New upstream version 18.09.0-pre1+dfsg (c2e7bf8c) · Commits · Debian Med / libsis-jhdf5-java

.classpath

+11 −11

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		@@ -3,19 +3,19 @@
		<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="lib" path="libs/test/hamcrest-core.jar"/>
		<classpathentry kind="lib" path="libs/test/hamcrest-integration.jar"/>
		<classpathentry kind="lib" path="libs/test/hamcrest-library.jar"/>
		<classpathentry kind="lib" path="libs/test/jmock.jar"/>
		<classpathentry kind="lib" path="libs/test/objenesis-1.0.jar"/>
		<classpathentry kind="lib" path="libs/test/testng-jdk15.jar"/>
		<classpathentry kind="lib" path="libs/build/ecj-4.6.1.jar"/>
		<classpathentry kind="lib" path="libs/prod/cisd-args4j-9.11.2.jar" sourcepath="libs/prod/cisd-args4j-9.11.2-sources.jar"/>
		<classpathentry kind="lib" path="libs/prod/commons-lang3-3.7.jar" sourcepath="libs/prod/commons-lang3-3.7-sources.jar"/>
		<classpathentry kind="lib" path="libs/prod/commons-io-2.6.jar" sourcepath="libs/prod/commons-io-2.6-sources.jar"/>
		<classpathentry kind="lib" path="libs/prod/sis-base-18.08.0.jar" sourcepath="libs/prod/sis-base-18.08.0-sources.jar"/>
		<classpathentry kind="output" path="targets/classes"/>
		</classpath>

.gitignore

+1 −0

Original line number	Diff line number	Diff line
		@@ -7,3 +7,4 @@
		/test-output
		/source/c/build
		source/c/hdf5tar
		source/c/CMake*zip

build.gradle

+102 −189

Original line number	Diff line number	Diff line
		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:+'
		compile fileTree(dir: 'libs/prod', include: '*.jar')
		testCompile fileTree(dir: 'libs/test', include: '*.jar')
		}

		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/*/'
		}

		baseName "${project.group}-jhdf5"
		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'
		from ("libs/") {
		include 'native/jhdf5///*'
		}

		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(' ')
		attributes 'Class-Path': configurations.runtime.collect { it.getName().contains("-sources") ? "" : it.getName() + " " }.join('')
		}
		}

		task allJar(type: Jar, dependsOn: [compileJava]) {
		sourcesJar {
		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/*/'
		from ("targets/dist") {
		include "BUILD-jhdf5.INFO"
		}

		manifest {
		attributes 'Main-Class': 'ch.systemsx.cisd.hdf5.h5ar.HDF5ArchiverMain'
		}
		}

		task myJavadoc(type: Javadoc) {
		source = [ sourceSets.main.allJava, "base-src" ]
		classpath = configurations.compile
		task myJavadoc(type: Javadoc, dependsOn: [compileJava]) {
		source = [ sourceSets.main.allJava, "base-sources" ]
		classpath = files(sourceSets.main.output.classesDir) + fileTree(dir: 'libs/prod', include: '*.jar') + files("libs/build/restrictions-1.0.2.jar")
		options.memberLevel = JavadocMemberLevel.PUBLIC
		options.overview = "overview.html"
		include "ch/systemsx/cisd/hdf5/**"
		@@ -159,13 +54,24 @@ task myJavadoc(type: Javadoc) {
		exclude "ch/systemsx/cisd/hdf5/ReflectionUtils.java"
		}

		task javadocZip(type: Zip, dependsOn: myJavadoc) {
		archiveName "${project.group}-jhdf5-javadoc.zip"
		task javadocJar(type: Jar, dependsOn: myJavadoc) {
		archiveName "${project.group}-jhdf5-javadoc-${project.version}.jar"
		from javadoc.destinationDir
		from ("sourceExamples/java") {
		include '*/'
		}
		from ("dist/doc") {
		include 'JHDF5.pdf'
		}

		task exampleZip(type: Jar) {
		archiveName "${project.group}-jhdf5-examples-src.zip"
		from ("targets/dist") {
		include "BUILD-jhdf5.INFO"
		}

		}

		task exampleJar(type: Jar) {
		baseName "${project.group}-jhdf5-examples-sources"

		from ("sourceExamples/java") {
		include '*/'
		@@ -174,78 +80,101 @@ task exampleZip(type: Jar) {
		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"
		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')
		}
		}

		from (allJar.archivePath) {
		into "${project.group}-jhdf5/lib"
		rename '(.*)', "${project.group}-jhdf5.jar"
		task processDistFiles( type: Copy) {
		into "$buildDir/output/dist"

		from ("dist") {
		exclude 'doc/JHDF5.odt'
		}

		from (configurations.runtime) {
		exclude 'restriction'
		exclude 'bcel'
		into "${project.group}-jhdf5/lib"
		from ("dist") {
		include 'doc/JHDF5.odt'
		rename { "JHDF5-${version}.odt" }
		}

		from (zipTree(batteriesIncluded.archivePath)) {
		into "${project.group}-jhdf5/lib"
		include 'native/**'
		doLast {
		execute('lowriter', [ '--headless', '--convert-to', 'pdf', '--outdir', "$buildDir/output/dist/doc", "$buildDir/output/dist/doc/JHDF5-${version}.odt" ])
		}

		from (nativeJarLinuxIntel.archivePath) {
		into "${project.group}-jhdf5/lib/nativejar"
		}

