.classpath

@@ -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

@@ -7,3 +7,4 @@
 /test-output
 /source/c/build
 source/c/hdf5*tar*
+source/c/CMake*zip

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:+'
+    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"
                 }

debian/changelog

-libsis-jhdf5-java (18.08~pre+git20180805.da55947+dfsg-1) UNRELEASED; urgency=medium
+libsis-jhdf5-java (18.09.0-pre1+dfsg-1) UNRELEASED; urgency=medium
 
   * Pre-release to adapt to HDF5 1.10.3-pre1
-  * Use git mode in watch file
+  * Adapt watch file to upstream Gitlab clone tags
   * Drop now unneeded get-orig-source target
   * Fix homepage
   * Use gradle build system
   * Build-Depends: ant
+  * Versioned Build-Depends: libsis-base-java (>= 18.08.0~)
 
  -- Andreas Tille <tille@debian.org>  Mon, 13 Aug 2018 14:30:28 +0200
 

debian/control

@@ -12,7 +12,7 @@ Build-Depends: debhelper (>= 11~),
                ant,
                libcommons-lang-java,
                libcommons-io-java,
-               libsis-base-java,
+               libsis-base-java (>= 18.08.0~),
                libhdf5-dev (>> 1.8.13),
                junit4,
                testng,

debian/patches/fix_build_dir.patch

@@ -4,7 +4,7 @@ Description: Do not make wrong assumptions about directory name
 
 --- a/javaproject.gradle
 +++ b/javaproject.gradle
-@@ -50,7 +50,7 @@ sourceSets {
+@@ -50,13 +50,9 @@ sourceSets {
  buildDir = 'targets/gradle'
  
  buildscript {
@@ -12,4 +12,10 @@ Description: Do not make wrong assumptions about directory name
 +    apply from: 'repository.gradle'
      
      repositories repositoryConfig
+-    
+-    dependencies {
+-        classpath 'cisd:cisd-ant-tasks:+'
+-    }
+ }
  
+ repositories repositoryConfig

debian/rules

@@ -17,9 +17,9 @@ TESTIGNORE = sourceTest/java/ch/systemsx/cisd/hdf5/HDF5RoundtripTest.java \
              sourceTest/java/ch/systemsx/cisd/hdf5/io/HDF5DataSetRandomAccessFileTest.java
 
 %:
-	dh $@ --buildsystem=gradle --with javahelper
+	dh $@ --with javahelper #  --buildsystem=gradle
 
-_override_dh_auto_clean:
+override_dh_auto_clean:
 	rm -rf build *.jar
 	rm -rf source/c/*.log
 	rm -rf source/c/*.so
@@ -31,19 +31,19 @@ _override_dh_auto_clean:
 	#Things that we'd probably exclude from the orig.tar.gz anyway
 	rm -rf jsrc lib ./sourceTest/java/jni
 
-_override_dh_auto_build:
+override_dh_auto_build:
 	# C build
 	cd source/c && \
 		$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS)  -shared -fPIC -Wl,--exclude-libs,ALL \
 		-I/usr/lib/jvm/default-java/include/ -I/usr/include/hdf5/serial \
-	       	jhdf5/*.c hdf-java/*.c -o libsis-jhdf5.so -lz -lhdf5_serial
+	       	*.c jni/*.c -o libsis-jhdf5.so -lz -lhdf5_serial
 	# Java build - see README.source about the file being removed
 	mkdir jsrc ; cp -r source/java/ch source/java/ncsa jsrc
 	rm jsrc/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java
 	# This line is still needed on Ubuntu 14.04
 	jh_build sis-jhdf5.jar jsrc
 
-_override_dh_auto_test:
+override_dh_auto_test:
 	# FIXME
 	# Due to bug #842815 several tests are failing
 	# To get at least some installable package these tests are ignored here

debian/watch

 version=4
 
-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
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+  https://sissource.ethz.ch/sispub/jhdf5/tags .*/archive/.+/jhdf5-(\d[-\d.pre]+)@ARCHIVE_EXT@
 
-# 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
+#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

dist/CONTENT

-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

 /*
- * 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.

dist/COPYING-args4j

 Copyright (c) 2003, Kohsuke Kawaguchi
+Copyright 2007 - 2009 ETH Zuerich, CISD.
 All rights reserved.
 
 Redistribution and use in source and binary forms,

dist/COPYING-commons

 Apache Commons Lang and Commons IO
-Copyright 2001-2008 The Apache Software Foundation
+Copyright 2001-2018 The Apache Software Foundation
 
 This product includes software developed by
 The Apache Software Foundation (http://www.apache.org/).

dist/COPYING-hdf5

@@ -4,7 +4,7 @@ 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.
+Copyright 2006-2018 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.

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
+set /p version=<%~dp0..\version.txt
+java -Dnative.libpath=%~dp0..\lib\native -jar %~dp0..\lib\sis-jhdf5-%version%.jar %1 %2 %3 %4 %5 %6 %7 %8 %9

dist/bin/h5ar.sh

@@ -19,4 +19,5 @@ while [ -n "${LINK}" ]; do
 done
 BINDIR="${SCRIPT%/*}"
 JHDFDIR="${BINDIR%/*}"
-java -Dnative.libpath="${JHDFDIR}/lib/native" -jar "${JHDFDIR}/lib/sis-jhdf5-tools.jar" "$@"
+VERSION=`cat "${JHDFDIR}/version.txt"`
+java -Dnative.libpath="${JHDFDIR}/lib/native" -jar "${JHDFDIR}/lib/sis-jhdf5-${VERSION}.jar" "$@"

