[med-svn] [Git][med-team/kaptive][master] 3 commits: Revert "Removed workaround with singlethread mode in autopkgtest since bug #970344 was resolved"

[Aaron M. Ucko]

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 <tille at debian.org>  Mon, 21 Sep 2020 07:56:29 +0200
+ -- Aaron M. Ucko <ucko at debian.org>  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
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