[med-svn] r5961 - in trunk/packages: . libjebl2-java libjebl2-java/trunk libjebl2-java/trunk/debian libjebl2-java/trunk/debian/patches libjebl2-java/trunk/debian/source
Andreas Tille
tille at alioth.debian.org
Sat Feb 12 17:06:43 UTC 2011
Author: tille
Date: 2011-02-12 17:06:39 +0000 (Sat, 12 Feb 2011)
New Revision: 5961
Added:
trunk/packages/libjebl2-java/
trunk/packages/libjebl2-java/trunk/
trunk/packages/libjebl2-java/trunk/debian/
trunk/packages/libjebl2-java/trunk/debian/changelog
trunk/packages/libjebl2-java/trunk/debian/compat
trunk/packages/libjebl2-java/trunk/debian/control
trunk/packages/libjebl2-java/trunk/debian/copyright
trunk/packages/libjebl2-java/trunk/debian/get-orig-source
trunk/packages/libjebl2-java/trunk/debian/libjebl2-java-doc.javadoc
trunk/packages/libjebl2-java/trunk/debian/libjebl2-java.jlibs
trunk/packages/libjebl2-java/trunk/debian/patches/
trunk/packages/libjebl2-java/trunk/debian/patches/do_not_build_jam.patch
trunk/packages/libjebl2-java/trunk/debian/patches/javadoc.patch
trunk/packages/libjebl2-java/trunk/debian/patches/series
trunk/packages/libjebl2-java/trunk/debian/rules
trunk/packages/libjebl2-java/trunk/debian/source/
trunk/packages/libjebl2-java/trunk/debian/source/format
trunk/packages/libjebl2-java/trunk/debian/watch
Log:
Inject libjebl2-java
Added: trunk/packages/libjebl2-java/trunk/debian/changelog
===================================================================
--- trunk/packages/libjebl2-java/trunk/debian/changelog (rev 0)
+++ trunk/packages/libjebl2-java/trunk/debian/changelog 2011-02-12 17:06:39 UTC (rev 5961)
@@ -0,0 +1,5 @@
+jebl2 (0.0.r6-1) unstable; urgency=low
+
+ * Initial Debian Upload (Closes: #??????)
+
+ -- Andreas Tille <tille at debian.org> Thu, 10 Feb 2011 10:26:38 +0100
Added: trunk/packages/libjebl2-java/trunk/debian/compat
===================================================================
--- trunk/packages/libjebl2-java/trunk/debian/compat (rev 0)
+++ trunk/packages/libjebl2-java/trunk/debian/compat 2011-02-12 17:06:39 UTC (rev 5961)
@@ -0,0 +1 @@
+7
Added: trunk/packages/libjebl2-java/trunk/debian/control
===================================================================
--- trunk/packages/libjebl2-java/trunk/debian/control (rev 0)
+++ trunk/packages/libjebl2-java/trunk/debian/control 2011-02-12 17:06:39 UTC (rev 5961)
@@ -0,0 +1,43 @@
+Source: jebl2
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7.1), javahelper (>=0.25)
+Build-Depends-Indep: default-jdk, default-jdk-doc, libtrove-java, libtrove-java-doc, ant
+Standards-Version: 3.9.1
+Section: java
+Homepage: http://code.google.com/p/jebl2/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/libjebl2-java/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/libjebl2-java/trunk/
+
+
+Package: libjebl2-java
+Architecture: all
+Depends: ${java:Depends}, ${misc:Depends}
+Recommends: ${java:Recommends}
+Description: Java Evolutionary Biology Library
+ A Java library for evolutionary biology and bioinformatics, including
+ objects representing biomolecular sequences, multiple sequence
+ alignments and phylogenetic trees.
+ .
+ This is a branch of the original JEBL on
+ http://sourceforge.net/projects/jebl/ to develop a new API and class
+ library.
