Merge branch 'master' into 708-rename-defaultpublicregistry-to-defaul…

…tcommunityregistry

.github/workflows/build.yml

@@ -30,7 +30,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java_version: [19]
+        java_version: [21]
 
     steps:
       - name: Environment
@@ -66,7 +66,7 @@ jobs:
           AWS_SECRET_ACCESS_KEY: ${{secrets.TOWER_CI_AWS_SECRET}}
           DOCKER_USER: ${{ secrets.DOCKER_USER }}
           DOCKER_PAT: ${{ secrets.DOCKER_PAT }}
-          QUAY_USER: ${{ secrets.QUAY_USER }}
+          QUAY_USER: "pditommaso+wave_ci_tests"
           QUAY_PAT: ${{ secrets.QUAY_PAT }}
           AZURECR_USER: ${{ secrets.AZURECR_USER }}
           AZURECR_PAT: ${{ secrets.AZURECR_PAT }}

.github/workflows/seqera_docs_changelog.yml

@@ -0,0 +1,61 @@
+name: Push changelog to Seqera Docs
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      release_name:
+        description: 'Release version (e.g. 1.0.0)'
+        required: true
+      release_body:
+        description: 'Release changelog content'
+        required: true
+
+jobs:
+  update-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Clone seqeralabs/docs
+        run: |
+          git clone https://github.com/seqeralabs/docs.git seqeralabs-docs
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Create changelog file
+        run: |
+          mkdir -p seqeralabs-docs/changelog/wave
+          cat << EOF > seqeralabs-docs/changelog/wave/${{ github.event.release.name || inputs.release_name }}.mdx
+          ---
+          title: Wave ${{ github.event.release.name || inputs.release_name }}
+          date: $(date +%Y-%m-%d)
+          tags: [wave]
+          ---
+
+          ${{ github.event.release.body || inputs.release_body }}
+          EOF
+
+      - uses: actions/create-github-app-token@v1
+        id: generate-token
+        with:
+          app-id: ${{ secrets.DOCS_BOT_APP_ID }}
+          private-key: ${{ secrets.DOCS_BOT_APP_PRIVATE_KEY }}
+          owner: seqeralabs
+          repositories: docs
+
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ steps.generate-token.outputs.token }}
+          branch-token: ${{ steps.generate-token.outputs.token }}
+          path: seqeralabs-docs
+          commit-message: "Changelog: Wave ${{ github.event.release.name || inputs.release_name }}"
+          title: "Changelog: Wave ${{ github.event.release.name || inputs.release_name }}"
+          body: |
+            This PR adds the changelog for Wave ${{ github.event.release.name || inputs.release_name }} to the Seqera documentation.
+
+            This is an automated PR created from the Wave repository.
+          branch: changelog-wave-${{ github.event.release.name || inputs.release_name }}
+          base: master
+          delete-branch: true

.gitignore

@@ -37,3 +37,6 @@ deployment-url.txt
 tsp-output/
 node_modules/
 package-lock.json
+
+# Seqera Docs clone
+seqeralabs-docs

Makefile

@@ -1,4 +1,4 @@
-config ?= compileClasspath
+config ?= runtimeClasspath
 
 ifdef module
 mm = :${module}:

README.md

@@ -18,7 +18,7 @@ images.
 * Push and cache built containers to a user-provided container repository;
 * Build Singularity native containers both using a Singularity spec file, Conda package(s);
 * Push Singularity native container images to OCI-compliant registries;
-
+* Scan container images for security vulnerabilities
 
 ### How it works
 
@@ -34,7 +34,7 @@ container registry where the image is stored, while the instrumented layers are
 
 ### Requirements
 
-* Java 19 or later
+* Java 21 or later
 * Linux or macOS
 * Redis 6.2 (or later)
 * Docker engine (for development)

