Issue with Python 3.12.0rc1

[mwtoews]

There is a potential issue with Python 3.12.0rc1 shown here:

  platform linux -- Python 3.12.0rc1, pytest-7.4.0, pluggy-1.2.0
  cachedir: .tox/py312/.pytest_cache
  rootdir: /project
  collected 38 items
  tests/test_index.py ........x............F...............                [ 97%]
  tests/test_tpr.py .                                                      [100%]
  =================================== FAILURES ===================================
  _____________________ IndexSerialization.test_interleaving _____________________
  self = <tests.test_index.IndexSerialization testMethod=test_interleaving>
      def test_interleaving(self) -> None:
          """Streaming against a persisted index without interleaving"""
      
          def data_gen(
              interleaved: bool = True,
          ) -> Iterator[Tuple[int, Tuple[float, float, float, float], int]]:
              for i, (minx, miny, maxx, maxy) in enumerate(self.boxes15):
                  if interleaved:
                      yield (i, (minx, miny, maxx, maxy), 42)
                  else:
                      yield (i, (minx, maxx, miny, maxy), 42)
      
          p = index.Property()
          tname = tempfile.mktemp()
          idx = index.Index(
              tname, data_gen(interleaved=False), properties=p, interleaved=False
          )
          hits1 = sorted(list(idx.intersection((0, 60, 0, 60))))
          self.assertTrue(len(hits1), 10)
          self.assertEqual(hits1, [0, 4, 16, 27, 35, 40, 47, 50, 76, 80])
      
  >       leaves = idx.leaves()
  /project/tests/test_index.py:475: 
  _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
  self = rtree.index.Index(bounds=[-186.673789279, 184.761387556, -96.7177218184, 96.6043699778], size=100)
      def leaves(self):
          leaf_node_count = ctypes.c_uint32()
          p_leafsizes = ctypes.pointer(ctypes.c_uint32())
          p_leafids = ctypes.pointer(ctypes.c_int64())
          pp_childids = ctypes.pointer(ctypes.pointer(ctypes.c_int64()))
      
          pp_mins = ctypes.pointer(ctypes.pointer(ctypes.c_double()))
          pp_maxs = ctypes.pointer(ctypes.pointer(ctypes.c_double()))
          dimension = ctypes.c_uint32(0)
      
          core.rt.Index_GetLeaves(
              self.handle,
              ctypes.byref(leaf_node_count),
              ctypes.byref(p_leafsizes),
              ctypes.byref(p_leafids),
              ctypes.byref(pp_childids),
              ctypes.byref(pp_mins),
              ctypes.byref(pp_maxs),
              ctypes.byref(dimension),
          )
      
          output = []
      
          count = leaf_node_count.value
          sizes = ctypes.cast(p_leafsizes, ctypes.POINTER(ctypes.c_uint32 * count))
          ids = ctypes.cast(p_leafids, ctypes.POINTER(ctypes.c_int64 * count))
          child = ctypes.cast(
              pp_childids, ctypes.POINTER(ctypes.POINTER(ctypes.c_int64) * count)
          )
          mins = ctypes.cast(
              pp_mins, ctypes.POINTER(ctypes.POINTER(ctypes.c_double) * count)
          )
          maxs = ctypes.cast(
              pp_maxs, ctypes.POINTER(ctypes.POINTER(ctypes.c_double) * count)
          )
          for i in range(count):
              p_child_ids = child.contents[i]
      
              id = ids.contents[i]
              size = sizes.contents[i]
              child_ids_array = ctypes.cast(
                  p_child_ids, ctypes.POINTER(ctypes.c_int64 * size)
              )
      
              child_ids = []
              for j in range(size):
  >               child_ids.append(child_ids_array.contents[j])
  E               ValueError: NULL pointer access
  /project/rtree/index.py:1311: ValueError
  =============================== warnings summary ===============================
  tests/test_index.py::IndexSerialization::test_interleaving
    /project/rtree/index.py:283: DeprecationWarning: index.get_size() is deprecated, use len(index) instead
      warnings.warn(
  -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
  =========================== short test summary info ============================
  FAILED tests/test_index.py::IndexSerialization::test_interleaving - ValueErro...
  ============== 1 failed, 36 passed, 1 xfailed, 1 warning in 0.62s ==============

It's possible this is a Python issue rather than with rtree. It would be nice to resolve before Python 3.12.0 is finalized.

[musicinmybrain]

From the Fedora package (for which I which I just took over as primary maintainer), it looks like this worked fine up through 3.12.0b4, and was probably broken by a change in 3.12.0rc1.

[musicinmybrain]

The code here does look superficially similar to the reproducer in python/cpython#107940.

[mwtoews]

Thanks for the xrefs @musicinmybrain it seems well reported upstream, hopefully it will be resolved by rc2.

[musicinmybrain]

I confirm this is fixed by Python 3.12.0rc2.

[mwtoews]

Thanks for checking @musicinmybrain !