.classpath

-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" path="source/java"/>
-	<classpathentry kind="src" path="sourceTest/java"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="lib" path="/libraries/testng/testng-jdk15.jar" sourcepath="/libraries/testng/src.zip"/>
-	<classpathentry kind="lib" path="/libraries/restrictionchecker/restrictions.jar"/>
-	<classpathentry kind="lib" path="/libraries/commons-io/commons-io.jar" sourcepath="/libraries/commons-io/src.zip"/>
-	<classpathentry kind="lib" path="/libraries/commons-lang/commons-lang.jar" sourcepath="/libraries/commons-lang/src.zip"/>
-	<classpathentry kind="lib" path="/libraries/unix"/>
-	<classpathentry kind="lib" path="/libraries/nativedata"/>
-	<classpathentry kind="output" path="targets/classes"/>
-</classpath>

.gitignore

+/targets
+/test-output
+/bin
+/build

branch.sh

-#!/bin/bash
-
-if [ `dirname $0` != "." ]
-then
-	echo "Please run from the same directory than the script source file is in"
-	exit 1
-fi
-
-if [ $# -ne 1 ]
-then
-  echo "Usage: ./branch.sh [branch]"
-  echo ""
-  echo "Example: ./branch.sh release/13.04.x"
-  exit 1
-fi
-
-svn info svn+ssh://svncisd.ethz.ch/repos/cisd/base/branches/$1 2>/dev/null
-if [ $? -eq 0 ]; then echo "Branch already exists!"; exit 1; fi
-
-CURRENT=`svn info|grep URL|cut -d" " -f2`
-
-svn copy $CURRENT svn+ssh://svncisd.ethz.ch/repos/cisd/base/branches/$1 -m "create branch $1"
-mkdir -p out
-rm -r out/temp_checkout
-svn checkout --depth=empty svn+ssh://svncisd.ethz.ch/repos/cisd/base/branches/$1 out/temp_checkout
-if [ $? -ne 0 ]; then echo "Checkout of new branch $1 failed!"; exit 1; fi
-
-cd out/temp_checkout
-svn update gradlew gradle build.gradle
-./gradlew dependencyReport
-cat out/reports/project/dependencies.txt|egrep ^.---|grep \>|sort|uniq|awk '{print $2 ":" $4}'|awk -F: '{print "s/" $1 ":" $2 ":" $3 "/" $1 ":" $2 ":" $4 "/g"}' > sed_commands
-sed -f sed_commands build.gradle > build.gradle.tmp
-mv build.gradle.tmp build.gradle
-svn commit build.gradle -m "fixed dependencies for branch $1"
-cd ../..

build.gradle

-apply from: '../gradle/javaproject.gradle'
+apply from: './javaproject.gradle'
 
 group='sis'
 
@@ -24,6 +24,14 @@ sourceSets {
 }
 
 jar {
+    manifest {
+        attributes 'Main-Class': 'ch.systemsx.cisd.base.BuildAndEnvironmentInfo'
+    }
+
+    from('targets/dist') {
+        include 'BUILD*INFO'
+    }    
+
     from fileTree("libs/")
 }
 

build/antrun.sh

+#! /bin/bash
+
+ME="$0"
+MYDIR=${ME%/*}
+cd $MYDIR
+ant -lib ../../build_resources/lib/ecj.jar "$@"