+
+
+Package: libjebl2-java-doc
+Section: doc
+Architecture: all
+Depends: ${java:Depends}, ${misc:Depends}
+Recommends: ${java:Recommends}
+Description: Java Evolutionary Biology Library (documentation)
+ A Java library for evolutionary biology and bioinformatics, including
+ objects representing biomolecular sequences, multiple sequence
+ alignments and phylogenetic trees.
+ .
+ This is a branch of the original JEBL on
+ http://sourceforge.net/projects/jebl/ to develop a new API and class
+ library.
+ .
+ This package provides the documentation for the library
Added: trunk/packages/libjebl2-java/trunk/debian/copyright
===================================================================
--- trunk/packages/libjebl2-java/trunk/debian/copyright (rev 0)
+++ trunk/packages/libjebl2-java/trunk/debian/copyright 2011-02-12 17:06:39 UTC (rev 5961)
@@ -0,0 +1,28 @@
+Format: http://dep.debian.net/deps/dep5/
+Upstream-Name: JEBL
+Upstream-Contact: Andrew Rambaut <a.rambaut at ed.ac.uk>
+Source: http://code.google.com/p/jebl2/source/checkout
+
+Files: *
+Copyright: © 2009-2010 Andrew Rambaut <a.rambaut at ed.ac.uk>
+Licence: LGPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+Comment:
+ On Debian systems, you can read the full text of the GNU Lesser General Public
+ License in ‘/usr/share/common-licenses/LGPL-3’.
+
+Files: debian/*
+Copyright: © 2011 Andreas Tille <tille at debian.org>
+License: PD
+ The packaging work is in the public domain unless stated otherwise.
Added: trunk/packages/libjebl2-java/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/libjebl2-java/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/libjebl2-java/trunk/debian/get-orig-source 2011-02-12 17:06:39 UTC (rev 5961)
@@ -0,0 +1,17 @@
+#!/bin/sh
+# get source for jebl-lib from SVN
+
+NAME=jebl2
+
+rm -f ../detail
+mkdir -p ../tarballs
+cd ../tarballs
+# svn export concerves time stamps of the files, checkout does not
+REV=`LC_ALL=C svn export http://${NAME}.googlecode.com/svn/trunk/ ${NAME} | tail -n 1 | sed 's/^.*revision \([0-9]\+\)./\1/'`
+VERSION=0.0.r${REV}
+
+find ${NAME} -name .svn -type d -exec rm -rf \{\} \;
+rm -f ${NAME}/lib/*.jar
+
+GZIP="--best --no-name" tar -czf "$NAME"_"$VERSION".orig.tar.gz "${NAME}"
+rm -rf "${NAME}"
Property changes on: trunk/packages/libjebl2-java/trunk/debian/get-orig-source
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/libjebl2-java/trunk/debian/libjebl2-java-doc.javadoc
===================================================================
--- trunk/packages/libjebl2-java/trunk/debian/libjebl2-java-doc.javadoc (rev 0)
+++ trunk/packages/libjebl2-java/trunk/debian/libjebl2-java-doc.javadoc 2011-02-12 17:06:39 UTC (rev 5961)
@@ -0,0 +1 @@
+doc /usr/share/doc/libjebl2-java/api
Added: trunk/packages/libjebl2-java/trunk/debian/libjebl2-java.jlibs
===================================================================
--- trunk/packages/libjebl2-java/trunk/debian/libjebl2-java.jlibs (rev 0)
+++ trunk/packages/libjebl2-java/trunk/debian/libjebl2-java.jlibs 2011-02-12 17:06:39 UTC (rev 5961)
@@ -0,0 +1 @@
+dist/*.jar
Added: trunk/packages/libjebl2-java/trunk/debian/patches/do_not_build_jam.patch
===================================================================
--- trunk/packages/libjebl2-java/trunk/debian/patches/do_not_build_jam.patch (rev 0)
+++ trunk/packages/libjebl2-java/trunk/debian/patches/do_not_build_jam.patch 2011-02-12 17:06:39 UTC (rev 5961)
