[med-svn] r9453 - in trunk/packages/phy-spread/trunk/debian: . patches scripts
Andreas Tille
tille at alioth.debian.org
Fri Jan 27 16:11:51 UTC 2012
Author: tille
Date: 2012-01-27 16:11:51 +0000 (Fri, 27 Jan 2012)
New Revision: 9453
Added:
trunk/packages/phy-spread/trunk/debian/README.Debian
trunk/packages/phy-spread/trunk/debian/get-orig-source
trunk/packages/phy-spread/trunk/debian/install
trunk/packages/phy-spread/trunk/debian/manifest
trunk/packages/phy-spread/trunk/debian/patches/follow_hint_from_README.patch
trunk/packages/phy-spread/trunk/debian/scripts/
trunk/packages/phy-spread/trunk/debian/scripts/phy-spread
Removed:
trunk/packages/phy-spread/trunk/debian/libkmlframework-java.jlibs
Modified:
trunk/packages/phy-spread/trunk/debian/changelog
trunk/packages/phy-spread/trunk/debian/control
trunk/packages/phy-spread/trunk/debian/copyright
trunk/packages/phy-spread/trunk/debian/patches/build_xml.patch
trunk/packages/phy-spread/trunk/debian/patches/series
trunk/packages/phy-spread/trunk/debian/rules
trunk/packages/phy-spread/trunk/debian/watch
Log:
Finally get the right stuff into spread packaging ...
Added: trunk/packages/phy-spread/trunk/debian/README.Debian
===================================================================
--- trunk/packages/phy-spread/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/phy-spread/trunk/debian/README.Debian 2012-01-27 16:11:51 UTC (rev 9453)
@@ -0,0 +1,9 @@
+SPREAD for Debian
+-----------------
+
+Please note:
+
+ Originally this program is named "spread". However, there is just such a
+ package inside Debian and thus a 'phy-' for phylogeny was prepended.
+
+ -- Andreas Tille <tille at debian.org> Thu, 26 Jan 2012 18:51:29 +0100
Modified: trunk/packages/phy-spread/trunk/debian/changelog
===================================================================
--- trunk/packages/phy-spread/trunk/debian/changelog 2012-01-27 15:19:21 UTC (rev 9452)
+++ trunk/packages/phy-spread/trunk/debian/changelog 2012-01-27 16:11:51 UTC (rev 9453)
@@ -1,5 +1,5 @@
-libkmlframework-java (0.0.20090718-1) UNRELEASED; urgency=low
+phy-spread (1.0.2-1) UNRELEASED; urgency=low
- * Initial release Closes: #????
+ * Initial release. (Closes: #657585)
- -- Andreas Tille <tille at debian.org> Tue, 17 Jan 2012 13:12:16 +0100
+ -- Andreas Tille <tille at debian.org> Thu, 26 Jan 2012 18:51:29 +0100
Modified: trunk/packages/phy-spread/trunk/debian/control
===================================================================
--- trunk/packages/phy-spread/trunk/debian/control 2012-01-27 15:19:21 UTC (rev 9452)
+++ trunk/packages/phy-spread/trunk/debian/control 2012-01-27 16:11:51 UTC (rev 9453)
@@ -1,20 +1,29 @@
-Source: libkmlframework-java
-Section: java
+Source: phy-spread
+Section: non-free/science
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 (>= 8), javahelper (>=0.25), default-jdk, ant, libservlet2.5-java
+Build-Depends: debhelper (>= 8), javahelper (>=0.25),
+ ant, ant-optional, openjdk-6-jdk | default-jdk,
+ libcolorpicker-java, libjebl2-java, libcolt-java,
+ libprocessing-core-java
Standards-Version: 3.9.2
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/libkmlframework-java/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/libkmlframework-java/trunk/
-Homepage: http://code.google.com/p/kmlframework/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/phy-spread/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/phy-spread/trunk/
+XS-Autobuild: yes
+Homepage: http://www.kuleuven.be/aidslab/phylogeography/SPREAD.html
-Package: libkmlframework-java
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}
-Recommends: ${java:Recommends}
-Description: library/framework for generating Google Earth KML
- The KML Framework is a library/framework for generating Google Earth
- KML (Keyhole Markup Language) documents. The framework is based on the
- work done by Eivind Bøhn as a part of his Master Thesis.
+Package: phy-spread
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}, openjdk-6-jre | java-jre
+Description: analyze and visualize phylogeographic reconstructions
+ SPREAD is a user-friendly application to analyze and visualize
+ phylogeographic reconstructions resulting from Bayesian inference of
+ spatio-temporal diffusion.
