build.gradle

plugins {
    id 'java'
    id 'idea'
    id 'application'
    //id "us.kirchmeier.capsule" version "1.0.1"
    //id "jacoco"
    id 'com.github.johnrengelman.shadow' version '2.0.0'
    id 'com.gradle.build-scan' version '1.16'
}



mainClassName = 'uk.ac.ox.oxfish.Main'

repositories {
    mavenLocal()
    mavenCentral()

}

sourceSets
        {
  main {
    java {
      srcDir 'src/main/java'
    }
    resources {
      srcDir 'src/main/resources'
    }
  }
  test {
    java {
      srcDir 'src/test/java'
    }
    resources {
      srcDir 'src/test/resources'
    }
  }
}



//here we add all the dependencies notice that mason and geomason are not on maven so we need to add them separately
dependencies
{
    //mason libraries. They aren't on maven so we have to lug their jars around
    compile fileTree(dir: 'libs/mason', include: '*.jar')
    compile fileTree(dir: 'libs/geomason', include: '*.jar')
    //a jury-rigged version of OSMOSE, hopefully linkable with this simulation
    compile fileTree(dir: 'libs/osmose', include: '*.jar')


    //metawidget + apache binders. Useful for the gui
    compile "org.metawidget.modules:metawidget-all:4.1"
    compile "commons-beanutils:commons-beanutils:1.8.3"

    //csv helper
    compile "com.opencsv:opencsv:3.8"


    //logger:
    compile "com.esotericsoftware:minlog:1.3.0"
    //serializer
    compile fileTree(dir: 'libs/xstream/lib', include: '*.jar')
    compile "org.ogce:xpp3:1.1.6"

    //kd tree
    compile fileTree(dir: 'libs/rednaxela', include: '*.jar')

    //jung social network:
    compile "net.sf.jung:jung-api:2.0.1"
    compile 'net.sf.jung:jung-graph-impl:2.0.1'
    compile 'net.sf.jung:jung-io:2.0.1'
    compile 'net.sf.jung:jung-algorithms:2.0.1'

    //yaml parser, useful for reading configuration files
    compile 'org.yaml:snakeyaml:1.15'
    //jcommander, useful to parse command line
    compile "com.beust:jcommander:1.48"

    //commons math
    compile group: 'org.apache.commons', name: 'commons-math3', version: '3.2'

    //burlap : Reinforcement Learning helper
    compile group: 'edu.brown.cs.burlap', name: 'burlap', version: '3.0.1'

    //discrete choosers
    compile fileTree(dir: 'libs/discrete-choosers', include: '*.jar')


    // maximizer
    compile group: 'de.openea', name : 'eva2', version : '2.2.0'

    //annotations
    compile group: 'com.intellij', name: 'annotations', version: '12.0'

    //testing:
    testCompile "junit:junit:4.12"
    testCompile "org.mockito:mockito-all:1.9.5"

    //guava. Useful for PreConditions and sometimes specialized collections
    compile "com.google.guava:guava:23.0"
    compile "com.google.code.findbugs:jsr305:3.0.2"


}


//this makes tests multi-threaded when called from gradle. Useful!
test{
        maxParallelForks = Math.min(Runtime.runtime.availableProcessors(),3)
}





task shadowJarFoo(type: com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar) {
    archiveName = 'foo.jar'
    from sourceSets.main.output //tells the task to include the project code
    configurations = [ configurations.runtime ] //tells the task to shadow in the jars files in the 'runtime' scope
}


