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3.14 free-threading environment, it is likely caused by C-extensions (like pyteomics.cmass or pyyaml) compiled with an outdated version of Cython.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

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Author: Rappsilber Laboratory

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Data verified by PyPI on Sep 3, 2026
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Python >=3.10.1

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Release history Release notifications | RSS feed

This release

1.0.9 This release

16 files

1.0.8

13 files

1.0.7

13 files

1.0.6

13 files

1.0.4

13 files

Pre-release

1.0.3rc1

13 files

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