+ .
+ There is a tutorial for SPREAD online at
+ http://www.kuleuven.be/aidslab/phylogeography/tutorial/spread_tutorial.html
+ .
+ Originally this program is named "spread". However, there is just such a
+ package inside Debian and thus a 'phy' for phylogeny was prepended.
Modified: trunk/packages/phy-spread/trunk/debian/copyright
===================================================================
--- trunk/packages/phy-spread/trunk/debian/copyright 2012-01-27 15:19:21 UTC (rev 9452)
+++ trunk/packages/phy-spread/trunk/debian/copyright 2012-01-27 16:11:51 UTC (rev 9453)
@@ -1,32 +1,31 @@
Format: http://dep.debian.net/deps/dep5/
-Upstream-Name: KML framework
-Upstream-Contact: Eivind Bøhn <eivind at boehn.org>
-Source: http://code.google.com/p/kmlframework/downloads/list
+Upstream-Name: Spread
+Upstream-Contact: Filip Bielejec <filip.bielejec at rega.kuleuven.be>
+Original-Source: http://www.kuleuven.be/aidslab/phylogeography/SPREAD.html
-Files: *
-Copyright: © 2007-2009 Eivind Bøhn <eivind at boehn.org>
-License: BSD 2-Clause License
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are
- met:
- * Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in the
- documentation and/or other materials provided with the distribution.
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
- IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
- TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
- PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
- HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
- SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
- TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+Copyright: 2004-2011 Filip Bielejec <filip.bielejec at rega.kuleuven.be>,
+ Andrew Rambaut <a.rambaut at ed.ac.uk>,
+ Marc A. Suchard <msuchard at gmail.com>,
+ Philippe Lemey
+License: 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 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/>.
+ .
+ On a Debian GNU/Linux system, the GNU Lesser GPL license version 3 is included
+ in the file ‘/usr/share/common-licenses/LGPL-3’, and the GNU GPL license
+ version 3 is included in the file ‘/usr/share/common-licenses/GPL-3’.
Files: debian/*
-Copyright: © 2012 Andreas Tille
-License: BSD 2-Clause License
- Same as source code itself
+Copyright: © 2012 Andreas Tille <tille at debian.org>
+License: LGPL-3+
+ Same license as the software itself
Added: trunk/packages/phy-spread/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/phy-spread/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/phy-spread/trunk/debian/get-orig-source 2012-01-27 16:11:51 UTC (rev 9453)
@@ -0,0 +1,33 @@
+#!/bin/sh
+# unpack spread tarball to get rid of several binaries
+
+set -e
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+UPSTREAMNAME=`echo $NAME | sed 's/phy-//'`
+
+if ! echo $@ | grep -q upstream-version ; then
+ VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+else
+ VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${UPSTREAMNAME}.*?\1?"`
+ if echo "$VERSION" | grep -q "upstream-version" ; then
+ echo "Unable to parse version number"
+ exit
+ fi
+fi
+
+TARDIR=${UPSTREAMNAME}-${VERSION}
+mkdir -p ../tarballs
+cd ../tarballs
+mv ../${TARDIR}.tar.gz .
+tar -xzf ${TARDIR}.tar.gz
+
+# Remove useless binaries
+rm -rf ${TARDIR}/release/Mac
+rm -rf ${TARDIR}/release/Windows
+rm -rf ${TARDIR}/release/tools
+
+# Remove debian packaged jars
+rm -rf ${TARDIR}/lib/*
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -czf "$NAME"_"$VERSION".orig.tar.gz "${TARDIR}"
+rm -rf ${TARDIR}
Property changes on: trunk/packages/phy-spread/trunk/debian/get-orig-source
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/phy-spread/trunk/debian/install
===================================================================
--- trunk/packages/phy-spread/trunk/debian/install (rev 0)
+++ trunk/packages/phy-spread/trunk/debian/install 2012-01-27 16:11:51 UTC (rev 9453)
@@ -0,0 +1,2 @@
+dist/*.jar usr/share/java
+debian/scripts/* usr/bin
Deleted: trunk/packages/phy-spread/trunk/debian/libkmlframework-java.jlibs
