Fix native image build issues

- Register conf/native-image as a nativeCompile input, so editing the
  reflection config actually triggers a rebuild instead of reporting
  UP-TO-DATE and shipping the previous binary.

- Drop the graalvmNative agent block. It only takes effect with -Pagent,
  and generateNativeImageConfig does the tracing instead.

- Make the simulator send workspace/didChangeConfiguration. This is what
  initializes the language services, so without it every language feature
  returned an empty result and the tracing agent observed almost nothing
  but lsp4j plumbing. The resulting binary answered "initialize" but was
  dead for real use: it could not deserialize DidChangeConfigurationParams
  or ExecuteCommandParams, and reported false errors such as
  "Unrecognized process input qualifier val".

- Also send workspace/executeCommand, use a real temp workspace instead of
  hardcoded /Users paths, and wait for outstanding async requests before
  shutdown -- responses arrive out of order and "exit" was truncating them.

- Strengthen the binary test. Checking only for an "initialize" response
  passes on a binary whose language features are all broken; also check for
  missing-metadata errors and for a non-empty documentSymbol result.

- Fix the release job: it collected *.tar.gz while the build uploaded a
  bare binary, and read the version from refs/tags while the workflow
  ignored tags. Package the binary as a tarball and trigger the release on
  v* tags.

- Limit push builds to main and tags, so a PR no longer builds four native
  images twice. Add timeout-minutes, and use the free macos-latest runner
  for Apple Silicon instead of the billed macos-latest-xlarge.

- Remove duplicatesStrategy from the jar task and the redundant copy it was
  masking; processResources already puts definitions.json in spec/.

- Rename the binary from nlsp to nextflow-lsp.

Author: bentsherman

.github/workflows/build-native.yml

@@ -3,28 +3,22 @@ name: Build Native Image
 on:
   push:
     branches:
-      - '*'
-      - '!refs/tags/.*'
-    tags-ignore:
-      - '*'
+      - 'main'
+    tags:
+      - 'v*'
   pull_request:
     types: [opened, reopened, synchronize]
-    branches:
-      - '*'
-      - '!refs/tags/.*'
-    tags-ignore:
-      - '*'
+  workflow_dispatch:
 
 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]')"
+    timeout-minutes: 60
     strategy:
       fail-fast: false
       matrix:
@@ -33,9 +27,10 @@ jobs:
             platform: linux-amd64
           - os: ubuntu-24.04-arm
             platform: linux-arm64
+          # NOTE: there is no free Intel macOS runner; this one is billed per minute
           - os: macos-latest-large
             platform: macos-intel
-          - os: macos-latest-xlarge
+          - os: macos-latest
             platform: macos-silicon
 
     steps:
@@ -57,25 +52,27 @@ jobs:
           chmod +x ./gradlew ./lsp-simulator.sh ./build-native.sh
           ./build-native.sh
 
+      - name: Package binary
+        run: |
+          tar -czf nextflow-lsp-${{ matrix.platform }}.tar.gz \
+            -C build/native/nativeCompile nextflow-lsp
+
       - name: Upload artifact
         uses: actions/upload-artifact@v4
         with:
-          name: nf-language-server-${{ matrix.platform }}
-          path: build/native/nativeCompile/nlsp
+          name: nextflow-lsp-${{ matrix.platform }}
+          path: nextflow-lsp-${{ matrix.platform }}.tar.gz
           retention-days: 7
 
   release:
     name: Create Release
     needs: build
     runs-on: ubuntu-latest
-    if: contains(github.event.head_commit.message, '[release]')
+    if: startsWith(github.ref, 'refs/tags/v')
     permissions:
       contents: write
 
