Add GraalVM native image compilation support

.github/workflows/build-native.yml

@@ -0,0 +1,107 @@
+name: Build Native Image
+
+on:
+  push:
+    branches:
+      - '*'
+      - '!refs/tags/.*'
+    tags-ignore:
+      - '*'
+  pull_request:
+    types: [opened, reopened, synchronize]
+    branches:
+      - '*'
+      - '!refs/tags/.*'
+    tags-ignore:
+      - '*'
+
+env:
+  GRAALVM_VERSION: '21'
+  GRAALVM_DISTRIBUTION: 'graalvm'
+  JAVA_VERSION: '21'
+
+jobs:
+  build:
+    name: Build ${{ matrix.platform }}
+    runs-on: ${{ matrix.os }}
+    if: "!contains(github.event.head_commit.message, '[skip ci]')"
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            platform: linux-amd64
+          - os: ubuntu-24.04-arm
+            platform: linux-arm64
+          - os: macos-latest-large
+            platform: macos-intel
+          - os: macos-latest-xlarge
+            platform: macos-silicon
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Setup GraalVM
+        uses: graalvm/setup-graalvm@v1
+        with:
+          java-version: ${{ env.JAVA_VERSION }}
+          distribution: ${{ env.GRAALVM_DISTRIBUTION }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Setup Gradle
+        uses: gradle/actions/setup-gradle@v4
+
+      - name: Build native image
+        run: |
+          chmod +x ./gradlew ./lsp-simulator.sh ./build-native.sh
+          ./build-native.sh
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: nf-language-server-${{ matrix.platform }}
+          path: build/native/nativeCompile/nlsp
+          retention-days: 7
+
+  release:
+    name: Create Release
+    needs: build
+    runs-on: ubuntu-latest
+    if: contains(github.event.head_commit.message, '[release]')
+    permissions:
+      contents: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Download all artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: artifacts
+
+      - name: Prepare release assets
+        run: |
+          mkdir -p release
+          find artifacts -name "*.tar.gz" -exec cp {} release/ \;
+          cd release
+          sha256sum *.tar.gz > checksums.txt
+          cat checksums.txt
+
+      - name: Extract version from tag
+        id: version
+        run: echo "VERSION=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          name: Release ${{ steps.version.outputs.VERSION }}
+          draft: false
+          prerelease: ${{ contains(github.ref, '-rc') || contains(github.ref, '-beta') || contains(github.ref, '-alpha') }}
+          generate_release_notes: true
+          files: |
+            release/*.tar.gz
+            release/checksums.txt
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -1,2 +1,3 @@
 .gradle/
-build/
+.idea/
+build/

