Merge branch 'master' into azure_batch_no_container_spec

Signed-off-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>

Author: adamrtalbot

.github/CODEOWNERS

@@ -1,3 +1,7 @@
 # DOCUMENTATION -------------------------------------------------------
 # Docs folder ownership
 /docs/ @nextflow-io/docs
+
+# COMPILER ------------------------------------------------------------
+# nf-lang module
+/modules/nf-lang/ @nextflow-io/lang 

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,24 +1,23 @@
 ---
 name: Bug report
-about: Create a report to help us improve
+about: Report a bug to help us improve
 ---
 
 ## Bug report 
 
-(Please follow this template replacing the text between parentheses with the requested information)
+(Please follow this template by replacing the text between parentheses with the requested information)
 
 ### Expected behavior and actual behavior
 
-(Give an brief description of the expected behavior 
-and actual behavior)
+(Give a brief description of the expected behavior and actual behavior)
 
 ### Steps to reproduce the problem
 
-(Provide a test case that reproduce the problem either with a self-contained script or GitHub repository)
+(Provide a test case that reproduces the problem either with a self-contained script or GitHub repository)
 
 ### Program output 
 
-(Copy and paste here output produced by the failing execution. Please highlight it as a code block. Whenever possible upload the `.nextflow.log` file.)
+(Copy and paste the output produced by the failing execution. Please highlight it as a code block. Whenever possible upload the `.nextflow.log` file.)
 
 ### Environment 
 

.github/ISSUE_TEMPLATE/general_question.md

@@ -1,19 +1,8 @@
 ---
 name: General question 
-about: Need for help on Nextflow language and usage
+about: Ask for help with Nextflow language and usage
 ---
 
 Hi! Thanks for using Nextflow. 
 
-If you need help about Nextflow scripting language, 
-configuration options and general Nextflow usage the better 
-channels to post this kind of questions are: 
-
-* GitHub discussions: https://github.com/nextflow-io/nextflow/discussions
-* Slack community chat: https://www.nextflow.io/slack-invite.html
-
-
-Also you may also want to have a look at the patterns page 
-for common solutions to recurrent implementation problems: 
-http://nextflow-io.github.io/patterns/index.html
-
+If you need help using or developing Nextflow pipelines, the best place to ask questions is the [community forum](https://community.seqera.io/).

.github/ISSUE_TEMPLATE/new_feature.md

@@ -1,22 +1,16 @@
 ---
 name: New feature
-about: Submit a new feature proposal
+about: Propose a new feature or enhancement
 ---
 
 ## New feature
 
-Hi! Thanks for using Nextflow and submitting the proposal 
-for a new feature or the enhancement of an existing functionality. 
+(Hi! Thanks for using Nextflow and for proposing a new feature or enhancement. Please replace this text with a brief description of your proposal.)
 
-Please replace this text providing a short description of your 
-proposal.
+## Use case 
 
-## Usage scenario 
+(What's the main use case and deployment scenario addressed by this proposal)
 
-(What's the main usage case and the deployment scenario addressed by this proposal)
-
-## Suggest implementation 
+## Suggested implementation 
 
 (Highlight the main building blocks of a possible implementation and/or related components)
-
-

.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

@@ -1,16 +1,7 @@
-Hi! Thanks for contributing to Nextflow project.
+Hi! Thanks for contributing to Nextflow.
 
-When submitting a Pull Request please make sure to not include
-in the changeset any modification in these files:
-
-* `nextflow`
-* `modules/nf-commons/src/main/nextflow/Const.groovy`
-
-Also, please sign-off the DCO [1] to certify you are the author of the contribution
-and you adhere to Nextflow open source license [2] adding a `Signed-off-by` line to
-the contribution commit message. For more details check [3].
+When submitting a Pull Request, please sign-off the DCO [1] to certify that you are the author of the contribution and you adhere to Nextflow's open source license [2] by adding a `Signed-off-by` line to the contribution commit message. See [3] for more details.
 