gradle/wrapper/gradle-wrapper.properties

@@ -3,4 +3,4 @@ distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=http\://svnsis.ethz.ch/repos/cisd/ivy-repository/trunk/gradle/distribution/2.3/gradle-2.3-all.zip
+distributionUrl=http\://svnsis.ethz.ch/repos/cisd/ivy-repository/trunk/gradle/distribution/4.9/gradle-4.9-all.zip

javaproject.gradle

@@ -19,8 +19,8 @@ configurations.all {
 }
 
 task wrapper(type: Wrapper) {
-    gradleVersion = '2.3'
-    distributionUrl = "http://svnsis.ethz.ch/repos/cisd/ivy-repository/trunk/gradle/distribution/2.3/gradle-2.3-all.zip"
+    gradleVersion = '4.9'
+    distributionUrl = "http://svnsis.ethz.ch/repos/cisd/ivy-repository/trunk/gradle/distribution/4.9/gradle-4.9-all.zip"
 }
 
 sourceCompatibility='1.8'
@@ -50,17 +50,8 @@ sourceSets {
 buildDir = 'targets/gradle'
 
 buildscript {
-    apply from: '../jhdf5/repository.gradle'
-    
-    repositories repositoryConfig
-    
-    dependencies {
-        classpath 'cisd:cisd-ant-tasks:+'
-    }
 }
 
-repositories repositoryConfig
-
 def execute(command, arguments) {
     new ByteArrayOutputStream().withStream { os ->
         print "execute: ${command}"
@@ -89,114 +80,70 @@ def execute_working_dir(command, arguments, working_dir) {
     }
 }
 
-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() {
-    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'], '.')
-        return output.length == 1 && output[0].length() == 0 ? 'clean' : 'dirty'
+def getDirtyFiles() {
+    if (isGitProject()) {
+        return execute_working_dir('git', ['status', '--porcelain'], '.')
     } else {
-    	return 'dirty'
-    }
+    	return [ 'Workspace is not under revision control.' ].toArray()
     }
-
-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 describe --tags'.execute().text.trim()
+    def humanReadableBuildInfo = ""
+    if (isGitProject()) {
+        def gitlogoutput = execute_working_dir('git', ['log', '-1', '--format=%at-%H'], '../' + project.name)
+        def rev = gitlogoutput[0].split("-")
+        project.ext.revisionNumber = Integer.parseInt(rev[0])
+        def commitHash = rev[1]
+        def commitDate = new java.text.SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssX").format(new Date(revisionNumber * 1000L))
+        def dirtyFiles = getDirtyFiles()
+        project.ext.cleanFlag = dirtyFiles.length == 1 && dirtyFiles[0].length() == 0 ? 'clean' : 'dirty'
+        project.ext.revisionInfo = "${commitHash} [${commitDate}]"
+        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
         }
+        humanReadableBuildInfo = "Version: ${project.ext.versionNumber}\n"
+        humanReadableBuildInfo += "GIT Revision SHA1 Hash: ${commitHash}\n"
+        humanReadableBuildInfo += "GIT Revision Date: ${commitDate}\n"
+        if (project.ext.cleanFlag == 'dirty') {
+            humanReadableBuildInfo += "Uncommitted Files in Build Workspace:\n"
+            humanReadableBuildInfo += "   " + dirtyFiles.join("\n   ") + "\n"
+        }
     } else {
+        project.ext.revisionInfo = '?'
         project.ext.revisionNumber = 1
         project.ext.versionNumber = 'SNAPSHOT'
+        project.ext.cleanFlag = 'dirty'
+        humanReadableBuildInfo += "Build workspace not under revision control.\n"
     }
 
-    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}:${project.ext.cleanFlag}"
+    version = project.ext.versionNumber.startsWith('SNAPSHOT') ? "${project.ext.revisionNumber}" : project.ext.versionNumber
+    project.ext.revisionForPublication = project.ext.versionNumber.startsWith('SNAPSHOT') ? "${project.ext.revisionNumber}" : project.ext.versionNumber
+    def buildInfo = "${project.ext.versionNumber}::${project.ext.revisionInfo}::${project.ext.cleanFlag}"
+    project.ext.buildInfo = buildInfo
     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
+    file("${project.projectDir}/$targetsDist/build.txt") << humanReadableBuildInfo
+    file("${project.projectDir}/$targetsDist/version.txt") << version
 }
 
 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()
@@ -231,10 +178,9 @@ test {
     testLogging.showStandardStreams = true
     ignoreFailures = true
 }
-test.dependsOn checkRestrictions
 
 dependencies {
-    ecj "eclipse:ecj:+"
+    ecj files('libs/build/ecj-4.6.1.jar')
 }
 
 compileJava {
@@ -261,18 +207,9 @@ compileTestJava {
 
 def createJvmArgs() {
     def args = ['-cp', configurations.ecj.asPath, 'org.eclipse.jdt.internal.compiler.batch.Main', '-nowarn']
-    appendCompatibilityOption(args, '-source', sourceCompatibility)
-    appendCompatibilityOption(args, '-target', targetCompatibility)
     return args
 }
 
-def appendCompatibilityOption(args, option, versionCompatibility) {
-    if (JavaVersion.current().equals(JavaVersion.toVersion(versionCompatibility))) {
-        args.add(option)
-        args.add(versionCompatibility.toString())
-    }
-}
-
 processTestResources {
     fileMode=0666
 }
@@ -288,7 +225,7 @@ eclipse {
 
 eclipse.classpath.file {
     whenMerged{ classpath ->
-        def projectRefs = classpath.entries.findAll{entry -> entry.kind =='src' && entry.path.startsWith('/')}
+        def projectRefs = classpath.entries.findAll{entry -> entry.kind =='sources' && entry.path.startsWith('/')}
         classpath.entries.removeAll(projectRefs)
         classpath.entries.addAll(projectRefs)   
     }