.checkstyle

+<?xml version="1.0" encoding="UTF-8"?>
+<fileset-config file-format-version="1.2.0" simple-config="false">
+    <local-check-config name="CISD Checks" location="/build_resources/checkstyle/cisd_checkstyle.xml" type="project" description="">
+        <additional-data name="protect-config-file" value="false"/>
+    </local-check-config>
+    <fileset name="all" enabled="true" check-config-name="CISD Checks" local="true">
+        <file-match-pattern match-pattern=".+ch/systemsx/cisd.+" include-pattern="true"/>
+    </fileset>
+</fileset-config>

.classpath

+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="source/java"/>
+	<classpathentry kind="src" path="sourceExamples/java"/>
+	<classpathentry kind="src" path="sourceTest/java"/>
+	<classpathentry kind="lib" path="/libraries/commons-lang/commons-lang.jar" sourcepath="/libraries/commons-lang/src.zip"/>
+	<classpathentry kind="lib" path="/libraries/commons-io/commons-io.jar" sourcepath="/libraries/commons-io/src.zip"/>
+	<classpathentry kind="lib" path="/libraries/cisd-args4j/cisd-args4j.jar"/>
+	<classpathentry kind="lib" path="/libraries/restrictionchecker/restrictions.jar"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
+	<classpathentry kind="lib" path="/libraries/testng/testng-jdk15.jar" sourcepath="/libraries/testng/src.zip"/>
+	<classpathentry kind="lib" path="/libraries/jmock/jmock.jar"/>
+	<classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-core.jar"/>
+	<classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-integration.jar"/>
+	<classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-library.jar"/>
+	<classpathentry kind="lib" path="/libraries/jmock/objenesis/objenesis-1.0.jar"/>
+	<classpathentry kind="lib" path="libs"/>
+	<classpathentry kind="lib" path="/libraries/sis-base/sis-base.jar" sourcepath="/libraries/sis-base/sis-base-src.zip"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="output" path="targets/classes"/>
+</classpath>

.gitignore

+/bin
+/build
+/.gradle
+/targets
+/.project
+/.settings
+/test-output
+/source/c/build
+source/c/hdf5*tar*

.shadow_dependencies

+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="lib" path="/libraries/unix"/>
+</classpath>

