PartSegCore-compiled-backend 0.15.14__tar.gz → 0.15.15__tar.gz

{partsegcore_compiled_backend-0.15.14 → partsegcore_compiled_backend-0.15.15}/.pre-commit-config.yaml

@@ -1,10 +1,10 @@
 repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.13.1
+    rev: v0.16.8
     hooks:
       # Run the linter.
-      - id: ruff
+      - id: ruff-check
       # Run the formatter.
       - id: ruff-format
 -   repo: https://github.com/pre-commit/pre-commit-hooks
@@ -22,18 +22,26 @@ repos:
     rev: v1.10.0
     hooks:
     -   id: rst-backticks
--   repo: https://github.com/markdownlint/markdownlint
-    rev: v0.12.0  # Use the ref you want to point at
+-   repo: https://github.com/executablebooks/mdformat
+    rev: 1.0.0  # Use the ref you want to point at
     hooks:
-    - id: markdownlint
+    - id: mdformat
+      exclude: TEST_FAIL_TEMPLATE.md|bug_report.md|feature_request.md
+      args: ["--number"]
+      additional_dependencies:
+          - mdformat-gfm
+          - mdformat-footnote
+          - mdformat-gfm-alerts
+          - mdformat-ruff
+          - mdformat-toc
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.4.1
+    rev: v2.4.3
     hooks:
     - id: codespell
       additional_dependencies:
       - tomli
 -   repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v21.1.1  # Use the sha / tag you want to point at
+    rev: v23.1.1  # Use the sha / tag you want to point at
     hooks:
     - id: clang-format
       args: ["-style=Google"]

{partsegcore_compiled_backend-0.15.14 → partsegcore_compiled_backend-0.15.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: PartSegCore_compiled_backend
-Version: 0.15.14
+Version: 0.15.15
 Summary: PartSegCore compiled backend,
 Keywords: bioimaging
 Author-Email: Grzegorz Bokota <g.bokota@cent.uw.edu.pl>

{partsegcore_compiled_backend-0.15.14 → partsegcore_compiled_backend-0.15.15}/pyproject.toml

@@ -130,9 +130,11 @@ test-command = "pytest {project}/src/tests"
 test-extras = ["test"]
 skip = "pp*macos* pp31* pp39-manylinux*"
 build = "*64"
-enable = ["pypy", "cpython-freethreading"]
+enable = ["pypy"]
 
 [tool.cibuildwheel.macos]
+# libomp (LLVM 23) uses aligned_alloc, available since macOS 10.15
+environment = { MACOSX_DEPLOYMENT_TARGET = "10.15" }
 before-all = [
     "set",
     "bash {project}/build_utils/build_libomp.sh",

{partsegcore_compiled_backend-0.15.14 → partsegcore_compiled_backend-0.15.15}/src/PartSegCore_compiled_backend/triangulation/intersection.hpp

@@ -133,8 +133,12 @@ enum Orientation {
  */
 inline Orientation _orientation(const point::Point& p, const point::Point& q,
                                 const point::Point& r) {
-  double val1 = ((q.y - p.y) * (r.x - q.x));
-  double val2 = ((r.y - q.y) * (q.x - p.x));
+  // Promote to double before multiplying: the float products lose precision
+  // and can flip the result for nearly collinear points.
+  double val1 =
+      (static_cast<double>(q.y) - p.y) * (static_cast<double>(r.x) - q.x);
+  double val2 =
+      (static_cast<double>(r.y) - q.y) * (static_cast<double>(q.x) - p.x);
   // This commented code if for debugging purposes of differences between macOS
   // and linux double val = ((q.y - p.y) * (r.x - q.x)) - ((r.y - q.y) * (q.x -
   // p.x)); if (val!= 0 && val1 == val2) {
@@ -337,15 +341,16 @@ inline std::unordered_set<OrderedPair> _find_intersections(
  */
 inline std::vector<point::Point> _find_intersection(const point::Segment& s1,
                                                     const point::Segment& s2) {
+  // To reduce problems with float precision, the same pair of segments
+  // should always be calculated in the same order.
+  if (s2 < s1) return _find_intersection(s2, s1);
   // ReSharper disable CppJoinDeclarationAndAssignment
-  point::Point::coordinate_t a1, b1, a2, b2, det, x, y, t;
-  //  point::Point::coordinate_t c1, c2, u;
-  a1 = s1.top.y - s1.bottom.y;
-  b1 = s1.bottom.x - s1.top.x;
-  // c1 = a1 * s1.bottom.x + b1 * s1.bottom.y;
-  a2 = s2.top.y - s2.bottom.y;
-  b2 = s2.bottom.x - s2.top.x;
-  // c2 = a2 * s2.bottom.x + b2 * s2.bottom.y;
+  double a1, b1, a2, b2, det, t;
+  point::Point::coordinate_t x, y;
+  a1 = static_cast<double>(s1.top.y) - s1.bottom.y;
+  b1 = static_cast<double>(s1.bottom.x) - s1.top.x;
+  a2 = static_cast<double>(s2.top.y) - s2.bottom.y;
+  b2 = static_cast<double>(s2.bottom.x) - s2.top.x;
   det = a1 * b2 - a2 * b1;
   if (det == 0) {
     // collinear case
@@ -356,15 +361,13 @@ inline std::vector<point::Point> _find_intersection(const point::Segment& s1,
     if (s2.point_on_line(s1.top)) res.push_back(s1.top);
     return res;
   }
-  t = ((s2.top.x - s1.top.x) * (s2.bottom.y - s2.top.y) -
-       (s2.top.y - s1.top.y) * (s2.bottom.x - s2.top.x)) /
+  t = ((static_cast<double>(s2.top.x) - s1.top.x) * -a2 -
+       (static_cast<double>(s2.top.y) - s1.top.y) * b2) /
       det;
-  // u = ((s2.top.x - s1.top.x) * (s1.bottom.y - s1.top.y) -
-  //     (s2.top.y - s1.top.y) * (s2.bottom.x - s2.top.x)) / det;
   if (t < 0) return {s1.top};
   if (t > 1) return {s1.bottom};
-  x = s1.top.x + t * b1;
-  y = s1.top.y + t * (-a1);
+  x = s1.top.x + static_cast<point::Point::coordinate_t>(t * b1);
+  y = s1.top.y + static_cast<point::Point::coordinate_t>(t * (-a1));
   return {{x, y}};
 }
 }  // namespace partsegcore::intersection