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-
       - name: Download all artifacts
         uses: actions/download-artifact@v4
         with:
@@ -84,21 +81,17 @@ jobs:
       - name: Prepare release assets
         run: |
           mkdir -p release
-          find artifacts -name "*.tar.gz" -exec cp {} 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 }}
+          name: Release ${{ github.ref_name }}
           draft: false
-          prerelease: ${{ contains(github.ref, '-rc') || contains(github.ref, '-beta') || contains(github.ref, '-alpha') }}
+          prerelease: ${{ contains(github.ref_name, '-rc') || contains(github.ref_name, '-beta') || contains(github.ref_name, '-alpha') }}
           generate_release_notes: true
           files: |
             release/*.tar.gz

build-native.sh

@@ -105,7 +105,7 @@ 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${BINARY_EXT}"
+    local BINARY_PATH="build/native/nativeCompile/nextflow-lsp${BINARY_EXT}"
     if [[ -f "$BINARY_PATH" ]]; then
         log_info "Native image built successfully: $BINARY_PATH"
         ls -lh "$BINARY_PATH"
@@ -119,18 +119,41 @@ build_native_image() {
 test_native_binary() {
     log_info "Testing native binary..."
 
-    local BINARY_PATH="build/native/nativeCompile/nlsp${BINARY_EXT}"
+    local BINARY_PATH="build/native/nativeCompile/nextflow-lsp${BINARY_EXT}"
     local OUTPUT
 
-    OUTPUT=$(./lsp-simulator.sh | "$BINARY_PATH" 2>&1 | head -20)
+    OUTPUT=$(./lsp-simulator.sh | "$BINARY_PATH" 2>&1) || true
 
-    if echo "$OUTPUT" | grep -q '"id":1,"result"'; then
-        log_info "Native binary test passed - LSP initialize succeeded"
-    else
+    # A binary missing reflection metadata still answers `initialize` -- it
+    # fails later, when lsp4j tries to deserialize a request it was never
+    # traced with. So check for those failures, and for a request that only
+    # succeeds once the language services are actually running.
+    local FAILED=false
+
+    if ! echo "$OUTPUT" | grep -q '"id":1,"result"'; then
+        log_error "LSP initialize did not succeed"
+        FAILED=true
+    fi
+
+    if echo "$OUTPUT" | grep -q 'was never registered'; then
+        log_error "Missing reflection metadata:"
+        echo "$OUTPUT" | grep 'was never registered' | sort -u
+        FAILED=true
+    fi
+
+    if ! echo "$OUTPUT" | grep -q '"id":6,"result":\[{'; then
+        log_error "textDocument/documentSymbol returned no symbols -- the"
+        log_error "language services are not working in the native binary"
+        FAILED=true
+    fi
+
+    if [[ "$FAILED" == "true" ]]; then
         log_error "Native binary test failed"
-        echo "$OUTPUT"
+        echo "$OUTPUT" | head -60
         exit 1
     fi
+
+    log_info "Native binary test passed"
 }
 
 
@@ -179,7 +202,7 @@ main() {
 
     echo ""
     log_info "Build completed successfully!"
-    log_info "Binary: build/native/nativeCompile/nlsp${BINARY_EXT}"
+    log_info "Binary: build/native/nativeCompile/nextflow-lsp${BINARY_EXT}"
 }
 
 main "$@"

build.gradle

@@ -99,11 +99,6 @@ processResources {
 
 jar {
   dependsOn buildSpec
-  duplicatesStrategy = DuplicatesStrategy.EXCLUDE
-  from("$buildDir/generated") {
-    include 'definitions.json'
-    into 'spec'
-  }
 }
 
 application {
@@ -141,30 +136,23 @@ task generateNativeImageConfig(type: Exec) {
 
 tasks.named('nativeCompile') {
   dependsOn generateNativeImageConfig
+  // native-image reads these via -H:ConfigurationFileDirectories, so Gradle
+  // needs to be told about them or config edits won't trigger a rebuild
+  inputs.dir("$projectDir/conf/native-image")
 }
 
 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'
+      imageName = 'nextflow-lsp'
       mainClass = 'nextflow.lsp.NextflowLanguageServer'
       buildArgs.addAll([
         '--no-fallback',
         '--enable-url-protocols=http,https',
         '-H:+ReportExceptionStackTraces',
+        // required: Groovy's indy call sites reach MethodHandleNatives
+        // methods that native-image cannot compile ahead of time. Deprecated
+        // upstream, so this will need another answer in a future GraalVM.
         '--report-unsupported-elements-at-runtime',
         '--initialize-at-build-time=org.slf4j',
         '--initialize-at-build-time=org.apache.groovy',