New upstream version 18.08~pre+git20180805.da55947+dfsg (c1b883f0) · Commits · Debian Med / libsis-jhdf5-java

.checkstyle

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		<?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

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		<?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

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		/bin
		/build
		/.gradle
		/targets
		/.project
		/.settings
		/test-output
		/source/c/build
		source/c/hdf5tar

.shadow_dependencies

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

build.gradle

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		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