ci(pre-commit.ci): autoupdate (#158)

* ci(pre-commit.ci): autoupdate

updates:
- [github.com/crate-ci/typos: v1.23.6 → typos-dict-v0.11.37](crate-ci/typos@v1.23.6...typos-dict-v0.11.37)
- [github.com/astral-sh/ruff-pre-commit: v0.5.6 → v0.8.1](astral-sh/ruff-pre-commit@v0.5.6...v0.8.1)
- [github.com/psf/black: 24.8.0 → 24.10.0](psf/black@24.8.0...24.10.0)
- [github.com/abravalheri/validate-pyproject: v0.18 → v0.23](abravalheri/validate-pyproject@v0.18...v0.23)
- [github.com/pre-commit/mirrors-mypy: v1.11.1 → v1.13.0](pre-commit/mirrors-mypy@v1.11.1...v1.13.0)

* style(pre-commit.ci): auto fixes [...]

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -5,28 +5,28 @@ ci:
 
 repos:
   - repo: https://github.com/crate-ci/typos
-    rev: v1.23.6
+    rev: typos-dict-v0.11.37
     hooks:
       - id: typos
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.6
+    rev: v0.8.1
     hooks:
       - id: ruff
         args: [--fix]
 
   - repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
 
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.18
+    rev: v0.23
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.1
+    rev: v1.13.0
     hooks:
       - id: mypy
         files: "^src/"

examples/ctc.ipynb

@@ -15,7 +15,6 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "from pathlib import Path\n",
     "import pprint\n",
     "import urllib.request\n",
     "import zipfile\n",
@@ -101,7 +100,7 @@
     "    name='Hela-01_GT'\n",
     ")\n",
     "pred_data = load_ctc_data(\n",
-    "    'sample-data/Fluo-N2DL-HeLa/01_RES', \n",
+    "    'sample-data/Fluo-N2DL-HeLa/01_RES',\n",
     "    'sample-data/Fluo-N2DL-HeLa/01_RES/res_track.txt',\n",
     "    name='Hela-01_RES'\n",
     ")"
@@ -181,9 +180,9 @@
    ],
    "source": [
     "ctc_results = run_metrics(\n",
-    "    gt_data=gt_data, \n",
-    "    pred_data=pred_data, \n",
-    "    matcher=CTCMatcher(), \n",
+    "    gt_data=gt_data,\n",
+    "    pred_data=pred_data,\n",
+    "    matcher=CTCMatcher(),\n",
     "    metrics=[CTCMetrics(), DivisionMetrics(frame_buffer=(0,1,2))],\n",
     ")\n",
     "pp.pprint(ctc_results)"
@@ -244,10 +243,10 @@
    ],
    "source": [
     "iou_results = run_metrics(\n",
-    "    gt_data=gt_data, \n",
-    "    pred_data=pred_data, \n",
-    "    matcher=IOUMatcher(iou_threshold=0.1), \n",
-    "    metrics=[DivisionMetrics(frame_buffer=(0,1,2))], \n",
+    "    gt_data=gt_data,\n",
+    "    pred_data=pred_data,\n",
+    "    matcher=IOUMatcher(iou_threshold=0.1),\n",
+    "    metrics=[DivisionMetrics(frame_buffer=(0,1,2))],\n",
     ")\n",
     "pp.pprint(iou_results)"
    ]

src/traccuracy/__init__.py

@@ -10,4 +10,4 @@
 from ._run_metrics import run_metrics
 from ._tracking_graph import EdgeFlag, NodeFlag, TrackingGraph
 
-__all__ = ["TrackingGraph", "run_metrics", "NodeFlag", "EdgeFlag"]
+__all__ = ["EdgeFlag", "NodeFlag", "TrackingGraph", "run_metrics"]

src/traccuracy/loaders/__init__.py

@@ -8,4 +8,4 @@
 
 from ._ctc import _check_ctc, _get_node_attributes, _load_tiffs, load_ctc_data
 
-__all__ = ["load_ctc_data", "_check_ctc", "_load_tiffs", "_get_node_attributes"]
+__all__ = ["_check_ctc", "_get_node_attributes", "_load_tiffs", "load_ctc_data"]

src/traccuracy/matchers/__init__.py

@@ -31,4 +31,4 @@
 from ._ctc import CTCMatcher
 from ._iou import IOUMatcher
 
-__all__ = ["CTCMatcher", "IOUMatcher", "get_labels_with_overlap", "Matched"]
+__all__ = ["CTCMatcher", "IOUMatcher", "Matched", "get_labels_with_overlap"]

src/traccuracy/metrics/__init__.py

@@ -2,4 +2,4 @@
 from ._divisions import DivisionMetrics
 from ._track_overlap import TrackOverlapMetrics
 
-__all__ = ["CTCMetrics", "DivisionMetrics", "AOGMMetrics", "TrackOverlapMetrics"]
+__all__ = ["AOGMMetrics", "CTCMetrics", "DivisionMetrics", "TrackOverlapMetrics"]

tests/bench.py

@@ -4,6 +4,7 @@
 
 import pandas as pd
 import pytest
+
 from traccuracy.loaders import (
     _check_ctc,
     _get_node_attributes,

tests/loaders/test_ctc.py

@@ -1,6 +1,7 @@
 import os
 
 import pandas as pd
+
 from traccuracy._tracking_graph import TrackingGraph
 from traccuracy.loaders import _ctc
 

tests/matchers/test_base.py

@@ -1,8 +1,7 @@
+from tests.test_utils import get_movie_with_graph
 from traccuracy._tracking_graph import TrackingGraph
 from traccuracy.matchers._base import Matched, Matcher
 
