Aaron M. Ucko pushed to branch master at Debian Med / kaptive
Commits: 84098a09 by Aaron M. Ucko at 2021-04-09T17:39:09-04:00 Revert "Removed workaround with singlethread mode in autopkgtest since bug #970344 was resolved" This reverts commit 2be57b96a8671bebd6597f2fa3d27769b578df3c. Per on arm64), and we should keep new changes minimal at this point in the release cycle. Leave a changelog stub. - - - - - 2fdf56cf by Aaron M. Ucko at 2021-04-09T18:03:05-04:00 Add debian/patches/extend_bad_versions (#986592). Extend the range of tblastn versions that might not be entirely stable with multiple threads through 2.11.x, switching to a regular expression along the way. - - - - - 83b9e367 by Aaron M. Ucko at 2021-04-09T18:08:17-04:00 Finalize kaptive 0.7.3-2 for unstable, urgency high per #986592. Team upload. - - - - - 4 changed files: - debian/changelog - + debian/patches/extend_bad_versions - debian/patches/series - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,9 +1,12 @@ -kaptive (0.7.3-2) UNRELEASED; urgency=medium +kaptive (0.7.3-2) unstable; urgency=high - * Removed workaround with singlethread mode in autopkgtest since - bug #970344 was resolved + * Team upload. + * debian/patches/extend_bad_versions: Extend the range of tblastn + versions that might not be entirely stable with multiple threads + through 2.11.x, switching to a regular expression along the way. + (Closes: #986592.) - -- Andreas Tille <[email protected]> Mon, 21 Sep 2020 07:56:29 +0200 + -- Aaron M. Ucko <[email protected]> Fri, 09 Apr 2021 18:08:16 -0400 kaptive (0.7.3-1) unstable; urgency=medium ===================================== debian/patches/extend_bad_versions ===================================== @@ -0,0 +1,19 @@ +--- a/kaptive.py ++++ b/kaptive.py +@@ -49,6 +49,7 @@ import fcntl + import gzip + import copy + import random ++import re + from collections import OrderedDict + from Bio import SeqIO + +@@ -912,7 +913,7 @@ def get_blast_hits(database, query, thre + # A known crash can occur with tblastn and recent versions of BLAST+ when multiple threads + # are used. Check for this case and display an informative error message if so. + version = get_blast_version(command[0]) +- bad_version = (version == '2.4.0') or (version == '2.5.0') or (version == '2.6.0') ++ bad_version = re.match(r'2\.(?:[4-9]|1[01])\.\d+$', version) + if threads > 1 and bad_version: + msg += '\nYou are using BLAST+ v' + version + ' which may crash when running with ' + msg += 'multiple threads.\n\n' ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ blastdb_4 +extend_bad_versions ===================================== debian/tests/run-unit-test ===================================== @@ -14,4 +14,6 @@ cd "${AUTOPKGTEST_TMP}" gunzip -r * -kaptive.py -a exact_match.fasta -k /usr/share/${pkg}/reference_database/Klebsiella_k_locus_primary_reference.gbk -o output/test +echo "FIXME: Due to bug #970344 we are using single threaded mode (-t 1) here." +kaptive.py -t 1 -a exact_match.fasta -k /usr/share/${pkg}/reference_database/Klebsiella_k_locus_primary_reference.gbk -o output/test +echo "FIXME: Make sure to remove '-t 1' from the kaptive call once bug #970344 is fixed." View it on GitLab: https://salsa.debian.org/med-team/kaptive/-/compare/2be57b96a8671bebd6597f2fa3d27769b578df3c...83b9e367940a3e606c145c23c7d382f11b2e885a -- View it on GitLab: https://salsa.debian.org/med-team/kaptive/-/compare/2be57b96a8671bebd6597f2fa3d27769b578df3c...83b9e367940a3e606c145c23c7d382f11b2e885a You're receiving this email because of your account on salsa.debian.org.
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