MDAnalysis fails with Cython 3.1.0

[IAlibay]

Originally reported and debugged by @yuxuanzhuang

We're getting Pytest worker crashes with Cython 3.1, see: https://github.com/MDAnalysis/mdanalysis/actions/runs/15360620736/job/43227245666?pr=5055

Pinning to <3.1 seems to be fixing the problem, see #5056

[tylerjereddy]

Everything seems "ok" (full suite passes) in a pip/PyPI-centric environment with Python 3.13.2 and Cython 3.1.1 locally on x86_64 Linux. Perhaps conda-land specific?

[yuxuanzhuang]

It turns out the crash is caused by both Cython and coverage.

Disabling line tracing in the Cython build prevents the crash: https://github.com/yuxuanzhuang/mdanalysis/actions/runs/15505516411/job/43659816415?pr=8

related cython/cython#6658

[minowau]

Is this issue still open. Please let me know.