@@ -0,0 +1,99 @@
+--- jebl2.orig/build.xml
++++ jebl2/build.xml
+@@ -7,7 +7,6 @@
+ <!-- set global properties for this build -->
+ <property name="src" location="src"/>
+ <property name="build" location="build"/>
+- <property name="build-mac-only" location="build-mac-only"/>
+
+ <property name="lib" location="lib"/>
+ <property name="dist" location="dist"/>
+@@ -19,31 +18,9 @@
+ <tstamp/>
+ <!-- Create the build directory structure used by compile -->
+ <mkdir dir="${build}"/>
+- <mkdir dir="${build-mac-only}"/>
+ <mkdir dir="${dist}"/>
+ </target>
+
+- <target name="compile-jam" depends="init">
+- <!-- Compile the java code from ${jamsrc} into ${build} -->
+-
+- <condition property="isMac">
+- <os family="mac"/>
+- </condition>
+- <javac source="1.5" srcdir="${src}" target="1.5" destdir="${build}" debug="true">
+- <include name="org/**/*"/>
+- <exclude name="org/**/maconly/*" unless = "isMac"/>
+- </javac>
+-
+- <!-- Utils.class was getting included in jebl.jar -->
+- <!-- twice and Pack200 was having issues. -->
+- <!-- Doesn't seem to be the case for me, the class is missing! RM-->
+- <!--<delete file="${build}/org/virion/jam/mac/Utils.class"/>-->
+-
+- <copy todir="${build}">
+- <fileset dir="${src}" includes="org/**/*.png"/>
+- </copy>
+- </target>
+-
+ <target name="clean">
+ <mkdir dir="${build}"/>
+ <delete includeEmptyDirs="true">
+@@ -52,38 +29,6 @@
+
+ </target>
+
+- <target name="compile-jam-mac-only" depends="init">
+- <!-- Compile the java code from ${jamsrc} into ${build} -->
+- <condition property="isMac">
+- <os family="mac"/>
+- </condition>
+- <javac source="1.5" srcdir="${src}" target="1.5" destdir="${build-mac-only}">
+- <include name="org/**/maconly/*"/>
+- </javac>
+- </target>
+-
+- <target name="dist-jam-mac-only" depends="compile-jam-mac-only" description="generate the -mac-only distribution">
+- <!-- Create the distribution directory -->
+- <mkdir dir="${dist}"/>
+-
+- <!-- create the mac-only jar file -->
+- <jar jarfile="${lib}/jam-mac-only.jar">
+- <fileset dir="${build-mac-only}" includes="**/mac*/**/*.class,*.properties"/>
+- </jar>
+- </target>
+-
+-
+- <target name="dist-jam" depends="compile-jam" description="generate the JAM distribution">
+- <!-- Create the distribution directory -->
+- <mkdir dir="${dist}"/>
+- <delete file="${dist}/jam.jar"/>
+- <!-- Put everything in ${build} into the jam.jar file -->
+- <jar jarfile="${dist}/jam.jar">
+- <fileset dir="${build}" includes="org/**/*.class,org/**/*.properties,org/**/*.png"/>
+- <zipgroupfileset dir="${lib}" includes="jam-mac-only.jar"/>
+- </jar>
+- </target>
+-
+ <target name="compile-jebl" depends="init">
+ <!-- Compile the java code from ${src} into ${build} -->
+ <javac source="1.5" srcdir="${src}" destdir="${build}" debug="true" target="1.5">
+@@ -105,7 +50,7 @@
+ </jar>
+ </target>
+
+- <target name="dist" depends="dist-jebl,dist-jam" description="generate the distribution">
++ <target name="dist" depends="dist-jebl" description="generate the distribution">
+ <!-- Create the distribution directory -->
+ <mkdir dir="${dist}"/>
+
+@@ -116,7 +61,7 @@
+ </jar>
+ </target>
+
+- <target name="dist-clean" depends="clean,compile-jebl,compile-jam" description="generate the distribution">
++ <target name="dist-clean" depends="clean,compile-jebl" description="generate the distribution">
+ <!-- For some reason I don't fully understand, running the standard distribute
