Merge branch 'master' into update-spidx-2.0.0

.pre-commit-config.yaml

@@ -1,25 +1,27 @@
+ci:
+  autoupdate_schedule: quarterly
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
-    -   id: check-yaml
-    -   id: end-of-file-fixer
-    -   id: trailing-whitespace
+    - id: check-yaml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
   - repo: https://github.com/python-jsonschema/check-jsonschema
     rev: 0.27.3
     hooks:
-    -   id: check-github-workflows
-        args: ["--verbose"]
-  - repo: https://github.com/psf/black
-    rev: 23.9.1
-    hooks:
-    -   id: black
+    - id: check-github-workflows
+      args: ["--verbose"]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.291
+    rev: v0.5.0
     hooks:
-    -   id: ruff
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.5.1
     hooks:
-    -   id: mypy
-        exclude: 'docs/.'
+    - id: mypy
+      exclude: 'docs/.'

pyproject.toml

@@ -48,10 +48,6 @@ version = {attr = "rtree.__version__"}
 [tool.setuptools.package-data]
 rtree = ["py.typed"]
 
-[tool.black]
-target-version = ["py38", "py39", "py310", "py311", "py312"]
-color = true
-
 [tool.cibuildwheel]
 build = "cp38-*"
 build-verbosity = 3
@@ -96,11 +92,14 @@ exclude_lines = [
     "@overload",
 ]
 
-[tool.isort]
-profile = "black"
-known_first_party = ["rtree"]
-skip_gitignore = true
-color_output = true
+[tool.ruff.lint]
+select = [
+    "E", "W",  # pycodestyle
+    "F",   # Pyflakes
+    "UP",  # pyupgrade
+    "I",   # isort
+    "NPY",  # NumPy-specific
+]
 
 [tool.mypy]
 exclude = ["docs", "build"]

rtree/__init__.py

@@ -4,6 +4,7 @@
 Rtree provides Python bindings to libspatialindex for quick
 hyperrectangular intersection queries.
 """
+
 from __future__ import annotations
 
 __version__ = "1.2.0"

rtree/exceptions.py

@@ -3,4 +3,5 @@
 
 class RTreeError(Exception):
     "RTree exception, indicates a RTree-related error."
+
     pass

rtree/finder.py

@@ -1,6 +1,7 @@
 """
 Locate `libspatialindex` shared library and header files.
 """
+
 from __future__ import annotations
 
 import ctypes

rtree/index.py

@@ -246,7 +246,7 @@ def __init__(self, *args: Any, **kwargs: Any) -> None:
 
             d = os.path.dirname(p)
             if not os.access(d, os.W_OK):
-                message = "Unable to open file '%s' for index storage" % f
+                message = f"Unable to open file '{f}' for index storage"
                 raise OSError(message)
         elif storage:
             self.properties.storage = RT_Custom
@@ -296,9 +296,7 @@ def __len__(self) -> int:
             return 0
 
     def __repr__(self) -> str:
-        return "rtree.index.Index(bounds={}, size={})".format(
-            self.bounds, self.get_size()
-        )
+        return f"rtree.index.Index(bounds={self.bounds}, size={self.get_size()})"
 
     def __getstate__(self) -> dict[str, Any]:
         state = self.__dict__.copy()
@@ -575,18 +573,17 @@ def _countTP(
         return p_num_results.value
 
     @overload
-    def contains(self, coordinates: Any, objects: Literal[True]) -> Iterator[Item]:
-        ...
+    def contains(self, coordinates: Any, objects: Literal[True]) -> Iterator[Item]: ...
 
     @overload
     def contains(
         self, coordinates: Any, objects: Literal[False] = False
-    ) -> Iterator[int] | None:
-        ...
+    ) -> Iterator[int] | None: ...
 
     @overload
-    def contains(self, coordinates: Any, objects: Literal["raw"]) -> Iterator[object]:
-        ...
+    def contains(
+        self, coordinates: Any, objects: Literal["raw"]
+    ) -> Iterator[object]: ...
 
     def contains(
         self, coordinates: Any, objects: bool | Literal["raw"] = False
@@ -724,20 +721,19 @@ def __or__(self, other: Index) -> Index:
         return new_idx
 
     @overload
-    def intersection(self, coordinates: Any, objects: Literal[True]) -> Iterator[Item]:
-        ...
+    def intersection(
+        self, coordinates: Any, objects: Literal[True]
+    ) -> Iterator[Item]: ...
 
     @overload
     def intersection(
         self, coordinates: Any, objects: Literal[False] = False
-    ) -> Iterator[int]:
-        ...
+    ) -> Iterator[int]: ...
 
     @overload
     def intersection(
         self, coordinates: Any, objects: Literal["raw"]
-    ) -> Iterator[object]:
-        ...
+    ) -> Iterator[object]: ...
 
     def intersection(
         self, coordinates: Any, objects: bool | Literal["raw"] = False
@@ -952,20 +948,17 @@ def _nearest_obj(self, coordinates, num_results, objects):
     @overload
     def nearest(
         self, coordinates: Any, num_results: int, objects: Literal[True]
-    ) -> Iterator[Item]:
-        ...
+    ) -> Iterator[Item]: ...
 
     @overload
     def nearest(
         self, coordinates: Any, num_results: int, objects: Literal[False] = False
-    ) -> Iterator[int]:
-        ...
+    ) -> Iterator[int]: ...
 
