update to maven-publish plugin

build.gradle

@@ -7,7 +7,7 @@ buildscript {
 plugins {
     id 'java'
     id 'scala'
-    id 'maven'
+    id 'maven-publish'
     id 'signing'
     id 'jacoco'
     id 'com.palantir.git-version' version '0.11.0'
@@ -22,7 +22,6 @@ repositories {
 jacocoTestReport {
     group = "Reporting"
     description = "Generate Jacoco coverage reports after running tests."
-    getAdditionalSourceDirs().from(sourceSets.main.allJava.srcDirs)
 
     reports {
         xml.enabled = true // codecov depends on xml format report
@@ -58,6 +57,8 @@ group = 'com.github.samtools'
 
 defaultTasks 'jar'
 
+
+
 jar {
     manifest {
         attributes 'Implementation-Title': 'HTSJDK',
@@ -145,72 +146,62 @@ task sourcesJar(type: Jar) {
     archiveClassifier.set('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") }
+    required { isRelease && gradle.taskGraph.hasTask("publishHtsjdkPublicationToMavenRepository") }
     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"))
-            }
+publishing {
+    publications {
+        htsjdk(MavenPublication) {
+            from components.java
+            artifact javadocJar
+            artifact sourcesJar
 
-            snapshotRepository(url: "https://broadinstitute.jfrog.io/broadinstitute/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/'
+            pom {
+                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'
+                        id = 'picard'
+                        name = 'Picard Team'
+                        url = 'http://broadinstitute.github.io/picard'
                     }
                 }
 
                 scm {
-                    url '[email protected]:samtools/htsjdk.git'
-                    connection 'scm:git:[email protected]:samtools/htsjdk.git'
+                    url = '[email protected]:samtools/htsjdk.git'
+                    connection = 'scm:git:[email protected]:samtools/htsjdk.git'
                 }
 
                 licenses {
                     license {
-                        name 'MIT License'
-                        url 'http://opensource.org/licenses/MIT'
-                        distribution 'repo'
+                        name = 'MIT License'
+                        url = 'http://opensource.org/licenses/MIT'
+                        distribution = 'repo'
                     }
                 }
             }
         }
     }
-    doFirst{
-        System.out.println("Uploading version $version")
+
+    repositories {
+        maven {
+            credentials {
+                username = isRelease ? project.findProperty("sonatypeUsername") : System.env.ARTIFACTORY_USERNAME
+                password = isRelease ? project.findProperty("sonatypePassword") : System.env.ARTIFACTORY_PASSWORD
+            }
+            def release = "https://oss.sonatype.org/service/local/staging/deploy/maven2/"
+            def snapshot = "https://broadinstitute.jfrog.io/broadinstitute/libs-snapshot-local/"
+            url = isRelease ? release : snapshot
+        }
     }
 }
+
+task install(dependsOn:publishToMavenLocal)