+ script doesn't always work if you have done a previous build on a previous version
+ of the source code. For some reason, it just doesn't compile some files. This
Added: trunk/packages/libjebl2-java/trunk/debian/patches/javadoc.patch
===================================================================
--- trunk/packages/libjebl2-java/trunk/debian/patches/javadoc.patch (rev 0)
+++ trunk/packages/libjebl2-java/trunk/debian/patches/javadoc.patch 2011-02-12 17:06:39 UTC (rev 5961)
@@ -0,0 +1,25 @@
+--- /dev/null
++++ jebl2/javadoc.xml
+@@ -0,0 +1,22 @@
++<project name="jebl2" default="javadoc" basedir=".">
++ <property name="src" location="src" />
++ <property name="doc" location="doc" />
++ <target name="init">
++ <!-- Create the doc folder -->
++ <mkdir dir="${doc}" />
++ </target>
++ <target name="javadoc" depends="init" description="generate the javadocs">
++ <javadoc
++ destdir="${doc}"
++ author="true"
++ version="true"
++ use="true"
++ windowtitle="JEBL2 lib API"
++ access="public">
++ <packageset dir="${src}" />
++ <doctitle><![CDATA[<h1>JEBL2</h1>]]></doctitle>
++ <bottom><![CDATA[<i>http://code.google.com/p/jebl2/</i>]]></bottom>
++ <link href="http://java.sun.com/j2se/1.4.1/docs/api/"/>
++ </javadoc>
++ </target>
++</project>
Added: trunk/packages/libjebl2-java/trunk/debian/patches/series
===================================================================
--- trunk/packages/libjebl2-java/trunk/debian/patches/series (rev 0)
+++ trunk/packages/libjebl2-java/trunk/debian/patches/series 2011-02-12 17:06:39 UTC (rev 5961)
@@ -0,0 +1,2 @@
+javadoc.patch
+do_not_build_jam.patch
Added: trunk/packages/libjebl2-java/trunk/debian/rules
===================================================================
--- trunk/packages/libjebl2-java/trunk/debian/rules (rev 0)
+++ trunk/packages/libjebl2-java/trunk/debian/rules 2011-02-12 17:06:39 UTC (rev 5961)
@@ -0,0 +1,17 @@
+#!/usr/bin/make -f
+
+JAVA_HOME=/usr/lib/jvm/default-java
+
+%:
+ dh $@ --with javahelper
+
+override_dh_auto_clean:
+ # build.xml does not provide a clean target
+ rm -rf dist build doc
+
+override_dh_auto_build:
+ dh_auto_build
+ ant -buildfile javadoc.xml
+
+get-orig-source:
+ . debian/get-orig-source
Property changes on: trunk/packages/libjebl2-java/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/libjebl2-java/trunk/debian/source/format
===================================================================
--- trunk/packages/libjebl2-java/trunk/debian/source/format (rev 0)
+++ trunk/packages/libjebl2-java/trunk/debian/source/format 2011-02-12 17:06:39 UTC (rev 5961)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/libjebl2-java/trunk/debian/watch
===================================================================
--- trunk/packages/libjebl2-java/trunk/debian/watch (rev 0)
+++ trunk/packages/libjebl2-java/trunk/debian/watch 2011-02-12 17:06:39 UTC (rev 5961)
@@ -0,0 +1,10 @@
+# Obtaining the source tarball of jebl is a bit tricky because there is no
+# explicite link to a downloadable tarball on the web page and the source is
+# only in SVN. There is even no versioning scheme and this watch file is just
+# checking for a new SVN commit
+
+version=3
+opts="dversionmangle=s/0.0.r//" \
+ http://code.google.com/p/jebl2/source/list \
+ detail\?r=([\d]+) \
+ debian debian/get-orig-source
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