From 2aadceb016f9590af4cd3ed522fd6e067b655734 Mon Sep 17 00:00:00 2001
From: Talley Lambert <talley.lambert@gmail.com>
Date: Wed, 9 Sep 2026 16:07:11 +0200
Subject: [PATCH] fix: update Cython dependency to avoid ABI collisions and add
 warning for import failures

---
 pyproject.toml                    |  9 ++++++++-
 src/spatial_graph/_rtree/rtree.py | 15 +++++++++++++++
 2 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 62d786b..ac0d95d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,7 +2,14 @@
 requires = [
   "setuptools>=77",
   "setuptools-scm>=8",
-  "Cython>=3.1",
+  # Cython 3.3.0 makes the __pyx_CyFunctionObject layout depend on the
+  # limited-API target (an extra func_is_coroutine field below 0x030B0000)
+  # without reflecting that in the name of the module its shared types live in,
+  # so our cp311 modules collide with any cp310 abi3 module built by the same
+  # Cython -- uharfbuzz >=0.56.1, via pygfx -- and whichever imports second dies
+  # with "Shared Cython type ... has the wrong size". Fixed in cython/cython#7916
+  # (unreleased at time of writing), so this skips the one bad release.
+  "Cython>=3.1,!=3.3.0",
   "CT3>=3.3.3",
   "numpy",  # imported (not linked) while rendering the wrappers
 ]
diff --git a/src/spatial_graph/_rtree/rtree.py b/src/spatial_graph/_rtree/rtree.py
index 8c79055..2ff787a 100644
--- a/src/spatial_graph/_rtree/rtree.py
+++ b/src/spatial_graph/_rtree/rtree.py
@@ -2,6 +2,7 @@
 
 import importlib
 import sys
+import warnings
 from pathlib import Path
 from typing import ClassVar
 
@@ -31,6 +32,20 @@ def _load_prebuilt(
         module = importlib.import_module(f"{PREBUILT_PACKAGE}.{name}")
     except ImportError:
         return None
+    except TypeError as e:  # pragma: no cover
+        # A Cython module already loaded in this process can claim the same
+        # shared-ABI module name as ours while disagreeing about the layout of
+        # the types in it, and the loser of that race is whoever imports second
+        # ("Shared Cython type ... has the wrong size"). Falling back to the JIT
+        # path costs a compiler, but beats taking the process down.
+        warnings.warn(
+            f"Could not import prebuilt {name} ({e}); compiling it instead. "
+            "This usually means another extension module in this process was "
+            "built against an incompatible Cython ABI.",
+            RuntimeWarning,
+            stacklevel=2,
+        )
+        return None
     return module.RTree