Merge branch 'master' into remove-testonly-constructors

Signed-off-by: Ben Sherman <[email protected]>

.github/workflows/build.yml

@@ -25,18 +25,32 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java_version: [11, 17, 22]
+        java_version: [17, 23]
 
     steps:
-      - name: Environment
-        run: env | sort
-
       - name: Checkout
         uses: actions/checkout@v4
         with:
           fetch-depth: 1
           submodules: true
 
+      - name: Get the commit message
+        id: get_commit_message
+        run: |
+            if [ "${{ github.event_name }}" = "pull_request" ]; then
+                echo "GitHub event=pull_request"
+                COMMIT_SHA=${{ github.event.pull_request.head.sha }}
+                COMMIT_MESSAGE=$(curl -s \
+                  -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
+                  https://api.github.com/repos/${{ github.repository }}/commits/$COMMIT_SHA | jq -r '.commit.message')
+                echo "Commit message=$COMMIT_MESSAGE" | head -n 1
+                echo "commit_message=$COMMIT_MESSAGE" | head -n 1 >> $GITHUB_OUTPUT
+            else
+               echo "GitHub event=${{ github.event_name }}"
+               echo "Commit message=${{ github.event.head_commit.message }}" | head -n 1
+               echo "commit_message=${{ github.event.head_commit.message }}" | head -n 1 >> $GITHUB_OUTPUT
+            fi 
+
       - name: Get changed files
         id: changed-files
         uses: tj-actions/changed-files@v43
@@ -76,6 +90,7 @@ jobs:
       - name: Test
         if: steps.changed-files.outputs.any_changed == 'true'
         run: |
+            env | sort
             # configure test env
             if [[ "$GOOGLE_SECRET" ]]; then
             echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json
@@ -106,16 +121,17 @@ jobs:
 
     outputs:
       any_changed: ${{ steps.changed-files.outputs.any_changed }}
+      commit_message: ${{ steps.get_commit_message.outputs.commit_message }}
 
   test:
-    if: ${{ !contains(github.event.head_commit.message, '[ci fast]') && needs.build.outputs.any_changed == 'true' }}
+    if: ${{ !contains(needs.build.outputs.commit_message, '[ci fast]') && needs.build.outputs.any_changed == 'true' }}
     needs: build
     runs-on: ubuntu-latest
     timeout-minutes: 90
     strategy:
       fail-fast: false
       matrix:
-        java_version: [11, 21]
+        java_version: [17, 23]
         test_mode: ["test_integration", "test_docs", "test_aws", "test_azure", "test_google", "test_wave"]
     steps:
       - name: Checkout
@@ -142,6 +158,12 @@ jobs:
 
       - name: Run tests
         run: |
+          env | sort
+          # configure test env
+          if [[ "$GOOGLE_SECRET" ]]; then
+          echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json
+          export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json
+          fi
           cat $HOME/.nextflow/scm
           make clean assemble install
           bash test-ci.sh
@@ -173,5 +195,51 @@ jobs:
         with:
           name: report-${{ matrix.test_mode }}-jdk-${{ matrix.java_version }}
           path: |
-            validation/**
+            validation/**/*
+            validation/**/.*
             integration-tests.tar
+
+  test-e2e:
+      if: ${{ contains(needs.build.outputs.commit_message,'[e2e stage]') || contains(needs.build.outputs.commit_message,'[e2e prod]') }}
+      needs: build
+      runs-on: ubuntu-latest
+      timeout-minutes: 10
+      permissions:
+          actions: write  # Allow writing to actions
+          contents: write # Allow writing to repository contents
+      steps:
+          - name: Checkout
+            uses: actions/checkout@v4
+            with:
+                fetch-depth: 1
+                submodules: true
+
+          - name: Setup Java 17
+            uses: actions/setup-java@v4
+            with:
+                java-version: 17
+                distribution: 'temurin'
+                architecture: x64
+                cache: gradle
+
+          - name: Setup env
+            run: |
+                wget -q -O wave https://github.com/seqeralabs/wave-cli/releases/download/v1.4.1/wave-1.4.1-linux-x86_64
+                chmod +x wave
+                mv wave /usr/local/bin/
+                echo "COMMIT_MESSAGE=\"${{ needs.build.outputs.commit_message }}\"" >> $GITHUB_ENV
+
+          - name : Docker Login to Seqera public CR
+            uses : docker/login-action@v3
+            with :
+                registry : "public.cr.seqera.io"
+                username : "public-cr-admin"
+                password : ${{ secrets.SEQERA_PUBLIC_CR_PASSWORD }}
+
+          - name: Launch tests
+            run: |
+                cd test-e2e
+                bash run.sh
+            env:
+                GITHUB_TOKEN: ${{ secrets.AUTOMATION_GITHUB_TOKEN }}
+                GRADLE_OPTS: '-Dorg.gradle.daemon=false'

