Merge remote-tracking branch 'upstream/main' into clean-gsoc-git-support-init

Author: wanling0000

.github/ghprcomment.yml

@@ -154,7 +154,16 @@
     See [CONTRIBUTING.md](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md#pull-request-process) for more details.
 
 
-# PR text
+# PR hygiene
+
+- jobName: 'Ensure that contributor is assigned (fails if not commented on issue)'
+  workflowName: 'On PR opened/updated'
+  message: >
+    You did not assign yourself to the issue.
+    Thus, it looks like you skipped reading our [CONTRIBUTING.md](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md), which explains exactly how to participate. No worries, it happens to the best of us.
+
+
+    Give it a read, and you’ll discover the ancient wisdom of assigning issues to yourself. Trust me, it’s worth it. 🚀
 
 - jobName: 'PR title must not start with "Fix for issue <number>"'
   workflowName: 'PR Tests'

.github/workflows/on-pr-opened-updated.yml

@@ -85,6 +85,7 @@ jobs:
           skip-if-not-in-project: true
   ensure_assignment:
     name: Ensure that contributor is assigned (fails if not commented on issue)
+    if: github.event.pull_request.head.repo.full_name != 'JabRef/jabref'
     # after determine_issue_number to ensure that there is only one failure because of no ticket number
     needs: determine_issue_number
     runs-on: ubuntu-latest
@@ -114,10 +115,25 @@ jobs:
           # Append the new assignee
           UPDATED_ASSIGNEES=$(echo "$ASSIGNEES" | jq --arg new "${{ github.event.pull_request.user.login }}" '. + [$new]')
 
+          LABELS=$(gh api repos/${{ github.repository }}/issues/${{ needs.determine_issue_number.outputs.issue_number }}/labels --jq '.[].name')
+          LABEL=$(echo "$LABELS" | grep -E '^good (first|second|third|forth) issue$' || true)
+          if [ -n "$LABEL" ]; then
+            echo "✅ Found label: $LABEL"
+            SILENT=false
+            # Apply label
+            gh issue edit "${{ github.event.pull_request.number }}" --add-label "$LABEL"
+          else
+            echo "🚫 Silent fail if not possible to add assignee"
+            SILENT=true
+          fi
+
           # Update issue with the new assignee list
           echo "Updating issue #${{ needs.determine_issue_number.outputs.issue_number }} updated with assignees: $UPDATED_ASSIGNEES..."
-          gh api -X PATCH /repos/JabRef/jabref/issues/${{ needs.determine_issue_number.outputs.issue_number }} --input <(echo "{\"assignees\": $UPDATED_ASSIGNEES}")
-
+          if [ "$SILENT" = true ]; then
+            gh api -X PATCH /repos/JabRef/jabref/issues/${{ needs.determine_issue_number.outputs.issue_number }} --input <(echo "{\"assignees\": $UPDATED_ASSIGNEES}") || true
+          else
+            gh api -X PATCH /repos/JabRef/jabref/issues/${{ needs.determine_issue_number.outputs.issue_number }} --input <(echo "{\"assignees\": $UPDATED_ASSIGNEES}")
+          fi
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - name: Add label "📌 Pinned"

.github/workflows/pr-comment.yml

@@ -7,7 +7,7 @@ name: Comment on PR
 
 on:
   workflow_run:
-    workflows: ["Tests", "On PR opened/updated"]
+    workflows: ["Source Code Tests", "On PR opened/updated", "PR Tests"]
     # https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#running-a-workflow-based-on-the-conclusion-of-another-workflow
     types: [completed]
   workflow_dispatch:

.github/workflows/run-openrewrite.yml

@@ -0,0 +1,69 @@
+name: Run OpenRewrite
+
+permissions:
+  contents: write
+  pull-requests: read
+
+on:
+  workflow_dispatch:
+    inputs:
+      pr_number:
+        description: 'Pull Request number'
+        required: true
+        type: number
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}-${{ github.event_name }}"
+  cancel-in-progress: true
+
+jobs:
+  rewrite:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Fetch PR branch
+        run: |
+          gh pr checkout ${{ inputs.pr_number }}
+        env:
+          GH_TOKEN: ${{secrets.GH_TOKEN_JABREF_MACHINE_PR_APPROVE}}
+
+      - name: Set up JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: 24.0.1
+          distribution: 'zulu'
+      - name: Setup Gradle
+        uses: gradle/actions/setup-gradle@v4
+      - name: Generate JBang cache key
+        id: cache-key
+        shell: bash
+        run: |
+          echo "cache_key=jbang-$(date +%F)" >> $GITHUB_OUTPUT
+      - name: Use cache
+        uses: actions/cache@v4
+        with:
+          lookup-only: true
+          path: ~/.jbang
+          key: ${{ steps.cache-key.outputs.cache_key }}
+          restore-keys:
+            jbang-
+      - name: Setup JBang
+        uses: jbangdev/setup-jbang@main
+
+      - name: Run rewrite
+        run: ./gradlew rewriteRun
+
+      - name: Commit and push changes
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          if git diff --quiet; then
+            echo "No changes to commit."
+          else
+            git add .
+            git commit -m "Fix issues using OpenRewrite"
+            git push
+          fi

