Build and test on Java 11

* Changes to allow htsjdk to build and run on Java 11.
  * Fix broken javadoc that fail in 11
  * Fix String.lines conflict: see scala/bug#11125
* Changes to the build:
  * Update gradle 4.8.1 -> 5.2.1
  * Update shadow plugin 2.0.4 -> 4.0.4
  * Update scala test plugin 0.22 -> 0.23
  * Switch publishing plugin from maven -> maven-publish
* Add Java 11 to travis matrix

Co-authored-by: Louis Bergelson <louisb@broadinstitute.org>

.travis.yml

@@ -11,6 +11,7 @@ cache:
 jdk:
   - oraclejdk8
   - openjdk8
+  - openjdk11
 matrix:
   fast_finish: true
   allow_failures: 
@@ -36,5 +37,5 @@ after_success:
   - echo "TRAVIS_BRANCH='$TRAVIS_BRANCH'";
     echo "JAVA_HOME='$JAVA_HOME'";
     if [ "$TRAVIS_BRANCH" == "master" ]; then
-       ./gradlew uploadArchives;
+       ./gradlew publish;
     fi

build.gradle

@@ -7,12 +7,12 @@ buildscript {
 plugins {
     id 'java'
     id 'scala'
-    id 'maven'
+    id 'maven-publish'
     id 'signing'
     id 'jacoco'
     id 'com.palantir.git-version' version '0.11.0'
-    id 'com.github.johnrengelman.shadow' version '2.0.4'
-    id 'com.github.maiflai.scalatest' version '0.22'
+    id 'com.github.johnrengelman.shadow' version '4.0.4'
+    id 'com.github.maiflai.scalatest' version '0.23'
 }
 
 repositories {
@@ -22,7 +22,6 @@ repositories {
 jacocoTestReport {
     group = "Reporting"
     description = "Generate Jacoco coverage reports after running tests."
-    additionalSourceDirs = files(sourceSets.main.allJava.srcDirs)
 
     reports {
         xml.enabled = true // codecov depends on xml format report
@@ -38,7 +37,7 @@ dependencies {
     compile "org.tukaani:xz:1.5"
     compile "gov.nih.nlm.ncbi:ngs-java:2.9.0"
 
-    testCompile "org.scala-lang:scala-library:2.12.6"
+    testCompile "org.scala-lang:scala-library:2.12.8"
     testCompile "org.scalatest:scalatest_2.12:3.0.5"
     testRuntime 'org.pegdown:pegdown:1.6.0' // Necessary for generating HTML reports with ScalaTest
     testCompile "org.testng:testng:6.14.3"
@@ -58,6 +57,8 @@ group = 'com.github.samtools'
 
 defaultTasks 'jar'
 
+
+
 jar {
     manifest {
         attributes 'Implementation-Title': 'HTSJDK',
@@ -141,92 +142,79 @@ task testExternalApis(type: Test) {
 }
 
 wrapper {
-    gradleVersion = '4.8.1'
+    gradleVersion = '5.2.1'
 }
 
-// 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')
-    }
+tasks.withType(Javadoc) {
+    options.addStringOption('Xdoclint:none', '-quiet')
 }
 
 task javadocJar(type: Jar, dependsOn: javadoc) {
-    classifier = 'javadoc'
+    archiveClassifier.set('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
+    archiveClassifier.set('sources')
 }
 
 /**
  * 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) }
+publishing {
+    publications {
+        htsjdk(MavenPublication) {
+            from components.java
+            artifact javadocJar
+            artifact sourcesJar
 
-            repository(url: "https://oss.sonatype.org/service/local/staging/deploy/maven2/") {
-                authentication(userName: project.findProperty("sonatypeUsername"), password: project.findProperty("sonatypePassword"))
-            }
-
-            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 'git@github.com:samtools/htsjdk.git'
-                    connection 'scm:git:git@github.com:samtools/htsjdk.git'
+                    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'
+                        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)

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.8.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-5.2.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -28,7 +28,7 @@ APP_NAME="Gradle"
 APP_BASE_NAME=`basename "$0"`
 
 # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS=""
+DEFAULT_JVM_OPTS='"-Xmx64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD="maximum"

src/main/java/htsjdk/samtools/util/MergingIterator.java

@@ -87,17 +87,11 @@ public MergingIterator(final Comparator<T> comparator, final Collection<Closeabl
 		// should we throw? it's prob'ly an error.
 	}
 
-	/**
-	 * @see java.util.Iterator<T>.hasNext
-	 */
 	@Override
 	public boolean hasNext() {
 		return ! this.queue.isEmpty();
 	}
 
-	/**
-	 * @see java.util.Iterator<T>.next
-	 */
 	@Override
 	public T next() {
 		if ( ! this.hasNext()) throw new NoSuchElementException();

src/test/scala/htsjdk/samtools/fastq/FastqReaderWriterTest.scala

@@ -143,7 +143,7 @@ class FastqReaderWriterTest extends UnitSpec {
       """.stripMargin.trim
 
     Range.inclusive(1, 3).foreach { n =>
-      val text   = fastq.lines.take(n).mkString("\n")
+      val text   = fastq.linesIterator.take(n).mkString("\n")
       val reader = new BufferedReader(new StringReader(text))
       an[Exception] shouldBe thrownBy { new FastqReader(null, reader).iterator().toSeq }
     }

src/test/scala/htsjdk/samtools/util/StringUtilTest.scala

@@ -118,8 +118,8 @@ class StringUtilTest extends UnitSpec {
 
   it should "wrap text when lines are longer than length give" in {
     val result = StringUtil.wordWrap(textForWrapping, 15)
-    result.lines.size shouldBe 5
-    result.lines.foreach(line => line.length should be <= 15)
+    result.linesIterator.size shouldBe 5
+    result.linesIterator.foreach(line => line.length should be <= 15)
   }
 
   "StringUtil.intValuesToString(int[])" should "generate a CSV string of ints" in {