===================================================================
--- trunk/packages/phy-spread/trunk/debian/libkmlframework-java.jlibs 2012-01-27 15:19:21 UTC (rev 9452)
+++ trunk/packages/phy-spread/trunk/debian/libkmlframework-java.jlibs 2012-01-27 16:11:51 UTC (rev 9453)
@@ -1 +0,0 @@
-lib/*.jar
Added: trunk/packages/phy-spread/trunk/debian/manifest
===================================================================
--- trunk/packages/phy-spread/trunk/debian/manifest (rev 0)
+++ trunk/packages/phy-spread/trunk/debian/manifest 2012-01-27 16:11:51 UTC (rev 9453)
@@ -0,0 +1,3 @@
+/usr/share/java/spread.jar:
+ Class-Path: /usr/share/java/processing-core.jar /usr/share/java/jebl.jar /usr/share/java/org.boehn.kmlframework.jar /usr/share/java/colt.jar /usr/share/java/ColorPicker.jar
+ Main-class: gui.SpreadApp
Modified: trunk/packages/phy-spread/trunk/debian/patches/build_xml.patch
===================================================================
--- trunk/packages/phy-spread/trunk/debian/patches/build_xml.patch 2012-01-27 15:19:21 UTC (rev 9452)
+++ trunk/packages/phy-spread/trunk/debian/patches/build_xml.patch 2012-01-27 16:11:51 UTC (rev 9453)
@@ -1,49 +1,39 @@
---- /dev/null
-+++ libkmlframework-java-20090718/src/build.xml
-@@ -0,0 +1,46 @@
-+<project name="kmlframework" basedir="." default="dist">
-+
-+ <property environment="env" />
-+
-+ <property name="version" value="1.2" />
-+ <property name="build.nb" value="0" />
-+
-+ <patternset id="java.libs" includes="*.jar" />
-+ <path id="mylibs">
-+ <fileset dir="/usr/share/java">
-+ <patternset refid="java.libs" />
-+ </fileset>
-+ </path>
-+
-+ <property name="src.dir" value="." />
-+ <property name="bin.dir" value="../bin" />
-+ <property name="lib.dir" value="../lib" />
-+
-+ <patternset id="java.libs" includes="*.jar" />
-+
-+ <target name="clean" description="Delete all generated files">
-+ <delete dir="${bin.dir}" />
-+ </target>
-+
-+ <target name="compile" description="Compile src files"
-+ depends="clean">
-+ <delete dir="${bin.dir}" />
-+ <mkdir dir="${bin.dir}" />
-+ <javac classpathref="mylibs" srcdir="${src.dir}" destdir="${bin.dir}">
-+ </javac>
-+ </target>
-+
-+ <target name="create-jar" description="Create jar file" depends="compile">
-+ <jar destfile="${lib.dir}/org.boehn.kmlframework.jar" basedir="${bin.dir}"
-+ update="true">
-+ <manifest>
-+ <!-- <attribute name="Main-Class" value="THE MAIN CLASS OF THE PROGRAM" /> -->
-+ <attribute name="Implementation-Version" value="${version}" />
-+ <attribute name="Implementation-Build" value="${build.nb}" />
-+ </manifest>
-+ </jar>
-+ </target>
-+
-+ <target name="dist" depends="create-jar" />
-+
-+</project>
+--- spread-1.0.2.orig/build.xml
++++ spread-1.0.2/build.xml
+@@ -34,11 +34,11 @@
+ <attribute name="Main-Class" value="${main_class_SpreadApp}" />
+ </manifest>
+ <fileset dir="classes"/>
+- <zipgroupfileset dir="lib" includes="core.jar"/>
+- <zipgroupfileset dir="lib" includes="jebl.jar"/>
+- <zipgroupfileset dir="lib" includes="org.boehn.kmlframework_20090320.jar"/>
+- <zipgroupfileset dir="lib" includes="colt.jar"/>
+- <zipgroupfileset dir="lib" includes="ColorPicker.jar"/>
++ <zipgroupfileset dir="/usr/share/java" includes="processing-core.jar"/>
++ <zipgroupfileset dir="/usr/share/java" includes="jebl.jar"/>
++ <zipgroupfileset dir="/usr/share/java" includes="org.boehn.kmlframework.jar"/>
++ <zipgroupfileset dir="/usr/share/java" includes="colt.jar"/>
++ <zipgroupfileset dir="/usr/share/java" includes="ColorPicker.jar"/>
+ <!--
+ <zipgroupfileset dir="lib" includes="quaqua.jar"/>
+ -->
+--- spread-1.0.2.orig/.classpath
++++ spread-1.0.2/.classpath
+@@ -1,12 +1,11 @@
+ <?xml version="1.0" encoding="UTF-8"?>
+ <classpath>
+ <classpathentry kind="src" path="src"/>
+- <classpathentry kind="lib" path="lib/core.jar"/>
+- <classpathentry kind="lib" path="lib/jebl.jar"/>
+- <classpathentry kind="lib" path="lib/org.boehn.kmlframework_20090320.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/processing-core.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/jebl.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/org.boehn.kmlframework.jar"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+- <classpathentry kind="lib" path="lib/colt.jar"/>
