Merge pull request #817 from viash-io/fix-backport-nxf

Port PR 812 to Viash 0.8.x

Author: hcannoodt

.github/workflows/ns_test.yml

@@ -9,12 +9,15 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - name: Set up sbt
+    - name: Set up java
       uses: actions/setup-java@v4
       with:
         distribution: temurin
         java-version: '11'
 
+    - name: Set up sbt
+      uses: sbt/setup-sbt@v1
+
     - name: Build viash
       run: |
         echo "${HOME}/.local/bin" >> $GITHUB_PATH

.github/workflows/prep_release.yml

@@ -0,0 +1,66 @@
+name: Prepare Viash Release
+
+on:
+  workflow_dispatch:
+    
+jobs:
+  build-and-release:
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Set up JDK 17
+      uses: actions/setup-java@v4
+      with:
+        java-version: '17'
+        distribution: 'temurin'
+
+    - name: Set up sbt
+      uses: sbt/setup-sbt@v1
+
+    - name: Set up Scala
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y scala
+
+    - name: Build Viash
+      run: |
+        ./configure
+        make
+        make tools
+        bin/viash export json_schema --format=json --output=bin/schema.json
+
+    - name: Get Version
+      id: get_version
+      run: |
+        viash_version=$(bin/viash --version | cut -d ' ' -f 2)
+        echo "Detected Viash version: $viash_version"
+        echo "viash_version=$viash_version" >> "$GITHUB_OUTPUT"
+        
+        # fetch relevant changelog section
+        changelog_section=$(awk "/# Viash ${viash_version}.*/{flag=1;next}/^# /{flag=0}flag" CHANGELOG.md)
+        
+        echo "changelog_section<<GITHUB_EOF" >> "$GITHUB_OUTPUT"
+        echo "$changelog_section" >> "$GITHUB_OUTPUT"
+        echo "GITHUB_EOF" >> "$GITHUB_OUTPUT"
+
+    - name: Create release
+      uses: softprops/action-gh-release@v2
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        tag_name: ${{ steps.get_version.outputs.viash_version }}
+        target_commitish: ${{ github.sha }}
+        name: Viash ${{ steps.get_version.outputs.viash_version }}
+        body: ${{ steps.get_version.outputs.changelog_section }}
+        draft: true
+        fail_on_unmatched_files: true
+        files: |
+          bin/viash
+          bin/schema.json
+          bin/viash_install

.github/workflows/sbt_test.yml

@@ -16,20 +16,14 @@ jobs:
         java:
           - { ver: '11', run_nextflow: true, run_coverage: false, nxf_ver: "22.04.5" }
           - { ver: '17', run_nextflow: true, run_coverage: true, nxf_ver: latest }
-          - { ver: '20', run_nextflow: true, run_coverage: false, nxf_ver: latest-edge }
+          - { ver: '21', run_nextflow: true, run_coverage: false, nxf_ver: latest-edge }
 
     steps:
     - uses: actions/checkout@v4
 
-    - uses: viash-io/viash-actions/update-docker-engine@v5
+    - uses: viash-io/viash-actions/project/update-docker-engine@v6
       if: runner.os == 'Linux'
 
-    - name: Set up Nextflow
-      if: ${{ runner.os == 'Linux' && matrix.java.run_nextflow }}
-      uses: nf-core/setup-nextflow@v1
-      with:
-        version: ${{ matrix.java.nxf_ver }}
-
     - name: Set up R
       uses: r-lib/actions/setup-r@v2
       with:
@@ -42,18 +36,14 @@ jobs:
           processx
           testthat
 
-    - name: Set up java & sbt
+    - name: Set up java
       uses: actions/setup-java@v4
       with:
         distribution: temurin
         java-version: ${{ matrix.java.ver }}
 
-    - name: Set up sbt specifically on macOS on arm64 if needed
-      if: ${{ runner.os == 'macOS' && runner.arch == 'ARM64'}}
-      run: |
-        if ! command -v sbt &> /dev/null; then
-          brew install sbt
-        fi
+    - name: Set up sbt
+      uses: sbt/setup-sbt@v1
 
     - name: Set up Scala
       run: |
@@ -69,6 +59,12 @@ jobs:
       with:
         python-version: '3.x'
 
+    - name: Set up Nextflow
+      if: ${{ runner.os == 'Linux' && matrix.java.run_nextflow }}
+      uses: nf-core/setup-nextflow@v2
+      with:
+        version: ${{ matrix.java.nxf_ver }}
+
     - name: Run tests
       run: |
         if [[ "${{ matrix.config.name }}" =~ ^ubuntu.*$ ]] && [[ "${{ matrix.java.run_coverage }}" == "true" ]]; then

CHANGELOG.md

@@ -1,11 +1,17 @@
-# Viash 0.x.x (yyyy-MM-dd): TODO Add title
+# Viash 0.8.7 (2025-04-01): Backport support upcoming version of Nextflow
 
-TODO add summary
+The upcoming release of Nextflow introduces a new class for loading scripts and renamed the old class.
+This release supports this change by using reflection to detect the available class.
 
 ## BUG FIXES
 
 * `viash build`: Fix error handling of non-generic errors in the build process or while pushing docker containers (PR #696).
 
+* `NextflowRunner`: ScriptParser was renamed to ScriptLoaderV1 in Nextflow 25.02.0-edge (PR #817). Backport from Viash 0.9.3 (PR #812).
+  This fix uses reflection to detect whether ScriptParser exists -- if not the ScriptLoaderFactory is used instead.
+
+* `NextflowRunner`: Backport path handling for `meta.resources_dir` for when symlinks are used (PR #817).
+
 # Viash 0.8.6 (2024-04-26): Bug fixes and improvements for CI
 
 Fix some issues in some edge cases.

build.sbt

@@ -2,7 +2,7 @@ name := "viash"
 
 version := "0.8.7-dev"
 
-scalaVersion := "2.13.10"
+scalaVersion := "2.13.12"
 
 libraryDependencies ++= Seq(
   "org.scalactic" %% "scalactic" % "3.2.15" % "test",
@@ -74,4 +74,4 @@ generateWorkflowHelper := {
 }
 
 assembly := ((assembly) dependsOn generateWorkflowHelper).value
-Test / testOptions := ((Test / testOptions) dependsOn generateWorkflowHelper).value
+Test / testOptions := ((Test / testOptions) dependsOn generateWorkflowHelper).value

project/build.properties

@@ -1 +1 @@
-sbt.version=1.6.1
+sbt.version=1.9.7

project/plugins.sbt

@@ -1,3 +1,3 @@
 addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "2.1.1")
-addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.5")
+addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.9")
 addSbtPlugin("de.heikoseeberger" % "sbt-header" % "5.9.0")

src/main/resources/io/viash/platforms/nextflow/VDSL3Helper.nf

@@ -315,7 +315,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -328,3 +328,24 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // retrieve and return process from meta
   return scriptMeta.getProcess(procKey)
 }
+
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}

src/main/scala/io/viash/platforms/NextflowPlatform.scala

@@ -256,7 +256,7 @@ case class NextflowPlatform(
       |
       |// create meta object
       |meta = [
-      |  "resources_dir": moduleDir,
+      |  "resources_dir": moduleDir.toRealPath().normalize(),
       |  "config": ${NextflowHelper.generateConfigStr(config)}
       |]
       |