[med-svn] [Git][med-team/pychopper][master] try to fix FTBS

[Karsten Schöke (@karso)]

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 <karsten.schoeke at geobasis-bb.de>  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?= <karsten.schoeke at geobasis-bb.de>
+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
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