.github/workflows/generate-send-dependencies.yml

@@ -0,0 +1,27 @@
+name: Generate and submit dependency graph for nextflow
+on:
+    push:
+      branches: ['master']
+
+permissions:
+  contents: write
+
+jobs:
+  dependency-submission:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        components: ["nextflow", "plugins:nf-google", "plugins:nf-amazon", "plugins:nf-azure", "plugins:nf-cloudcache", "plugins:nf-codecommit", "plugins:nf-console", "plugins:nf-tower", "plugins:nf-wave"]
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-java@v4
+      with:
+        distribution: temurin
+        java-version: 21
+
+    - name: Generate and submit dependency graph for nextflow
+      uses: gradle/actions/dependency-submission@v4
+      with:
+        dependency-resolution-task: ":${{ matrix.components }}:dependencies"
+        additional-arguments: "--configuration runtimeClasspath"
+        dependency-graph: generate-and-submit

.github/workflows/seqeradocs-changelog.yml

@@ -0,0 +1,62 @@
+name: Push release change log 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: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Create changelog file
+        run: |
+          mkdir -p seqeralabs-docs/changelog/nextflow
+          cat << EOF > seqeralabs-docs/changelog/nextflow/${{ github.event.release.name || inputs.release_name }}.mdx
+          ---
+          title: Nextflow ${{ github.event.release.name || inputs.release_name }}
+          date: $(date +%Y-%m-%d)
+          tags: [nextflow]
+          ---
+
+          ${{ 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: Nextflow ${{ github.event.release.name || inputs.release_name }}"
+          title: "Changelog: Nextflow ${{ github.event.release.name || inputs.release_name }}"
+          body: |
+            This PR adds the changelog for Nextflow ${{ github.event.release.name || inputs.release_name }} to the Seqera documentation.
+
+            This is an automated PR created from the Nextflow repository.
+          branch: changelog-nextflow-${{ github.event.release.name || inputs.release_name }}
+          base: master
+          delete-branch: true

VERSION

@@ -1 +1 @@
-24.07.0-edge
+24.11.0-edge

build.gradle

@@ -15,7 +15,7 @@
  */
 
 plugins {
-    id "io.codearte.nexus-staging" version "0.21.2"
+    id "io.codearte.nexus-staging" version "0.30.0"
     id 'java'
     id 'idea'
 }
@@ -73,12 +73,12 @@ allprojects {
     }
 
     compileJava {
-        options.release.set(11)
+        options.release.set(17)
     }
 
     tasks.withType(GroovyCompile) {
-        sourceCompatibility = '11'
-        targetCompatibility = '11'
+        sourceCompatibility = '17'
+        targetCompatibility = '17'
     }
 
     idea {
@@ -109,8 +109,8 @@ allprojects {
 
         // Documentation required libraries
         groovyDoc 'org.fusesource.jansi:jansi:2.4.0'
-        groovyDoc "org.apache.groovy:groovy-groovydoc:4.0.22"
-        groovyDoc "org.apache.groovy:groovy-ant:4.0.22"
+        groovyDoc "org.apache.groovy:groovy-groovydoc:4.0.24"
+        groovyDoc "org.apache.groovy:groovy-ant:4.0.24"
     }
 
     test {
@@ -147,7 +147,6 @@ allprojects {
     // Required to run tests on Java 9 and higher in compatibility mode
     tasks.withType(Test) {
         jvmArgs ([
-            '-Dorg.spockframework.mock.ignoreByteBuddy=true',
             '--enable-preview',
             '--add-opens=java.base/java.lang=ALL-UNNAMED',
             '--add-opens=java.base/java.io=ALL-UNNAMED',

buildSrc/build.gradle

@@ -11,7 +11,7 @@ version = "1.0.1"
 group = "io.nextflow"
 
 dependencies {
-    implementation ('com.amazonaws:aws-java-sdk-s3:1.12.129')
+    implementation ('com.amazonaws:aws-java-sdk-s3:1.12.777')
     implementation 'com.google.code.gson:gson:2.10.1'
 }