import psutil
 
-from cli.runners.all_pairs_cflr_tool_runner import AbstractAllPairsCflrToolRunner, CflrToolRunResult
-from src.grammar.cnf_grammar_template import CnfGrammarTemplate
-from src.graph.label_decomposed_graph import LabelDecomposedGraph
-from src.problems.Base.template_cfg.utils import explode_indices
+from cfpq_eval.runners.all_pairs_cflr_tool_runner import AbstractAllPairsCflrToolRunner, CflrToolRunResult
+from cfpq_model.cnf_grammar_template import CnfGrammarTemplate
+from cfpq_model.label_decomposed_graph import LabelDecomposedGraph
+from cfpq_model.utils import explode_indices
 
 
 class GraspanAllPairsCflrToolRunner(AbstractAllPairsCflrToolRunner):
diff --git a/cfpq_eval/runners/pearl_algo_all_pairs_cflr_tool_runner.py b/cfpq_eval/runners/pearl_algo_all_pairs_cflr_tool_runner.py
@@ -4,7 +4,7 @@
 from pathlib import Path
 from typing import Optional
 
-from cli.runners.all_pairs_cflr_tool_runner import AbstractAllPairsCflrToolRunner, CflrToolRunResult
+from cfpq_eval.runners.all_pairs_cflr_tool_runner import AbstractAllPairsCflrToolRunner, CflrToolRunResult
 
 
 class PearlAllPairsCflrToolRunner(AbstractAllPairsCflrToolRunner):
diff --git a/cfpq_eval/runners/pocr_algo_all_pairs_cflr_tool_runner.py b/cfpq_eval/runners/pocr_algo_all_pairs_cflr_tool_runner.py
@@ -2,7 +2,7 @@
 import subprocess
 from typing import Optional
 
-from cli.runners.all_pairs_cflr_tool_runner import AbstractAllPairsCflrToolRunner, CflrToolRunResult
+from cfpq_eval.runners.all_pairs_cflr_tool_runner import AbstractAllPairsCflrToolRunner, CflrToolRunResult
 
 
 class PocrAllPairsCflrToolRunner(AbstractAllPairsCflrToolRunner):
diff --git a/cfpq_eval/runners/py_algo_all_pairs_cflr_tool_runner.py b/cfpq_eval/runners/py_algo_all_pairs_cflr_tool_runner.py
@@ -2,7 +2,7 @@
 import subprocess
 from typing import Optional
 
-from cli.runners.all_pairs_cflr_tool_runner import AbstractAllPairsCflrToolRunner, CflrToolRunResult
+from cfpq_eval.runners.all_pairs_cflr_tool_runner import AbstractAllPairsCflrToolRunner, CflrToolRunResult
 
 
 class PyAlgoAllPairsCflrToolRunner(AbstractAllPairsCflrToolRunner):
diff --git a/cfpq_matrix/abstract_optimized_matrix_decorator.py b/cfpq_matrix/abstract_optimized_matrix_decorator.py
@@ -4,7 +4,7 @@
 from graphblas.core.dtypes import DataType
 from graphblas.core.matrix import Matrix
 
-from src.matrix.optimized_matrix import OptimizedMatrix, MatrixFormat
+from cfpq_matrix.optimized_matrix import OptimizedMatrix, MatrixFormat
 
 
 class AbstractOptimizedMatrixDecorator(OptimizedMatrix, ABC):
diff --git a/cfpq_matrix/block/block_matrix.py b/cfpq_matrix/block/block_matrix.py
@@ -3,10 +3,10 @@
 from graphblas.core.matrix import Matrix
 from graphblas.core.operator import Monoid, Semiring
 
-from src.matrix.abstract_optimized_matrix_decorator import AbstractOptimizedMatrixDecorator
-from src.matrix.optimized_matrix import OptimizedMatrix
-from src.matrix.block.block_matrix_space import BlockMatrixSpace, BlockMatrixOrientation
-from src.utils.subtractable_semiring import SubOp
+from cfpq_matrix.abstract_optimized_matrix_decorator import AbstractOptimizedMatrixDecorator
+from cfpq_matrix.optimized_matrix import OptimizedMatrix
+from cfpq_matrix.block.block_matrix_space import BlockMatrixSpace, BlockMatrixOrientation
+from cfpq_model.subtractable_semiring import SubOp
 
 
 class BlockMatrix(AbstractOptimizedMatrixDecorator, ABC):
diff --git a/cfpq_matrix/block/block_matrix_space.py b/cfpq_matrix/block/block_matrix_space.py
@@ -6,7 +6,7 @@
 from graphblas.core.matrix import Matrix
 from graphblas.core.operator import Monoid
 
-from src.matrix.optimized_matrix import OptimizedMatrix
+from cfpq_matrix.optimized_matrix import OptimizedMatrix
 
 
 class BlockMatrixOrientation(Enum):
diff --git a/cfpq_matrix/block/block_matrix_space_impl.py b/cfpq_matrix/block/block_matrix_space_impl.py
@@ -5,9 +5,9 @@
 import graphblas.monoid
 from graphblas.core.operator import Monoid
 