		from (nativeJarMacIntel.archivePath) {
		into "${project.group}-jhdf5/lib/nativejar"
		task distributionZip(type: Zip, dependsOn: [jar, javadocJar, sourcesJar, exampleJar, processDistFiles]) {
		baseName "${project.group}-jhdf5"

		from('targets/dist') {
		into "${project.group}-jhdf5"
		include 'version.txt'
		include 'build.txt'
		}

		from (nativeJarWindowsIntel.archivePath) {
		into "${project.group}-jhdf5/lib/nativejar"
		from ("$buildDir/output/dist") {
		into "${project.group}-jhdf5"
		include '*'
		}

		from (batteriesIncluded.archivePath) {
		into "${project.group}-jhdf5/lib/batteries_included"
		from ("$buildDir/output/dist") {
		into "${project.group}-jhdf5"
		include 'bin/*'
		}

		from ("dist") {
		from ("$buildDir/output/dist") {
		into "${project.group}-jhdf5"
		include 'doc/*'
		}

		from (javadocZip.archivePath) {
		from (javadocJar.archivePath) {
		into "${project.group}-jhdf5/doc"
		}

		from (exampleZip.archivePath) {
		from (exampleJar.archivePath) {
		into "${project.group}-jhdf5/doc"
		}

		from (configurations.runtime) {
		include '-sources'
		into "${project.group}-jhdf5/sources"
		}

		from (sourcesJar.archivePath) {
		into "${project.group}-jhdf5/src"
		rename '(.*)', "${project.group}-jhdf5-src.zip"
		into "${project.group}-jhdf5/sources"
		}

		// 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 $buildDir/tmp/expandedArchives".tokenize()
		from (jar.archivePath) {
		into "${project.group}-jhdf5/lib"
		}

		from (configurations.runtime) {
		exclude 'restriction'
		exclude 'bcel'
		exclude '-sources'
		into "${project.group}-jhdf5/lib"
		}

		from ("libs") {
		into "${project.group}-jhdf5/lib"
		include 'native/**'
		}

		from (configurations.runtime.collect {zipTree(it)}) {
		into "${project.group}-jhdf5/lib"
		include 'native/*/'
		}

		}
		@@ -258,22 +187,6 @@ if (project == project.rootProject)
		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"
		}

dist/CONTENT

+53 −37

Original line number	Diff line number	Diff line
		Documentation
		doc/jhdf5-javadoc.zip
		General Information:
		build.txt
		The build information of this distribution in human readable form.
		version.txt
		The version information of this distribution in machine readable form.
		CONTENT
		This file.
		COPYING
		Copyright notice of the JHDF5 and the SIS base libraries.
		COPYING-hdf5
		Copyright notice of the HDF5 library.
		COPYING-commons
		Copyright notice of the Apache "Commons IO" and "Commons Lang3" libraries.
		COPYING-args4j
		Copyright notice of the CISD args4j library.
		LICENSE
		The Apache Sofware License 2.0.

		doc/cisd-jhdf5-examples-src.zip
		Example programs for some of the features of JHDF5
		Documentation:
		doc/sis-jhdf5-javadoc-<VERSION>.jar
		The Javadoc of JHDF5.

		Source
		src/jhdf5-src.zip
		doc/sis-jhdf5-examples-sources-<VERSION>.jar
		Simple example programs showing some features of JHDF5.

		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).
		doc/JHDF5-<VERSION>.pdf
		A simple (and incomplete) introduction into JHDF5 (in Portable Document Format).

		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).
		doc/JHDF5-<VERSION>.odt
		A simple (and incomplete) introduction into JHDF5 (in OpenDocument Text Format).

		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
		Source Code:
		sources/jhdf5-sources-<VERSION>.jar
		The source code of jhdf5.
		sources/sis-base-18.08.0-sources.jar
		The source code of the SIS base library.
		sources/cisd-args4j-9.11.2-sources.jar
		The source code of the CISD args4j library.
		sources/commons-io-2.6-sources.jar
		The source code of the Apache "Commons IO" library.
		sources/commons-lang3-3.7-sources.jar
		The source code of the Apache "Commons Lang3" library.

		Libraries:
		lib/sis-jhdf5.jar:
		The Java class files of the JHDF5 library, the h5ar archiver and the hdf5 native libraries.
		Requires commons-io-2.6.jar, commons-lang3-3.7.jar, sis-base-18.08.0.jar and cisd-args4j-9.11.2
		(only needed for h5ar archiver) on the class path.
		lib/sis-base-18.08.0.jar
		The Java class files of the SIS base library. Requires commons-io-2.6.jar, commons-lang3-3.7.jar
		on the class path.
		lib/cisd-args4j-9.11.2.jar
		The Java class files of the CISD args4j library.
		lib/commons-lang3-3.7.jar
		The Java class files of the Apache "Commons Lang3" library.
		lib/commons-io-2.6.jar
		The Java class files of the Apache "Commons IO" library.
		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
		Wrapper Executables:
		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

dist/COPYING

+1 −1

Original line number	Diff line number	Diff line
		/*
		* Copyright 2008-2012 ETH Zuerich, CISD
		* Copyright 2007 - 2018 ETH Zuerich, CISD and SIS.
		*
		* Licensed under the Apache License, Version 2.0 (the "License");
		* you may not use this file except in compliance with the License.