TST: test_extending failures on free-threaded Windows wheel build #22039
Description
Observed for a test wheel build in gh-22024; sample log for the three test failures: https://github.com/scipy/scipy/actions/runs/12240251798/job/34142804841?pr=22024
FAILED linalg/tests/test_extending.py::test_cython - subprocess.CalledProcessError: Command '['meson', 'compile', '-vv']' returned non-zero exit status 1.
FAILED optimize/tests/test_extending.py::test_cython - subprocess.CalledProcessError: Command '['meson', 'compile', '-vv']' returned non-zero exit status 1.
FAILED special/tests/test_extending.py::test_cython - subprocess.CalledProcessError: Command '['meson', 'compile', '-vv']' returned non-zero exit status 1.
A sample of 1 of the 3 tracebacks is below the fold. Each failure scenario seems to ultimately involve a missing .pxd file it seems.
Details
_________________________________ test_cython _________________________________
..\venv-test\Lib\site-packages\scipy\special\tests\test_extending.py:19: in test_cython
extensions, extensions_cpp = _test_cython_extension(tmp_path, srcdir)
srcdir = 'C:\\Users\\runneradmin\\AppData\\Local\\Temp\\cibw-run-hxclyq60\\cp313t-win_amd64\\venv-test\\Lib\\site-packages\\scipy\\special'
tmp_path = WindowsPath('C:/Users/runneradmin/AppData/Local/Temp/pytest-of-runneradmin/pytest-0/test_cython2')
..\venv-test\Lib\site-packages\scipy\_lib\_testutils.py:316: in _test_cython_extension
subprocess.check_call(["meson", "compile", "-vv"], cwd=target_dir)
build_dir = WindowsPath('C:/Users/runneradmin/AppData/Local/Temp/pytest-of-runneradmin/pytest-0/test_cython2/3216/special/tests/_cython_examples')
f = <_io.TextIOWrapper name='C:\\Users\\runneradmin\\AppData\\Local\\Temp\\pytest-of-runneradmin\\pytest-0\\test_cython2\\3216\\special\\tests\\_cython_examples\\interpreter-native-file.ini' mode='w' encoding='cp1252'>
mod_name = 'special'
native_file = 'C:\\Users\\runneradmin\\AppData\\Local\\Temp\\pytest-of-runneradmin\\pytest-0\\test_cython2\\3216\\special\\tests\\_cython_examples\\interpreter-native-file.ini'
pytest = <module 'pytest' from 'C:\\Users\\runneradmin\\AppData\\Local\\Temp\\cibw-run-hxclyq60\\cp313t-win_amd64\\venv-test\\Lib\\site-packages\\pytest\\__init__.py'>
srcdir = 'C:\\Users\\runneradmin\\AppData\\Local\\Temp\\cibw-run-hxclyq60\\cp313t-win_amd64\\venv-test\\Lib\\site-packages\\scipy\\special'
target_dir = WindowsPath('C:/Users/runneradmin/AppData/Local/Temp/pytest-of-runneradmin/pytest-0/test_cython2/3216/special/tests/_cython_examples/build')
tmp_path = WindowsPath('C:/Users/runneradmin/AppData/Local/Temp/pytest-of-runneradmin/pytest-0/test_cython2/3216')
..\..\..\..\pypa\cibuildwheel\Cache\nuget-cpython\python-freethreaded.3.13.0\tools\Lib\subprocess.py:419: in check_call
raise CalledProcessError(retcode, cmd)
E subprocess.CalledProcessError: Command '['meson', 'compile', '-vv']' returned non-zero exit status 1.
