xicommon

Troubleshooting

Segmentation Faults during pytest (Python 3.14 free-threading)

If you encounter segmentation faults when running pytest in a Python 3.14 free-threading environment, it is likely caused by C-extensions (like pyteomics.cmass or pyyaml) compiled with an outdated version of Cython.

Fix: Ensure Cython is at least version 3.3.0 before installing dependencies.

1. Upgrade Cython: pip install "cython>=3.3.0"
2. Reinstall affected packages (e.g., pyteomics) to trigger a rebuild against the new Cython version.

Compilation Error: unknown type name '__pyx_vectorcallfunc'

When running pytest after upgrading Cython, if pyximport fails with a compilation error regarding __pyx_vectorcallfunc in dynamically generated .c files, the .pyxbld cache contains stale C files generated by the old Cython version.

Fix: Clear the pyximport build cache to force regeneration of the C files: rm -rf ~/.pyxbld