VERSION

@@ -1 +1 @@
-1.13.5
+1.15.5

build.gradle

@@ -2,10 +2,10 @@ import java.time.OffsetDateTime
 import java.time.format.DateTimeFormatter
 
 plugins {
-    id 'java-library'
+    id 'io.seqera.wave.java-library-conventions'
     id 'io.seqera.wave.groovy-application-conventions'
-    id "com.github.johnrengelman.shadow" version "7.1.1"
-    id "io.micronaut.minimal.application" version "3.7.0"
+    id "com.github.johnrengelman.shadow" version "8.1.1"
+    id "io.micronaut.minimal.application" version "4.1.1"
     id "com.google.cloud.tools.jib" version "3.4.2"
     id 'org.asciidoctor.jvm.convert' version '3.3.2'
     id 'jacoco'
@@ -29,73 +29,83 @@ repositories {
 }
 
 dependencies {
-    annotationProcessor("io.micronaut:micronaut-http-validation")
-    compileOnly("io.micronaut.data:micronaut-data-processor")
-    compileOnly("io.micronaut:micronaut-inject-groovy")
-    compileOnly("io.micronaut:micronaut-http-validation")
-    implementation("jakarta.persistence:jakarta.persistence-api:3.0.0")
-    api 'io.seqera:lib-mail:1.0.0'
-    api 'io.seqera:wave-api:0.13.3'
-    api 'io.seqera:wave-utils:0.14.1'
-    implementation("io.micronaut:micronaut-http-client")
-    implementation("io.micronaut:micronaut-jackson-databind")
-    implementation("io.micronaut.groovy:micronaut-runtime-groovy")
-    implementation("io.micronaut.reactor:micronaut-reactor")
-    implementation("io.micronaut.reactor:micronaut-reactor-http-client")
-    implementation("jakarta.annotation:jakarta.annotation-api")
-    implementation("io.micronaut:micronaut-validation")
+    annotationProcessor 'io.micronaut.validation:micronaut-validation-processor'
+    annotationProcessor 'io.micronaut:micronaut-http-validation'
+    compileOnly 'io.micronaut.data:micronaut-data-processor'
+    compileOnly 'io.micronaut:micronaut-inject-groovy'
+    compileOnly 'io.micronaut:micronaut-http-validation'
+    implementation 'jakarta.persistence:jakarta.persistence-api:3.0.0'
+    api 'io.seqera:lib-mail:1.2.1'
+    api 'io.seqera:wave-api:0.14.0'
+    api 'io.seqera:wave-utils:0.15.0'
+    implementation 'io.seqera:lib-crypto:1.0.0'
+    implementation 'io.micronaut:micronaut-http-client'
+    implementation 'io.micronaut:micronaut-jackson-databind'
+    implementation 'io.micronaut.groovy:micronaut-runtime-groovy'
+    implementation 'io.micronaut.reactor:micronaut-reactor'
+    implementation 'io.micronaut.reactor:micronaut-reactor-http-client'
+    implementation 'jakarta.annotation:jakarta.annotation-api'
+    implementation 'io.micronaut.validation:micronaut-validation'
     implementation 'io.micronaut.security:micronaut-security'
-    implementation "org.codehaus.groovy:groovy-json"
-    implementation "org.codehaus.groovy:groovy-nio"
-    implementation 'com.google.guava:guava:32.1.2-jre'
+    implementation 'io.micronaut:micronaut-websocket'
+    implementation 'org.apache.groovy:groovy-json'
+    implementation 'org.apache.groovy:groovy-nio'
+    implementation 'com.google.guava:guava:33.3.1-jre'
     implementation 'dev.failsafe:failsafe:3.1.0'
-    implementation('io.projectreactor:reactor-core')
-    implementation("io.seqera:tower-crypto:22.4.0-watson") { transitive = false }  // to be replaced with 22.4.0 once released
-    implementation 'org.apache.commons:commons-compress:1.24.0'
-    implementation 'org.apache.commons:commons-lang3:3.12.0'
-    implementation 'io.kubernetes:client-java:19.0.0'
-    implementation 'io.kubernetes:client-java-api-fluent:18.0.1'
-    implementation 'com.google.code.gson:gson:2.9.0'
-    implementation "com.fasterxml.jackson.datatype:jackson-datatype-jsr310"
+    implementation 'io.micronaut.reactor:micronaut-reactor'
+    implementation 'io.micronaut.reactor:micronaut-reactor-http-client'
+    implementation 'org.apache.commons:commons-compress:1.27.1'
+    implementation 'org.apache.commons:commons-lang3:3.17.0'
+    implementation 'io.kubernetes:client-java:21.0.1'
+    implementation 'io.kubernetes:client-java-api-fluent:21.0.1'
+    implementation 'com.google.code.gson:gson:2.10.1'
+    implementation 'com.fasterxml.jackson.datatype:jackson-datatype-jsr310'
     implementation 'com.fasterxml.jackson.dataformat:jackson-dataformat-yaml'
-    implementation 'com.squareup.moshi:moshi:1.14.0'
-    implementation 'com.squareup.moshi:moshi-adapters:1.14.0'
-    implementation 'redis.clients:jedis:5.0.2'
-    implementation "io.github.resilience4j:resilience4j-ratelimiter:0.17.0"
+    implementation 'com.squareup.moshi:moshi:1.15.1'
+    implementation 'com.squareup.moshi:moshi-adapters:1.15.1'
+    implementation 'redis.clients:jedis:5.1.3'
+    implementation 'io.github.resilience4j:resilience4j-ratelimiter:0.17.0'
+    implementation 'io.micronaut:micronaut-retry'
     // caching deps
-    implementation("io.micronaut.cache:micronaut-cache-core")
-    implementation("io.micronaut.cache:micronaut-cache-caffeine")
-    implementation("io.micronaut.aws:micronaut-aws-parameter-store")
-    implementation "software.amazon.awssdk:ecr"
-    implementation "software.amazon.awssdk:ecrpublic"
+    implementation 'io.micronaut.cache:micronaut-cache-core'
+    implementation 'io.micronaut.cache:micronaut-cache-caffeine'
+    implementation 'io.micronaut.aws:micronaut-aws-parameter-store'
+    implementation 'software.amazon.awssdk:ecr'
+    implementation 'software.amazon.awssdk:ecrpublic'
     implementation 'software.amazon.awssdk:ses'
-    implementation 'org.yaml:snakeyaml:2.0'
+    implementation 'org.yaml:snakeyaml:2.2'
     implementation 'com.github.ben-manes.caffeine:caffeine:3.1.8'
     implementation 'org.luaj:luaj-jse:3.0.1'
     //object storage dependency
-    implementation("io.micronaut.objectstorage:micronaut-object-storage-aws")
+    implementation 'io.micronaut.objectstorage:micronaut-object-storage-aws'
     // include sts to allow the use of service account role - https://stackoverflow.com/a/73306570
     // this sts dependency is require by micronaut-aws-parameter-store,
     // not directly used by the app, for this reason keeping `runtimeOnly`
-    runtimeOnly "software.amazon.awssdk:sts"
-
-    runtimeOnly("io.netty:netty-tcnative-boringssl-static:2.0.0.Final")
-    runtimeOnly("javax.xml.bind:jaxb-api:2.3.1")
-    testImplementation("org.testcontainers:testcontainers")
-    testImplementation("org.testcontainers:mysql:1.17.3")
+    runtimeOnly 'software.amazon.awssdk:sts'
+    runtimeOnly 'io.netty:netty-tcnative-boringssl-static:2.0.0.Final'
+    runtimeOnly 'javax.xml.bind:jaxb-api:2.3.1'
+    testImplementation 'org.testcontainers:testcontainers'
+    testImplementation 'org.testcontainers:mysql:1.17.3'
 
