Migrate to Java 17

.github/workflows/tests.yml

@@ -14,18 +14,15 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        java: [ 8, 11 ]
+        java: [ 17 ]
         experimental: [false]
-#        include:
-#          - java: 17
-#            experimental: true
       fail-fast: false
     continue-on-error: ${{ matrix.experimental }}
     name: Java ${{ matrix.Java }} build and test
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up java ${{ matrix.Java }}
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
           java-version: ${{ matrix.Java }}
           distribution: 'adopt'
@@ -40,11 +37,9 @@ jobs:
         run: scripts/htsget-scripts/start-htsget-test-server.sh
       - name: Run tests
         run: ./gradlew test jacocoTestReport
-#      - name: Upload to codecov
-#        run:  bash <(curl -s https://raw.githubusercontent.com/broadinstitute/codecov-bash-uploader/main/codecov-verified.bash)
       - name: Upload test results
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: test-results-${{ matrix.Java }}
           path: build/reports/tests
@@ -53,11 +48,11 @@ jobs:
     runs-on: ubuntu-latest
     name: Tests that require external APIs
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up java 8
-        uses: actions/setup-java@v2
+      - uses: actions/checkout@v3
+      - name: Set up java 17
+        uses: actions/setup-java@v3
         with:
-          java-version: '8'
+          java-version: '17'
           distribution: 'adopt'
           cache: gradle
       - name: Grant execute permission for gradlew
@@ -70,7 +65,7 @@ jobs:
 #        run: bash <(curl -s https://raw.githubusercontent.com/broadinstitute/codecov-bash-uploader/main/codecov-verified.bash)
       - name: Upload test results
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: test-results-external-apis
           path: build/reports/tests
@@ -79,11 +74,11 @@ jobs:
     runs-on: ubuntu-latest
     name: FTP tests
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up java 8
-        uses: actions/setup-java@v2
+      - uses: actions/checkout@v3
+      - name: Set up java 17
+        uses: actions/setup-java@v3
         with:
-          java-version: '8'
+          java-version: '17'
           distribution: 'adopt'
           cache: gradle
       - name: Grant execute permission for gradlew
@@ -96,19 +91,19 @@ jobs:
 #        run: bash <(curl -s https://raw.githubusercontent.com/broadinstitute/codecov-bash-uploader/main/codecov-verified.bash)
       - name: Upload test results
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: test-results-ftp
           path: build/reports/tests
   spotBugs:
     runs-on: ubuntu-latest
     name: SpotBugs
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up java 8
-        uses: actions/setup-java@v2
+      - uses: actions/checkout@v3
+      - name: Set up java 17
+        uses: actions/setup-java@v3
         with:
-          java-version: '8'
+          java-version: '17'
           distribution: 'adopt'
           cache: gradle
       - name: Grant execute permission for gradlew
@@ -117,7 +112,7 @@ jobs:
         run: ./gradlew spotBugsMain spotBugsTest
       - name: Upload spotBugs Report
         if: failure()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: spotBugs-Report
           path: build/reports/spotbugs

README.md

@@ -1,4 +1,3 @@
-[![Coverage Status](https://codecov.io/gh/samtools/htsjdk/branch/master/graph/badge.svg)](https://codecov.io/gh/samtools/htsjdk)
 [![Build and Test](https://github.com/samtools/htsjdk/actions/workflows/tests.yml/badge.svg?branch=master&event=push)](https://github.com/samtools/htsjdk/actions/workflows/tests.yml)
 [![Maven Central](https://maven-badges.herokuapp.com/maven-central/com.github.samtools/htsjdk/badge.svg)](http://search.maven.org/#search%7Cga%7C1%7Cg%3A%22com.github.samtools%22%20AND%20a%3A%22htsjdk%22)
 [![License](http://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/samtools/htsjdk)
@@ -26,7 +25,7 @@ To receive announcements of releases and other significant project news please s
 
 ### Building HTSJDK
 
-HTSJDK is now built using [gradle](http://gradle.org/).
+HTSJDK is built using [gradle](http://gradle.org/).
 
 A wrapper script (`gradlew`) is included which will download the appropriate version of gradle on the first invocation.
 
@@ -102,16 +101,19 @@ Broadly speaking the majority of the code is covered under the MIT license with
 ### Java Minimum Version Support Policy
 
 Htsjdk currently targets Java 8 and is tested on both 8 and 11.
-We do not currently plan to support versions of Java which are not long-term-support releases (ex: 9, 10, or 12).  
 
-We will notify the community at least 6 months before we plan to stop support for Java 8.  
+We intend to drop support for 8/11 and switch exclusively to 17+ in our next release (4.0.0).
+
+Given our promise of 6 months of warning before a move off of 8, we will atttempt to provide 3.x releases on demand if
+any critical bugs are discovered in the next 6 months.
 
