fixing circular import by moving NO_PARENTS to constants files

ultrack/cli/data_summary.py

@@ -10,9 +10,10 @@
 
 from ultrack.cli.utils import config_option
 from ultrack.config import MainConfig
-from ultrack.core.database import NO_PARENT, LinkDB, NodeDB
+from ultrack.core.database import LinkDB, NodeDB
 from ultrack.core.export.utils import solution_dataframe_from_sql
 from ultrack.tracks.graph import add_track_ids_to_tracks_df
+from ultrack.utils.constants import NO_PARENT
 from ultrack.utils.printing import pretty_print_df
 
 

ultrack/core/database.py

@@ -24,9 +24,7 @@
 
 from ultrack.config.dataconfig import DatabaseChoices, DataConfig
 from ultrack.utils.array import assert_same_length
-
-# constant value to indicate it has no parent
-NO_PARENT = -1
+from ultrack.utils.constants import NO_PARENT
 
 Base = declarative_base()
 

ultrack/core/export/_test/test_ctc.py

@@ -2,9 +2,9 @@
 import pandas as pd
 import pytest
 
-from ultrack.core.database import NO_PARENT
 from ultrack.core.export.ctc import ctc_compress_forest, stitch_tracks_df
 from ultrack.tracks.graph import add_track_ids_to_tracks_df
+from ultrack.utils.constants import NO_PARENT
 
 
 @pytest.fixture

ultrack/core/export/_test/test_networkx.py

@@ -1,8 +1,8 @@
 import pandas as pd
 import pytest
 
-from ultrack.core.database import NO_PARENT
 from ultrack.core.export import tracks_layer_to_networkx
+from ultrack.utils.constants import NO_PARENT
 
 
 @pytest.mark.parametrize("children_to_parent", [True, False])

ultrack/core/export/_test/test_trackmate.py

@@ -4,8 +4,8 @@
 import pandas as pd
 import pytest
 
-from ultrack.core.database import NO_PARENT
 from ultrack.core.export.trackmate import tracks_layer_to_trackmate
+from ultrack.utils.constants import NO_PARENT
 
 pytrackmate = pytest.importorskip("pytrackmate")
 

ultrack/core/export/ctc.py

@@ -19,7 +19,7 @@
 
 from ultrack.config.config import MainConfig
 from ultrack.config.dataconfig import DataConfig
-from ultrack.core.database import NO_PARENT, NodeDB
+from ultrack.core.database import NodeDB
 from ultrack.core.export.utils import (
     export_segmentation_generic,
     filter_nodes_generic,
@@ -32,6 +32,7 @@
     tracks_df_forest,
 )
 from ultrack.tracks.stats import estimate_drift
+from ultrack.utils.constants import NO_PARENT
 from ultrack.utils.data import validate_and_overwrite_path
 
 logging.basicConfig()

ultrack/core/export/networkx.py

@@ -4,9 +4,9 @@
 import pandas as pd
 
 from ultrack.config.config import MainConfig
-from ultrack.core.database import NO_PARENT
 from ultrack.core.export.tracks_layer import to_tracks_layer
 from ultrack.tracks.graph import _create_tracks_forest
+from ultrack.utils.constants import NO_PARENT
 
 LOG = logging.getLogger(__name__)
 

ultrack/core/export/trackmate.py

@@ -6,8 +6,8 @@
 import pandas as pd
 
 from ultrack.config.config import MainConfig
-from ultrack.core.database import NO_PARENT
 from ultrack.core.export.tracks_layer import to_tracks_layer
+from ultrack.utils.constants import NO_PARENT
 
 
 def _set_filter_elem(elem: ET.Element) -> None:

ultrack/core/export/utils.py

@@ -9,8 +9,9 @@
 from toolz import curry
 
 from ultrack.config.dataconfig import DataConfig
-from ultrack.core.database import NO_PARENT, NodeDB
+from ultrack.core.database import NodeDB
 from ultrack.core.segmentation.node import Node
+from ultrack.utils.constants import NO_PARENT
 from ultrack.utils.multiprocessing import multiprocessing_apply
 
 LOG = logging.getLogger(__name__)

ultrack/core/linking/_test/test_link_utils.py

@@ -3,8 +3,9 @@
 from sqlalchemy.orm import Session
 
 from ultrack.config.config import MainConfig
-from ultrack.core.database import NO_PARENT, LinkDB, NodeDB
+from ultrack.core.database import LinkDB, NodeDB
 from ultrack.core.linking.utils import clear_linking_data
+from ultrack.utils.constants import NO_PARENT
 
 
 @pytest.mark.parametrize(

ultrack/core/solve/_test/test_sql_tracking.py

@@ -6,8 +6,9 @@
 
 from ultrack import solve, to_tracks_layer
 from ultrack.config.config import MainConfig
-from ultrack.core.database import NO_PARENT, LinkDB, NodeDB, VarAnnotation
+from ultrack.core.database import LinkDB, NodeDB, VarAnnotation
 from ultrack.core.solve.sqltracking import SQLTracking
+from ultrack.utils.constants import NO_PARENT
 
 _CONFIG_PARAMS = {
     "segmentation.n_workers": 4,

ultrack/core/solve/solver/heuristic/heuristic_solver.py

@@ -7,12 +7,12 @@
 from skimage.util._map_array import ArrayMap
 
 from ultrack.config.config import TrackingConfig
-from ultrack.core.database import NO_PARENT
 from ultrack.core.solve.solver.base_solver import BaseSolver
 from ultrack.core.solve.solver.heuristic._numba_heuristic_solver import (
     NumbaHeuristicSolver,
 )
 from ultrack.utils.array import assert_same_length
+from ultrack.utils.constants import NO_PARENT
 