cmd = ['meson', 'compile', '-vv']
kwargs = {'cwd': WindowsPath('C:/Users/runneradmin/AppData/Local/Temp/pytest-of-runneradmin/pytest-0/test_cython2/3216/special/tests/_cython_examples/build')}
popenargs = (['meson', 'compile', '-vv'],)
retcode = 1
---------------------------- Captured stdout call -----------------------------
1.6.99
The Meson build system
Version: 1.6.99
Source dir: C:\Users\runneradmin\AppData\Local\Temp\pytest-of-runneradmin\pytest-0\test_cython2\3216\special\tests\_cython_examples
Build dir: C:\Users\runneradmin\AppData\Local\Temp\pytest-of-runneradmin\pytest-0\test_cython2\3216\special\tests\_cython_examples\build
Build type: native build
Project name: random-build-examples
Project version: undefined
Activating VS 16.11.42
C compiler for the host machine: cl (msvc 19.29.30157 "Microsoft (R) C/C++ Optimizing Compiler Version 19.29.30157 for x64")
C linker for the host machine: link link 14.29.30157.0
C++ compiler for the host machine: cl (msvc 19.29.30157 "Microsoft (R) C/C++ Optimizing Compiler Version 19.29.30157 for x64")
C++ linker for the host machine: link link 14.29.30157.0
Cython compiler for the host machine: cython (cython 3.1.0)
Host machine cpu family: x86_64
Host machine cpu: x86_64
Program python found: YES (C:\Users\runneradmin\AppData\Local\Temp\cibw-run-hxclyq60\cp313t-win_amd64\venv-test\Scripts\python.exe)
Run-time dependency python found: YES 3.13
Build targets in project: 3
random-build-examples undefined
User defined options
Native files: C:\Users\runneradmin\AppData\Local\Temp\pytest-of-runneradmin\pytest-0\test_cython2\3216\special\tests\_cython_examples\interpreter-native-file.ini
buildtype : release
vsenv : true
Found ninja-1.11.1.git.kitware.jobserver-1 at C:\Users\runneradmin\AppData\Local\Temp\cibw-run-hxclyq60\cp313t-win_amd64\build\venv\Scripts\ninja.EXE
Visual Studio environment is needed to run Ninja. It is recommended to use Meson wrapper:
C:\Users\runneradmin\AppData\Local\Temp\cibw-run-hxclyq60\cp313t-win_amd64\build\venv\Scripts\meson compile -C .
[1/7] "C:\Users\runneradmin\AppData\Local\Temp\cibw-run-hxclyq60\cp313t-win_amd64\build\venv\Scripts\meson" "--internal" "copy" "../extending.pyx" "extending_cpp.pyx"
[2/7] "cython" "-M" "--fast-fail" "-3" C:/Users/runneradmin/AppData/Local/Temp/pytest-of-runneradmin/pytest-0/test_cython2/3216/special/tests/_cython_examples/extending.pyx -o extending.cp313t-win_amd64.pyd.p/extending.pyx.c
FAILED: extending.cp313t-win_amd64.pyd.p/extending.pyx.c
"cython" "-M" "--fast-fail" "-3" C:/Users/runneradmin/AppData/Local/Temp/pytest-of-runneradmin/pytest-0/test_cython2/3216/special/tests/_cython_examples/extending.pyx -o extending.cp313t-win_amd64.pyd.p/extending.pyx.c
Error compiling Cython file:
------------------------------------------------------------
...
#!/usr/bin/env python3
#cython: language_level=3
#cython: boundscheck=False
#cython: wraparound=False
from scipy.special.cython_special cimport beta, gamma
^
------------------------------------------------------------
C:\Users\runneradmin\AppData\Local\Temp\pytest-of-runneradmin\pytest-0\test_cython2\3216\special\tests\_cython_examples\extending.pyx:6:0: 'scipy\special\cython_special.pxd' not found
[3/7] "cython" "-M" "--fast-fail" "-3" "--cplus" extending_cpp.pyx -o extending_cpp.cp313t-win_amd64.pyd.p/extending_cpp.pyx.cpp
FAILED: extending_cpp.cp313t-win_amd64.pyd.p/extending_cpp.pyx.cpp
"cython" "-M" "--fast-fail" "-3" "--cplus" extending_cpp.pyx -o extending_cpp.cp313t-win_amd64.pyd.p/extending_cpp.pyx.cpp
Error compiling Cython file:
------------------------------------------------------------
...
#!/usr/bin/env python3
#cython: language_level=3
#cython: boundscheck=False
#cython: wraparound=False
from scipy.special.cython_special cimport beta, gamma
^
------------------------------------------------------------
extending_cpp.pyx:6:0: 'scipy\special\cython_special.pxd' not found
ninja: build stopped: subcommand failed.
Activating VS 16.11.42
INFO: automatically activated MSVC compiler environment
INFO: autodetecting backend as ninja
INFO: calculating backend command to run: C:\Users\runneradmin\AppData\Local\Temp\cibw-run-hxclyq60\cp313t-win_amd64\build\venv\Scripts\ninja.EXE -v
The "regular" (not free threaded) 3.13 + Windows version of the wheel build is green. That doesn't necessarily mean that it is a thread-safety issue though, it could also relate to some other aspect -- i.e., free-threaded wheel builds have build isolation disabled, or some other subtle difference in workflow/dep version.