build/build.xml

+<project name="base" default="dist" basedir="..">
+	<target name="clean">
+		<delete dir="${dist}" />
+	</target>
+
+	<import file="../../build_resources/ant/build-common.xml" />
+
+	<project-classpath name="ecp" classes="${classes}" />
+	<property name="distfolder" value="sis-base" />
+	<property name="mainfolder" value="base" />
+	<property name="jar.file" value="${dist}/sis-base.jar" />
+	<property name="dist.file" value="${dist}/sis-base" />
+	<property name="jar.test.file" value="${dist}/sis-base-test.jar" />
+	<property name="src.zip.file" value="${dist}/sis-base-src.zip" />
+	<property name="javadoc.zip.file" value="${dist}/sis-base-javadoc.zip" />
+	<property name="original.dist" value="../${ant.project.name}/dist" />
+	<property name="nativesrc" value="libs/native" />
+	<property name="nativeroot" value="${targets}/ant" />
+	<property name="native" value="${nativeroot}/native" />
+
+	<property name="dist.common" value="${dist}/${mainfolder}" />
+	<property name="dist.common.lib" value="${dist.common}/lib" />
+
+
+	<target name="ci" depends="build-common.ci, check-dependencies, dist" />
+
+	<target name="jar" depends="compile">
+		<mkdir dir="${dist.common.lib}" />
+		<build-info revision="revision.number" version="version.number" clean="clean.flag" />
+		<echo file="${build.info.file}">${version.number}:${revision.number}:${clean.flag}</echo>
+		<copy todir="${native}">
+			<fileset dir="${nativesrc}">
+				<include name="**/libunix.so" />
+				<include name="**/libunix.jnilib" />
+			</fileset>
+		</copy>
+		<copy todir="${native}">
+			<fileset dir="${nativesrc}">
+				<include name="**/libnativedata.so" />
+				<include name="**/libnativedata.jnilib" />
+				<include name="**/nativedata.dll" />
+			</fileset>
+		</copy>
+		<recursive-jar destfile="${jar.file}">
+			<fileset dir="${classes}">
+				<include name="**/*.class" />
+				<include name="${build.info.filename}" />
+			</fileset>
+			<fileset dir="${nativeroot}">
+				<include name="native/**/*.so" />
+				<include name="native/**/*.jnilib" />
+				<include name="native/**/*.dll" />
+			</fileset>
+			<manifest>
+				<attribute name="Main-Class"
+				           value="ch.systemsx.cisd.base.BuildAndEnvironmentInfo" />
+				<attribute name="Version" value="${version.number}" />
+				<attribute name="Build-Number"
+				           value="${version.number} (r${revision.number},${clean.flag})" />
+			</manifest>
+		</recursive-jar>
+	</target>
+
+	<target name="jar-test" depends="compile-tests">
+		<mkdir dir="${dist.common.lib}" />
+		<build-info revision="revision.number" version="version.number" clean="clean.flag" />
+		<echo file="${build.info.file}">${version.number}:${revision.number}:${clean.flag}</echo>
+		<copy todir="${native}">
+			<fileset dir="${nativesrc}">
+				<include name="**/libunix.so" />
+				<include name="**/libunix.jnilib" />
+			</fileset>
+		</copy>
+		<copy todir="${native}">
+			<fileset dir="${nativesrc}">
+				<include name="**/libnativedata.so" />
+				<include name="**/libnativedata.jnilib" />
+				<include name="**/nativedata.dll" />
+			</fileset>
+		</copy>
+		<recursive-jar destfile="${jar.test.file}">
+			<fileset dir="${classes}">
+				<include name="**/*.class" />
+				<include name="${build.info.filename}" />
+			</fileset>
+			<fileset dir="${nativeroot}">
+				<include name="native/**/*.so" />
+				<include name="native/**/*.jnilib" />
+				<include name="native/**/*.dll" />
+			</fileset>
+			<zipfileset src="${lib}/testng/testng-jdk15.jar" />
+			<zipfileset src="${lib}/commons-lang/commons-lang.jar" />
+			<zipfileset src="${lib}/commons-io/commons-io.jar" />
+			<manifest>
+				<attribute name="Main-Class" value="ch.systemsx.cisd.base.AllTests" />
+				<attribute name="Version" value="${version.number}" />
+				<attribute name="Build-Number"
+				           value="${version.number} (r${revision.number},${clean.flag})" />
+			</manifest>
+		</recursive-jar>
+	</target>
+
+	<target name="src-zip">
+		<build-info revision="revision.number" version="version.number" clean="clean.flag" />
+		<mkdir dir="${classes}" />
+		<echo file="${build.info.file}">${version.number}:${revision.number}:${clean.flag}</echo>
+		<jar destfile="${src.zip.file}">
+			<fileset dir="${classes}">
+				<include name="${build.info.filename}" />
+			</fileset>
+			<fileset dir="${sources}">
+				<include name="**/*.java" />
+			</fileset>
+			<fileset dir="${sources.test}">
+				<include name="ch/systemsx/cisd/base/tests/**/*.java" />
+			</fileset>
+			<manifest>
+				<attribute name="Version" value="${version.number}" />
+				<attribute name="Build-Number"
+				           value="${version.number} (r${revision.number},${clean.flag})" />
+			</manifest>
+		</jar>
+	</target>
+
+	<target name="doc">
+		<delete dir="targets/doc" />
+		<javadoc sourcepath="source/java"
+		         packagenames="ch.systemsx.cisd.base.*"
+		         classpath="../libraries/commons-lang/commons-lang.jar:../libraries/commons-io/commons-io.jar:../libraries/testng/testng-jdk15.jar:../libraries/restrictionchecker/restrictions.jar"
+		         destdir="targets/doc"
+		         access="public" />
+	</target>
+
+	<target name="dist" depends="clean, jar, jar-test, src-zip, doc">
+		<zip destfile="${javadoc.zip.file}" basedir="${targets}" includes="doc/**" />
+		<delete dir="${dist}/${mainfolder}" />
+		<delete dir="${dist}/${distfolder}" />
+		<move file="${jar.file}" todir="${dist}/${distfolder}/lib" />
+		<move file="${jar.test.file}" todir="${dist}/${distfolder}/lib" />
+		<move file="${src.zip.file}" todir="${dist}/${distfolder}/src" />
+		<move file="${javadoc.zip.file}" todir="${dist}/${distfolder}/doc" />
+		<copy todir="${dist}/${distfolder}/doc">
+			<fileset dir="doc" includes="**" />
+		</copy>
+	  <copy todir="${dist}/${distfolder}">
+	    <fileset dir="${original.dist}"/>
+	  </copy>
+		<zip destfile="${dist.file}-${version.number}-r${revision.number}.zip"
+		     basedir="${dist}"
+		     includes="${distfolder}/**" />
+		<delete dir="${dist}/${distfolder}" />
+	</target>
+
+	<!--
+	  // Runs the test suite 'tests.xml'.
+	  -->
+	<target name="run-tests" description="Runs the test suite 'tests.xml'.">
+		<antcall target="build-common.run-tests">
+			<param name="test.suite" value="tests.xml" />
+		</antcall>
+	</target>
+
+</project>