 LOG = logging.getLogger(__name__)
 

ultrack/core/solve/solver/mip_solver.py

@@ -10,9 +10,9 @@
 from skimage.util._map_array import ArrayMap
 
 from ultrack.config.config import TrackingConfig
-from ultrack.core.database import NO_PARENT
 from ultrack.core.solve.solver.base_solver import BaseSolver
 from ultrack.utils.array import assert_same_length
+from ultrack.utils.constants import NO_PARENT
 
 LOG = logging.getLogger(__name__)
 

ultrack/reader/_test/test_napari_reader.py

@@ -7,8 +7,8 @@
 from napari.plugins import _initialize_plugins
 from napari.viewer import ViewerModel
 
-from ultrack.core.database import NO_PARENT
 from ultrack.reader.napari_reader import napari_get_reader
+from ultrack.utils.constants import NO_PARENT
 
 
 @pytest.fixture

ultrack/tracks/_test/test_tracks_gap_closing.py

@@ -3,8 +3,8 @@
 import zarr
 import zarr.storage
 
-from ultrack.core.database import NO_PARENT
 from ultrack.tracks import close_tracks_gaps
+from ultrack.utils.constants import NO_PARENT
 
 
 def test_gap_closing() -> None:

ultrack/tracks/_test/test_tracks_graph.py

@@ -2,13 +2,13 @@
 import pandas as pd
 import pytest
 
-from ultrack.core.database import NO_PARENT
 from ultrack.tracks import (
     filter_short_sibling_tracks,
     get_paths_to_roots,
     get_subgraph,
     split_trees,
 )
+from ultrack.utils.constants import NO_PARENT
 
 
 @pytest.fixture

ultrack/tracks/_test/test_tracks_sorting.py

@@ -4,13 +4,13 @@
 import pandas as pd
 from numba import typed, types
 
-from ultrack.core.database import NO_PARENT
 from ultrack.tracks import (
     left_first_search,
     sort_track_ids,
     sort_trees_by_length,
     sort_trees_by_max_radius,
 )
+from ultrack.utils.constants import NO_PARENT
 
 
 def test_sortrees_by_length() -> None:

ultrack/tracks/_test/test_tracks_stats.py

@@ -4,13 +4,13 @@
 import pandas as pd
 import pytest
 
-from ultrack.core.database import NO_PARENT
 from ultrack.tracks.stats import (
     estimate_drift,
     tracks_df_movement,
     tracks_length,
     tracks_profile_matrix,
 )
+from ultrack.utils.constants import NO_PARENT
 
 
 def spatial_df(group_drift: Sequence[int], length_per_group: int = 10) -> pd.DataFrame:

ultrack/tracks/_test/test_tracks_video.py

@@ -6,12 +6,12 @@
 import pytest
 from napari.viewer import ViewerModel
 
-from ultrack.core.database import NO_PARENT
 from ultrack.tracks.video import (
     tracks_df_to_3D_video,
     tracks_df_to_moving_2D_plane_video,
     tracks_df_to_videos,
 )
+from ultrack.utils.constants import NO_PARENT
 
 pytest.importorskip("napari_animation")
 

ultrack/tracks/gap_closing.py

@@ -7,7 +7,7 @@
 from scipy.spatial.distance import cdist
 from zarr.storage import Store
 
-from ultrack.core.database import NO_PARENT
+from ultrack.utils.constants import NO_PARENT
 from ultrack.utils.segmentation import SegmentationPainter, copy_segments
 
 

ultrack/tracks/graph.py

@@ -8,7 +8,7 @@
 from numpy.typing import ArrayLike
 from zarr.storage import Store
 
-from ultrack.core.database import NO_PARENT
+from ultrack.utils.constants import NO_PARENT
 from ultrack.utils.segmentation import SegmentationPainter, copy_segments
 
 LOG = logging.getLogger(__name__)

ultrack/tracks/sorting.py

@@ -7,13 +7,13 @@
 from scipy.spatial.distance import pdist
 from tqdm import tqdm
 
-from ultrack.core.database import NO_PARENT
 from ultrack.tracks.graph import (
     inv_tracks_df_forest,
     left_first_search,
     split_trees,
     tracks_df_forest,
 )
+from ultrack.utils.constants import NO_PARENT
 
 LOG = logging.getLogger(__name__)
 

ultrack/tracks/stats.py

@@ -4,8 +4,8 @@
 import numpy as np
 import pandas as pd
 
-from ultrack.core.database import NO_PARENT
 from ultrack.tracks.sorting import sort_track_ids
+from ultrack.utils.constants import NO_PARENT
 
 LOG = logging.getLogger(__name__)
 

ultrack/utils/constants.py

@@ -1,3 +1,5 @@
 import os
 
+NO_PARENT = -1
+
 ULTRACK_DEBUG = bool(int(os.environ.get("ULTRACK_DEBUG", False)))

ultrack/validation/_test/test_link_validation.py

@@ -4,7 +4,7 @@
 import pandas as pd
 from napari.viewer import ViewerModel
 
-from ultrack.core.database import NO_PARENT
+from ultrack.utils.constants import NO_PARENT
 from ultrack.validation.link_validation import Annotation, LinkValidation
 
 

ultrack/validation/link_validation.py

@@ -10,7 +10,7 @@
 from qtpy.QtGui import QKeySequence
 from qtpy.QtWidgets import QLabel, QPushButton, QVBoxLayout, QWidget
 
-from ultrack.core.database import NO_PARENT
+from ultrack.utils.constants import NO_PARENT
 
 LOG = logging.getLogger(__name__)