[med-svn] r14355 - in trunk/packages/biojava3/trunk/debian: . patches

[olivier sallou]

Author: osallou-guest
Date: 2013-08-06 11:31:55 +0000 (Tue, 06 Aug 2013)
New Revision: 14355

Modified:
   trunk/packages/biojava3/trunk/debian/build.xml
   trunk/packages/biojava3/trunk/debian/changelog
   trunk/packages/biojava3/trunk/debian/control
   trunk/packages/biojava3/trunk/debian/get-orig-source
   trunk/packages/biojava3/trunk/debian/patches/fix_code_to_support_latest_jmol
   trunk/packages/biojava3/trunk/debian/watch
Log:
new upstream release 3.0.6, using github repo

Modified: trunk/packages/biojava3/trunk/debian/build.xml
===================================================================
--- trunk/packages/biojava3/trunk/debian/build.xml	2013-08-05 15:07:14 UTC (rev 14354)
+++ trunk/packages/biojava3/trunk/debian/build.xml	2013-08-06 11:31:55 UTC (rev 14355)
@@ -21,13 +21,14 @@
 	<property environment="env"/>
 	<property name="project.jarfile.name" value="BJLIB.jar"/>	
 	
-	<property name="class.path" value="${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit4.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar ${lib.dir}/Jmol.jar /usr/share/icedtea-web/netx.jar ${lib.dir}/hamcrest.jar ${lib.dir}/json_simple.jar ${lib.dir}/commons-codec.jar ${lib.dir}/itext5.jar ${lib.dir}/Jmol.jar"/>
+	<property name="class.path" value="${lib.dir}/commons-logging.jar ${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit4.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar ${lib.dir}/Jmol.jar /usr/share/icedtea-web/netx.jar ${lib.dir}/hamcrest.jar ${lib.dir}/json_simple.jar ${lib.dir}/commons-codec.jar ${lib.dir}/itext5.jar ${lib.dir}/Jmol.jar"/>
 								
 	<path id="compile.classpath">
                         <fileset dir="${lib.dir}">
 				<include name="commons-cli.jar"/>
 				<include name="commons-collections.jar"/>
 				<include name="commons-dbcp.jar"/>
+				<include name="commons-logging.jar"/>
 				<include name="commons-pool.jar"/>
 				<include name="commons-codec.jar"/>
 				<include name="itext5.jar"/>

Modified: trunk/packages/biojava3/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava3/trunk/debian/changelog	2013-08-05 15:07:14 UTC (rev 14354)
+++ trunk/packages/biojava3/trunk/debian/changelog	2013-08-06 11:31:55 UTC (rev 14355)
@@ -1,3 +1,12 @@
+biojava3-live (3.0.6-1) UNRELEASED; urgency=low
+
+  * New upstream release
+    TODO: needs Apache commons logging >= 2.0
+   
+   [debian/watch]: use new upstream GitHub repository
+
+ -- Olivier Sallou <osallou at debian.org>  Tue, 18 Jun 2013 14:40:39 +0200
+
 biojava3-live (3.0.5-3) unstable; urgency=low
 
   * Fix issue wit itext5 >= 5.4.1 related to API change (Closes: #712359)

Modified: trunk/packages/biojava3/trunk/debian/control
===================================================================
--- trunk/packages/biojava3/trunk/debian/control	2013-08-05 15:07:14 UTC (rev 14354)
+++ trunk/packages/biojava3/trunk/debian/control	2013-08-06 11:31:55 UTC (rev 14355)
@@ -5,6 +5,7 @@
 Uploaders: Olivier Sallou <osallou at debian.org>
 Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
  libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1),
+ libcommons-logging-java,
  libcommons-cli-java, libguava-java (>= 11.0.1),
  libcommons-codec-java, libitext5-java (>= 5.4.1), libjmol-java,
  default-jdk (>= 1:1.6), junit4,javahelper (>=0.25),
@@ -21,6 +22,7 @@
  libcommons-pool-java (>= 1.1),
  libcommons-collections-java (>= 2.1),
  libcommons-dbcp-java (>= 1.1),
+ libcommons-logging-java,
  libhsqldb-java,
  libbytecode-java,
  icedtea-netx,

Modified: trunk/packages/biojava3/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/biojava3/trunk/debian/get-orig-source	2013-08-05 15:07:14 UTC (rev 14354)
+++ trunk/packages/biojava3/trunk/debian/get-orig-source	2013-08-06 11:31:55 UTC (rev 14355)
@@ -12,11 +12,11 @@
 
 cd ../tarballs
 #biojava-3.0.4-all.tar.gz
-UTAR="biojava-${VERSION}-all.tar.gz"
+UTAR="biojava-${VERSION}.tar.gz"
 mv ../${UTAR} .
 tar -xzf ${UTAR}
 
-mv bj${VERSION} $PKG-${VERSION}.orig # .orig is requested by Developers Reference 3.4.4 §6.7.8.2
+mv biojava-biojava-${VERSION} $PKG-${VERSION}.orig # .orig is requested by Developers Reference 3.4.4 §6.7.8.2
 
 cd $PKG-${VERSION}.orig
 	rm -rf target

Modified: trunk/packages/biojava3/trunk/debian/patches/fix_code_to_support_latest_jmol
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/fix_code_to_support_latest_jmol	2013-08-05 15:07:14 UTC (rev 14354)
+++ trunk/packages/biojava3/trunk/debian/patches/fix_code_to_support_latest_jmol	2013-08-06 11:31:55 UTC (rev 14355)
@@ -5,15 +5,7 @@
 
 --- a/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java
 +++ b/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java
-@@ -29,6 +29,7 @@
- import javax.swing.JTextField;
- 
- import org.jmol.api.JmolStatusListener;
-+import org.jmol.constant.EnumCallback;
- 
- public class MyJmolStatusListener implements JmolStatusListener {
- 
-@@ -40,7 +41,17 @@
+@@ -42,7 +42,17 @@
  	public void setTextField (JTextField statusField) {
  		status = statusField;
  	}

Modified: trunk/packages/biojava3/trunk/debian/watch
===================================================================
--- trunk/packages/biojava3/trunk/debian/watch	2013-08-05 15:07:14 UTC (rev 14354)
+++ trunk/packages/biojava3/trunk/debian/watch	2013-08-06 11:31:55 UTC (rev 14355)
@@ -1,4 +1,5 @@
 version=3
 
-http://biojava.org/wiki/BioJava:Download http://biojava.org/download/bj.*/biojava-(.*)-all\.tar\.gz
+opts=filenamemangle=s/.+\/biojava-?(\d\S*)\.tar\.gz/biojava-$1.tar.gz/  \
+  https://github.com/biojava/biojava/tags .*/biojava-?(\d\S*)\.tar\.gz