     // --
-    implementation("ch.qos.logback:logback-classic:1.4.8")
+    implementation 'ch.qos.logback:logback-classic:1.5.12'
 
     // rate limit
-    implementation 'com.github.seqeralabs:spillway:7b72700293'
+    implementation 'com.coveo:spillway:3.0.0'
 
     // monitoring
-    implementation "io.micronaut.micrometer:micronaut-micrometer-registry-prometheus"
+    implementation 'io.micronaut.micrometer:micronaut-micrometer-core'
+    implementation 'io.micronaut.micrometer:micronaut-micrometer-registry-prometheus'
     // Also required to enable endpoint
-    implementation "io.micronaut:micronaut-management"
+    implementation 'io.micronaut:micronaut-management'
     //views
-    implementation("io.micronaut.views:micronaut-views-handlebars")
+    implementation 'io.micronaut.views:micronaut-views-handlebars'
+
+    // upgrade indirect dependencies 
+    runtimeOnly 'org.bouncycastle:bcpkix-jdk18on:1.78'
+    runtimeOnly 'org.bitbucket.b_c:jose4j:0.9.4'
+    runtimeOnly 'io.netty:netty-bom:4.1.115.Final'
+    runtimeOnly 'com.google.protobuf:protobuf-java:4.27.5'
 }
 
