build.gradle

apply plugin: 'java'
//apply plugin: 'maven'

group = 'ch.psi'
version = '0.13.0'

description = """"""

sourceCompatibility = 1.8
targetCompatibility = 1.8


repositories {
    mavenCentral()
    maven { url "http://artifacts.psi.ch/artifactory/libs-releases" }
    maven { url "http://maven.imagej.net/content/repositories/public/" }
    flatDir {
        dirs 'lib'
    }
}

// define a provided scope
configurations {
    provided
    compile.extendsFrom provided
}

dependencies {

    compile name: 'sis-jhdf5-19.04.0'
    compile name: 'sis-base-18.09.0'
    compile name: 'commons-io-2.6'
//    compile name: 'sis-base-18.09.0'
//    compile group: 'cisd', name: 'jhdf5', version: '14.12.6'
//    compile group: 'hdf5', name: 'hdf', version:'2.10.0'
//    compile group: 'hdf5', name: 'hdfobj', version:'2.10.0'
//    compile group: 'hdf5', name: 'hdf5', version:'2.10.0'
//    compile group: 'hdf5', name: 'hdf5obj', version:'2.10.0'
    compile group: 'org.slf4j', name: 'slf4j-api', version: '1.7.6'
    testCompile group: 'junit', name: 'junit', version: '4.11'


    provided group: 'net.imagej', name: 'ij', version: '1.53e'
}

task fatJar(type: Jar) {
//    manifest {
//        attributes 'Implementation-Title': 'CaView',
//                'Implementation-Version': version,
//                'Main-Class': 'ch.psi.caview.CaView'
//    }
    archiveBaseName = 'HDF5_Viewer'
    from { (configurations.compile - configurations.provided).collect { it.isDirectory() ? it : zipTree(it) } }
    with jar
}

//task distributionZip(type: Zip, dependsOn: [fatJar]) {
//    baseName "${project.group}-jhdf5"
//
//    from('targets/dist') {
//        into "${project.group}-jhdf5"
//        include 'version.txt'
//        include 'build.txt'
//    }
//
//    from ("$buildDir/output/dist") {
//        into "${project.group}-jhdf5"
//        include '*'
//    }
//
//    from ("$buildDir/output/dist") {
//        into "${project.group}-jhdf5"
//        include 'bin/*'
//    }
//
//    from ("$buildDir/output/dist") {
//        into "${project.group}-jhdf5"
//        include 'doc/*'
//    }
//
//    from (javadocJar.archivePath) {
//        into "${project.group}-jhdf5/doc"
//    }
//
//    from (exampleJar.archivePath) {
//        into "${project.group}-jhdf5/doc"
//    }
//
//    from (configurations.runtime) {
//        include '*-sources*'
//        into "${project.group}-jhdf5/sources"
//    }
//
//    from (sourcesJar.archivePath) {
//        into "${project.group}-jhdf5/sources"
//    }
//
//    from (jar.archivePath) {
//        into "${project.group}-jhdf5/lib"
//    }
//
//    from (h5arCLIJar.archivePath) {
//        into "${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/**/*'
//    }
//
//}