-from tests.test_utils import get_movie_with_graph
-
 
 class DummyMatcher(Matcher):
     def _compute_mapping(

tests/matchers/test_compute_overlap.py

@@ -1,10 +1,10 @@
 import pytest
+
+from tests.test_utils import get_annotated_image
 from traccuracy.matchers._compute_overlap import (
     get_labels_with_overlap,
 )
 
-from tests.test_utils import get_annotated_image
-
 
 @pytest.mark.parametrize("overlap", ["iou", "iogt"])
 def test_get_labels_with_overlap(overlap):

tests/matchers/test_ctc.py

@@ -1,10 +1,10 @@
 import networkx as nx
 import numpy as np
 import pytest
-from traccuracy._tracking_graph import TrackingGraph
-from traccuracy.matchers._ctc import CTCMatcher
 
 from tests.test_utils import get_annotated_movie
+from traccuracy._tracking_graph import TrackingGraph
+from traccuracy.matchers._ctc import CTCMatcher
 
 
 def test_match_ctc():

tests/matchers/test_iou.py

@@ -1,6 +1,8 @@
 import networkx as nx
 import numpy as np
 import pytest
+
+from tests.test_utils import get_annotated_image, get_movie_with_graph
 from traccuracy._tracking_graph import TrackingGraph
 from traccuracy.matchers._iou import (
     IOUMatcher,
@@ -9,8 +11,6 @@
     match_iou,
 )
 
-from tests.test_utils import get_annotated_image, get_movie_with_graph
-
 
 def get_two_to_one(w, h, imw, imh):
     """Basic two cell merge/split

tests/metrics/test_ctc_metrics.py

@@ -2,12 +2,12 @@
 from pathlib import Path
 
 import pytest
+
+from tests.test_utils import get_movie_with_graph, gt_data
 from traccuracy.loaders import load_ctc_data
 from traccuracy.matchers import CTCMatcher
 from traccuracy.metrics import CTCMetrics
 
-from tests.test_utils import get_movie_with_graph, gt_data
-
 ROOT_DIR = Path(__file__).resolve().parents[2]
 
 

tests/metrics/test_divisions.py

@@ -2,13 +2,13 @@
 from pathlib import Path
 
 import pytest
+
+from tests.test_utils import download_gt_data, get_division_graphs
 from traccuracy import TrackingGraph
 from traccuracy.loaders import load_ctc_data
 from traccuracy.matchers import IOUMatcher, Matched
 from traccuracy.metrics._divisions import DivisionMetrics
 
-from tests.test_utils import download_gt_data, get_division_graphs
-
 ROOT_DIR = Path(__file__).resolve().parents[2]
 
 

tests/metrics/test_track_overlap_metrics.py

@@ -2,6 +2,7 @@
 
 import networkx as nx
 import pytest
+
 from traccuracy import TrackingGraph
 from traccuracy.matchers import Matched
 from traccuracy.metrics._track_overlap import TrackOverlapMetrics, _mapping_to_dict

tests/metrics/test_weighted_error_sums.py

@@ -1,4 +1,5 @@
 import pytest
+
 from traccuracy.metrics._ctc import (
     get_weighted_edge_error_sum,
     get_weighted_error_sum,

tests/test_run_metrics.py

@@ -1,10 +1,10 @@
 import pytest
+
+from tests.test_utils import get_movie_with_graph
 from traccuracy import run_metrics
 from traccuracy.matchers._base import Matcher
 from traccuracy.metrics._base import Metric
 
-from tests.test_utils import get_movie_with_graph
-
 
 class DummyMetric(Metric):
     def _compute(self, matched):

tests/test_tracking_graph.py

@@ -2,6 +2,7 @@
 
 import networkx as nx
 import pytest
+
 from traccuracy import EdgeFlag, NodeFlag, TrackingGraph
 
 

tests/test_utils.py

@@ -5,6 +5,7 @@
 import networkx as nx
 import numpy as np
 import skimage as sk
+
 from traccuracy._tracking_graph import TrackingGraph
 from traccuracy.loaders import load_ctc_data
 

tests/track_errors/test_ctc_errors.py

@@ -1,5 +1,6 @@
 import networkx as nx
 import numpy as np
+
 from traccuracy._tracking_graph import EdgeFlag, NodeFlag, TrackingGraph
 from traccuracy.matchers import Matched
 from traccuracy.track_errors._ctc import get_edge_errors, get_vertex_errors

tests/track_errors/test_divisions.py

@@ -1,6 +1,8 @@
 import networkx as nx
 import numpy as np
 import pytest
+
+from tests.test_utils import get_division_graphs
 from traccuracy import NodeFlag, TrackingGraph
 from traccuracy.matchers import Matched
 from traccuracy.track_errors.divisions import (
@@ -11,8 +13,6 @@
     _get_succ_by_t,
 )
 
-from tests.test_utils import get_division_graphs
-
 
 @pytest.fixture
 def g():