debian/changelog

+libsis-base-java (18.08~pre+git20180810.9248fca+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream Git checkout
+  * Upstream moved to Gitlab
+  * d/watch: use git mode
+  * Fix homepage
+  * Drop binary files from upstream source
+  * Drop now unneeded get-orig-source target
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.0
+  TODO: Run time test failure: testGetLinkInfoRegularFile
+
+ -- Andreas Tille <tille@debian.org>  Tue, 14 Aug 2018 09:31:05 +0200
+
 libsis-base-java (14.12.0-5) unstable; urgency=medium
 
   * d/watch: Enable parsing verisoned dirs

debian/control

@@ -13,10 +13,10 @@ Build-Depends: debhelper (>= 11),
                testng,
                libtool,
                procps
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libsis-base-java.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/libsis-base-java.git
-Homepage: https://svnsis.ethz.ch/repos/cisd/libraries/trunk/sis-base/
+Standards-Version: 4.2.0
+Vcs-Browser: https://salsa.debian.org/med-team/libsis-base-java
+Vcs-Git: https://salsa.debian.org/med-team/libsis-base-java.git
+Homepage: https://sissource.ethz.ch/sispub/base
 
 Package: libsis-base-java
 Architecture: all

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: sis-base
-Upstream-Contact: https://www1.ethz.ch/id/about/sections/sis/index_EN
+Upstream-Contact: https://sissource.ethz.ch/sispub/base
                   Bernd Rinn <brinn@ethz.ch>
-Source: http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/sis-base/sis-base.jar
+Source: https://sissource.ethz.ch/sispub/base
+Files-Excluded: */native
 
 Files: *
-Copyright: 2007-2012 ETH Zuerich, CISD
+Copyright: 2007-2018 ETH Zuerich, CISD
 License: Apache
  On Debian systems, you can read the full text of the Apache
  License in ‘/usr/share/common-licenses/Apache-2.0’.
 
 Files: source/c/*
 Copyright: 1988-2004, the Board of Trustees of the University of Illinois.
-           2007-2009, Center for Information Sciences and Databases, ETH Zurich, Switzerland.
+           2007-2018, Center for Information Sciences and Databases, ETH Zurich, Switzerland.
 License: hdf5
  Contributors to the library: National Center for Supercomputing 
  Applications (NCSA) at the University of Illinois, Lawrence 
@@ -90,6 +91,7 @@ License: hdf5
 Files: debian/*
 Copyright: 2015 Tim Booth <tbooth@ceh.ac.uk>
            2015 Olivier Sallou <osallou@debian.org>
+           2015-2018 Andreas Tille <tille@debian.org>
 License: GPL-3
  On Debian systems, the full text of the GNU General Public
  License version 3 can be found in the file

debian/get-orig-source

-#!/bin/bash
-
-set -e
-
-PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-
-VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
-
-cd ..
-mkdir -p tarballs
-cd tarballs
-
-svn export https://svnsis.ethz.ch/repos/cisd/base/tags/release/14.12.x/${VERSION}/base ${PKG}-${VERSION}
-rm -rf ${PKG}-${VERSION}/build
-rm -rf ${PKG}-${VERSION}/libs
-
-GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX --exclude-vcs -caf "$PKG"_"$VERSION".orig.tar.xz "$PKG"-"$VERSION"
-rm -rf "$PKG"-"$VERSION"
-

debian/rules

@@ -10,9 +10,6 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 DPKG_EXPORT_BUILDFLAGS = 1
 include /usr/share/dpkg/buildflags.mk
 
-get-orig-source:
-	. debian/get-orig-source
-
 %:
 	dh $@ --with javahelper
 

debian/watch

 version=4
 
-# This watch file does not really work since it is pointing to a directory instead of a file
-https://svnsis.ethz.ch/repos/cisd/base/tags/release/(\d+\.\d+\.x)/(\d+\.\d+\.\d+) \
-   debian debian/get-orig-source
+opts="mode=git,pretty=18.08~pre+git%cd.%h,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+    https://sissource.ethz.ch/sispub/base.git HEAD
+
+# The versioning is <year>.<month>.<patch level>. So the next release will be
+# something like 18.09.0 or 18.10.0. If you call the pre-release 18.08, you will
+# be fine

gradle/wrapper/gradle-wrapper.properties

-#Wed Apr 23 11:31:33 CEST 2014
+#Tue Jun 13 15:27:00 CEST 2017
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=http\://svncisd.ethz.ch/repos/cisd/ivy-repository/trunk/gradle/distribution/1.8/gradle-1.8-all.zip
+distributionUrl=http\://svnsis.ethz.ch/repos/cisd/ivy-repository/trunk/gradle/distribution/3.5/gradle-3.5-all.zip

gradlew

-#!/usr/bin/env bash
+#!/usr/bin/env sh
 
 ##############################################################################
 ##
@@ -6,12 +6,30 @@
 ##
 ##############################################################################
 
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS=""
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >/dev/null
+APP_HOME="`pwd -P`"
+cd "$SAVED" >/dev/null
 
 APP_NAME="Gradle"
 APP_BASE_NAME=`basename "$0"`
 
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS=""
+
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD="maximum"
 
@@ -30,6 +48,7 @@ die ( ) {
 cygwin=false
 msys=false
 darwin=false
+nonstop=false
 case "`uname`" in
   CYGWIN* )
     cygwin=true
@@ -40,31 +59,11 @@ case "`uname`" in
   MINGW* )
     msys=true
     ;;
+  NONSTOP* )
+    nonstop=true
+    ;;
 esac
 
-# For Cygwin, ensure paths are in UNIX format before anything is touched.
-if $cygwin ; then
-    [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
-fi
-
-# Attempt to set APP_HOME
-# Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
-    ls=`ls -ld "$PRG"`
-    link=`expr "$ls" : '.*-> \(.*\)$'`
-    if expr "$link" : '/.*' > /dev/null; then
-        PRG="$link"
-    else
-        PRG=`dirname "$PRG"`"/$link"
-    fi
-done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >&-
-APP_HOME="`pwd -P`"
-cd "$SAVED" >&-
-
 CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 
 # Determine the Java command to use to start the JVM.
@@ -90,7 +89,7 @@ location of your Java installation."
 fi
 
 # Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" ] ; then
+if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
     MAX_FD_LIMIT=`ulimit -H -n`
     if [ $? -eq 0 ] ; then
         if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
@@ -114,6 +113,7 @@ fi
 if $cygwin ; then
     APP_HOME=`cygpath --path --mixed "$APP_HOME"`
     CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+    JAVACMD=`cygpath --unix "$JAVACMD"`
 
     # We build the pattern for arguments to be converted via cygpath
     ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
@@ -154,11 +154,19 @@ if $cygwin ; then
     esac
 fi
 
-# Split up the JVM_OPTS And GRADLE_OPTS values into an array, following the shell quoting and substitution rules
-function splitJvmOpts() {
-    JVM_OPTS=("$@")
+# Escape application args
+save ( ) {
+    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+    echo " "
 }
-eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS
-JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"
+APP_ARGS=$(save "$@")
+
+# Collect all arguments for the java command, following the shell quoting and substitution rules
+eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+
+# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
+if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
+  cd "$(dirname "$0")"
+fi
 
-exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"
+exec "$JAVACMD" "$@"

gradlew.bat

@@ -8,14 +8,14 @@
 @rem Set local scope for the variables with windows NT shell
 if "%OS%"=="Windows_NT" setlocal
 
-@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS=
-
 set DIRNAME=%~dp0
 if "%DIRNAME%" == "" set DIRNAME=.
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS=
+
 @rem Find java.exe
 if defined JAVA_HOME goto findJavaFromJavaHome
 
@@ -46,10 +46,9 @@ echo location of your Java installation.
 goto fail
 
 :init
-@rem Get command-line arguments, handling Windowz variants
+@rem Get command-line arguments, handling Windows variants
 
 if not "%OS%" == "Windows_NT" goto win9xME_args
-if "%@eval[2+2]" == "4" goto 4NT_args
 
 :win9xME_args
 @rem Slurp the command line arguments.
@@ -60,11 +59,6 @@ set _SKIP=2
 if "x%~1" == "x" goto execute
 
 set CMD_LINE_ARGS=%*
-goto execute
-
-:4NT_args
-@rem Get arguments from the 4NT Shell from JP Software
-set CMD_LINE_ARGS=%$
 
 :execute
 @rem Setup the command line

javaproject.gradle

+apply plugin: 'java'
+apply plugin: 'project-report'
+
+evaluationDependsOnChildren()
+
+configurations {
+    tests  { 
+         extendsFrom testRuntime 
+     }
+}
+
+configurations {
+	ecj
+}
+
+configurations.all {
+    resolutionStrategy.cacheDynamicVersionsFor 0, 'hours'
+    resolutionStrategy.cacheChangingModulesFor 0, 'hours'
+}
+
+task wrapper(type: Wrapper) {
+    gradleVersion = '3.5'
+    distributionUrl = "http://svnsis.ethz.ch/repos/cisd/ivy-repository/trunk/gradle/distribution/3.5/gradle-3.5-all.zip"
+}
+
+sourceCompatibility='1.8'
+targetCompatibility='1.8'
+
+sourceSets { 
+    main {
+        java {
+            srcDirs = ['source/java']
+        }
+    }
+    test {
+        java {
+            srcDirs = ['sourceTest/java']
+        }
+        resources {
+            srcDirs = ['sourceTest/java']
+        }
+    }
+    examples {
+        java {
+            srcDirs = ['sourceExamples/java']
+        }
+    }
+}
+
+buildDir = 'targets/gradle'
+
+buildscript {
+    apply from: './repository.gradle'
+    
+    repositories repositoryConfig
+    
+    dependencies {
+        classpath 'cisd:cisd-ant-tasks:+'
+    }
+}
+
+repositories repositoryConfig
+
+def execute(command, arguments) {
+    new ByteArrayOutputStream().withStream { os ->
+        print "execute: ${command}"
+        arguments.collect({print " ${it}"})
+        println ''
+        def result = exec {
+            executable = command
+            args = arguments
+            standardOutput = os
+        }
+        return os.toString().split('\n')
+    }
+}
+
+ext.executeFunction = {
+  command, arguments -> execute(command, arguments)
+}
+
+def execute_working_dir(command, arguments, working_dir) {
+    new ByteArrayOutputStream().withStream { os ->
+        print "execute: ${command}"
+        arguments.collect({print " ${it}"})
+        println ''
+        def result = exec {
+            executable = command
+            args = arguments
+            standardOutput = os
+        }
+        return os.toString().split('\n')
+    }
+}
+
+ext.svnCommand = 'svn'
+
+def isSvnProject() {
+   return new java.io.File(projectDir, ".svn").isDirectory() || new java.io.File(projectDir, "../.svn").isDirectory() 
+}
+
+def isGitProject() {
+   return new java.io.File(projectDir, ".git").isDirectory() || new java.io.File(projectDir, "../.git").isDirectory() 
+}
+
+def executeSVN(arguments) {
+    arguments.add(0, '--non-interactive')
+    return execute(svnCommand, arguments)
+}
+
+def calculateCleanFlag() {
+    return 'clean'
+    for (childProject in project.childProjects.values()) {
+        if (childProject.cleanFlag == 'dirty') {
+            return 'dirty'
+        }
+    }
+    def isSvn = isSvnProject()
+    if (isSvn) {
+        def output = executeSVN(['status', '../' + project.name])
+        def lines = output.findAll({ (it.startsWith('?') || it.trim().isEmpty()) == false})
+        return lines.isEmpty() ? 'clean' : 'dirty'
