[med-svn] [Git][med-team/jaligner][master] 8 commits: Create changelog entries

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / jaligner


Commits:
d7e283e5 by Andreas Tille at 2020-07-03T11:37:15+02:00
Create changelog entries

- - - - -
02b3640b by Andreas Tille at 2020-07-03T11:37:51+02:00
routine-update: Standards-Version: 4.5.0

- - - - -
f085b1e8 by Andreas Tille at 2020-07-03T11:37:51+02:00
routine-update: debhelper-compat 13

- - - - -
f75ac2d7 by Andreas Tille at 2020-07-03T11:37:56+02:00
routine-update: Add salsa-ci file

- - - - -
3cb1b7f5 by Andreas Tille at 2020-07-03T11:37:56+02:00
routine-update: Rules-Requires-Root: no

- - - - -
ed265f6d by Andreas Tille at 2020-07-03T11:38:01+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.

Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

- - - - -
ac791a7e by Andreas Tille at 2020-07-03T11:47:51+02:00
Add patch from pull request fixing traceback of global alignments

- - - - -
2988fecb by Andreas Tille at 2020-07-03T11:57:58+02:00
Upload to unstable

- - - - -


7 changed files:

- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/f267efdf3bc29291eddd380bba127b8ed56f2dc2.patch
- + debian/patches/series
- + debian/salsa-ci.yml
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,26 @@
+jaligner (1.0+dfsg-7) unstable; urgency=medium
+
+  [ Steffen Moeller ]
+  * d/u/metadata: yamllint
+
+  [ Pranav Ballaney ]
+  * Install example and reference data
+  * Install docs
+  * Add autopkgtests
+  * Add Pranav Ballaney to Uploaders
+  * Include reference binary
+
+  [ Andreas Tille ]
+  * Standards-Version: 4.5.0 (routine-update)
+  * debhelper-compat 13 (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+    Repository-Browse.
+  * Add patch from pull request fixing traceback of global alignments
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com>  Fri, 03 Jul 2020 11:36:48 +0200
+
 jaligner (1.0+dfsg-6) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11


=====================================
debian/control
=====================================
@@ -5,17 +5,18 @@ Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
            Pranav Ballaney <ballaneypranav at gmail.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 13),
                default-jdk
 Build-Depends-Indep: junit4,
                      javahelper,
                      icedtea-netx,
                      asciidoctor,
                      maven-repo-helper
-Standards-Version: 4.2.1
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/jaligner
 Vcs-Git: https://salsa.debian.org/med-team/jaligner.git
 Homepage: https://github.com/ahmedmoustafa/JAligner
+Rules-Requires-Root: no
 
 Package: jaligner
 Architecture: all


=====================================
debian/patches/f267efdf3bc29291eddd380bba127b8ed56f2dc2.patch
=====================================
@@ -0,0 +1,19 @@
+From f267efdf3bc29291eddd380bba127b8ed56f2dc2 Mon Sep 17 00:00:00 2001
+From: Tobias Bertelsen <tobias.bertelsen at gmail.com>
+Date: Wed, 25 Feb 2015 16:04:08 +0100
+Subject: [PATCH] Fixing traceback of global alignments
+  See Pull request: https://github.com/ahmedmoustafa/JAligner/pull/1
+Origin: https://github.com/ahmedmoustafa/JAligner/commit/f267efdf3bc29291eddd380bba127b8ed56f2dc2.patch
+
+
+--- a/src/jaligner/NeedlemanWunschGotoh.java
++++ b/src/jaligner/NeedlemanWunschGotoh.java
+@@ -220,7 +220,7 @@ public final class NeedlemanWunschGotoh
+ 		} // loop rows
+ 
+ 		Cell cell = new Cell();
+-		cell.set(maxi, maxj, v[n - 1]);
++		cell.set(m-1, n-1, v[n - 1]);
+ 
+ 		logger.info("Finished.");
+ 


=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+f267efdf3bc29291eddd380bba127b8ed56f2dc2.patch


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/ahmedmoustafa/JAligner/issues
+Bug-Submit: https://github.com/ahmedmoustafa/JAligner/issues/new
 Registry:
  - Name: OMICtools
    Entry: OMICS_20021
@@ -5,3 +7,5 @@ Registry:
    Entry: NA
  - Name: SciCrunch
    Entry: NA
+Repository: https://github.com/ahmedmoustafa/JAligner.git
+Repository-Browse: https://github.com/ahmedmoustafa/JAligner



View it on GitLab: https://salsa.debian.org/med-team/jaligner/-/compare/01a98951682a3f5f013daa2a8723b74f89b1cb45...2988fecb8bf2a2e49742686b87d2c48c07534917

-- 
View it on GitLab: https://salsa.debian.org/med-team/jaligner/-/compare/01a98951682a3f5f013daa2a8723b74f89b1cb45...2988fecb8bf2a2e49742686b87d2c48c07534917
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200703/ba0c22c6/attachment-0001.html>