使用pytest运行shapely.geometry.box()触发Segmentation fault问题排查

问题复现 #

• 以下代码通过pytest运行时抛出Fatal Python error: Segmentation fault：

from shapely import geometry
def test_geometry_box(self) -> None:
    geom = geometry.box(*[1, 2, 3, 4])

• 但将代码放在独立文件中直接运行完全正常：

from shapely import geometry
geom = geometry.box(*[1, 2, 3, 4])

环境信息 #

• Shapely版本：1.8.4
• 安装方式：通过Poetry使用Shapely = "^1"配置安装

栈追踪信息 #

.../test.py Fatal Python error: Segmentation fault

Thread 0x000000030a67f000 (most recent call first):
  File ".../threading.py", line 316 in wait
  File ".../threading.py", line 581 in wait
  File ".../site-packages/tqdm/_monitor.py", line 60 in run
  File ".../threading.py", line 980 in _bootstrap_inner
  File ".../threading.py", line 937 in _bootstrap

Current thread 0x00000002045dce00 (most recent call first):
  File ".../site-packages/shapely/geometry/polygon.py", line 539 in geos_polygon_from_py
  File ".../site-packages/shapely/geometry/polygon.py", line 261 in __init__
  File ".../site-packages/shapely/geometry/geo.py", line 64 in box
  File "/test.py", line 55 in test_geometry_box
  File ".../site-packages/_pytest/python.py", line 192 in pytest_pyfunc_call
  File ".../site-packages/pluggy/_callers.py", line 39 in _multicall
  File ".../site-packages/pluggy/_manager.py", line 80 in _hookexec
  File ".../site-packages/pluggy/_hooks.py", line 265 in __call__
  File ".../site-packages/_pytest/python.py", line 1761 in runtest
  File ".../site-packages/_pytest/runner.py", line 166 in pytest_runtest_call
  File ".../site-packages/pluggy/_callers.py", line 39 in _multicall
  File ".../site-packages/pluggy/_manager.py", line 80 in _hookexec
  File ".../site-packages/pluggy/_hooks.py", line 265 in __call__
  File ".../site-packages/_pytest/runner.py", line 259 in <lambda>
  File ".../site-packages/_pytest/runner.py", line 338 in from_call
  File ".../site-packages/_pytest/runner.py", line 258 in call_runtest_hook
  File ".../site-packages/_pytest/runner.py", line 219 in call_and_report
  File ".../site-packages/_pytest/runner.py", line 130 in runtestprotocol
  File ".../site-packages/_pytest/runner.py", line 111 in pytest_runtest_protocol
  File ".../site-packages/pluggy/_callers.py", line 39 in _multicall
  File ".../site-packages/pluggy/_manager.py", line 80 in _hookexec
  File ".../site-packages/pluggy/_hooks.py", line 265 in __call__
  File ".../site-packages/_pytest/main.py", line 347 in pytest_runtestloop
  File ".../site-packages/pluggy/_callers.py", line 39 in _multicall
  File ".../site-packages/pluggy/_manager.py", line 80 in _hookexec
  File ".../site-packages/pluggy/_hooks.py", line 265 in __call__
  File ".../site-packages/_pytest/main.py", line 322 in _main
  File ".../site-packages/_pytest/main.py", line 268 in wrap_session
  File ".../site-packages/_pytest/main.py", line 315 in pytest_cmdline_main
  File ".../site-packages/pluggy/_callers.py", line 39 in _multicall
  File ".../site-packages/pluggy/_manager.py", line 80 in _hookexec
  File ".../site-packages/pluggy/_hooks.py", line 265 in __call__
  File ".../site-packages/_pytest/config/__init__.py", line 164 in main
  File ".../site-packages/_pytest/config/__init__.py", line 187 in console_main
  File ".../pytest", line 8 in <module>
zsh: segmentation fault  pytest

原因分析 #

段错误发生在Shapely调用GEOS库创建多边形的底层逻辑中，仅在pytest环境触发的核心原因包括：

• 多线程环境冲突：pytest的测试运行机制（如默认线程复用、并行测试）与Shapely 1.8.4依赖的GEOS库线程安全机制不兼容。栈追踪中出现的tqdm监控线程，可能引发GEOS资源访问的竞争冲突。
• 版本兼容性缺陷：Shapely 1.x系列存在已知的多线程环境下段错误问题，后续2.x版本重构了底层GEOS交互逻辑，已修复这类稳定性问题。
• 依赖版本不匹配：Poetry安装的依赖中，可能存在GEOS库与Shapely版本不兼容的情况，单线程直接运行时掩盖了冲突，但pytest的多线程/多进程环境触发了问题。

解决方案 #

• 升级Shapely版本：将Poetry依赖改为Shapely = "^2.0"，升级到2.x系列，彻底解决线程安全相关的底层问题。
• 禁用pytest并行机制：运行pytest时添加-n 1参数强制单进程运行，或修改pytest.ini配置禁用并行测试，避免多线程环境触发GEOS的线程安全问题。
• 排除tqdm干扰：如果测试中用到tqdm，可以设置环境变量TQDM_DISABLE_MONITOR=1临时禁用其监控线程，消除线程竞争诱因。

内容的提问来源于stack exchange，提问作者Jamie.Sgro