build.gradle

+apply from: 'javaproject.gradle'
+
+group='sis'
+sourceCompatibility='1.8'
+targetCompatibility='1.8'
+
+dependencies {
+    compile 'cisd:cisd-args4j:+',
+            'cisd:cisd-base:+',
+            'rinn:restrictions:+'
+    
+    testCompile 'testng:testng:+',
+                'jmock:jmock:+'
+}
+
+tasks.withType(Test) {
+    systemProperty "java.library.path", "libs/native/jhdf5/amd64-Linux:libs/native/jhdf5/amd64-Linux:libs/native/jhdf5/x86_64-Mac OS X:libs/native/jhdf5/x86_64-Mac OS X"
+}
+
+// Eclipse Gradle plugin always uses the default JRE, so we need to explicitly set it to 1.7.
+// (https://issues.gradle.org/browse/GRADLE-3100)
+eclipse {
+    classpath {
+         containers.remove('org.eclipse.jdt.launching.JRE_CONTAINER')
+         containers 'org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7'
+    }
+}
+
+jar {
+    baseName "${project.group}-jhdf5-core"
+    from (sourceSets.main.output.classesDir) { 
+        exclude('ch/systemsx/cisd/hdf5/h5ar') 
+        exclude('ch/systemsx/cisd/hdf5/io')
+    }
+    from('targets/dist') {
+        include 'BUILD*INFO'
+    }    
+    manifest {
+        attributes 'Main-Class': 'ch.systemsx.cisd.hdf5.BuildAndEnvironmentInfo'
+        attributes 'Class-Path': configurations.runtime.collect { it.getName() }.join(' ')
+    }
+    
+}
+
+task nativeJarLinuxIntel(type: Jar) {
+    archiveName 'hdf5-linux-intel.jar'
+    from ("libs") {
+        include 'native/jhdf5/amd64-Linux/**/*'
+        include 'native/jhdf5/arm-Linux/**/*'
+    }
+    
+    from('targets/dist') {
+        include 'BUILD*INFO'
+    }    
+}
+
+task nativeJarMacIntel(type: Jar) {
+    archiveName 'hdf5-macosx-intel.jar'
+    from ("libs") {
+        include 'native/jhdf5/x86_64-Mac OS X/**/*'
+    }
+    
+    from('targets/dist') {
+        include 'BUILD*INFO'
+    }    
+}
+
+task nativeJarWindowsIntel(type: Jar) {
+    archiveName 'hdf5-windows-intel.jar'
+    from ("libs") {
+        include 'native/jhdf5/amd64-Windows/**/*'
+    }
+    
+    from('targets/dist') {
+        include 'BUILD*INFO'
+    }    
+}
+
+task toolsJar(type: Jar, dependsOn: [compileJava]) {
+    baseName "${project.group}-jhdf5-tools"
+    from (sourceSets.main.output.classesDir) {
+        include('ch/systemsx/cisd/hdf5/h5ar/**/*') 
+        include('ch/systemsx/cisd/hdf5/io/**/*') 
+    }
+    
+    from('targets/dist') {
+        include 'BUILD*INFO'
+    }    
+    
+    manifest {
+        attributes 'Main-Class': 'ch.systemsx.cisd.hdf5.h5ar.HDF5ArchiverMain'
+        attributes 'Class-Path': configurations.runtime.collect { it.getName() }.join(' ') + " ${project.group}-jhdf5-core.jar " + [nativeJarLinuxIntel, nativeJarMacIntel, nativeJarWindowsIntel].collect {it.archiveName}.join(' ')
+    }
+}
+
+task allJar(type: Jar, dependsOn: [compileJava]) {
+    baseName "${project.group}-jhdf5"
+
+    from (sourceSets.main.output.classesDir) {
+        include '**/*'
+    }
+
+    from (configurations.runtime.collect {zipTree(it)}) {
+        exclude 'native/**/*'
+        exclude 'BUILD-*.INFO'
+    }
+
+    from('targets/dist') {
+        include 'BUILD*INFO'
+    }    
+    
+    manifest {
+        attributes 'Main-Class': 'ch.systemsx.cisd.hdf5.h5ar.HDF5ArchiverMain'
+        attributes 'Class-Path': [nativeJarLinuxIntel, nativeJarMacIntel, nativeJarWindowsIntel].collect {it.archiveName}.join(' ')
+    }
+}
+
+
+task batteriesIncluded(type: Jar, dependsOn: [allJar, nativeJarLinuxIntel, nativeJarMacIntel, nativeJarWindowsIntel]) {
+    archiveName "${project.group}-jhdf5-batteries_included.jar"
+    from (zipTree(allJar.archivePath)) {
+        include '**/*'
+    }
+    
+    from (configurations.runtime.collect {zipTree(it)}) {
+        include 'native/**/*'
+    }
+
+    from (zipTree(nativeJarLinuxIntel.archivePath)) {
+        include 'native/**/*'
+    }
+    from (zipTree(nativeJarMacIntel.archivePath)) {
+        include 'native/**/*'
+    }
+    from (zipTree(nativeJarWindowsIntel.archivePath)) {
+        include 'native/**/*'
+    }
+    
+    manifest {
+        attributes 'Main-Class': 'ch.systemsx.cisd.hdf5.h5ar.HDF5ArchiverMain'
+    }
+}
+
+task myJavadoc(type: Javadoc) {
+	source = [ sourceSets.main.allJava, "base-src" ]
+	classpath = configurations.compile
+	options.memberLevel = JavadocMemberLevel.PUBLIC
+	options.overview = "overview.html"
+	include "ch/systemsx/cisd/hdf5/**"
+	include "ch/ethz/sis/hdf5/**"
+	include "hdf/hdf5lib/exceptions/**"
+	exclude "ch/systemsx/cisd/hdf5/hdf5lib/**"
+	exclude "ch/ethz/sis/hdf5/hdf5lib/**"
+	exclude "ch/systemsx/cisd/hdf5/cleanup/**"
+	exclude "ch/systemsx/cisd/hdf5/BitSetConversionUtils.java"
+	exclude "ch/systemsx/cisd/hdf5/MatrixUtils.java"
+	exclude "ch/systemsx/cisd/hdf5/StringUtils.java"
+	exclude "ch/systemsx/cisd/hdf5/PaddingUtils.java"
+	exclude "ch/systemsx/cisd/hdf5/ReflectionUtils.java"
+}
+
+task javadocZip(type: Zip, dependsOn: myJavadoc) {
+    archiveName "${project.group}-jhdf5-javadoc.zip"
+    from javadoc.destinationDir
+}
+
+task exampleZip(type: Jar) {
+    archiveName "${project.group}-jhdf5-examples-src.zip"
+
+    from ("sourceExamples/java") {
+        include '**/*'
+    }
+    
+    from ("targets/dist") {
+        include "BUILD-jhdf5.INFO"
+    }
+}
+
+task distributionZip(type: Zip, dependsOn: [jar, toolsJar, allJar, nativeJarLinuxIntel, nativeJarMacIntel, nativeJarWindowsIntel, batteriesIncluded, javadocZip, sourcesJar, exampleZip]) {
+    baseName "${project.group}-jhdf5"
+
+    from (jar.archivePath) {
+        into "${project.group}-jhdf5/lib"
+        rename '(.*)', "${project.group}-jhdf5-core.jar"
+    }
+    
+    from (toolsJar.archivePath) {
+        into "${project.group}-jhdf5/lib"
+        rename '(.*)', "${project.group}-jhdf5-tools.jar"
+    }
+
+    from (allJar.archivePath) {
+        into "${project.group}-jhdf5/lib"
+        rename '(.*)', "${project.group}-jhdf5.jar"
+    }
+    
+    from (configurations.runtime) {
+        exclude '*restriction*'
+        exclude '*bcel*'
+        into "${project.group}-jhdf5/lib"
+    }
+    
+    from (zipTree(batteriesIncluded.archivePath)) {
+        into "${project.group}-jhdf5/lib"
+        include 'native/**'
+    }
+    
+    from (nativeJarLinuxIntel.archivePath) {
+        into "${project.group}-jhdf5/lib/nativejar"
+    }
+    
+    from (nativeJarMacIntel.archivePath) {
+        into "${project.group}-jhdf5/lib/nativejar"
+    }
+    
+    from (nativeJarWindowsIntel.archivePath) {
+        into "${project.group}-jhdf5/lib/nativejar"
+    }
+
+    from (batteriesIncluded.archivePath) {
+        into "${project.group}-jhdf5/lib/batteries_included"
+    }
+
+    from ("dist") {
+        into "${project.group}-jhdf5"
+    }
+    
+    from (javadocZip.archivePath) {
+        into "${project.group}-jhdf5/doc"
+    }
+    
+    from (exampleZip.archivePath) {
+        into "${project.group}-jhdf5/doc"
+    }    
+    
+    from (sourcesJar.archivePath) {
+        into "${project.group}-jhdf5/src"
+        rename '(.*)', "${project.group}-jhdf5-src.zip"
+    }
+
+	// BR 2014-06-09:
+	// This is a workaround for an issue in Gradle: if one of entries from a jar file gets extraced read-only, 
+	// overwriting it in a subsequent run will fail. It should be fixed in a future version of Gradle.
+	// See http://forums.gradle.org/gradle/topics/ziptree_unable_to_overwrite_temporary_read_only_files 
+    doLast {
+        exec {
+            commandLine = "chmod -R u+w $buildDir/tmp/expandedArchives".tokenize()
+        }
+    }
+
+}
+
+if (project == project.rootProject)
+{
+    publishing {
+        publications {
+            artifacts(IvyPublication) {
+                module "${project.group}-jhdf5"
+                revision project.revisionForPublication
+                from components.java
+                artifact(toolsJar) {
+                    name = "${project.group}-jhdf5-tools"
+                    conf = "runtime"
+                }
+                artifact(nativeJarLinuxIntel) {
+                    name = "hdf5-linux-intel"
+                    conf = "runtime"
+                }
+                artifact(nativeJarMacIntel) {
+                    name = "hdf5-macosx-intel"
+                    conf = "runtime"
+                }
+                artifact(nativeJarWindowsIntel) {
+                    name = "hdf5-windows-intel"
+                    conf = "runtime"
+                }
+                artifact(sourcesJar) {
+                    type = "source"
+                }
+                descriptor {
+                    withXml {
+                        asNode().dependencies.dependency.find { it.@org == 'rinn' }.replaceNode {}
+                    }
+                }
+            }
+        }
+    }
+}
+
+build.dependsOn distributionZip
+

build/antrun.sh

+#! /bin/bash
+
+SCRIPT="$0"
+if [ "${SCRIPT}" = "${SCRIPT#/}" ]; then
+  SCRIPT="`pwd`/${SCRIPT#./}"
+fi
+BINDIR="${SCRIPT%/*}"
+BASEDIR=${BINDIR%/*}
+cd $BASEDIR
+ant -lib ../build_resources/lib/ecj.jar -f build/build.xml "$@"

