[med-svn] [Git][med-team/macsyfinder][master] 2 commits: Add patch to fix random failure on systems with specific configuration (Closes: #1028774)

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / macsyfinder


Commits:
4cdf3fbb by Nilesh Patra at 2023-01-16T08:41:32+05:30
Add patch to fix random failure on systems with specific configuration (Closes: #1028774)

- - - - -
91126442 by Nilesh Patra at 2023-01-16T08:42:20+05:30
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/join-threads-for-concurrency.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,9 +1,15 @@
-macsyfinder (2.0-2) UNRELEASED; urgency=medium
+macsyfinder (2.0-2) unstable; urgency=medium
 
+  [ Andreas Tille ]
   * Team upload.
   * Create sensible upstream source filename
 
- -- Andreas Tille <tille at debian.org>  Tue, 20 Sep 2022 09:57:19 +0200
+  [ Nilesh Patra ]
+  * Bump Standards-Version to 4.6.2 (no changes needed)
+  * Add patch to fix random failure on systems with
+    specific configuration (Closes: #1028774)
+
+ -- Nilesh Patra <nilesh at debian.org>  Mon, 16 Jan 2023 08:42:05 +0530
 
 macsyfinder (2.0-1) unstable; urgency=medium
 


=====================================
debian/patches/join-threads-for-concurrency.patch
=====================================
@@ -0,0 +1,35 @@
+Description: The unpatched code does not make much sense as this is iterating over all threads
+ and later joining one of them. Instead keep joining rest of the threads, as was likely the intention
+Author: Nilesh Patra <nilesh at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1028774
+Forwarded: https://github.com/gem-pasteur/macsyfinder/issues/58
+Last-Update: 2023-01-16
+--- a/tests/test_Report.py
++++ b/tests/test_Report.py
+@@ -370,7 +370,7 @@
+         for t in threading.enumerate():
+             if t is main_thread:
+                 continue
+-        t.join()
++            t.join()
+ 
+         #          gene, model,     hit_id,        hit_seq_length replicon_name, pos_hit, i_eval,  score,
+         #          profile_coverage, sequence_coverage, begin_match, end_match
+@@ -461,7 +461,7 @@
+         for t in threading.enumerate():
+             if t is main_thread:
+                 continue
+-        t.join()
++            t.join()
+ 
+         #          gene, model,     hit_id,        hit_seq_length replicon_name, pos_hit, i_eval,  score,
+         #          profile_coverage, sequence_coverage, begin_match, end_match
+@@ -540,7 +540,7 @@
+         for t in threading.enumerate():
+             if t is main_thread:
+                 continue
+-        t.join()
++            t.join()
+ 
+         #          gene, model,     hit_id,        hit_seq_length replicon_name, pos_hit, i_eval,  score,
+         #          profile_coverage, sequence_coverage, begin_match, end_match


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ skip_failing_test.patch
 privacy
 fix-test-parse.patch
 do_not_test_parse_model_old_syntax.patch
+join-threads-for-concurrency.patch



View it on GitLab: https://salsa.debian.org/med-team/macsyfinder/-/compare/94dc7bcb4b612903d33699d7c27cf1667e93e901...91126442f92960a79501783ff9d2a4e3fa5bea6d

-- 
View it on GitLab: https://salsa.debian.org/med-team/macsyfinder/-/compare/94dc7bcb4b612903d33699d7c27cf1667e93e901...91126442f92960a79501783ff9d2a4e3fa5bea6d
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