build-native.sh

@@ -0,0 +1,185 @@
+#!/bin/bash
+set -euo pipefail
+
+#
+# Build script for GraalVM native image of nf-language-server
+# Supports: linux/amd64, linux/arm64, macos/amd64, macos/arm64 (Apple Silicon)
+#
+# Usage:
+#   ./build-native.sh [options]
+#
+# Options:
+#   --skip-test      Skip testing the native binary
+#   --help, -h       Show this help message
+#
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+cd "$SCRIPT_DIR"
+
+# Colors for output (disabled in CI)
+if [[ -t 1 ]] && [[ -z "${CI:-}" ]]; then
+    RED='\033[0;31m'
+    GREEN='\033[0;32m'
+    YELLOW='\033[1;33m'
+    NC='\033[0m'
+else
+    RED=''
+    GREEN=''
+    YELLOW=''
+    NC=''
+fi
+
+log_info() {
+    echo -e "${GREEN}[INFO]${NC} $1"
+}
+
+log_warn() {
+    echo -e "${YELLOW}[WARN]${NC} $1"
+}
+
+log_error() {
+    echo -e "${RED}[ERROR]${NC} $1"
+}
+
+# Check for required tools
+check_requirements() {
+    log_info "Checking requirements..."
+
+    # Check for Java
+    if ! command -v java &> /dev/null; then
+        log_error "Java is not installed or not in PATH"
+        exit 1
+    fi
+
+    JAVA_VERSION=$(java -version 2>&1 | head -1 | cut -d'"' -f2 | cut -d'.' -f1)
+    if [[ "$JAVA_VERSION" -lt 17 ]]; then
+        log_error "Java 17+ is required, found version $JAVA_VERSION"
+        exit 1
+    fi
+
+    # Check for native-image
+    if ! command -v native-image &> /dev/null; then
+        # Try to find it in JAVA_HOME
+        if [[ -n "${JAVA_HOME:-}" ]] && [[ -x "$JAVA_HOME/bin/native-image" ]]; then
+            export PATH="$JAVA_HOME/bin:$PATH"
+        elif [[ -n "${GRAALVM_HOME:-}" ]] && [[ -x "$GRAALVM_HOME/bin/native-image" ]]; then
+            export PATH="$GRAALVM_HOME/bin:$PATH"
+            export JAVA_HOME="$GRAALVM_HOME"
+        else
+            log_error "native-image not found. Please install GraalVM with native-image support."
+            log_error "You can use SDKMAN: sdk install java 21.0.1-graal && sdk use java 21.0.1-graal"
+            exit 1
+        fi
+    fi
+
+    # Verify native-image works
+    if ! native-image --version &> /dev/null; then
+        log_error "native-image is not working correctly"
+        exit 1
+    fi
+
+    log_info "Using Java: $(java -version 2>&1 | head -1)"
+    log_info "Using native-image: $(native-image --version 2>&1 | head -1)"
+}
+
+# Detect platform
+detect_platform() {
+    OS="$(uname -s | tr '[:upper:]' '[:lower:]')"
+
+    case "$OS" in
+        linux|darwin)
+            BINARY_EXT=""
+            ;;
+        mingw*|msys*|cygwin*)
+            BINARY_EXT=".exe"
+            ;;
+        *)
+            log_error "Unsupported OS: $OS"
+            exit 1
+            ;;
+    esac
+}
+
+# Build native image (includes shadow jar, tracing agent, and native compilation)
+build_native_image() {
+    log_info "Building native image (this includes JAR build and tracing agent)..."
+    ./gradlew nativeCompile --no-configuration-cache --no-daemon
+
+    local BINARY_PATH="build/native/nativeCompile/nlsp${BINARY_EXT}"
+    if [[ -f "$BINARY_PATH" ]]; then
+        log_info "Native image built successfully: $BINARY_PATH"
+        ls -lh "$BINARY_PATH"
+    else
+        log_error "Native image build failed - binary not found"
+        exit 1
+    fi
+}
+
+# Test the native binary
+test_native_binary() {
+    log_info "Testing native binary..."
+
+    local BINARY_PATH="build/native/nativeCompile/nlsp${BINARY_EXT}"
+    local OUTPUT
+
+    OUTPUT=$(./lsp-simulator.sh | "$BINARY_PATH" 2>&1 | head -20)
+
+    if echo "$OUTPUT" | grep -q '"id":1,"result"'; then
+        log_info "Native binary test passed - LSP initialize succeeded"
+    else
+        log_error "Native binary test failed"
+        echo "$OUTPUT"
+        exit 1
+    fi
+}
+
+
+# Main build process
+main() {
+    local SKIP_TEST=false
+
+    # Parse arguments
+    while [[ $# -gt 0 ]]; do
+        case $1 in
+            --skip-test)
+                SKIP_TEST=true
+                shift
+                ;;
+            --help|-h)
+                echo "Usage: $0 [options]"
+                echo ""
+                echo "Build GraalVM native image for nf-language-server"
+                echo ""
+                echo "Options:"
+                echo "  --skip-test     Skip testing the native binary"
+                echo "  --help, -h      Show this help message"
+                echo ""
+                echo "Requirements:"
+                echo "  - GraalVM 21+ with native-image"
+                echo "  - Use SDKMAN: sdk install java 21.0.1-graal"
+                exit 0
+                ;;
+            *)
+                log_error "Unknown option: $1"
+                exit 1
+                ;;
+        esac
+    done
+
+    log_info "Starting native image build..."
+    echo ""
+
+    check_requirements
+    detect_platform
+    build_native_image
+
+    if [[ "$SKIP_TEST" != "true" ]]; then
+        test_native_binary
+    fi
+
+    echo ""
+    log_info "Build completed successfully!"
+    log_info "Binary: build/native/nativeCompile/nlsp${BINARY_EXT}"
+}
+
+main "$@"

