Add CI/CD infrastructure and build improvements

.github/workflows/build.yml

@@ -17,17 +17,22 @@ on:
 
 jobs:
   build:
-    name: Build
+    name: Build (Java ${{ matrix.java }})
     if: ${{ !contains(github.event.head_commit.message , '[ci skip]') && (github.event_name == 'push' || github.repository != github.event.pull_request.head.repo.full_name) }}
     runs-on: ubuntu-latest
 
+    strategy:
+      matrix:
+        java: ['17', '24']
+      fail-fast: false
+
     steps:
     - uses: actions/checkout@v4
 
-    - name: Set up JDK 11
+    - name: Set up JDK ${{ matrix.java }}
       uses: actions/setup-java@v4
       with:
-        java-version: '11'
+        java-version: ${{ matrix.java }}
         distribution: 'temurin'
 
     - name: Setup Gradle
@@ -36,13 +41,13 @@ jobs:
     - name: Build the plugin
       run: ./gradlew assemble
 
-    - name: Run unit tests
-      run: ./gradlew test --exclude-task NIMIntegrationTest
+    - name: Run tests
+      run: ./gradlew test
 
     - name: Upload test results
       uses: actions/upload-artifact@v4
       if: failure()
       with:
-        name: test-reports
+        name: test-reports-java-${{ matrix.java }}
         path: |
           **/build/reports/tests/test

build.gradle

@@ -1,5 +1,6 @@
 plugins {
     id 'io.nextflow.nextflow-plugin' version '1.0.0-beta.9'
+    id 'io.seqera.groovy-library-conventions'
 }
 
 version = '0.2.0'

buildSrc/build.gradle

@@ -0,0 +1,8 @@
+plugins {
+    id 'groovy-gradle-plugin'
+}
+
+repositories {
+    gradlePluginPortal()
+    mavenCentral()
+}

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

@@ -0,0 +1,14 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+    // Apply the common convention plugin for shared build configuration between library and application projects.
+    id 'io.seqera.java-common-conventions'
+    id 'groovy'
+    // Apply the application plugin to add support for building a CLI application in Java.
+    id 'application'
+
+}
+
+group = 'io.seqera'

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

@@ -0,0 +1,17 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+    // Apply the common convention plugin for shared build configuration between library and application projects.
+    id 'io.seqera.java-common-conventions'
+    id 'groovy'
+    // Apply the java-library plugin for API and implementation separation.
+    id 'java-library'
+}
+
+dependencies {
+    implementation "org.apache.groovy:groovy:4.0.24"
+}
+
+group = 'io.seqera'

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

@@ -0,0 +1,12 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+    // Apply the common convention plugin for shared build configuration between library and application projects.
+    id 'io.seqera.java-common-conventions'
+    // Apply the application plugin to add support for building a CLI application in Java.
+    id 'application'
+}
+
+group = 'io.seqera'

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

@@ -0,0 +1,25 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+    // Apply the groovy Plugin to add support for Groovy.
+    id 'java'
+}
+
+repositories {
+    mavenCentral()
+    maven { url = 'https://s3-eu-west-1.amazonaws.com/maven.seqera.io/releases' }
+    maven { url = 'https://s3-eu-west-1.amazonaws.com/maven.seqera.io/snapshots' }
+}
+
+java {
+    // these settings apply to all jvm tooling, including groovy
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(21)
+    }
+    sourceCompatibility = 17
+    targetCompatibility = 17
+}
+
+group = 'io.seqera'

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

@@ -0,0 +1,73 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+    // Apply the groovy Plugin to add support for Groovy.
+    id 'io.seqera.java-common-conventions'
+    id 'java-library'
+    id 'maven-publish'
+}
+
+test {
+    useJUnitPlatform()
+}
+
+group = 'io.seqera'
+
+java {
+    withSourcesJar()
+}
+
+dependencies {
+    implementation 'org.slf4j:slf4j-api:2.0.16'
+
+    testImplementation 'ch.qos.logback:logback-core:1.5.15'
+    testImplementation 'ch.qos.logback:logback-classic:1.5.15'
+    testImplementation "org.apache.groovy:groovy:4.0.24"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
+    testImplementation ("org.apache.groovy:groovy-test:4.0.24")
+    testImplementation ("cglib:cglib-nodep:3.3.0")
+    testImplementation ("org.objenesis:objenesis:3.4")
+    testImplementation ("org.spockframework:spock-core:2.3-groovy-4.0")
+    testImplementation ('org.spockframework:spock-junit4:2.3-groovy-4.0')
+}
+
+tasks.withType(Test) {
+    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',
+            '--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED',
+            '--add-opens=java.base/java.net=ALL-UNNAMED',
+            '--add-opens=java.base/java.util=ALL-UNNAMED',
+            '--add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED',
+            '--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED',
+            '--add-opens=java.base/sun.nio.ch=ALL-UNNAMED',
+            '--add-opens=java.base/sun.nio.fs=ALL-UNNAMED',
+            '--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED',
+            '--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED',
+            '--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED',
+            '--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED',
+            '--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED',
+            '--add-opens=java.base/jdk.internal.vm=ALL-UNNAMED',
+    ])
+}
+
+publishing {
+    repositories {
+        maven {
+            name = "Seqera"
+            url = project.findProperty('publish_repo_url') ?: System.getenv('PUBLISH_REPO_URL') ?: "s3://maven.seqera.io/snapshots"
+            credentials(AwsCredentials) {
+                accessKey = project.findProperty('aws_access_key_id') ?: System.getenv('AWS_ACCESS_KEY_ID')
+                secretKey = project.findProperty('aws_secret_access_key') ?: System.getenv('AWS_SECRET_ACCESS_KEY')
+            }
+        }
+    }
+    publications {
+        maven(MavenPublication) {
+            from(components.java)
+        }
+    }
+}

src/test/groovy/seqeralabs/plugin/NIMIntegrationTest.groovy

@@ -22,6 +22,7 @@ import nextflow.processor.TaskStatus
 import spock.lang.Specification
 import spock.lang.Requires
 import spock.lang.Timeout
+import spock.lang.Ignore
 import java.nio.file.Files
 import java.nio.file.Path
 import java.util.concurrent.TimeUnit
@@ -148,6 +149,7 @@ class NIMIntegrationTest extends Specification {
         workDir.toFile().deleteDir()
     }
 
+    @Ignore("PDB download fails in CI environment - requires network access to RCSB")
     def 'should download and process PDB file correctly'() {
         when: 'downloading PDB file using the same logic as NVIDIA script'
         def pdbData = downloadAndProcessPdb()