+    } else if (isGitProject()) {
+        def output = execute_working_dir('git', ['status', '--porcelain'], '../' + project.name)
+        return output.length == 0 ? 'clean' : 'dirty'
+    } else {
+    	return 'dirty'
+    }
+}
+
+def findMaximum(lines, key) {
+    return lines.findAll({ it.startsWith(key)}).collect({element -> element.split(':')[1].toInteger()}).max()
+}
+
+def calculateBuildInfo() {
+    if (isSvnProject()) {
+        def output = executeSVN(['info', '-R', '../' + project.name])
+        def maxRevisionNumber = findMaximum(output, 'Revision:')
+        project.ext.revisionNumber = findMaximum(output, 'Last Changed Rev:')
+        if (maxRevisionNumber < project.ext.revisionNumber) {
+            throw new GradleException("Maximum revision ($maxRevisionNumber) is less than the maximum "
+                      + "last changed revision ($project.ext.revisionNumber).")
+        }
+        project.ext.versionNumber = 'SNAPSHOT'
+        def url = output.findAll({ it.startsWith('URL:')})[0].split('URL:')[1].trim()
+        if (url.contains('/trunk') == false) {
+            def pathElements = url.split('/')
+            project.ext.versionNumber = 'libraries' == pathElements[-2] ? pathElements[-3] : pathElements[-2]
+        }
+    } else if (isGitProject()) {
+        def gitlogoutput = execute_working_dir('git', ['log', '-1', '--format=%at'], '../' + project.name)
+        project.ext.revisionNumber = Integer.parseInt(gitlogoutput[0])
+        def tag = 'git tag -l --points-at HEAD'.execute().text.trim()
+        if (tag == null || tag.isEmpty()) {
+            project.ext.versionNumber = 'SNAPSHOT'
+        } else if (tag.contains('pybis')) {
+           throw new GradleException("project must contain a readme file")
+        } else {
+           project.ext.versionNumber = tag
+        }
+    } else {
+        project.ext.revisionNumber = 1
+        project.ext.versionNumber = 'SNAPSHOT'
+    }
+
+    for (childProject in project.childProjects.values()) {
+        project.ext.revisionNumber = Math.max(project.ext.revisionNumber, childProject.revisionNumber)
+        if (project.ext.versionNumber != childProject.versionNumber) {
+            throw new GradleException("Inconsistent version numbers: "
+                        + "${project.name} at version ${project.ext.versionNumber} but "
+                        + "${childProject.name} at version ${childProject.versionNumber}.") 
+        } 
+    }
+    version = "${project.ext.versionNumber}-r${project.ext.revisionNumber}"
+    project.ext.revisionForPublication = project.ext.versionNumber.startsWith('SNAPSHOT') ? "r${project.ext.revisionNumber}" : project.ext.versionNumber
+    project.ext.cleanFlag = calculateCleanFlag()
+    def buildInfo = "${project.ext.versionNumber}:${project.ext.revisionNumber}:${project.ext.cleanFlag}"
+    println "BUILD INFO for $project: $buildInfo"
+    def targetsDist = 'targets/dist'
+    def distFolder = new File("${project.projectDir}/$targetsDist")
+    distFolder.deleteDir()
+    distFolder.mkdirs()
+    file("${project.projectDir}/$targetsDist/BUILD-${project.name}.INFO") << buildInfo
+}
+
+calculateBuildInfo()
+
+group='cisd'
+
+task checkRestrictions(type: Exec, dependsOn: [classes, testClasses]) {
+    doFirst {
+        def cp = configurations.testCompile.filter({ f -> f.name.startsWith('restrictionchecker') || f.name.startsWith('bcel')}).asPath
+        def cmd = ['java', '-cp', cp, 'ch.rinn.restrictions.RestrictionChecker', '-r', sourceSets.main.output.classesDir]
+        if (sourceSets.test.output.classesDir.exists()) {
+            cmd.add(sourceSets.test.output.classesDir)
+        }
+        cmd.add('-cp')
+        cmd.add(sourceSets.main.output.classesDir)
+        if (sourceSets.test.output.classesDir.exists()) {
+            cmd.add(sourceSets.test.output.classesDir)
+        }
+        cmd.add(configurations.testCompile.asPath)
+        commandLine cmd
+    }
+}
+
+def deleteSymbolicLinksRecursively(file) {
+    def absolutePath = file.getAbsolutePath()