build.gradle

@@ -1,5 +1,6 @@
 plugins {
   id 'com.gradleup.shadow' version '8.3.5'
+  id 'org.graalvm.buildtools.native' version '0.10.4'
   id 'application'
   id 'groovy'
   id 'java'
@@ -93,6 +94,7 @@ processResources {
 
 jar {
   dependsOn buildSpec
+  duplicatesStrategy = DuplicatesStrategy.EXCLUDE
   from("$buildDir/generated") {
     include 'definitions.json'
     into 'spec'
@@ -106,3 +108,69 @@ application {
 shadowJar {
   archiveVersion = ''
 }
+
+task generateNativeImageConfig(type: Exec) {
+  description = 'Generate native-image configuration using tracing agent'
+  group = 'native'
+
+  dependsOn shadowJar
+
+  def agentOutputDir = file("$buildDir/native-image-agent")
+  def simulateScript = file("$projectDir/lsp-simulator.sh")
+
+  inputs.file(shadowJar.archiveFile)
+  inputs.file(simulateScript)
+  outputs.dir(agentOutputDir)
+
+  doFirst {
+    agentOutputDir.mkdirs()
+  }
+
+  commandLine 'bash', '-c', """
+    ${simulateScript.absolutePath} | java \\
+      -agentlib:native-image-agent=config-output-dir=${agentOutputDir.absolutePath} \\
+      -cp ${shadowJar.archiveFile.get().asFile.absolutePath} \\
+      nextflow.lsp.NextflowLanguageServer
+  """
+}
+
+tasks.named('nativeCompile') {
+  dependsOn generateNativeImageConfig
+}
+
+graalvmNative {
+  agent {
+    defaultMode = 'standard'
+    builtinCallerFilter = true
+    builtinHeuristicFilter = true
+    enableExperimentalPredefinedClasses = false
+    enableExperimentalUnsafeAllocationTracing = false
+    trackReflectionMetadata = true
+    metadataCopy {
+      inputTaskNames.add('run')
+      outputDirectories.add("$buildDir/native-image-agent")
+      mergeWithExisting = true
+    }
+  }
+  binaries {
+    main {
+      imageName = 'nlsp'
+      mainClass = 'nextflow.lsp.NextflowLanguageServer'
+      buildArgs.addAll([
+        '--no-fallback',
+        '--enable-url-protocols=http,https',
+        '-H:+ReportExceptionStackTraces',
+        '--report-unsupported-elements-at-runtime',
+        '--initialize-at-build-time=org.slf4j',
+        '--initialize-at-build-time=org.apache.groovy',
+        '--initialize-at-build-time=groovy',
+        '--initialize-at-build-time=org.codehaus.groovy',
+        '--initialize-at-build-time=groovyjarjarantlr4',
+        '--initialize-at-build-time=java.beans',
+        '--initialize-at-build-time=com.sun.beans',
+        "-H:ConfigurationFileDirectories=$buildDir/native-image-agent,$projectDir/conf/native-image"
+      ])
+    }
+  }
+  toolchainDetection = false
+}

conf/native-image/reflect-config.json

@@ -0,0 +1,12 @@
+[
+  {
+    "name": "[Ljava.lang.reflect.AccessFlag;",
+    "allPublicMethods": true,
+    "allPublicFields": true
+  },
+  {
+    "name": "java.lang.reflect.AccessFlag",
+    "allPublicMethods": true,
+    "allPublicFields": true
+  }
+]