     @overload
     def nearest(
         self, coordinates: Any, num_results: int, objects: Literal["raw"]
-    ) -> Iterator[object]:
-        ...
+    ) -> Iterator[object]: ...
 
     def nearest(
         self,
@@ -2104,7 +2097,7 @@ def __init__(self, *args: Any, **kwargs: Any) -> None:
                 or isinstance(args[0], bytes)
                 or isinstance(args[0], ICustomStorage)
             ):
-                raise ValueError("%s supports only in-memory indexes" % self.__class__)
+                raise ValueError(f"{self.__class__} supports only in-memory indexes")
         self._objects: dict[int, tuple[int, object]] = {}
         return super().__init__(*args, **kwargs)
 
@@ -2171,14 +2164,12 @@ def insert(self, obj: object, coordinates: Any) -> None:  # type: ignore[overrid
     add = insert  # type: ignore[assignment]
 
     @overload  # type: ignore[override]
-    def intersection(self, coordinates: Any, bbox: Literal[True]) -> Iterator[Item]:
-        ...
+    def intersection(self, coordinates: Any, bbox: Literal[True]) -> Iterator[Item]: ...
 
     @overload
     def intersection(
         self, coordinates: Any, bbox: Literal[False] = False
-    ) -> Iterator[object]:
-        ...
+    ) -> Iterator[object]: ...
 
     def intersection(
         self, coordinates: Any, bbox: bool = False
@@ -2252,14 +2243,12 @@ def intersection(
     @overload  # type: ignore[override]
     def nearest(
         self, coordinates: Any, num_results: int = 1, bbox: Literal[True] = True
-    ) -> Iterator[Item]:
-        ...
+    ) -> Iterator[Item]: ...
 
     @overload
     def nearest(
         self, coordinates: Any, num_results: int = 1, bbox: Literal[False] = False
-    ) -> Iterator[object]:
-        ...
+    ) -> Iterator[object]: ...
 
     def nearest(
         self, coordinates: Any, num_results: int = 1, bbox: bool = False
@@ -2367,5 +2356,5 @@ def leaves(self):
                 [self._objects[child_id][1] for child_id in child_ids],
                 bounds,
             )
-            for id, child_ids, bounds in super(RtreeContainer, self).leaves()
+            for id, child_ids, bounds in super().leaves()
         ]

scripts/repair_wheel.py

@@ -18,7 +18,7 @@ def main():
         os_ = "windows"
     else:
         raise NotImplementedError(
-            "sys.platform '{}' is not supported yet.".format(sys.platform)
+            f"sys.platform '{sys.platform}' is not supported yet."
         )
 
     p = argparse.ArgumentParser(

tests/test_index.py

@@ -256,7 +256,7 @@ def test_objects(self) -> None:
         hit = [h for h in hits if h.id == 4321][0]
         self.assertEqual(hit.id, 4321)
         self.assertEqual(hit.object, 42)
-        box = ["%.10f" % t for t in hit.bbox]
+        box = [f"{t:.10f}" for t in hit.bbox]
         expected = ["34.3776829412", "26.7375853734", "49.3776829412", "41.7375853734"]
         self.assertEqual(box, expected)
 

tests/test_tpr.py

@@ -7,6 +7,7 @@
 from typing import Any, Iterator
 
 import numpy as np
+from numpy.random import default_rng
 
 from rtree.index import Index, Property, RT_TPRTree
 
@@ -79,16 +80,18 @@ def data_generator(
     max_x: int = 1,
     max_y: int = 1,
 ) -> Iterator[tuple[str, int, Any]]:
+    rng = default_rng()
+
     def create_object(
         id_: float, time: float, x: float | None = None, y: float | None = None
     ) -> Cartesian:
         # Create object with random or defined x, y and random velocity
         if x is None:
-            x = np.random.uniform(min_x, max_x)
+            x = rng.uniform(min_x, max_x)
         if y is None:
-            y = np.random.uniform(min_y, max_y)
-        speed = np.random.uniform(min_speed, max_speed)
-        angle = np.random.uniform(-np.pi, np.pi)
+            y = rng.uniform(min_y, max_y)
+        speed = rng.uniform(min_speed, max_speed)
+        angle = rng.uniform(-np.pi, np.pi)
         x_vel, y_vel = speed * np.cos(angle), speed * np.sin(angle)
 
         # Set update time for when out of bounds, or max interval
@@ -123,9 +126,9 @@ def create_object(
                     continue
                 kill = object_.out_of_bounds
             else:
-                id_ = np.random.randint(0, dataset_size)
+                id_ = rng.integers(0, dataset_size)
                 while id_ in updated_ids:
-                    id_ = np.random.randint(0, dataset_size)
+                    id_ = rng.integers(0, dataset_size)
                 object_ = objects[id_]
 
             updated_ids.add(object_.id)
@@ -144,12 +147,12 @@ def create_object(
             yield "INSERT", t_now, object_
 
         for _ in range(queries_per_time_step):
-            x = np.random.uniform(min_x, max_x)
-            y = np.random.uniform(min_y, max_y)
-            dx = np.random.uniform(min_query_extent, max_query_extent)
-            dy = np.random.uniform(min_query_extent, max_query_extent)
-            dt = np.random.randint(min_query_interval, max_query_interval + 1)
-            t = np.random.randint(t_now, t_now + horizon - dt)
+            x = rng.uniform(min_x, max_x)
+            y = rng.uniform(min_y, max_y)
+            dx = rng.uniform(min_query_extent, max_query_extent)
+            dy = rng.uniform(min_query_extent, max_query_extent)
+            dt = rng.integers(min_query_interval, max_query_interval + 1)
+            t = rng.integers(t_now, t_now + horizon - dt)
 
             yield "QUERY", t_now, QueryCartesian(t, t + dt, x, y, dx, dy)