build/build.xml

+<project name="jhdf5" default="dist" basedir="..">
+	<import file="../../build_resources/ant/build-common.xml" />
+	<project-classpath name="ecp" classes="${classes}:${lib}/junit4/junit.jar" />
+
+	<property name="mainfolder" value="sis-${ant.project.name}" />
+	<property name="distfolder" value="${ant.project.name}" />
+	<property name="jar.file" value="${dist}/sis-jhdf5.jar" />
+	<property name="dist.file" value="${dist}/sis-jhdf5" />
+	<property name="jar.batteries-included.filename"
+	          value="sis-jhdf5-batteries_included.jar" />
+	<property name="jar.batteries-included.file" value="${dist}/${jar.batteries-included.filename}" />
+	<property name="jar.core.file" value="${dist}/sis-jhdf5-core.jar" />
+	<property name="jar.tools.file" value="${dist}/sis-jhdf5-tools.jar" />
+	<property name="sources.examples" value="sourceExamples/java" />
+	<property name="src.zip.file" value="${dist}/sis-jhdf5-src.zip" />
+	<property name="examples.src.zip.file" value="${dist}/sis-jhdf5-examples-src.zip" />
+	<property name="javadoc.zip.file" value="${dist}/sis-jhdf5-javadoc.zip" />
+	<property name="test.jar.file" value="${dist}/sis-jhdf5-test.jar" />
+	<property name="lib" value="../libraries" />
+	<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="${nativeroot}/native" />
+
+	<property name="dist.hdf5" value="${dist}/${mainfolder}" />
+	<property name="dist.hdf5.lib" value="${dist.hdf5}/lib" />
+
+	<!--
+      // Compile Java classes using the Eclipse compiler 
+      // Note: THIS IS A PRIVATE TARGET. It isn't intended to be used in other build scripts.
+      // Parameter: src = source folder
+      -->
+	<target name="_plain-compile">
+		<echo level="info">Compile all classes in ${basedir}/${src} and subfolders</echo>
+		<javac srcdir="${src}"
+		       destdir="${classes}"
+		       classpath="${ecp}"
+		       source="1.7"
+		       target="1.7"
+			     encoding="UTF-8"
+		       debug="true">
+			<compilerarg line="-warn:none" />
+		</javac>
+		<copy todir="${classes}">
+			<fileset dir="${src}">
+				<include name="**/*.xml" />
+				<include name="**/*.xsd" />
+				<include name="**/*.properties" />
+				<include name="**/*.jpg" />
+				<include name="**/*.png" />
+				<include name="**/*.gif" />
+			</fileset>
+		</copy>
+	</target>
+
+	<target name="clean">
+		<delete dir="${dist}" />
+		<delete dir="${targets}/ant" />
+	</target>
+
+	<target name="jar-test" depends="clean, compile-tests">
+		<mkdir dir="${dist.hdf5.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="**/libjhdf5.so" />
+				<include name="**/libjhdf5.jnilib" />
+				<include name="**/jhdf5.dll" />
+			</fileset>
+		</copy>
+		<recursive-jar destfile="${test.jar.file}">
+			<fileset dir="${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>
+			<fileset dir="${sources.test}/test/hdf5lib">
+				<include name="*.hdf" />
+			</fileset>
+			<zipfileset src="${lib}/testng/testng-jdk15.jar" />
+			<zipfileset src="${lib}/junit4/junit.jar" />
+			<zipfileset src="${lib}/jmock/hamcrest/hamcrest-core.jar" />
+			<zipfileset src="${lib}/sis-base/sis-base.jar" />
+			<zipfileset src="${lib}/cisd-args4j/cisd-args4j.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.hdf5.HDF5RoundtripTest" />
+				<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-complete" depends="compile">
+		<mkdir dir="${dist.hdf5.lib}" />
+		<build-info revision="revision.number" version="version.number" clean="clean.flag" />
+		<echo file="${build.info.file}">${version.number}:${revision.number}:${clean.flag}</echo>
+		<copy todir="${native}">
+			<fileset dir="${nativesrc}">
+				<include name="**/libjhdf5.so" />
+				<include name="**/libjhdf5.jnilib" />
+				<include name="**/jhdf5.dll" />
+			</fileset>
+		</copy>
+		<recursive-jar destfile="${jar.batteries-included.file}">
+			<fileset dir="${classes}">
+				<include name="${build.info.filename}" />
+				<include name="**/*.class" />
+			</fileset>
+			<fileset dir="${nativeroot}">
+				<include name="native/**/*.so" />
+				<exclude name="native/**/*-SunOS/*.so" />
+				<include name="native/**/*.jnilib" />
+				<include name="native/**/*.dll" />
+			</fileset>
+			<zipfileset src="${lib}/sis-base/sis-base.jar">
+				<exclude name="${build.info.filename}" />
+				<exclude name="native/**/*-SunOS/*.so" />
+			</zipfileset>
+			<zipfileset src="${lib}/cisd-args4j/cisd-args4j.jar">
+				<exclude name="${build.info.filename}" />
+				<exclude name="**/AbstractBuildAndEnvironmentInfo.class" />
+			</zipfileset>
+			<zipfileset src="${lib}/commons-lang/commons-lang.jar">
+				<exclude name="META-INF/LICENSE.txt" />
+				<exclude name="META-INF/NOTICE.txt" />
+			</zipfileset>
+			<zipfileset src="${lib}/commons-io/commons-io.jar">
+				<exclude name="META-INF/LICENSE.txt" />
+				<exclude name="META-INF/NOTICE.txt" />
+			</zipfileset>
+			<manifest>
+				<attribute name="Main-Class" value="ch.systemsx.cisd.hdf5.h5ar.HDF5ArchiverMain" />
+				<attribute name="Version" value="${version.number}" />
+				<attribute name="Build-Number"
+				           value="${version.number} (r${revision.number},${clean.flag})" />
+			</manifest>
+		</recursive-jar>
+		<recursive-jar destfile="${jar.file}">
+			<fileset dir="${classes}">
+				<include name="${build.info.filename}" />
+				<include name="**/*.class" />
+			</fileset>
+			<zipfileset src="${lib}/sis-base/sis-base.jar">
+				<exclude name="${build.info.filename}" />
+				<exclude name="native/**" />
+			</zipfileset>
+			<zipfileset src="${lib}/cisd-args4j/cisd-args4j.jar">
+				<exclude name="${build.info.filename}" />
+				<exclude name="**/AbstractBuildAndEnvironmentInfo.class" />
+			</zipfileset>
+			<zipfileset src="${lib}/commons-lang/commons-lang.jar">
