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Change pysam dependency to >=0.24.0 - #666
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pysam 0.24.0 fixes the Python 3.13 + pytest-cov failure (pysam-developers/pysam#1350) that the pysam==0.23.0 pin worked around (#560). Closes #653
korikuzma
approved these changes
Oct 5, 2026
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Closes #653.
Replaces the
pysam==0.23.0pin (#560) withpysam>=0.24.0. pysam 0.23.1–0.23.3 wheels were built with Cython 3.1, which brokepytest-covon Python 3.13 (ValueError: Firing event 10 with no exception setwhen iterating aVariantFile; pysam-developers/pysam#1350). pysam 0.24.0 fixed this.Verified the full suite passes with coverage on Python 3.10–3.13 with pysam 0.24.0 and 0.24.1, and that VCF annotation output is unchanged from 0.23.0.