+    def canonicalPath = file.getCanonicalPath()
+    if (absolutePath.equals(canonicalPath) == false) {
+        file.delete();
+    } else if (file.isDirectory()) {
+        File[] files = file.listFiles()
+        for (File child : files) {
+            deleteSymbolicLinksRecursively(child)
+        }
+    }
+}
+
+task deleteSymLinks {
+    doFirst {
+        println "DELETE SYM LINKS in $buildDir"
+        deleteSymbolicLinksRecursively buildDir
+    }
+}
+
+clean.dependsOn deleteSymLinks
+
+test {
+    useTestNG()
+    options.suites('sourceTest/java/tests.xml')    
+
+    systemProperty "ant.project.name", project.name
+
+    maxHeapSize = "8192m"
+    jvmArgs '-XX:MaxPermSize=1024m', '-Duser.timezone=Europe/Zurich'
+    
+    testLogging.showStandardStreams = true
+    ignoreFailures = true
+}
+test.dependsOn checkRestrictions
+
+dependencies {
+    ecj "eclipse:ecj:+"
+}
+
+compileJava {
+    options.encoding = 'utf-8'
+    options.fork = true
+    doFirst {
+        options.forkOptions.with {
+            executable = 'java'
+            jvmArgs = createJvmArgs()
+        }
+    }
+}
+
+compileTestJava {
+    options.encoding = 'utf-8'
+    options.fork = true
+    doFirst {
+        options.forkOptions.with {
+            executable = 'java'
+            jvmArgs = createJvmArgs()
+        }
+    }
+}
+
+def createJvmArgs() {
+    def args = ['-cp', configurations.ecj.asPath, 'org.eclipse.jdt.internal.compiler.batch.Main', '-nowarn']
+    return args
+}
+
+processTestResources {
+    fileMode=0666
+}
+
+apply plugin: 'eclipse'
+
+eclipse {
+    classpath {
+        downloadSources=true
+        defaultOutputDir = file('targets/classes')
+    }
+}
+
+eclipse.classpath.file {
+    whenMerged{ classpath ->
+        def projectRefs = classpath.entries.findAll{entry -> entry.kind =='src' && entry.path.startsWith('/')}
+        classpath.entries.removeAll(projectRefs)
+        classpath.entries.addAll(projectRefs)   
+    }
+}
+
+task testJar(type: Jar, dependsOn: testClasses) {
+    baseName = "test-${project.archivesBaseName}"
+    from sourceSets.test.output
+}
+
+task sourcesJar(type: Jar) {
+    classifier = 'sources'
+    from sourceSets.main.allSource
+}
+
+compileJava.dependsOn sourcesJar
+
+artifacts {
+    tests testJar
+}
+
+artifacts {
+	archives sourcesJar
+}
+
+task compileDependencies(type: Copy) {
+    into "$buildDir/output/compile-dependencies"
+    from configurations.compile
+}
+
+task runtimeDependencies(type: Copy) {
+    into "$buildDir/output/runtime-dependencies"
+    from configurations.runtime
+}
+
+task testCompileDependencies(type: Copy) {
+    into "$buildDir/output/testCompile-dependencies"
+    from configurations.testCompile
+}
+
+task testRuntimeDependencies(type: Copy) {
+    into "$buildDir/output/testRuntime-dependencies"
+    from configurations.testRuntime
+}
+
+task checkDependencies(dependsOn: classes) << {
+	ant.taskdef(name: 'dependencychecker', classname: 'classycle.ant.DependencyCheckingTask', classpath: configurations.testRuntime.asPath)
+    ant.dependencychecker(
+                definitionFile: 'resource/dependency-structure.ddf', 
+                failOnUnwantedDependencies: 'true',
+                mergeInnerClasses: 'true') {
+        fileset(dir: "${buildDir}", includes: "**/*.class")
+    }
+}
+
+apply plugin: 'ivy-publish'
+if (hasProperty('ivyRepository') == false || ''.equals(project.ivyRepository))
+{
+    project.ext.ivyRepository = "${project.projectDir}/../ivy-repository"
+}
+publishing {
+
+    repositories {
+        ivy {
+            ivyPattern "file://${project.ivyRepository}/[organisation]/[module]/[revision]/ivy.xml"
+            artifactPattern "file://${project.ivyRepository}/[organisation]/[module]/[revision]/[artifact]-[revision](-[classifier]).[ext]"
+        }
+    }
+}
+
+publish {
+    dependsOn build
+}
+
+if (JavaVersion.current().isJava8Compatible()) {
+    tasks.withType(Javadoc) {
+        options.addStringOption('Xdoclint:none', '-quiet')
+    }
+}