 application {
@@ -148,8 +158,7 @@ jib {
 
 run{
     def envs = findProperty('micronautEnvs')
-    // note: "--enable-preview" is required to use virtual threads on Java 19 and 20
-    def args = ["-Dmicronaut.environments=$envs","--enable-preview"]
+    def args = ["-Dmicronaut.environments=$envs","-Djdk.tracePinnedThreads=short", "--add-opens","java.base/java.lang=ALL-UNNAMED"]
     if( environment['JVM_OPTS'] ) args.add(environment['JVM_OPTS'])
     jvmArgs args
     systemProperties 'DOCKER_USER': project.findProperty('DOCKER_USER') ?: environment['DOCKER_USER'],

buildSrc/src/main/groovy/io.seqera.wave.groovy-application-conventions.gradle

@@ -11,8 +11,3 @@ plugins {
 }
 
 group = 'io.seqera'
-
-tasks.withType(Test) {
-    // note: "--enable-preview" is required to use virtual thread on Java 19 and 20
-    jvmArgs (["--enable-preview"])
-}

buildSrc/src/main/groovy/io.seqera.wave.groovy-common-conventions.gradle

@@ -14,17 +14,17 @@ repositories {
 
 java {
     toolchain {
-        languageVersion = JavaLanguageVersion.of(19)
+        languageVersion = JavaLanguageVersion.of(21)
     }
 }
 
 compileJava {
-    options.release.set(11)
+    options.release.set(17)
 }
 
-tasks.withType(GroovyCompile) {
-    sourceCompatibility = '11'
-    targetCompatibility = '11'
+tasks.withType(GroovyCompile).configureEach {
+    sourceCompatibility = '17'
+    targetCompatibility = '17'
 }
 
 group = 'io.seqera'

buildSrc/src/main/groovy/io.seqera.wave.java-library-conventions.gradle

@@ -16,17 +16,17 @@ repositories {
 
 java {
     toolchain {
-        languageVersion = JavaLanguageVersion.of(19)
+        languageVersion = JavaLanguageVersion.of(21)
     }
 }
 
 compileJava {
-    options.release.set(11)
+    options.release.set(17)
 }
 
-tasks.withType(GroovyCompile) {
-    sourceCompatibility = '11'
-    targetCompatibility = '11'
+tasks.withType(GroovyCompile).configureEach {
+    sourceCompatibility = '17'
+    targetCompatibility = '17'
 }
 
 test {
@@ -40,22 +40,22 @@ java {
 }
 
 dependencies {
-    implementation 'org.slf4j:slf4j-api:1.7.36'
+    implementation 'org.slf4j:slf4j-api:2.0.16'
+    implementation 'org.slf4j:slf4j-jdk-platform-logging:2.0.16'
 
-    testImplementation 'ch.qos.logback:logback-core:1.2.11'
-    testImplementation 'ch.qos.logback:logback-classic:1.2.11'
-    testImplementation "org.codehaus.groovy:groovy:3.0.15"
-    testImplementation "org.codehaus.groovy:groovy-nio:3.0.15"
-    testImplementation ("org.codehaus.groovy:groovy-test:3.0.17")
-    testImplementation ("cglib:cglib-nodep:3.3.0")
-    testImplementation ("org.objenesis:objenesis:3.2")
-    testImplementation ("org.spockframework:spock-core:2.3-groovy-3.0") { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
-    testImplementation ('org.spockframework:spock-junit4:2.3-groovy-3.0') { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
+    testImplementation 'ch.qos.logback:logback-core:1.5.12'
+    testImplementation 'ch.qos.logback:logback-classic:1.5.12'
+    testImplementation 'org.apache.groovy:groovy:4.0.15'
+    testImplementation 'org.apache.groovy:groovy-nio:4.0.15'
+    testImplementation 'org.apache.groovy:groovy-test:4.0.15'
+    testImplementation 'org.objenesis:objenesis:3.4'
+    testImplementation 'net.bytebuddy:byte-buddy:1.14.17'
+    testImplementation 'org.spockframework:spock-core:2.3-groovy-4.0'
+    testImplementation 'org.spockframework:spock-junit4:2.3-groovy-4.0'
 }
 
-tasks.withType(Test) {
-    jvmArgs ([
-            '--enable-preview',
+tasks.withType(Test).configureEach {
+    jvmArgs([
             '--add-opens=java.base/java.lang=ALL-UNNAMED',
             '--add-opens=java.base/java.io=ALL-UNNAMED',
             '--add-opens=java.base/java.nio=ALL-UNNAMED',