Dear maintainer, I've prepared an NMU for cyvcf2 (versioned as 0.30.11-1.1). The diff is attached to this message.
Also filed as https://salsa.debian.org/med-team/cyvcf2/-/merge_requests/1 Regards, SR
diff -Nru cyvcf2-0.30.11/debian/changelog cyvcf2-0.30.11/debian/changelog --- cyvcf2-0.30.11/debian/changelog 2021-08-15 07:35:52.000000000 -0400 +++ cyvcf2-0.30.11/debian/changelog 2021-11-21 08:38:57.000000000 -0400 @@ -1,3 +1,11 @@ +cyvcf2 (0.30.11-1.1) unstable; urgency=medium + + * Non-maintainer upload. + * Patch: Python 3.10 support - avoid a regression in gzip file handles + (Closes: #1000317) + + -- Stefano Rivera <stefa...@debian.org> Sun, 21 Nov 2021 08:38:57 -0400 + cyvcf2 (0.30.11-1) unstable; urgency=medium * Fix watch URL diff -Nru cyvcf2-0.30.11/debian/patches/python-3.10.patch cyvcf2-0.30.11/debian/patches/python-3.10.patch --- cyvcf2-0.30.11/debian/patches/python-3.10.patch 1969-12-31 20:00:00.000000000 -0400 +++ cyvcf2-0.30.11/debian/patches/python-3.10.patch 2021-11-21 08:38:57.000000000 -0400 @@ -0,0 +1,46 @@ +From: Stefano Rivera <stef...@rivera.za.net> +Date: Sun, 21 Nov 2021 08:29:40 -0400 +Subject: Avoid a Python 3.10 regression in iterating GzipFiles + +Open the file with a context manager, so we're holding onto a reference to it, for the lifetime of the iteration. + +This avoids hitting https://bugs.python.org/issue45475 which affects python3.10 3.10.0-4 in Debian. + +Bug-Debian: https://bugs.debian.org/1000317 +Forwarded: https://github.com/brentp/cyvcf2/pull/225 +--- + cyvcf2/tests/test_reader.py | 21 +++++++++++---------- + 1 file changed, 11 insertions(+), 10 deletions(-) + +diff --git a/cyvcf2/tests/test_reader.py b/cyvcf2/tests/test_reader.py +index 76cb9f8..f81b920 100644 +--- a/cyvcf2/tests/test_reader.py ++++ b/cyvcf2/tests/test_reader.py +@@ -456,16 +456,17 @@ def test_var_type(): + def _get_line_for(v): + import gzip + +- for i, line in enumerate(gzip.open(VCF_PATH), start=1): +- line = line.decode() +- if line[0] == "#": continue +- toks = line.strip().split("\t") +- if not (toks[0] == v.CHROM and int(toks[1]) == v.POS): continue +- if toks[3] != v.REF: continue +- if toks[4] not in v.ALT: continue +- return toks +- else: +- raise Exception("not found") ++ with gzip.open(VCF_PATH) as f: ++ for i, line in enumerate(f, start=1): ++ line = line.decode() ++ if line[0] == "#": continue ++ toks = line.strip().split("\t") ++ if not (toks[0] == v.CHROM and int(toks[1]) == v.POS): continue ++ if toks[3] != v.REF: continue ++ if toks[4] not in v.ALT: continue ++ return toks ++ else: ++ raise Exception("not found") + + + def _get_samples(v): diff -Nru cyvcf2-0.30.11/debian/patches/series cyvcf2-0.30.11/debian/patches/series --- cyvcf2-0.30.11/debian/patches/series 2021-08-08 07:32:31.000000000 -0400 +++ cyvcf2-0.30.11/debian/patches/series 2021-11-21 08:38:57.000000000 -0400 @@ -1,2 +1,3 @@ add_htslib_link_dependency.patch i386.patch +python-3.10.patch