+				<exclude name="META-INF/LICENSE.txt" />
+				<exclude name="META-INF/NOTICE.txt" />
+			</zipfileset>
+			<zipfileset src="${lib}/commons-io/commons-io.jar">
+				<exclude name="META-INF/LICENSE.txt" />
+				<exclude name="META-INF/NOTICE.txt" />
+			</zipfileset>
+			<manifest>
+				<attribute name="Main-Class" value="ch.systemsx.cisd.hdf5.h5ar.HDF5ArchiverMain" />
+				<attribute name="Version" value="${version.number}" />
+				<attribute name="Build-Number"
+				           value="${version.number} (r${revision.number},${clean.flag})" />
+				<attribute name="Class-Path"
+				           value="hdf5-linux-intel.jar hdf5-macosx-intel.jar hdf5-windows-intel.jar" />
+			</manifest>
+		</recursive-jar>
+	</target>
+
+	<target name="examples-src-zip">
+		<build-info revision="revision.number" version="version.number" clean="clean.flag" />
+		<echo file="${build.info.file}">${version.number}:${revision.number}:${clean.flag}</echo>
+		<recursive-jar destfile="${examples.src.zip.file}">
+			<fileset dir="${classes}">
+				<include name="${build.info.filename}" />
+			</fileset>
+			<fileset dir="${sources.examples}">
+				<include name="**/*.java" />
+			</fileset>
+			<manifest>
+				<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" />
+		<echo file="${build.info.file}">${version.number}:${revision.number}:${clean.flag}</echo>
+		<recursive-jar destfile="${src.zip.file}">
+			<fileset dir="${classes}">
+				<include name="${build.info.filename}" />
+			</fileset>
+			<fileset dir="${sources}">
+				<include name="**/*.java" />
+			</fileset>
+			<manifest>
+				<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-core" depends="compile">
+		<mkdir dir="${dist.hdf5.lib}" />
+		<build-info revision="revision.number" version="version.number" clean="clean.flag" />
+		<echo file="${build.info.file}">${version.number}:${revision.number}:${clean.flag}</echo>
+		<jar destfile="${jar.core.file}">
+			<fileset dir="${classes}">
+				<include name="${build.info.filename}" />
+				<include name="**/*.class" />
+				<exclude name="**/io/*.class" />
+				<exclude name="**/h5ar/*.class" />
+			</fileset>
+			<zipfileset src="${lib}/sis-base/sis-base.jar">
+				<include name="ch/systemsx/cisd/base/utilities/AbstractBuildAndEnvironmentInfo.class" />
+			</zipfileset>
+			<manifest>
+				<attribute name="Main-Class" value="ch.systemsx.cisd.hdf5.BuildAndEnvironmentInfo" />
+				<attribute name="Version" value="${version.number}" />
+				<attribute name="Build-Number"
+				           value="${version.number} (r${revision.number},${clean.flag})" />
+			</manifest>
+		</jar>
+	</target>
+
+	<target name="jar-tools" depends="compile">
+		<mkdir dir="${dist.hdf5.lib}" />
+		<build-info revision="revision.number" version="version.number" clean="clean.flag" />
+		<echo file="${build.info.file}">${version.number}:${revision.number}:${clean.flag}</echo>
+		<jar destfile="${jar.tools.file}">
+			<fileset dir="${classes}">
+				<include name="${build.info.filename}" />
+				<include name="**/io/*.class" />
+				<include name="**/h5ar/*.class" />
+				<include name="ch/systems/cisd/hdf5/BuildAndEnvironmentInfo*.class" />
+			</fileset>
+			<zipfileset src="${lib}/sis-base/sis-base.jar">
+				<include name="ch/systemsx/cisd/base/utilities/AbstractBuildAndEnvironmentInfo.class" />
+			</zipfileset>
+			<manifest>
+				<attribute name="Version" value="${version.number}" />
+				<attribute name="Build-Number"
+				           value="${version.number} (r${revision.number},${clean.flag})" />
+				<attribute name="Main-Class" value="ch.systemsx.cisd.hdf5.h5ar.HDF5ArchiverMain" />
+				<attribute name="Class-Path"
+				           value="commons-lang.jar commons-io.jar sis-base.jar cisd-args4j.jar sis-jhdf5-core.jar hdf5-linux-intel.jar hdf5-macosx-intel.jar hdf5-windows-intel.jar" />
+			</manifest>
+		</jar>
+	</target>
+
+	<target name="jar-all"
+	        depends="jar-complete, src-zip, examples-src-zip, jar-core, jar-tools, jar-platforms" />
+
+	<target name="jar-platforms"
+	        depends="jar-linux-intel, jar-macosx-intel, jar-windows-intel" />
+
+	<target name="jar-linux-intel" depends="compile">
+		<delete dir="${native}" />
+		<mkdir dir="${native}" />
+		<mkdir dir="${dist.hdf5.lib}" />
+		<build-info revision="revision.number" version="version.number" clean="clean.flag" />
+		<echo file="${build.info.file}">${version.number}:${revision.number}:${clean.flag}</echo>
+		<copy todir="${native}">
+			<fileset dir="${nativesrc}">
+				<include name="jhdf5/i386-Linux/libjhdf5.so" />
+				<include name="jhdf5/amd64-Linux/libjhdf5.so" />
+				<include name="jhdf5/arm-Linux/libjhdf5.so" />
+			</fileset>
+		</copy>
+		<jar destfile="${dist}/hdf5-linux-intel.jar">
+			<fileset dir="${classes}">
+				<include name="${build.info.filename}" />
+			</fileset>
+			<fileset dir="${nativeroot}">
+				<include name="native/**/*.so" />
+			</fileset>
+			<zipfileset src="${lib}/sis-base/sis-base.jar">
+				<include name="ch/systemsx/cisd/base/utilities/BuildAndEnvironmentInfo.class" />
+			</zipfileset>
+			<manifest>
+				<attribute name="Main-Class"
+				           value="ch.systemsx.cisd.base.utilities.BuildAndEnvironmentInfo" />
+				<attribute name="Version" value="${version.number}" />
+				<attribute name="Build-Number"
+				           value="${version.number} (r${revision.number},${clean.flag})" />
+			</manifest>
+		</jar>
+	</target>
+
+	<target name="jar-macosx-intel" depends="compile">
+		<delete dir="${native}" />
+		<mkdir dir="${native}" />
+		<mkdir dir="${dist.hdf5.lib}" />
+		<build-info revision="revision.number" version="version.number" clean="clean.flag" />
+		<echo file="${build.info.file}">${version.number}:${revision.number}:${clean.flag}</echo>