-from src.matrix.optimized_matrix import OptimizedMatrix
-from src.matrix.block.block_matrix import BlockMatrix, CellBlockMatrix, VectorBlockMatrix
-from src.matrix.block.block_matrix_space import BlockMatrixSpace, BlockMatrixOrientation
+from cfpq_matrix.optimized_matrix import OptimizedMatrix
+from cfpq_matrix.block.block_matrix import BlockMatrix, CellBlockMatrix, VectorBlockMatrix
+from cfpq_matrix.block.block_matrix_space import BlockMatrixSpace, BlockMatrixOrientation
 
 
 class BlockMatrixSpaceImpl(BlockMatrixSpace):
diff --git a/cfpq_matrix/empty_optimized_matrix.py b/cfpq_matrix/empty_optimized_matrix.py
@@ -1,9 +1,9 @@
 from graphblas.core.matrix import Matrix
 from graphblas.core.operator import Semiring, Monoid
 
-from src.matrix.abstract_optimized_matrix_decorator import AbstractOptimizedMatrixDecorator
-from src.matrix.optimized_matrix import OptimizedMatrix
-from src.utils.subtractable_semiring import SubOp
+from cfpq_matrix.abstract_optimized_matrix_decorator import AbstractOptimizedMatrixDecorator
+from cfpq_matrix.optimized_matrix import OptimizedMatrix
+from cfpq_model.subtractable_semiring import SubOp
 
 
 class EmptyOptimizedMatrix(AbstractOptimizedMatrixDecorator):
diff --git a/cfpq_matrix/format_optimized_matrix.py b/cfpq_matrix/format_optimized_matrix.py
@@ -3,9 +3,9 @@
 from graphblas.core.matrix import Matrix
 from graphblas.core.operator import Monoid, Semiring
 
-from src.matrix.abstract_optimized_matrix_decorator import AbstractOptimizedMatrixDecorator
-from src.matrix.optimized_matrix import OptimizedMatrix
-from src.utils.subtractable_semiring import SubOp
+from cfpq_matrix.abstract_optimized_matrix_decorator import AbstractOptimizedMatrixDecorator
+from cfpq_matrix.optimized_matrix import OptimizedMatrix
+from cfpq_model.subtractable_semiring import SubOp
 
 
 class FormatOptimizedMatrix(AbstractOptimizedMatrixDecorator):
diff --git a/cfpq_matrix/lazy_add_optimized_matrix.py b/cfpq_matrix/lazy_add_optimized_matrix.py
@@ -1,9 +1,9 @@
 from graphblas.core.matrix import Matrix
 from graphblas.core.operator import Monoid, Semiring
 
-from src.matrix.abstract_optimized_matrix_decorator import AbstractOptimizedMatrixDecorator
-from src.matrix.optimized_matrix import OptimizedMatrix
-from src.utils.subtractable_semiring import SubOp
+from cfpq_matrix.abstract_optimized_matrix_decorator import AbstractOptimizedMatrixDecorator
+from cfpq_matrix.optimized_matrix import OptimizedMatrix
+from cfpq_model.subtractable_semiring import SubOp
 
 
 class LazyAddOptimizedMatrix(AbstractOptimizedMatrixDecorator):
diff --git a/cfpq_matrix/matrix_to_optimized_adapter.py b/cfpq_matrix/matrix_to_optimized_adapter.py
@@ -4,8 +4,8 @@
 from graphblas.core.matrix import Matrix
 from graphblas.core.operator import Monoid, Semiring
 
-from src.matrix.optimized_matrix import OptimizedMatrix, MatrixFormat
-from src.utils.subtractable_semiring import SubOp
+from cfpq_matrix.optimized_matrix import OptimizedMatrix, MatrixFormat
+from cfpq_model.subtractable_semiring import SubOp
 
 
 class MatrixToOptimizedAdapter(OptimizedMatrix):
diff --git a/cfpq_matrix/optimized_matrix.py b/cfpq_matrix/optimized_matrix.py
@@ -7,7 +7,7 @@
 from graphblas.core.matrix import Matrix
 from graphblas.core.operator import Semiring, Monoid
 
-from src.utils.subtractable_semiring import SubOp
+from cfpq_model.subtractable_semiring import SubOp
 
 MatrixFormat = Optional[str]
 
diff --git a/cfpq_matrix/utils.py b/cfpq_matrix/utils.py
diff --git a/cfpq_model/cnf_grammar_template.py b/cfpq_model/cnf_grammar_template.py
diff --git a/cfpq_model/label_decomposed_graph.py b/cfpq_model/label_decomposed_graph.py
diff --git a/cfpq_model/subtractable_semiring.py b/cfpq_model/subtractable_semiring.py
diff --git a/cfpq_model/utils.py b/cfpq_model/utils.py
diff --git a/collect_diff_coverage.sh b/collect_diff_coverage.sh
diff --git a/test/algo/all_pairs/conftest.py b/test/algo/all_pairs/conftest.py
diff --git a/test/algo/all_pairs/test_cfg_all_pairs_reachability.py b/test/algo/all_pairs/test_cfg_all_pairs_reachability.py
diff --git a/test/cli/test_run_all_pairs_cflr.py b/test/cli/test_run_all_pairs_cflr.py
