Karsten Schöke pushed to branch master at Debian Med / pychopper
Commits: 9a11d314 by Karsten Schöke at 2026-05-15T15:02:08+02:00 try to fix FTBS Insert Handle-parasail-Result-objects-without-traceback.patch - - - - - 3 changed files: - debian/changelog - + debian/patches/Handle-parasail-Result-objects-without-traceback.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +pychopper (2.7.10-3) UNRELEASED; urgency=medium + + * Team upload + * Handle-parasail-Result-objects-without-traceback.patch: New + try to fix FTBS + + -- Karsten Schöke <[email protected]> Fri, 15 May 2026 14:54:06 +0200 + pychopper (2.7.10-2) unstable; urgency=medium * Team upload ===================================== debian/patches/Handle-parasail-Result-objects-without-traceback.patch ===================================== @@ -0,0 +1,32 @@ +From: =?utf-8?q?Karsten_Sch=C3=B6ke?= <[email protected]> +Date: Fri, 15 May 2026 14:44:54 +0200 +Subject: Handle parasail Result objects without traceback + On some architectures (notably arm64), parasail may return a Result object + without traceback support. In this case, accessing `aln.cigar` raises an + AttributeError, causing the alignment step to fail and abort processing. + . + This change gracefully skips such cases instead of failing the entire run. +Forwarded: not-needed +--- + pychopper/parasail_backend.py | 8 ++++++++ + 1 file changed, 8 insertions(+) + +diff --git a/pychopper/parasail_backend.py b/pychopper/parasail_backend.py +index 8fe608a..1dff062 100644 +--- a/pychopper/parasail_backend.py ++++ b/pychopper/parasail_backend.py +@@ -27,6 +27,14 @@ def process_alignment(aln, query, query_name, aln_params): + res['score'] = aln.score + max_score = float(aln_params['match'] * len(query)) + res['norm_score'] = (max_score - aln.score) / max_score ++ ++ try: ++ cigar = aln.cigar ++ except AttributeError as e: ++ if "no traceback" in str(e): ++ return None ++ raise ++ + fo = first_cigar(aln.cigar.decode.decode()) + res['ref_start'] = aln.cigar.beg_ref + res['ref_end'] = aln.end_ref + 1 ===================================== debian/patches/series ===================================== @@ -1,2 +1,3 @@ fixTests.patch fix-sphinx-scripts-path.patch +Handle-parasail-Result-objects-without-traceback.patch View it on GitLab: https://salsa.debian.org/med-team/pychopper/-/commit/9a11d3147e5c0b86e2c5bdf1ea9855380e99ed4b -- View it on GitLab: https://salsa.debian.org/med-team/pychopper/-/commit/9a11d3147e5c0b86e2c5bdf1ea9855380e99ed4b You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
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