+- <classpathentry kind="lib" path="lib/ColorPicker.jar"/>
+- <classpathentry kind="lib" path="release/Mac/lib/quaqua.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/colt.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/ColorPicker.jar"/>
+ <classpathentry kind="output" path="bin"/>
+ </classpath>
Added: trunk/packages/phy-spread/trunk/debian/patches/follow_hint_from_README.patch
===================================================================
--- trunk/packages/phy-spread/trunk/debian/patches/follow_hint_from_README.patch (rev 0)
+++ trunk/packages/phy-spread/trunk/debian/patches/follow_hint_from_README.patch 2012-01-27 16:11:51 UTC (rev 9453)
@@ -0,0 +1,18 @@
+Author: Andreas Tille <tille at debian.org>
+Description: README says:
+ Before exporting to a runnable jar change line 12 in templates.MapBackground.java:
+ boolean fromJar = false
+ to
+ boolean fromJar = true
+
+--- spread-1.0.2.orig/src/templates/MapBackground.java
++++ spread-1.0.2/src/templates/MapBackground.java
+@@ -11,7 +11,7 @@
+ public static int mapImageWidth = 2048;
+ public static int mapImageHeight = 1025;
+
+- boolean fromJar = false;
++ boolean fromJar = true;
+
+ public MapBackground(PApplet p) {
+
Modified: trunk/packages/phy-spread/trunk/debian/patches/series
===================================================================
--- trunk/packages/phy-spread/trunk/debian/patches/series 2012-01-27 15:19:21 UTC (rev 9452)
+++ trunk/packages/phy-spread/trunk/debian/patches/series 2012-01-27 16:11:51 UTC (rev 9453)
@@ -1 +1,2 @@
+follow_hint_from_README.patch
build_xml.patch
Modified: trunk/packages/phy-spread/trunk/debian/rules
===================================================================
--- trunk/packages/phy-spread/trunk/debian/rules 2012-01-27 15:19:21 UTC (rev 9452)
+++ trunk/packages/phy-spread/trunk/debian/rules 2012-01-27 16:11:51 UTC (rev 9453)
@@ -1,19 +1,18 @@
#!/usr/bin/make -f
# -*- makefile -*-
-# debian/rules file for libkmlframework-java
+# debian/rules file for spread
# Andreas Tille <tille at debian.org>
# GPL
+#export DH_VERBOSE=1
+
+DEBJAR := /usr/share/java
+CLASSPATH := $(DEBJAR)/jebl.jar:$(DEBJAR)/colt.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/ColorPicker.jar:$(DEBJAR)/processing-core.jar
+
%:
dh $@ --with javahelper
override_dh_auto_build:
- ant -f src/build.xml
-
-override_dh_clean:
- ant -f src/build.xml clean
- rm -rf lib
- dh_clean
-
-get-orig-source:
- uscan --verbose --force-download --repack --rename
+ # no idea why setting CLASSPATH explicitely this way, however patching
+ # build.xml and .classpath seems not to be sufficient
+ CLASSPATH=$(CLASSPATH) ant jar
Added: trunk/packages/phy-spread/trunk/debian/scripts/phy-spread
===================================================================
--- trunk/packages/phy-spread/trunk/debian/scripts/phy-spread (rev 0)
+++ trunk/packages/phy-spread/trunk/debian/scripts/phy-spread 2012-01-27 16:11:51 UTC (rev 9453)
@@ -0,0 +1,4 @@
+#!/bin/sh
+
+DEBJAR="/usr/share/java"
+java -Xms64m -Xmx512m -jar /usr/share/java/spread.jar $*
Property changes on: trunk/packages/phy-spread/trunk/debian/scripts/phy-spread
___________________________________________________________________
Added: svn:executable
+ *
Modified: trunk/packages/phy-spread/trunk/debian/watch
===================================================================
--- trunk/packages/phy-spread/trunk/debian/watch 2012-01-27 15:19:21 UTC (rev 9452)
+++ trunk/packages/phy-spread/trunk/debian/watch 2012-01-27 16:11:51 UTC (rev 9453)
@@ -1,2 +1,5 @@
version=3
-http://googlecode.debian.net/p/kmlframework/org.boehn.kmlframework_(\d+).zip
+http://www.kuleuven.be/aidslab/phylogeography/SPREAD.html \
+ https://github.com/.*/phylogeography/SPREAD/spread-([.\d]+)\.tar\.gz
+
+# https://github.com/phylogeography/spread/tags .*/tarball/(.*)
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