build.gradle

buildscript {
    repositories {
        mavenCentral()
    }
}

plugins {
    id "java"
    id 'maven'
    id 'signing'
    id 'jacoco'
    id 'com.palantir.git-version' version '0.5.1'
    id 'com.github.johnrengelman.shadow' version '1.2.3'
    id "com.github.kt3k.coveralls" version "2.6.3"
}

repositories {
    mavenCentral()
}

jacocoTestReport {
    dependsOn test
    group = "Reporting"
    description = "Generate Jacoco coverage reports after running tests."
    additionalSourceDirs = files(sourceSets.main.allJava.srcDirs)

    reports {
        xml.enabled = true // coveralls plugin depends on xml format report
        html.enabled = true
    }
}

jacoco {
    toolVersion = "0.7.5.201505241946"
}

dependencies {
    compile "org.apache.commons:commons-jexl:2.1.1"
    compile "commons-logging:commons-logging:1.1.1"
    compile "org.xerial.snappy:snappy-java:1.0.3-rc3"
    compile "org.apache.commons:commons-compress:1.4.1"
    compile "org.tukaani:xz:1.5"
    compile "gov.nih.nlm.ncbi:ngs-java:1.2.4"

    testCompile "org.testng:testng:6.9.9"
}

sourceCompatibility = 1.8
targetCompatibility = 1.8

final isRelease = Boolean.getBoolean("release")
final gitVersion = gitVersion().replaceAll(".dirty", "")
version = isRelease ? gitVersion : gitVersion + "-SNAPSHOT"

logger.info("build for version:" + version)
group = 'com.github.samtools'

defaultTasks 'jar'

jar {
    manifest {
        attributes 'Implementation-Title': 'HTSJDK',
                'Implementation-Vendor' : 'Samtools Organization',
                'Implementation-Version': version
    }
}

import org.gradle.internal.os.OperatingSystem;

tasks.withType(Test) {
    outputs.upToDateWhen { false } // tests will always rerun
    useTestNG()

    // set heap size for the test JVM(s)
    minHeapSize = "1G"
    maxHeapSize = "2G"

    jvmArgs '-Djava.awt.headless=true'  //this prevents awt from displaying a java icon while the tests are running

    if (System.env.CI == "true") {  //if running under a CI output less into the logs
        int count = 0

        beforeTest { descriptor ->
            count++
            if( count % 100 == 0) {
                logger.lifecycle("Finished "+ Integer.toString(count++) + " tests")
            }
        }
    } else {
        // show standard out and standard error of the test JVM(s) on the console
        testLogging.showStandardStreams = true
        beforeTest { descriptor ->
            logger.lifecycle("Running Test: " + descriptor)
        }

        // listen to standard out and standard error of the test JVM(s)
        onOutput { descriptor, event ->
            logger.lifecycle("Test: " + descriptor + " produced standard out/err: " + event.message )
        }
    }

    testLogging {
        testLogging {
            events "skipped", "failed"
            exceptionFormat = "full"
        }
        afterSuite { desc, result ->
            if (!desc.parent) { // will match the outermost suite
                println "Results: ${result.resultType} (${result.testCount} tests, ${result.successfulTestCount} successes, ${result.failedTestCount} failures, ${result.skippedTestCount} skipped)"
            }
        }
    }
}

test {
    description = "Runs the unit tests other than the SRA tests"

    useTestNG {
        if( OperatingSystem.current().isUnix() ){
            excludeGroups "slow", "broken", "sra"
        } else {
            excludeGroups "slow", "broken", "unix", "sra"
        }
    }
}

task testSRA(type: Test) {
    jvmArgs '-Dsamjdk.sra_libraries_download=true'

    description "Run the SRA tests"
    useTestNG {
        configFailurePolicy 'continue'
        includeGroups "sra"
    }
}

task wrapper(type: Wrapper) {
    description = "Regenerate the gradle wrapper"
    gradleVersion = '2.13'
}

// This is a hack to disable the java 8 default javadoc lint until we fix the html formatting
if (JavaVersion.current().isJava8Compatible()) {
    tasks.withType(Javadoc) {
        options.addStringOption('Xdoclint:none', '-quiet')
    }
}

task javadocJar(type: Jar, dependsOn: javadoc) {
    classifier = 'javadoc'
    from 'build/docs/javadoc'
}

task sourcesJar(type: Jar) {
    from sourceSets.main.allSource
    classifier = 'sources'
}

/**
 *This specifies what artifacts will be built and uploaded when performing a maven upload.
 */
artifacts {
    archives jar
    archives javadocJar
    archives sourcesJar
}

/**
 * Sign non-snapshot releases with our secret key.  This should never need to be invoked directly.
 */
signing {
    required { isRelease && gradle.taskGraph.hasTask("uploadArchives") }
    sign configurations.archives
}

/**
 * Upload a release to sonatype.  You must be an authorized uploader and have your sonatype
 * username and password information in your gradle properties file.  See the readme for more info.
 *
 * For releasing to your local maven repo, use gradle install
 */
uploadArchives {
    repositories {
        mavenDeployer {
            beforeDeployment { MavenDeployment deployment -> signing.signPom(deployment) }

            repository(url: "https://oss.sonatype.org/service/local/staging/deploy/maven2/") {
                authentication(userName: project.findProperty("sonatypeUsername"), password: project.findProperty("sonatypePassword"))
            }

            snapshotRepository(url: "https://artifactory.broadinstitute.org/artifactory/libs-snapshot-local/") {
                authentication(userName: System.env.ARTIFACTORY_USERNAME, password: System.env.ARTIFACTORY_PASSWORD)
            }

            pom.project {
                name 'HTSJDK'
                packaging 'jar'
                description 'A Java API for high-throughput sequencing data (HTS) formats'
                url 'http://samtools.github.io/htsjdk/'

                developers {
                    developer {
                        id 'picard'
                        name 'Picard Team'
                        url 'http://broadinstitute.github.io/picard'
                    }
                }

                scm {
                    url 'git@github.com:samtools/htsjdk.git'
                    connection 'scm:git:git@github.com:samtools/htsjdk.git'
                }

                licenses {
                    license {
                        name 'MIT License'
                        url 'http://opensource.org/licenses/MIT'
                        distribution 'repo'
                    }
                }
            }
        }
    }
    doFirst{
        System.out.println("Uploading version $version")
    }
}