 1. https://developercertificate.org/
 2. https://github.com/nextflow-io/nextflow/blob/master/COPYING
 3. https://github.com/apps/dco
-

.github/workflows/build.yml

@@ -39,34 +39,20 @@ jobs:
         run: |
             if [ "${{ github.event_name }}" = "pull_request" ]; then
                 echo "GitHub event=pull_request"
-                COMMIT_SHA=${{ github.event.pull_request.head.sha }}
-                COMMIT_MESSAGE=$(curl -s \
+                COMMIT_SHA="${{ github.event.pull_request.head.sha }}"
+                COMMIT_MESSAGE="$(curl -s \
                   -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
-                  https://api.github.com/repos/${{ github.repository }}/commits/$COMMIT_SHA | jq -r '.commit.message')
+                  https://api.github.com/repos/${{ 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
-        with:
-          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
+                echo "GitHub event=${{ github.event_name }}"
+                COMMIT_MESSAGE="${{ github.event.head_commit.message }}"
+                echo "Commit message=$COMMIT_MESSAGE" | head -n 1
+                echo "commit_message=$COMMIT_MESSAGE" | head -n 1 >> $GITHUB_OUTPUT
+            fi
 
       - name: Setup env
-        if: steps.changed-files.outputs.any_changed == 'true'
         run: |
              rm -f $HOME/.gitconfig;
              mkdir -p "$HOME/.nextflow";
@@ -75,7 +61,6 @@ jobs:
           NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
 
       - name: Setup Java ${{ matrix.java_version }}
-        if: steps.changed-files.outputs.any_changed == 'true'
         uses: actions/setup-java@v4
         with:
           java-version: ${{matrix.java_version}}
@@ -84,11 +69,9 @@ jobs:
           cache: gradle
 
       - name: Compile
-        if: steps.changed-files.outputs.any_changed == 'true'
         run: make assemble
 
       - name: Test
-        if: steps.changed-files.outputs.any_changed == 'true'
         run: |
             env | sort
             # configure test env
@@ -113,26 +96,24 @@ jobs:
 
       - name: Publish tests report
         uses: actions/upload-artifact@v4
-        if: steps.changed-files.outputs.any_changed == 'true' && always()
         with:
           name: report-unit-tests-jdk-${{ matrix.java_version }}
           path: |
             **/build/reports/tests/test
 
     outputs:
-      any_changed: ${{ steps.changed-files.outputs.any_changed }}
       commit_message: ${{ steps.get_commit_message.outputs.commit_message }}
 
   test:
-    if: ${{ !contains(needs.build.outputs.commit_message, '[ci fast]') && needs.build.outputs.any_changed == 'true' }}
+    if: ${{ !contains(needs.build.outputs.commit_message, '[ci fast]') }}
     needs: build
     runs-on: ubuntu-latest
     timeout-minutes: 90
     strategy:
       fail-fast: false
       matrix:
         java_version: [17, 23]
-        test_mode: ["test_integration", "test_docs", "test_aws", "test_azure", "test_google", "test_wave"]
+        test_mode: ["test_integration", "test_parser_v2", "test_docs", "test_aws", "test_azure", "test_google", "test_wave"]
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -187,17 +168,18 @@ jobs:
 
       - name: Tar integration tests
         if: always()
-        run: tar -cvf integration-tests.tar tests/checks
+        run: | 
+            tar -cvf integration-tests.tar.gz tests/checks
+            tar -cvf validation-tests.tar.gz validation
 
       - name: Publish tests report
         uses: actions/upload-artifact@v4
         if: always()
         with:
           name: report-${{ matrix.test_mode }}-jdk-${{ matrix.java_version }}
           path: |
-            validation/**/*
-            validation/**/.*
-            integration-tests.tar
+            validation-tests.tar.gz
+            integration-tests.tar.gz
 
   test-e2e:
       if: ${{ contains(needs.build.outputs.commit_message,'[e2e stage]') || contains(needs.build.outputs.commit_message,'[e2e prod]') }}

.github/workflows/codespell.yml

@@ -27,6 +27,16 @@ else
 mm = 
 endif 
 
+compile:
+	./gradlew compile exportClasspath
+	@echo "DONE `date`"
+
+assemble:
+	./gradlew buildInfo compile assemble
+
+check:
+	./gradlew check
+
 clean:
 	rm -rf .nextflow*
 	rm -rf work 
@@ -38,21 +48,11 @@ clean:
 	rm -rf plugins/*/build
 	./gradlew clean
 
-compile:
-	./gradlew compile exportClasspath
-	@echo "DONE `date`"
-
-assemble:
-	./gradlew buildInfo compile assemble
-
-check:
-	./gradlew check
-
 #
 # install compiled artifacts in Maven local dir
 # 
 install:
-	BUILD_PACK=1 ./gradlew installLauncher publishToMavenLocal -Dmaven.repo.local=${HOME}/.nextflow/capsule/deps/
+	BUILD_PACK=1 ./gradlew installLauncher publishToMavenLocal
 
 #
 # Show dependencies try `make deps config=runtime`, `make deps config=google`

Makefile

@@ -1 +1 @@
-24.11.0-edge
+25.02.1-edge

VERSION

@@ -67,18 +67,12 @@ allprojects {
     apply plugin: 'jacoco'
 
     java {
+        // these settings apply to all jvm tooling, including groovy
         toolchain {
             languageVersion = JavaLanguageVersion.of(21)
         }
-    }
-
-    compileJava {
-        options.release.set(17)
-    }
-
-    tasks.withType(GroovyCompile) {
-        sourceCompatibility = '17'
-        targetCompatibility = '17'
+        sourceCompatibility = 17
+        targetCompatibility = 17
     }
 
     idea {
@@ -109,8 +103,8 @@ allprojects {
 
         // Documentation required libraries
         groovyDoc 'org.fusesource.jansi:jansi:2.4.0'
-        groovyDoc "org.apache.groovy:groovy-groovydoc:4.0.24"
-        groovyDoc "org.apache.groovy:groovy-ant:4.0.24"
+        groovyDoc "org.apache.groovy:groovy-groovydoc:4.0.26"
+        groovyDoc "org.apache.groovy:groovy-ant:4.0.26"
     }
 
     test {
@@ -243,7 +237,7 @@ task compile {
 
 def getRuntimeConfigs() {
     def names = subprojects
-            .findAll { prj -> prj.name in ['nextflow','nf-commons','nf-httpfs'] }
+            .findAll { prj -> prj.name in ['nextflow','nf-commons','nf-httpfs','nf-lang'] }
             .collect { it.name }
 
     FileCollection result = null
@@ -269,7 +263,7 @@ task exportClasspath {
         def home = System.getProperty('user.home')
         def all = getRuntimeConfigs()
         def libs = all.collect { File file ->  /*println file.canonicalPath.replace(home, '$HOME');*/ file.canonicalPath;  }
-        ['nextflow','nf-commons','nf-httpfs'].each {libs << file("modules/$it/build/libs/${it}-${version}.jar").canonicalPath }
+        ['nextflow','nf-commons','nf-httpfs','nf-lang'].each {libs << file("modules/$it/build/libs/${it}-${version}.jar").canonicalPath }
         file('.launch.classpath').text = libs.unique().join(':')
     }
 }
@@ -282,7 +276,7 @@ ext.nexusEmail = project.findProperty('nexusEmail')
 // `signing.keyId` property needs to be defined in the `gradle.properties` file
 ext.enableSignArchives = project.findProperty('signing.keyId')
 
-ext.coreProjects = projects( ':nextflow', ':nf-commons', ':nf-httpfs' )
+ext.coreProjects = projects( ':nextflow', ':nf-commons', ':nf-httpfs', ':nf-lang' )
 
 configure(coreProjects) {
     group = 'io.nextflow'