+		<copy todir="${native}">
+			<fileset dir="${nativesrc}">
+				<include name="jhdf5/i386-Mac OS X/libjhdf5.jnilib" />
+				<include name="jhdf5/x86_64-Mac OS X/libjhdf5.jnilib" />
+			</fileset>
+		</copy>
+		<jar destfile="${dist}/hdf5-macosx-intel.jar">
+			<fileset dir="${classes}">
+				<include name="${build.info.filename}" />
+			</fileset>
+			<fileset dir="${nativeroot}">
+				<include name="native/**/*.jnilib" />
+			</fileset>
+			<zipfileset src="${lib}/sis-base/sis-base.jar">
+				<include name="ch/systemsx/cisd/base/utilities/BuildAndEnvironmentInfo.class" />
+			</zipfileset>
+			<manifest>
+				<attribute name="Main-Class"
+				           value="ch.systemsx.cisd.base.utilities.BuildAndEnvironmentInfo" />
+				<attribute name="Version" value="${version.number}" />
+				<attribute name="Build-Number"
+				           value="${version.number} (r${revision.number},${clean.flag})" />
+			</manifest>
+		</jar>
+	</target>
+
+	<target name="jar-windows-intel" depends="compile">
+		<delete dir="${native}" />
+		<mkdir dir="${native}" />
+		<mkdir dir="${dist.hdf5.lib}" />
+		<build-info revision="revision.number" version="version.number" clean="clean.flag" />
+		<echo file="${build.info.file}">${version.number}:${revision.number}:${clean.flag}</echo>
+		<copy todir="${native}">
+			<fileset dir="${nativesrc}">
+				<include name="jhdf5/x86-Windows/jhdf5.dll" />
+				<include name="jhdf5/amd64-Windows/jhdf5.dll" />
+			</fileset>
+		</copy>
+		<jar destfile="${dist}/hdf5-windows-intel.jar">
+			<fileset dir="${classes}">
+				<include name="${build.info.filename}" />
+			</fileset>
+			<fileset dir="${nativeroot}">
+				<include name="native/**/*.dll" />
+			</fileset>
+			<zipfileset src="${lib}/sis-base/sis-base.jar">
+				<include name="ch/systemsx/cisd/base/utilities/BuildAndEnvironmentInfo.class" />
+			</zipfileset>
+			<manifest>
+				<attribute name="Main-Class"
+				           value="ch.systemsx.cisd.base.utilities.BuildAndEnvironmentInfo" />
+				<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="${targets}/doc" />
+		<delete dir="${targets}/source-base" />
+		<unzip src="../libraries/sis-base/sis-base-src.zip" dest="${targets}/source-base" />
+		<javadoc classpath="../base/targets/classes:../libraries/sis-base/sis-base.jar:../libraries/commons-lang/commons-lang.jar:../libraries/commons-io/commons-io.jar:../libraries/restrictionchecker/restrictions.jar:../libraries/cisd-args4j/cisd-args4j.jar"
+		         destdir="targets/doc"
+		         doctitle="JHDF5 14.12"
+		         author="false"
+		         overview="overview.html"
+		         access="public">
+			<fileset dir="source/java" defaultexcludes="yes">
+				<include name="ch/systemsx/cisd/hdf5/**/*.java" />
+				<include name="ncsa/hdf/hdf5lib/exceptions/**/*.java" />
+				<exclude name="ch/systemsx/cisd/hdf5/hdf5lib/**/*.java" />
+				<exclude name="ch/systemsx/cisd/hdf5/cleanup/**/*.java" />
+				<exclude name="ch/systemsx/cisd/hdf5/MatrixUtils.java" />
+				<exclude name="ch/systemsx/cisd/hdf5/StringUtils.java" />
+				<exclude name="ch/systemsx/cisd/hdf5/ReflectionUtils.java" />
+				<exclude name="ch/systemsx/cisd/hdf5/BitSetConversionUtils.java" />
+			</fileset>
+			<fileset dir="${targets}/source-base" defaultexcludes="yes">
+				<include name="ch/systemsx/cisd/base/mdarray/**/*.java" />
+			</fileset>
+		</javadoc>
+		<copy todir="${targets}/doc">
+			<fileset dir="${sources.examples}" />
+		</copy>
+		<copy file="${original.dist}/doc/JHDF5.pdf" todir="${targets}/doc" />
+	</target>
+
+	<target name="dist" depends="clean, jar-all, doc">
+		<zip destfile="${javadoc.zip.file}" basedir="${targets}" includes="doc/**" />
+		<delete dir="${dist}/${mainfolder}" />
+		<copy file="${lib}/cisd-args4j/cisd-args4j.jar" todir="${dist}/${distfolder}/lib" />
+		<copy file="${lib}/sis-base/sis-base.jar" todir="${dist}/${distfolder}/lib" />
+		<copy file="${lib}/commons-lang/commons-lang.jar" todir="${dist}/${distfolder}/lib" />
+		<copy file="${lib}/commons-io/commons-io.jar" todir="${dist}/${distfolder}/lib" />
+		<move file="${jar.batteries-included.file}"
+		      todir="${dist}/${distfolder}/lib/batteries_included" />
+		<move file="${dist}/hdf5-linux-intel.jar" todir="${dist}/${distfolder}/lib/nativejar" />
+		<move file="${dist}/hdf5-macosx-intel.jar" todir="${dist}/${distfolder}/lib/nativejar" />
+		<move file="${dist}/hdf5-windows-intel.jar" todir="${dist}/${distfolder}/lib/nativejar" />
+		<move todir="${dist}/${distfolder}/lib">
+			<fileset dir="${dist}">
+				<include name="*.jar" />
+			</fileset>
+		</move>
+		<unzip src="${dist}/${distfolder}/lib/batteries_included/${jar.batteries-included.filename}"
+		       dest="${dist}/${distfolder}/lib">
+			<patternset>
+				<include name="native/**" />
+			</patternset>
+		</unzip>
+		<move file="${src.zip.file}" todir="${dist}/${distfolder}/src" />
+		<move file="${javadoc.zip.file}" todir="${dist}/${distfolder}/doc" />
+		<move file="${examples.src.zip.file}" todir="${dist}/${distfolder}/doc" />
+		<copy todir="${dist}/${distfolder}">
+			<fileset dir="${original.dist}" />
+		</copy>
+		<zip destfile="${dist.file}-${version.number}-r${revision.number}.zip">
+			<zipfileset dir="${dist}/${distfolder}" prefix="${mainfolder}" excludes="**/*.sh" />
+			<zipfileset dir="${dist}/${distfolder}"
+			            prefix="${mainfolder}"
+			            includes="**/*.sh"
+			            filemode="755" />
+		</zip>
+		<delete dir="${dist}/${distfolder}" />
+	</target>
+
+	<!--
+	// Task for continuous integration server.
+	-->
+	<target name="ci"
+	        depends="build-common.ci, check-dependencies"
+	        description="Task for continuous integration server." />
+
+</project>

