chore: Update pybind11 submodule to commit 3e9dfa2

cpp/prtree.h

@@ -51,36 +51,38 @@ namespace py = pybind11;
 template <class T>
 using vec = std::vector<T>;
 
-template <typename Sequence >
-inline py::array_t<typename Sequence::value_type> as_pyarray(Sequence& seq) {
+template <typename Sequence>
+inline py::array_t<typename Sequence::value_type> as_pyarray(Sequence &seq)
+{
 
   auto size = seq.size();
   auto data = seq.data();
   std::unique_ptr<Sequence> seq_ptr = std::make_unique<Sequence>(std::move(seq));
-  auto capsule = py::capsule(seq_ptr.get(), [](void *p) { std::unique_ptr<Sequence>(reinterpret_cast<Sequence*>(p)); });
+  auto capsule = py::capsule(seq_ptr.get(), [](void *p)
+                             { std::unique_ptr<Sequence>(reinterpret_cast<Sequence *>(p)); });
   seq_ptr.release();
   return py::array(size, data, capsule);
 }
 
 template <typename T>
-auto list_list_to_arrays(vec<vec<T>> out_ll){
+auto list_list_to_arrays(vec<vec<T>> out_ll)
+{
   vec<T> out_s;
   out_s.reserve(out_ll.size());
   std::size_t sum = 0;
-  for (auto &&i : out_ll) {
+  for (auto &&i : out_ll)
+  {
     out_s.push_back(i.size());
     sum += i.size();
   }
   vec<T> out;
   out.reserve(sum);
-  for(const auto &v: out_ll)
+  for (const auto &v : out_ll)
     out.insert(out.end(), v.begin(), v.end());
 
   return make_tuple(
-      std::move(as_pyarray(out_s))
-      ,
-      std::move(as_pyarray(out))
-  );
+      std::move(as_pyarray(out_s)),
+      std::move(as_pyarray(out)));
 }
 
 template <class T, size_t StaticCapacity>
@@ -242,7 +244,7 @@ class BB
     }
     for (int i = 0; i < D; ++i)
     {
-      flags[i] = -minima[i] < maxima[i];
+      flags[i] = -minima[i] <= maxima[i];
     }
     for (int i = 0; i < D; ++i)
     {
@@ -1291,7 +1293,8 @@ class PRTree
     return out;
   }
 
-  auto find_all_array(const py::array_t<float> &x){
+  auto find_all_array(const py::array_t<float> &x)
+  {
     return list_list_to_arrays(std::move(find_all(x)));
   }
 
@@ -1334,6 +1337,7 @@ class PRTree
     };
 
     bfs<T, B, D>(std::move(find_func), flat_tree, target);
+    std::sort(out.begin(), out.end());
     return out;
   }
 

requirements.txt

@@ -1,3 +1,3 @@
-numpy>=1.16
+numpy>=1.16,<2.0
 pybind11; platform_machine != "x86_64" and platform_machine != "amd64" and platform_machine != "AMD64" and sys_platform == 'darwin'  # for m1 mac
 cmake; platform_machine != "x86_64" and platform_machine != "amd64" and platform_machine != "AMD64" and sys_platform == 'darwin'  # for m1 mac

setup.py

@@ -9,7 +9,7 @@
 from setuptools import Extension, find_packages, setup
 from setuptools.command.build_ext import build_ext
 
-version = "v0.6.0"
+version = "v0.6.1"
 
 sys.path.append("./tests")
 
@@ -109,6 +109,10 @@ def build_extension(self, ext):
     classifiers=[
         "License :: OSI Approved :: MIT License",
         "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
     ],
 )

tests/test_PRTree.py

@@ -139,3 +139,32 @@ def test_obj(seed, PRTree, dim, tmp_path):
     idx = prtree.query(q)
     return_obj = prtree2.query(q, return_obj=True)
     assert set(return_obj) == set([obj[i] for i in idx])
+
+
+def test_readme():
+    idxes = np.array([1, 2])
+    rects = np.array([[0.0, 0.0, 1.0, 0.5], [1.0, 1.5, 1.2, 3.0]])
+    prtree = PRTree2D(idxes, rects)
+
+    # batch query
+    q = np.array([[0.5, 0.2, 0.6, 0.3], [0.8, 0.5, 1.5, 3.5]])
+    result = prtree.batch_query(q)
+    assert result == [[1], [1, 2]]
+
+    # Insert
+    prtree.insert(3, [1.0, 1.0, 2.0, 2.0])
+    q = np.array([[0.5, 0.2, 0.6, 0.3], [0.8, 0.5, 1.5, 3.5]])
+    result = prtree.batch_query(q)
+    assert result == [[1], [1, 2, 3]]
+
+    # Erase
+    prtree.erase(2)
+    result = prtree.batch_query(q)
+    assert result == [[1], [1, 3]]
+
+    # non-batch query
+    assert prtree.query([0.5, 0.5, 1.0, 1.0]) == [1, 3]
+
+    # point query
+    assert prtree.query([0.5, 0.5]) == [1]
+    assert prtree.query(0.5, 0.5) == [1]