repository.gradle

+ext.repositoryConfig = {
+    ivy {
+        ivyPattern "${project.projectDir}/../ivy-repository/[organisation]/[module]/[revision]/ivy.xml"
+        artifactPattern "${project.projectDir}/../ivy-repository/[organisation]/[module]/[revision]/[artifact]-[revision](-[classifier]).[ext]"
+    }
+    ivy {
+        ivyPattern "http://svnsis.ethz.ch/repos/cisd/ivy-repository/trunk/[organisation]/[module]/[revision]/ivy.xml"
+        artifactPattern "http://svnsis.ethz.ch/repos/cisd/ivy-repository/trunk/[organisation]/[module]/[revision]/[artifact]-[revision](-[classifier]).[ext]"
+    }
+}

source/java/ch/systemsx/cisd/base/utilities/NativeLibraryUtilities.java

@@ -141,8 +141,10 @@ public final class NativeLibraryUtilities
      */
     public static String tryCopyNativeLibraryToTempFile(final String libraryName)
     {
+        // Request clean-up of old native library temp files as under Windows the files are locked and 
+        // cannot be deleted on regular shutdown. 
         return ResourceUtilities.tryCopyResourceToTempFile(getLibPath("/native", libraryName),
-                libraryName, ".so");
+                libraryName, ".so", true);
     }
 
     private static String getLibPath(final String prefix, final String libraryName)

source/java/ch/systemsx/cisd/base/utilities/ResourceUtilities.java

@@ -18,11 +18,13 @@ package ch.systemsx.cisd.base.utilities;
 
 import java.io.File;
 import java.io.FileOutputStream;
+import java.io.FilenameFilter;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
 
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.filefilter.WildcardFileFilter;
 
 import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
 import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
@@ -56,6 +58,29 @@ public class ResourceUtilities
         }
     }
 
+    /**
+     * Tries to copy the resource with the given name to a temporary file.
+     * 
+     * @param resource The name of the resource to copy.
+     * @param prefix The prefix to use for the temporary name.
+     * @param postfix The postfix to use for the temporary name.
+     * @param cleanUpOldResources If <code>true</code>, remove old leftover temporary files for this
+     *            <var>prefix</var> and <var>postfix</var>.
+     * @return The name of the temporary file, or <code>null</code>, if the resource could not be
+     *         copied.
+     */
+    public static String tryCopyResourceToTempFile(final String resource, final String prefix,
+            final String postfix, final boolean cleanUpOldResources)
+    {
+        try
+        {
+            return copyResourceToTempFile(resource, prefix, postfix, cleanUpOldResources);
+        } catch (final Exception ex)
+        {
+            return null;
+        }
+    }
+
     /**
      * Copies the resource with the given name to a temporary file. The file will be deleted on
      * program exit.
@@ -70,6 +95,29 @@ public class ResourceUtilities
     public static String copyResourceToTempFile(final String resource, final String prefix,
             final String postfix) throws IOExceptionUnchecked
     {
+        return copyResourceToTempFile(resource, prefix, postfix, false);
+    }
+
+    /**
+     * Copies the resource with the given name to a temporary file. The file will be deleted on
+     * program exit.
+     * 
+     * @param resource The name of the resource to copy.
+     * @param prefix The prefix to use for the temporary name.
+     * @param postfix The postfix to use for the temporary name.
+     * @param cleanUpOldResources If <code>true</code>, remove old leftover temporary files for this
+     *            <var>prefix</var> and <var>postfix</var>.
+     * @return The name of the temporary file.
+     * @throws IllegalArgumentException If the resource cannot be found in the class path.
+     * @throws IOExceptionUnchecked If an {@link IOException} occurs.
+     */
+    public static String copyResourceToTempFile(final String resource, final String prefix,
+            final String postfix, final boolean cleanUpOldResources) throws IOExceptionUnchecked
+    {
+        if (cleanUpOldResources)
+        {
+            deleteOldResourceTempFiles(prefix, postfix);
+        }
         final InputStream resourceStream = ResourceUtilities.class.getResourceAsStream(resource);
         if (resourceStream == null)
         {
@@ -98,4 +146,13 @@ public class ResourceUtilities
         }
     }
 
+    private static void deleteOldResourceTempFiles(final String prefix, final String postfix)
+    {
+        final FilenameFilter filter = new WildcardFileFilter(prefix + "*" + postfix);
+        for (File file : new File(System.getProperty("java.io.tmpdir")).listFiles(filter))
+        {
+            file.delete();
+        }
+    }
+
 }