Migrate to macos-13 runner image

.azure-pipelines.yml

@@ -67,7 +67,7 @@ stages:
               CXX: g++
               BUILD_PYTHON_API: ON
             mac:
-              imageName: 'macOS-12'
+              imageName: 'macOS-13'
               python.version: '3.7'
               CXX: clang++
               BUILD_PYTHON_API: ON

.github/workflows/macos.yml

@@ -18,7 +18,7 @@ env:
   MACOSX_DEPLOYMENT_TARGET: "11"
 jobs:
   libtiledbvcf:
-    runs-on: macos-12
+    runs-on: macos-13
     steps:
       - uses: actions/checkout@v4
       - name: Setup to build htslib from source
@@ -64,7 +64,7 @@ jobs:
           # USAGE: run-cli-tests.sh <build-dir> <inputs-dir>
           libtiledbvcf/test/run-cli-tests.sh libtiledbvcf/build libtiledbvcf/test/inputs
   python:
-    runs-on: macos-12
+    runs-on: macos-13
     needs: libtiledbvcf
     env:
       DYLD_LIBRARY_PATH: "${{ github.workspace }}/dist/lib"
@@ -98,7 +98,7 @@ jobs:
       - name: Confirm linking
         run: otool -L /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tiledbvcf/libtiledbvcf.cpython-*-darwin.so
   java:
-    runs-on: macos-12
+    runs-on: macos-13
     needs: libtiledbvcf
     steps:
       - uses: actions/checkout@v4
@@ -114,7 +114,7 @@ jobs:
       - name: Test
         run: cd apis/java && ./gradlew test
   python-standalone:
-    runs-on: macos-12
+    runs-on: macos-13
     steps:
       - uses: actions/checkout@v4
         with:

.github/workflows/nightly.yml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macos-12, ubuntu-latest]
+        os: [macos-13, ubuntu-latest]
         branches:
           - {libtiledb: release-2.26, tiledb-py: 0.32.0}
           - {libtiledb: dev, tiledb-py: dev}

apis/java/build.gradle

@@ -2,8 +2,8 @@ plugins {
     id 'java'
     id 'idea'
     id 'maven-publish'
-    id 'com.github.sherter.google-java-format' version '0.8'
-    id 'com.github.johnrengelman.shadow' version '4.0.3'
+    id 'com.github.sherter.google-java-format' version '0.9'
+    id 'com.github.johnrengelman.shadow' version '8.1.1'
 }
 
 ext.getVersionName = { ->
@@ -29,8 +29,10 @@ ext.getVersionName = { ->
 group 'io.tiledb'
 version getVersionName()
 
-sourceCompatibility = 1.8
-targetCompatibility = 1.8
+java {
+    sourceCompatibility = 1.8
+    targetCompatibility = 1.8
+}
 
 sourceSets {
     main {
@@ -51,9 +53,9 @@ repositories {
 
 dependencies {
     // https://mvnrepository.com/artifact/commons-io/commons-io
-    compile group: 'commons-io', name: 'commons-io', version: '2.6'
+    implementation group: 'commons-io', name: 'commons-io', version: '2.17.0'
 
-    testCompile group: 'junit', name: 'junit', version: '4.12'
+    testImplementation group: 'junit', name: 'junit', version: '4.12'
 }
 
 test {
@@ -106,6 +108,10 @@ shadowJar {
 import com.github.sherter.googlejavaformatgradleplugin.GoogleJavaFormat
 import com.github.sherter.googlejavaformatgradleplugin.VerifyGoogleJavaFormat
 
+googleJavaFormat {
+    toolVersion = '1.7'
+}
+
 task format(type: GoogleJavaFormat) {
     source = sourceSets*.allJava
     include '**/*.java'
@@ -206,12 +212,13 @@ assemble {
 }
 
 task sourceJar(type: Jar) {
-    classifier "sources"
+    archiveClassifier.set("sources")
     from sourceSets.main.allJava
+    duplicatesStrategy = DuplicatesStrategy.EXCLUDE
 }
 
 task javadocJar(type: Jar, dependsOn: javadoc) {
-    classifier "javadoc"
+    archiveClassifier.set("javadoc")
     from javadoc.destinationDir
 }
 

apis/java/gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.6-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.10.2-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists