Merge branch 'master' into 4033-fix-cli-params-case

Signed-off-by: Ben Sherman <bentshermann@gmail.com>

.github/CODEOWNERS

@@ -0,0 +1,3 @@
+# DOCUMENTATION -------------------------------------------------------
+# Docs folder ownership
+/docs/ @nextflow-io/docs

.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

@@ -4,7 +4,6 @@ When submitting a Pull Request please make sure to not include
 in the changeset any modification in these files:
 
 * `nextflow`
-* `docs/conf.py`
 * `modules/nf-commons/src/main/nextflow/Const.groovy`
 
 Also, please sign-off the DCO [1] to certify you are the author of the contribution

.github/workflows/build.yml

@@ -32,16 +32,24 @@ jobs:
         run: env | sort
 
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
           submodules: true
 
       - name: Get changed files
         id: changed-files
-        uses: tj-actions/changed-files@v41
+        uses: tj-actions/changed-files@v43
         with:
-          files_ignore: docs
+          files_ignore: docs/**
+
+      - name: List all changed files
+        env:
+            ALL_CHANGED_FILES: ${{ steps.changed-files.outputs.all_changed_files }}
+        run: |
+            for file in ${ALL_CHANGED_FILES}; do
+                echo "$file was changed"
+            done
 
       - name: Setup env
         if: steps.changed-files.outputs.any_changed == 'true'
@@ -54,7 +62,7 @@ jobs:
 
       - name: Setup Java ${{ matrix.java_version }}
         if: steps.changed-files.outputs.any_changed == 'true'
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: ${{matrix.java_version}}
           distribution: 'temurin'
@@ -67,7 +75,14 @@ jobs:
 
       - name: Test
         if: steps.changed-files.outputs.any_changed == 'true'
-        run: make test
+        run: |
+            # 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
+            # run tests
+            make test
         env:
           AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
           AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
@@ -82,7 +97,7 @@ jobs:
           AZURE_BATCH_ACCOUNT_KEY: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }}
 
       - name: Publish tests report
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: steps.changed-files.outputs.any_changed == 'true' && always()
         with:
           name: report-unit-tests-jdk-${{ matrix.java_version }}
@@ -96,14 +111,15 @@ jobs:
     if: ${{ !contains(github.event.head_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]
         test_mode: ["test_integration", "test_docs", "test_aws", "test_azure", "test_google", "test_wave"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
           submodules: true
@@ -117,7 +133,7 @@ jobs:
           NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
 
       - name: Setup Java ${{ matrix.java_version }}
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: ${{matrix.java_version}}
           distribution: 'temurin'
@@ -152,7 +168,7 @@ jobs:
         run: tar -cvf integration-tests.tar tests/checks
 
       - name: Publish tests report
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: always()
         with:
           name: report-${{ matrix.test_mode }}-jdk-${{ matrix.java_version }}

.github/workflows/cffconvert.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out a copy of the repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Check whether the citation metadata from CITATION.cff is valid
         uses: citation-file-format/cffconvert-github-action@2.0.0

.github/workflows/codespell.yml

@@ -17,6 +17,6 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Codespell
         uses: codespell-project/actions-codespell@v2

.github/workflows/docs.yml

@@ -10,7 +10,7 @@ jobs:
     name: Build
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: '3.9'

Makefile

@@ -1,5 +1,5 @@
 #
-#  Copyright 2013-2023, Seqera Labs
+#  Copyright 2013-2024, Seqera Labs
 #
 #  Licensed under the Apache License, Version 2.0 (the "License");
 #  you may not use this file except in compliance with the License.

NOTICE

@@ -1,6 +1,6 @@
 NEXTFLOW
 
-Copyright 2013-2023, Seqera Labs
+Copyright 2013-2024, Seqera Labs
 
 
 This software includes source code and libraries developed by:
@@ -142,7 +142,7 @@ This software includes source code and libraries developed by:
 
     Spack
     https://github.com/spack/spack
-    Copyright 2013-2023 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details.
+    Copyright 2013-2024 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details.
     Licensed under Apache License, Version 2.0
 
 Nextflow is a registered trademark of Seqera Labs, Spain.

VERSION

@@ -1 +1 @@
-23.12.0-edge
+24.04.0-edge

build.gradle

@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2023, Seqera Labs
+ * Copyright 2013-2024, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -32,7 +32,7 @@ if (groovyVer) {
 
         configurations.all {
             resolutionStrategy.eachDependency { DependencyResolveDetails details ->
-                if (details.requested.group == 'org.codehaus.groovy') {
+                if (details.requested.group == 'org.apache.groovy') {
                     if( groovyVer.contains(':') )
                         details.useTarget(groovyVer)
                     else
@@ -69,6 +69,10 @@ allprojects {
     java {
         toolchain {
             languageVersion = JavaLanguageVersion.of(19)
+            // note: the use of Java 21 causes the error "NoClassDefFoundError: java/util/SequencedCollection"
+            // see also
+            //   https://aphyr.com/posts/369-classnotfoundexception-java-util-sequencedcollection
+            //   https://www.baeldung.com/java-21-sequenced-collections
         }
     }
 
@@ -95,8 +99,8 @@ allprojects {
 
     configurations {
         // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
-        all*.exclude group: 'org.codehaus.groovy', module: 'groovy-all'
-        all*.exclude group: 'org.codehaus.groovy', module: 'groovy-cli-picocli'
+        all*.exclude group: 'org.apache.groovy', module: 'groovy-all'
+        all*.exclude group: 'org.apache.groovy', module: 'groovy-cli-picocli'
         // groovydoc libs
         groovyDoc.extendsFrom runtime
     }
@@ -108,15 +112,15 @@ allprojects {
         }
 
         // Documentation required libraries
-        groovyDoc 'org.fusesource.jansi:jansi:1.11'
-        groovyDoc "org.codehaus.groovy:groovy-groovydoc:3.0.19"
-        groovyDoc "org.codehaus.groovy:groovy-ant:3.0.19"
+        groovyDoc 'org.fusesource.jansi:jansi:2.4.0'
+        groovyDoc "org.apache.groovy:groovy-groovydoc:4.0.21"
+        groovyDoc "org.apache.groovy:groovy-ant:4.0.21"
     }
 
     test {
         useJUnitPlatform()
     }
-    
+
     // this is required due to this IDEA bug
     // https://youtrack.jetbrains.com/issue/IDEA-129282
     sourceSets {
@@ -145,28 +149,27 @@ allprojects {
     }
 
     // Required to run tests on Java 9 and higher in compatibility mode
-    if (JavaVersion.current() >= JavaVersion.VERSION_1_9) {
-        tasks.withType(Test) {
-            jvmArgs ([
-                    '--enable-preview',
-                    '--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',
-            ])
-        }
+    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',
+            '--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',
+        ])
     }
 
     /**
@@ -213,21 +216,13 @@ task buildInfo { doLast {
     timestamp=${System.currentTimeMillis()}
     commitId=${project.property('commitId')}
     """.stripIndent()
-    
+
     // -- update 'nextflow' wrapper
     file0 = file('nextflow')
     src = file0.text
     src = src.replaceAll(/NXF_VER\=\$\{NXF_VER:-'.*'\}/, 'NXF_VER=\\${NXF_VER:-\'' + version + '\'}')
     file0.text = src
 
-    // -- update sphynx
-    def major = version.split(/\./)[0..1].join('.')
-    file0 = file('docs/conf.py')
-    src = file0.text
-    src = src.replaceAll(/version *= *'[0-9a-zA-Z_\-\.]+'/, "version = '$major'" as String)
-    src = src.replaceAll(/release *= *'[0-9a-zA-Z_\-\.]+'/, "release = '$version'" as String)
-    file0.text = src
-
     // -- update dockerfile
     file0 = file('docker/Dockerfile')
     src = file0.text

buildSrc/src/main/groovy/io/nextflow/gradle/tasks/GithubUploader.groovy

@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2023, Seqera Labs
+ * Copyright 2013-2024, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.