debian/changelog

+libsis-jhdf5-java (18.08~pre+git20180805.da55947+dfsg-1) UNRELEASED; urgency=medium
+
+  * Pre-release to adapt to HDF5 1.10.3-pre1
+  * Use git mode in watch file
+  * Drop now unneeded get-orig-source target
+
+ -- Andreas Tille <tille@debian.org>  Mon, 13 Aug 2018 14:30:28 +0200
+
 libsis-jhdf5-java (14.12.6-2) unstable; urgency=medium
 
   * Add upstream contact

debian/copyright

@@ -3,6 +3,7 @@ Upstream-Name: JHDF5 (HDF5 for Java)
 Upstream-Contact: https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=26609113
                   Bernd Rinn <brinn@ethz.ch>
 Source: http://svnsis.ethz.ch/repos/cisd/jhdf5/tags/release/
+Files-Excluded: */native
 
 Files: * 
 Copyright: Copyright (C) The HDF Group.

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
-
-rm -rf ${PKG}-${VERSION} ; mkdir ${PKG}-${VERSION} ; cd ${PKG}-${VERSION}
-svn export http://svnsis.ethz.ch/repos/cisd/jhdf5/tags/release/14.12.x/${VERSION}/jhdf5/source
-svn export http://svnsis.ethz.ch/repos/cisd/jhdf5/tags/release/14.12.x/${VERSION}/jhdf5/sourceTest
-cd ..
-
-tar --owner=root --group=root --mode=a+rX --exclude-vcs -caf "$PKG"_"$VERSION".orig.tar.xz "$PKG"-"$VERSION"
-rm -rf "$PKG"-"$VERSION"
-

debian/rules

@@ -19,9 +19,6 @@ TESTIGNORE = sourceTest/java/ch/systemsx/cisd/hdf5/HDF5RoundtripTest.java \
 %:
 	dh $@ --with javahelper
 
-get-orig-source:
-	debian/get-orig-source
-
 override_dh_auto_clean:
 	rm -rf build *.jar
 	rm -rf source/c/*.log

debian/watch

 version=4
-http://svnsis.ethz.ch/repos/cisd/jhdf5/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/jhdf5.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

dist/CONTENT

+Documentation
+  doc/jhdf5-javadoc.zip
+  
+  doc/cisd-jhdf5-examples-src.zip
+    Example programs for some of the features of JHDF5
+
+Source
+  src/jhdf5-src.zip
+  
+Library
+  lib/cisd-jhdf5-core.jar: 
+    The Java class files of the JHDF5 library. Requires commons-io.jar, commons-lang.jar and  
+    cisd-base.jar on the class path. Requires the native libraries to be provided separately (see 
+    below at lib/native).
+
+  lib/cisd-jhdf5-tools.jar: 
+    The Java class files of the h5ar archiver. It can be used like 'java -jar cisd-jhdf5-tools.jar'. 
+    Requires commons-io.jar, commons-lang.jar, cisd-base.jar, cisd-args4j.jar and cisd-jhdf5-core.jar in 
+    the class path. Requires the native libraries to be provided separately (see below at lib/native).
+
+  lib/cisd-jhdf5.jar: 
+    All Java class files packaged in one jar file. Requires the native libraries to be provided 
+    separately. 
+
+  lib/batteries_included:
+    Includes all Java class files of the JHDF5 library and the h5ar archiver and all native 
+    libraries necessary to use JHDF5.
+    No other file is needed when using one of these jar files. 
+
+	  All supported platforms:
+	    lib/batteries_included/cisd-jhdf5-batteries_included_lin_win_mac_sol.jar 
+	  
+	  Linux/MacOS X/Windows, but no Solaris support: 
+	    lib/batteries_included/cisd-jhdf5-batteries_included_lin_win_mac.jar
+	    
+  lib/native:
+    The native libraries as files in folders jhdf5 and unix. In order to use them ensure that you 
+    point the Java property native.libpath to the root of this hierarchy,
+    e.g.: "-Dnative.libpath=/home/joe/lib/native"
+
+  lib/nativejar:
+    The jar files in this folder contain the native libraries for each platform, e.g. 
+    hdf5-linux-intel.jar has the shared libraries for Linux on Intel/AMD. Note that these jar 
+    files do not contain the Java class files. In order to make use of these jar files you need
+    to ensure that the file for your platform is in the class path of the jre.
+ 
+Wrapper
+  bin/h5ar.sh:
+    A script that calls h5ar by invoking the JRE with appropriate parameters. Suitable for being 
+    symlinked to e.g. /usr/local/bin
+  bin/h5ar.bar:
+    Example script on how to most easily invoke h5ar on Windows. Needs to be adapted to have the 
+    fully qualified path to the jar file.
+

dist/COPYING

+/*
+ * Copyright 2008-2012 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */

dist/COPYING-args4j

+Copyright (c) 2003, Kohsuke Kawaguchi
+All rights reserved.
+
+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 OWNER 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.

dist/COPYING-commons

+Apache Commons Lang and Commons IO
+Copyright 2001-2008 The Apache Software Foundation
+
+This product includes software developed by
+The Apache Software Foundation (http://www.apache.org/).
\ No newline at end of file

