[Debian-med-packaging] Bug#1000317: cyvcf2: FTBFS with Python 3.10

[Stefano Rivera]

Source: cyvcf2
Version: 0.30.11-1
Severity: serious
Tags: ftbfs patch
Justification: FTBFS

https://buildd.debian.org/status/fetch.php?pkg=cyvcf2&arch=amd64&ver=0.30.11-1%2Bb1&stamp=1637483151&raw=0

Tests fail with:
======================================================================
ERROR: cyvcf2.tests.test_reader.test_info_dict
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_cyvcf2/build/cyvcf2/tests/test_reader.py", line 226, in test_info_dict
    toks = _get_line_for(variant)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_cyvcf2/build/cyvcf2/tests/test_reader.py", line 459, in _get_line_for
    for i, line in enumerate(gzip.open(VCF_PATH), start=1):
ValueError: readline of closed file

======================================================================
ERROR: cyvcf2.tests.test_reader.test_gt_types
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_cyvcf2/build/cyvcf2/tests/test_reader.py", line 518, in test_gt_types
    o = _get_samples(variant)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_cyvcf2/build/cyvcf2/tests/test_reader.py", line 485, in _get_samples
    toks = _get_line_for(v)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_cyvcf2/build/cyvcf2/tests/test_reader.py", line 459, in _get_line_for
    for i, line in enumerate(gzip.open(VCF_PATH), start=1):
ValueError: readline of closed file

----------------------------------------------------------------------
Ran 95 tests in 0.647s

Should be resolved by applying this patch: https://github.com/brentp/cyvcf2/pull/225

I'll do a 0-day NMU for it.

SR