 Java SE Major Release | End of Java SE Oracle Public Updates / OpenJDK support | Proposed End of Support in HTSJDK | Actual End of Support in HTSJDK
----- | ---- | ---- | ----
-6  | Feb 2013 | Aug 2013 | Oct 2015
-7  | Apr 2015 | Oct 2015 | Oct 2015
-8  | Jan 2019 | TBD      | TBD
-11 | Sep 2022 | TBD      | TBD
+---- | ---- |-----------------------------------| ----
+6  | Feb 2013 | Aug 2013                          | Oct 2015
+7  | Apr 2015 | Oct 2015                          | Oct 2015
+8  | Jan 2019 | Feb 2022                          | TBD
+11 | Sep 2022 | Feb 2022                          | TBD
+17 | TBD      | TBD                               | TBD
 
 
 ### Meaning of the Htsjdk version number

build.gradle

@@ -10,7 +10,7 @@ plugins {
     id 'signing'
     id 'jacoco'
     id 'com.palantir.git-version' version '0.11.0'
-    id 'com.github.johnrengelman.shadow' version '4.0.4'
+    id 'com.github.johnrengelman.shadow' version '7.1.2'
     id 'com.github.spotbugs' version "5.0.13"
 }
 
@@ -37,17 +37,25 @@ dependencies {
         exclude group: "junit"
     }
 
+    implementation 'org.openjdk.nashorn:nashorn-core:15.4'
+
+
     api "gov.nih.nlm.ncbi:ngs-java:2.9.0"
     api "org.apache.commons:commons-jexl:2.1.1"
 
-    testImplementation "org.testng:testng:6.14.3"
-    testImplementation "com.google.jimfs:jimfs:1.1"
-    testImplementation "com.google.guava:guava:26.0-jre"
+    testImplementation 'org.testng:testng:7.7.0'
+    testImplementation 'com.google.jimfs:jimfs:1.1'
+    testImplementation "com.google.guava:guava:31.1-jre"
     testImplementation "org.apache.commons:commons-lang3:3.7"
 }
 
-sourceCompatibility = 1.8
-targetCompatibility = 1.8
+java {
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(17)
+    }
+    withJavadocJar()
+    withSourcesJar()
+}
 
 final isRelease = Boolean.getBoolean("release")
 final gitVersion = gitVersion().replaceAll(".dirty", "")
@@ -64,6 +72,7 @@ tasks.withType(JavaCompile) {
 
 tasks.withType(Javadoc) {
     options.addStringOption('encoding', 'UTF-8')
+    options.addStringOption('Xdoclint:none', '-quiet')
 }
 
 jar {
@@ -159,20 +168,6 @@ if(project == rootProject) {
     }
 }
 
-tasks.withType(Javadoc) {
-    options.addStringOption('Xdoclint:none', '-quiet')
-}
-
-task javadocJar(type: Jar, dependsOn: javadoc) {
-    archiveClassifier.set('javadoc')
-    from 'build/docs/javadoc'
-}
-
-task sourcesJar(type: Jar) {
-    from sourceSets.main.allSource
-    archiveClassifier.set('sources')
-}
-
 spotbugs {
     reportLevel = 'high'
     excludeFilter = file('gradle/spotbugs-exclude.xml')
@@ -197,8 +192,6 @@ publishing {
     publications {
         htsjdk(MavenPublication) {
             from components.java
-            artifact javadocJar
-            artifact sourcesJar
 
             pom {
                 name = 'HTSJDK'
@@ -250,6 +243,7 @@ signing {
     required { isRelease && gradle.taskGraph.hasTask("publishHtsjdkPublicationToMavenRepository") }
     sign publishing.publications.htsjdk
 }
+
 gradle.taskGraph.beforeTask { Task task ->
     println "executing $task ..."
 }

src/main/java/htsjdk/samtools/Defaults.java

@@ -166,7 +166,7 @@ public static SortedMap<String, Object> allDefaults(){
     private static String getStringProperty(final String name, final String def) {
         try {
             return System.getProperty(Defaults.SAMJDK_PREFIX + name, def);
-        } catch (final java.security.AccessControlException error) {
+        } catch (final SecurityException error) {
             log.warn(error,"java Security Manager forbids 'System.getProperty(\"" + name + "\")' , returning default value: " + def );
             return def;
         }
@@ -178,7 +178,7 @@ private static String getStringProperty(final String name, final String def) {
     private static boolean hasProperty(final String name){
         try {
             return null != System.getProperty(Defaults.SAMJDK_PREFIX + name);
-        } catch (final java.security.AccessControlException error) {
+        } catch (final SecurityException error) {
             log.warn(error,"java Security Manager forbids 'System.getProperty(\"" + name + "\")' , returning false");
             return false;
         }

src/main/java/htsjdk/samtools/TextTagCodec.java

@@ -204,7 +204,7 @@ else if (SAMUtils.isValidUnsignedIntegerAttribute(lValue)) {
             }
         } else if (type.equals("f")) {
             try {
-                return new Float(stringVal);
+                return Float.parseFloat(stringVal);
             } catch (NumberFormatException e) {
                 throw new SAMFormatException("Tag of type f should have single-precision floating point value");
             }