dist/COPYING-hdf5

+
+Copyright Notice and License Terms for 
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+-----------------------------------------------------------------------------
+
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright 2006-2010 by The HDF Group.
+
+NCSA HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright 1998-2006 by the Board of Trustees of the University of Illinois.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted for any purpose (including commercial purposes) 
+provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, 
+   this list of conditions, and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, 
+   this list of conditions, and the following disclaimer in the documentation 
+   and/or materials provided with the distribution.
+
+3. In addition, redistributions of modified forms of the source or binary 
+   code must carry prominent notices stating that the original code was 
+   changed and the date of the change.
+
+4. All publications or advertising materials mentioning features or use of 
+   this software are asked, but not required, to acknowledge that it was 
+   developed by The HDF Group and by the National Center for Supercomputing 
+   Applications at the University of Illinois at Urbana-Champaign and 
+   credit the contributors.
+
+5. Neither the name of The HDF Group, the name of the University, nor the 
+   name of any Contributor may be used to endorse or promote products derived 
+   from this software without specific prior written permission from 
+   The HDF Group, the University, or the Contributor, respectively.
+
+DISCLAIMER: 
+THIS SOFTWARE IS PROVIDED BY THE HDF GROUP AND THE CONTRIBUTORS 
+"AS IS" WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED.  In no 
+event shall The HDF Group or the Contributors be liable for any damages 
+suffered by the users arising out of the use of this software, even if 
+advised of the possibility of such damage. 
+
+-----------------------------------------------------------------------------
+-----------------------------------------------------------------------------
+
+Contributors:   National Center for Supercomputing Applications (NCSA) at 
+the University of Illinois, Fortner Software, Unidata Program Center (netCDF), 
+The Independent JPEG Group (JPEG), Jean-loup Gailly and Mark Adler (gzip), 
+and Digital Equipment Corporation (DEC).
+
+-----------------------------------------------------------------------------
+
+Portions of HDF5 were developed with support from the Lawrence Berkeley 
+National Laboratory (LBNL) and the United States Department of Energy 
+under Prime Contract No. DE-AC02-05CH11231.
+
+-----------------------------------------------------------------------------
+
+Portions of HDF5 were developed with support from the University of 
+California, Lawrence Livermore National Laboratory (UC LLNL).  
+The following statement applies to those portions of the product and must 
+be retained in any redistribution of source code, binaries, documentation, 
+and/or accompanying materials:
+
+   This work was partially produced at the University of California, 
+   Lawrence Livermore National Laboratory (UC LLNL) under contract 
+   no. W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy 
+   (DOE) and The Regents of the University of California (University) 
+   for the operation of UC LLNL.
+
+   DISCLAIMER: 
+   This work was prepared as an account of work sponsored by an agency of 
+   the United States Government. Neither the United States Government nor 
+   the University of California nor any of their employees, makes any 
+   warranty, express or implied, or assumes any liability or responsibility 
+   for the accuracy, completeness, or usefulness of any information, 
+   apparatus, product, or process disclosed, or represents that its use 
+   would not infringe privately- owned rights. Reference herein to any 
+   specific commercial products, process, or service by trade name, 
+   trademark, manufacturer, or otherwise, does not necessarily constitute 
+   or imply its endorsement, recommendation, or favoring by the United 
+   States Government or the University of California. The views and 
+   opinions of authors expressed herein do not necessarily state or reflect 
+   those of the United States Government or the University of California, 
+   and shall not be used for advertising or product endorsement purposes.
+-----------------------------------------------------------------------------
+
+