//this task creates a single executable jar ("fat" because it contains all its requirements); this is mostly what gets
//distributed

task fatJar(type: com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar) {
    mergeServiceFiles()
    archiveName = 'oxfish_executable.jar'
    from sourceSets.main.output //tells the task to include the project code
    configurations = [ project.configurations.compile ] //tells the task to shadow in the jars files in the 'runtime' scope
    manifest {
        attributes 'Main-Class': 'uk.ac.ox.oxfish.Main'
    }
}

task optimizerJar(type: com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar) {
    mergeServiceFiles()
    archiveName = 'maximizer.jar'
    from sourceSets.main.output //tells the task to include the project code
    configurations = [ project.configurations.compile ] //tells the task to shadow in the jars files in the 'runtime' scope
    manifest {
        attributes 'Main-Class': 'uk.ac.ox.oxfish.MainOptimizer'
    }
}

task calicatchFatJar(type: com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar) {
    mergeServiceFiles()
    archiveName = 'calicatch.jar'
    from sourceSets.main.output //tells the task to include the project code
    configurations = [ project.configurations.compile ] //tells the task to shadow in the jars files in the 'runtime' scope
    manifest {
        attributes 'Main-Class': 'uk.ac.ox.oxfish.experiments.CaliCatchCalibration'
    }
}

task inferenceFatJar(type: com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar) {
    mergeServiceFiles()
    archiveName = 'indirectInference.jar'
    from sourceSets.main.output //tells the task to include the project code
    configurations = [ project.configurations.compile ] //tells the task to shadow in the jars files in the 'runtime' scope
    manifest {
        attributes 'Main-Class': 'uk.ac.ox.oxfish.experiments.IndirectInferencePaper'
    }
}


//this task creates a single executable jar ("fat" because it contains all its requirements); this is mostly what gets
//distributed
task buildHeadless(type: com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar) {

    mergeServiceFiles()
    archiveName = 'yamler.jar'
    from sourceSets.main.output //tells the task to include the project code
    configurations = [ project.configurations.compile ] //tells the task to shadow in the jars files in the 'runtime' scope
    manifest {
        attributes 'Main-Class': 'uk.ac.ox.oxfish.YamlMain'
    }

}

//this task takes the yamler.jar from the build/libs folder and place it in the runs optimization folder. This is important
//to make optimization.py work correctly

task deployHeadless(type: Copy, dependsOn: buildHeadless) {
    from 'build/libs/'
    into 'runs/optimization/'
    include 'yamler.jar'
}



task fatJarBatch(type: com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar) {
    mergeServiceFiles()
    archiveName = 'oxfish_batch.jar'
    from sourceSets.main.output //tells the task to include the project code
    configurations = [ project.configurations.compile ] //tells the task to shadow in the jars files in the 'runtime' scope
    manifest {
        attributes 'Main-Class': 'uk.ac.ox.oxfish.gui.BatchRunnerSetup'
    }
}


//this task can be called as ./gradlew buildSampleFiles and simply rebuilds the "YAML Samples" folder
task buildSampleFiles(type: JavaExec){
    classpath = sourceSets.main.runtimeClasspath
    main = 'uk.ac.ox.oxfish.experiments.BuildSampleInputs'
}

task optimizer(type: JavaExec){
    classpath = sourceSets.main.runtimeClasspath
    main = 'uk.ac.ox.oxfish.MainOptimizer'
}


task sample_inputs(type:JavaExec){
    main = 'uk.ac.ox.oxfish.experiments.BuildSampleInputs'
    classpath = sourceSets.main.runtimeClasspath
}


task appendix(type:JavaExec){
    main = 'uk.ac.ox.oxfish.experiments.FirstPaper'
    classpath = sourceSets.main.runtimeClasspath
}

task execute(type:JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = project.hasProperty("mainClass") ? project.getProperty("mainClass") : "package.MyDefaultMain"

}


task algorithms(type:JavaExec){
    main = 'uk.ac.ox.oxfish.experiments.SocialTuningExercise'
    classpath = sourceSets.main.runtimeClasspath
}

task batch(type:JavaExec){
    main = 'uk.ac.ox.oxfish.gui.BatchRunnerSetup'
    classpath = sourceSets.main.runtimeClasspath
}


test {
  useJUnit()
  testLogging {
    events "passed", "skipped", "failed"
  }
}


buildScan {
    termsOfServiceUrl = 'https://gradle.com/terms-of-service'
    termsOfServiceAgree = 'yes'
}

idea{
    project {

    }
    module {
        downloadJavadoc = true // defaults to false
        downloadSources = true
    }
}