partsegcore_compiled_backend-0.15.15/src/PartSegCore_compiled_backend/version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '0.15.15'
+__version_tuple__ = version_tuple = (0, 15, 15)
+
+__commit_id__ = commit_id = 'gc7ec30e77'

partsegcore_compiled_backend-0.15.15/src/tests/data/create_holes_triangulation_failure.txt

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{partsegcore_compiled_backend-0.15.14 → partsegcore_compiled_backend-0.15.15}/src/tests/test_triangulate.py

@@ -1,3 +1,5 @@
+from pathlib import Path
+
 import numpy as np
 import pytest
 from PartSegCore_compiled_backend.triangulate import (
@@ -20,6 +22,8 @@ from PartSegCore_compiled_backend.triangulate import (
     triangulate_polygon_with_edge_numpy_li,
 )
 
+DATA_DIR = Path(__file__).parent / 'data'
+
 
 def test_on_segment():
     assert on_segment((0, 0), (0, 1), (0, 2))
@@ -743,3 +747,15 @@ def test_is_convex_regular_polygon(angle, n_vertex, reverse):
     rot = rotation_matrix(angle)
     rotated_poly = np.dot(poly, rot)
     assert is_convex(rotated_poly)
+
+
+def test_hole_triangulation_precision():
+    # Polygon with two holes (napari single path encoding) from napari/bermuda#194.
+    # Float precision errors in orientation/intersection used to silently drop ~30% of the area.
+    vertices = np.loadtxt(DATA_DIR / 'create_holes_triangulation_failure.txt', dtype=np.float32)
+    triangles, points = triangulate_polygon_numpy_li([vertices])
+    tri_points = points.astype(np.float64)[triangles]
+    v1 = tri_points[:, 1] - tri_points[:, 0]
+    v2 = tri_points[:, 2] - tri_points[:, 0]
+    area = np.abs(v1[:, 0] * v2[:, 1] - v1[:, 1] * v2[:, 0]).sum() / 2
+    assert area == pytest.approx(139420612.3, rel=1e-6)

partsegcore_compiled_backend-0.15.14/src/PartSegCore_compiled_backend/version.py

@@ -1,34 +0,0 @@
-# file generated by setuptools-scm
-# don't change, don't track in version control
-
-__all__ = [
-    "__version__",
-    "__version_tuple__",
-    "version",
-    "version_tuple",
-    "__commit_id__",
-    "commit_id",
-]
-
-TYPE_CHECKING = False
-if TYPE_CHECKING:
-    from typing import Tuple
-    from typing import Union
-
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-    COMMIT_ID = Union[str, None]
-else:
-    VERSION_TUPLE = object
-    COMMIT_ID = object
-
-version: str
-__version__: str
-__version_tuple__: VERSION_TUPLE
-version_tuple: VERSION_TUPLE
-commit_id: COMMIT_ID
-__commit_id__: COMMIT_ID
-
-__version__ = version = '0.15.14'
-__version_tuple__ = version_tuple = (0, 15, 14)
-
-__commit_id__ = commit_id = 'ga18220505'