dist/LICENSE

+/*
+ *                                 Apache License
+ *                           Version 2.0, January 2004
+ *                        http://www.apache.org/licenses/
+ *
+ *   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+ *
+ *   1. Definitions.
+ *
+ *      "License" shall mean the terms and conditions for use, reproduction,
+ *      and distribution as defined by Sections 1 through 9 of this document.
+ *
+ *      "Licensor" shall mean the copyright owner or entity authorized by
+ *      the copyright owner that is granting the License.
+ *
+ *      "Legal Entity" shall mean the union of the acting entity and all
+ *      other entities that control, are controlled by, or are under common
+ *      control with that entity. For the purposes of this definition,
+ *      "control" means (i) the power, direct or indirect, to cause the
+ *      direction or management of such entity, whether by contract or
+ *      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+ *      outstanding shares, or (iii) beneficial ownership of such entity.
+ *
+ *      "You" (or "Your") shall mean an individual or Legal Entity
+ *      exercising permissions granted by this License.
+ *
+ *      "Source" form shall mean the preferred form for making modifications,
+ *      including but not limited to software source code, documentation
+ *      source, and configuration files.
+ *
+ *      "Object" form shall mean any form resulting from mechanical
+ *      transformation or translation of a Source form, including but
+ *      not limited to compiled object code, generated documentation,
+ *      and conversions to other media types.
+ *
+ *      "Work" shall mean the work of authorship, whether in Source or
+ *      Object form, made available under the License, as indicated by a
+ *      copyright notice that is included in or attached to the work
+ *      (an example is provided in the Appendix below).
+ *
+ *      "Derivative Works" shall mean any work, whether in Source or Object
+ *      form, that is based on (or derived from) the Work and for which the
+ *      editorial revisions, annotations, elaborations, or other modifications
+ *      represent, as a whole, an original work of authorship. For the purposes
+ *      of this License, Derivative Works shall not include works that remain
+ *      separable from, or merely link (or bind by name) to the interfaces of,
+ *      the Work and Derivative Works thereof.
+ *
+ *      "Contribution" shall mean any work of authorship, including
+ *      the original version of the Work and any modifications or additions
+ *      to that Work or Derivative Works thereof, that is intentionally
+ *      submitted to Licensor for inclusion in the Work by the copyright owner
+ *      or by an individual or Legal Entity authorized to submit on behalf of
+ *      the copyright owner. For the purposes of this definition, "submitted"
+ *      means any form of electronic, verbal, or written communication sent
+ *      to the Licensor or its representatives, including but not limited to
+ *      communication on electronic mailing lists, source code control systems,
+ *      and issue tracking systems that are managed by, or on behalf of, the
+ *      Licensor for the purpose of discussing and improving the Work, but
+ *      excluding communication that is conspicuously marked or otherwise
+ *      designated in writing by the copyright owner as "Not a Contribution."
+ *
+ *      "Contributor" shall mean Licensor and any individual or Legal Entity
+ *      on behalf of whom a Contribution has been received by Licensor and
+ *      subsequently incorporated within the Work.
+ *
+ *   2. Grant of Copyright License. Subject to the terms and conditions of
+ *      this License, each Contributor hereby grants to You a perpetual,
+ *      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ *      copyright license to reproduce, prepare Derivative Works of,
+ *      publicly display, publicly perform, sublicense, and distribute the
+ *      Work and such Derivative Works in Source or Object form.
+ *
+ *   3. Grant of Patent License. Subject to the terms and conditions of
+ *      this License, each Contributor hereby grants to You a perpetual,
+ *      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ *      (except as stated in this section) patent license to make, have made,
+ *      use, offer to sell, sell, import, and otherwise transfer the Work,
+ *      where such license applies only to those patent claims licensable
+ *      by such Contributor that are necessarily infringed by their
+ *      Contribution(s) alone or by combination of their Contribution(s)
+ *      with the Work to which such Contribution(s) was submitted. If You
+ *      institute patent litigation against any entity (including a
+ *      cross-claim or counterclaim in a lawsuit) alleging that the Work
+ *      or a Contribution incorporated within the Work constitutes direct
+ *      or contributory patent infringement, then any patent licenses
+ *      granted to You under this License for that Work shall terminate
+ *      as of the date such litigation is filed.
+ *
+ *   4. Redistribution. You may reproduce and distribute copies of the
+ *      Work or Derivative Works thereof in any medium, with or without
+ *      modifications, and in Source or Object form, provided that You
+ *      meet the following conditions:
+ *
+ *      (a) You must give any other recipients of the Work or
+ *          Derivative Works a copy of this License; and
+ *
+ *      (b) You must cause any modified files to carry prominent notices
+ *          stating that You changed the files; and
+ *
+ *      (c) You must retain, in the Source form of any Derivative Works
+ *          that You distribute, all copyright, patent, trademark, and
+ *          attribution notices from the Source form of the Work,
+ *          excluding those notices that do not pertain to any part of
+ *          the Derivative Works; and
+ *
+ *      (d) If the Work includes a "NOTICE" text file as part of its
+ *          distribution, then any Derivative Works that You distribute must
+ *          include a readable copy of the attribution notices contained
+ *          within such NOTICE file, excluding those notices that do not
+ *          pertain to any part of the Derivative Works, in at least one
+ *          of the following places: within a NOTICE text file distributed
+ *          as part of the Derivative Works; within the Source form or
+ *          documentation, if provided along with the Derivative Works; or,
+ *          within a display generated by the Derivative Works, if and
+ *          wherever such third-party notices normally appear. The contents
+ *          of the NOTICE file are for informational purposes only and
+ *          do not modify the License. You may add Your own attribution
+ *          notices within Derivative Works that You distribute, alongside
+ *          or as an addendum to the NOTICE text from the Work, provided
+ *          that such additional attribution notices cannot be construed
+ *          as modifying the License.
+ *
+ *      You may add Your own copyright statement to Your modifications and
+ *      may provide additional or different license terms and conditions
+ *      for use, reproduction, or distribution of Your modifications, or
+ *      for any such Derivative Works as a whole, provided Your use,
+ *      reproduction, and distribution of the Work otherwise complies with
+ *      the conditions stated in this License.
+ *
+ *   5. Submission of Contributions. Unless You explicitly state otherwise,
+ *      any Contribution intentionally submitted for inclusion in the Work
+ *      by You to the Licensor shall be under the terms and conditions of
+ *      this License, without any additional terms or conditions.
+ *      Notwithstanding the above, nothing herein shall supersede or modify
+ *      the terms of any separate license agreement you may have executed
+ *      with Licensor regarding such Contributions.
+ *
+ *   6. Trademarks. This License does not grant permission to use the trade
+ *      names, trademarks, service marks, or product names of the Licensor,
+ *      except as required for reasonable and customary use in describing the
+ *      origin of the Work and reproducing the content of the NOTICE file.
+ *
+ *   7. Disclaimer of Warranty. Unless required by applicable law or
+ *      agreed to in writing, Licensor provides the Work (and each
+ *      Contributor provides its Contributions) on an "AS IS" BASIS,
+ *      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ *      implied, including, without limitation, any warranties or conditions
+ *      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+ *      PARTICULAR PURPOSE. You are solely responsible for determining the
+ *      appropriateness of using or redistributing the Work and assume any
+ *      risks associated with Your exercise of permissions under this License.
+ *
+ *   8. Limitation of Liability. In no event and under no legal theory,
+ *      whether in tort (including negligence), contract, or otherwise,
+ *      unless required by applicable law (such as deliberate and grossly
+ *      negligent acts) or agreed to in writing, shall any Contributor be
+ *      liable to You for damages, including any direct, indirect, special,
+ *      incidental, or consequential damages of any character arising as a
+ *      result of this License or out of the use or inability to use the
+ *      Work (including but not limited to damages for loss of goodwill,
+ *      work stoppage, computer failure or malfunction, or any and all
+ *      other commercial damages or losses), even if such Contributor
+ *      has been advised of the possibility of such damages.
+ *
+ *   9. Accepting Warranty or Additional Liability. While redistributing
+ *      the Work or Derivative Works thereof, You may choose to offer,
+ *      and charge a fee for, acceptance of support, warranty, indemnity,
+ *      or other liability obligations and/or rights consistent with this
+ *      License. However, in accepting such obligations, You may act only
+ *      on Your own behalf and on Your sole responsibility, not on behalf
+ *      of any other Contributor, and only if You agree to indemnify,
+ *      defend, and hold each Contributor harmless for any liability
+ *      incurred by, or claims asserted against, such Contributor by reason
+ *      of your accepting any such warranty or additional liability.
+ *
+ *   END OF TERMS AND CONDITIONS
+ *
+ *   APPENDIX: How to apply the Apache License to your work.
+ *
+ *      To apply the Apache License to your work, attach the following
+ *      boilerplate notice, with the fields enclosed by brackets "[]"
+ *      replaced with your own identifying information. (Don't include
+ *      the brackets!)  The text should be enclosed in the appropriate
+ *      comment syntax for the file format. We also recommend that a
+ *      file or class name and description of purpose be included on the
+ *      same "printed page" as the copyright notice for easier
+ *      identification within third-party archives.
+ *
+ *   Copyright [yyyy] [name of copyright owner]
+ *
+ *   Licensed under the Apache License, Version 2.0 (the "License");
+ *   you may not use this file except in compliance with the License.
+ *   You may obtain a copy of the License at
+ *
+ *       http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *   Unless required by applicable law or agreed to in writing, software
+ *   distributed under the License is distributed on an "AS IS" BASIS,
+ *   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *   See the License for the specific language governing permissions and
+ *   limitations under the License.
+ */

dist/bin/h5ar.bat

+@echo off
+
+java -Dnative.libpath=%~dp0..\lib\native -jar %~dp0..\lib\sis-jhdf5-tools.jar %1 %2 %3 %4 %5 %6 %7 %8 %9

dist/bin/h5ar.sh

+#! /bin/bash
+
+# This script requires the readlink binary. If your system lacks this binary, $JHDFDIR needs to be hard-coded
+
+SCRIPT="$0"
+if [ "${SCRIPT}" = "${SCRIPT#/}" ]; then
+  SCRIPT="`pwd`/${SCRIPT#./}"
+fi
+BINDIR="${SCRIPT%/*}"
+LINK="`readlink $0`"
+while [ -n "${LINK}" ]; do
+  if [ "${LINK#/}" = "${LINK}" ]; then
+    SCRIPT="${BINDIR}/${LINK}"
+  else
+    SCRIPT="${LINK}"
+  fi
+  BINDIR="${SCRIPT%/*}"
+  LINK="`readlink ${SCRIPT}`"
+done
+BINDIR="${SCRIPT%/*}"
+JHDFDIR="${BINDIR%/*}"
+java -Dnative.libpath="${JHDFDIR}/lib/native" -jar "${JHDFDIR}/lib/sis-jhdf5-tools.jar" "$@"