[med-svn] [Git][med-team/mauve-aligner][master] 9 commits: New upstream version 2.4.0+4736

Andreas Tille gitlab at salsa.debian.org
Wed Jul 4 21:53:06 BST 2018 

Andreas Tille pushed to branch master at Debian Med / mauve-aligner


Commits:
b05e1390 by Andreas Tille at 2018-07-04T22:43:09+02:00
New upstream version 2.4.0+4736
- - - - -
96a461fa by Andreas Tille at 2018-07-04T22:43:10+02:00
Update upstream source from tag 'upstream/2.4.0+4736'

Update to upstream version '2.4.0+4736'
with Debian dir 432d6d6b75afe412d4b0a4e69007fd8dc68b1925
- - - - -
774dc06b by Andreas Tille at 2018-07-04T22:44:57+02:00
New upstream SVN checkout

- - - - -
a89a26a8 by Andreas Tille at 2018-07-04T22:45:51+02:00
Fake watch file

- - - - -
45edeed5 by Andreas Tille at 2018-07-04T22:47:31+02:00
do not uselessly parse d/changelog

- - - - -
66ee7a92 by Andreas Tille at 2018-07-04T22:47:41+02:00
debhelper 11

- - - - -
4c7255b5 by Andreas Tille at 2018-07-04T22:48:39+02:00
Point Vcs fields to salsa.debian.org

- - - - -
88b32118 by Andreas Tille at 2018-07-04T22:48:39+02:00
Standards-Version: 4.1.4

- - - - -
c3646caf by Andreas Tille at 2018-07-04T22:51:53+02:00
Upload to unstable

- - - - -


16 changed files:

- debian/changelog
- debian/compat
- debian/control
- debian/rules
- debian/watch
- src/images/Back16.gif
- src/images/Down16.gif
- src/images/Forward16.gif
- src/images/Home16.gif
- src/images/Up16.gif
- src/images/Zoom16.gif
- src/images/ZoomIn16.gif
- src/images/ZoomIn24.gif
- src/images/ZoomOut16.gif
- src/images/ZoomOut24.gif
- src/org/gel/mauve/analysis/SnpExporter.java


Changes:

=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,14 @@
+mauve-aligner (2.4.0+4736-1) unstable; urgency=medium
+
+  * New upstream SVN checkout
+  * Fake watch file
+  * d/rules: do not uselessly parse d/changelog
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.4
+
+ -- Andreas Tille <tille at debian.org>  Wed, 04 Jul 2018 22:48:39 +0200
+
 mauve-aligner (2.4.0+4734-3) unstable; urgency=high
 
   * Add explicit dependency on libbiojava-java to enable


=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11


=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -1,11 +1,10 @@
 Source: mauve-aligner
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders:
-	Andreas Tille <tille at debian.org>,
-	Afif Elghraoui <afif at ghraoui.name>,
+Uploaders: Andreas Tille <tille at debian.org>,
+           Afif Elghraoui <afif at ghraoui.name>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
                javahelper,
                default-jdk,
                ant,
@@ -17,10 +16,10 @@ Build-Depends: debhelper (>= 9),
                libzeus-jscl-java,
                icedtea-netx-common,
                libunixsocket-java,
-	       imagemagick,
-Standards-Version: 3.9.6
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mauve-aligner.git
-Vcs-Git: git://anonscm.debian.org/debian-med/mauve-aligner.git
+               imagemagick
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/mauve-aligner
+Vcs-Git: https://salsa.debian.org/med-team/mauve-aligner.git
 Homepage: http://darlinglab.org/mauve/
 
 Package: mauve-aligner
@@ -28,7 +27,7 @@ Architecture: any
 Depends: ${java:Depends},
          java-wrappers,
          ${misc:Depends},
-	 libbiojava-java,
+         libbiojava-java,
          progressivemauve
 Recommends: ${java:Recommends}
 Description: multiple genome alignment


=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -6,8 +6,6 @@
 
 #export DH_VERBOSE=1
 
-PACKAGE := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
-
 JAVA_HOME  := /usr/lib/jvm/default-java
 
 DEBJAR    := /usr/share/java


=====================================
debian/watch
=====================================
--- a/debian/watch
+++ b/debian/watch
@@ -1 +1,4 @@
-# There is no tarball download location, libMuscle is only available in SVN
+version=4
+
+opts=dversionmangle=s/.*/0.No-Release/ \
+  https://people.debian.org/~eriberto/ FakeWatchNoUpstreamReleaseForThisPackage-(\d\S+)\.gz


=====================================
src/images/Back16.gif
=====================================
Binary files a/src/images/Back16.gif and b/src/images/Back16.gif differ


=====================================
src/images/Down16.gif
=====================================
Binary files a/src/images/Down16.gif and b/src/images/Down16.gif differ


=====================================
src/images/Forward16.gif
=====================================
Binary files a/src/images/Forward16.gif and b/src/images/Forward16.gif differ


=====================================
src/images/Home16.gif
=====================================
Binary files a/src/images/Home16.gif and b/src/images/Home16.gif differ


=====================================
src/images/Up16.gif
=====================================
Binary files a/src/images/Up16.gif and b/src/images/Up16.gif differ


=====================================
src/images/Zoom16.gif
=====================================
Binary files a/src/images/Zoom16.gif and b/src/images/Zoom16.gif differ


=====================================
src/images/ZoomIn16.gif
=====================================
Binary files a/src/images/ZoomIn16.gif and b/src/images/ZoomIn16.gif differ


=====================================
src/images/ZoomIn24.gif
=====================================
Binary files a/src/images/ZoomIn24.gif and b/src/images/ZoomIn24.gif differ


=====================================
src/images/ZoomOut16.gif
=====================================
Binary files a/src/images/ZoomOut16.gif and b/src/images/ZoomOut16.gif differ


=====================================
src/images/ZoomOut24.gif
=====================================
Binary files a/src/images/ZoomOut24.gif and b/src/images/ZoomOut24.gif differ


=====================================
src/org/gel/mauve/analysis/SnpExporter.java
=====================================
--- a/src/org/gel/mauve/analysis/SnpExporter.java
+++ b/src/org/gel/mauve/analysis/SnpExporter.java
@@ -130,6 +130,7 @@ public class SnpExporter {
 		for (int i = 0; i < snps.length; i++){
 			output.write(snps[i].toString()+"\n");
 		}
+        output.flush(); // don't forget to flush!
 	}
 	
 	public static void exportGaps(XmfaViewerModel model, XMFAAlignment xmfa, BufferedWriter output) throws IOException {
@@ -139,6 +140,7 @@ public class SnpExporter {
 		for (Gap[] ar: gaps)
 			for (Gap g: ar)
 				output.write(g.toString()+"\n");
+        output.flush(); // don't forget to flush!
 	}
 	
 	public static SNP[] getSNPs(XmfaViewerModel model){



View it on GitLab: https://salsa.debian.org/med-team/mauve-aligner/compare/cf12f0e9266670e6294d76593c06f373206d852d...c3646cafd58b37e51e135dfa4146a70bfea1ef04

-- 
View it on GitLab: https://salsa.debian.org/med-team/mauve-aligner/compare/cf12f0e9266670e6294d76593c06f373206d852d...c3646cafd58b37e51e135dfa4146a70bfea1ef04
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