.github/workflows/tests-pr.yml

@@ -39,9 +39,14 @@ jobs:
           if echo "$TITLE" | grep -Eiq '^Fix for issue #?[0-9]+'; then
             echo "❌ Title starts with 'Fix for issue <number>' — not allowed."
             exit 1
-          else
-            echo "✅ Title format OK"
           fi
+
+          if echo "$TITLE" | grep -Eiq '^Fixed the issue'; then
+            echo "❌ Title starts with 'Fixed the issue' — not allowed."
+            exit 1
+          fi
+
+          echo "✅ Title format OK"
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 

.jbang/JabSrvLauncher.java

@@ -56,11 +56,11 @@
 //DEPS org.tinylog:slf4j-tinylog:2.7.0
 //DEPS org.tinylog:tinylog-impl:2.7.0
 //DEPS org.slf4j:jul-to-slf4j:2.0.17
-//DEPS org.apache.logging.log4j:log4j-to-slf4j:2.25.0
+//DEPS org.apache.logging.log4j:log4j-to-slf4j:2.25.1
 //DEPS info.picocli:picocli:4.7.7
 //DEPS org.postgresql:postgresql:42.7.7
 //DEPS org.bouncycastle:bcprov-jdk18on:1.81
-//DEPS com.konghq:unirest-modules-gson:4.4.7
+//DEPS com.konghq:unirest-modules-gson:4.4.12
 //DEPS jakarta.ws.rs:jakarta.ws.rs-api:4.0.0
 //DEPS org.glassfish.jersey.core:jersey-server:3.1.10
 //DEPS org.glassfish.jersey.inject:jersey-hk2:3.1.10
@@ -72,7 +72,7 @@
 //DEPS org.glassfish.grizzly:grizzly-framework:4.0.2
 //DEPS jakarta.validation:jakarta.validation-api:3.1.1
 //DEPS org.hibernate.validator:hibernate-validator:9.0.1.Final
-//DEPS com.konghq:unirest-modules-gson:4.4.7
+//DEPS com.konghq:unirest-modules-gson:4.4.12
 //DEPS com.google.guava:guava:33.4.8-jre
 //DEPS org.jabref:afterburner.fx:2.0.0
 //DEPS net.harawata:appdirs:1.4.0

CHANGELOG.md

@@ -74,6 +74,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where Document Viewer showed technical exceptions when opening entries with non-PDF files. [#13198](https://github.com/JabRef/jabref/issues/13198)
 - When creating a library, if you drag a PDF file containing only a single column, the dialog will now automatically close. [#13262](https://github.com/JabRef/jabref/issues/13262)
 - We fixed an issue where the tab showing the fulltext search results would appear blank after switching library. [#13241](https://github.com/JabRef/jabref/issues/13241)
+- Enhanced field selection logic in the Merge Entries dialog when fetching from DOI to prefer valid years and entry types. [#12549](https://github.com/JabRef/jabref/issues/12549)
 
 ### Removed
 

build-logic/build.gradle.kts

@@ -12,7 +12,7 @@ dependencies {
     implementation("com.adarshr:gradle-test-logger-plugin:4.0.0")
     implementation("com.autonomousapps:dependency-analysis-gradle-plugin:2.19.0")
     implementation("com.github.andygoossens:gradle-modernizer-plugin:1.11.0")
-    implementation("org.gradlex:extra-java-module-info:1.12")
+    implementation("org.gradlex:extra-java-module-info:1.13")
     implementation("org.gradlex:java-module-dependencies:1.9.2")
     implementation("org.gradlex:java-module-packaging:1.1") // required for platform-specific packaging of JavaFX dependencies
     implementation("org.gradlex:java-module-testing:1.7")

build-logic/src/main/kotlin/org.jabref.gradle.base.dependency-rules.gradle.kts

@@ -82,6 +82,7 @@ jvmDependencyConflicts.patch {
 
 extraJavaModuleInfo {
     failOnAutomaticModules = true
+    failOnModifiedDerivedModuleNames = true
     skipLocalJars = true
 
     knownModule("com.github.hypfvieh:dbus-java-core", "org.freedesktop.dbus")
@@ -147,7 +148,8 @@ extraJavaModuleInfo {
     }
     module("com.konghq:unirest-modules-gson", "unirest.modules.gson")
     module("com.squareup.okhttp3:okhttp", "okhttp3")
-    module("com.squareup.okhttp3:okhttp-sse", "okhttp3.sse")
+    module("com.squareup.okhttp3:okhttp-jvm", "okhttp3")
+    module("com.squareup.okhttp3:okhttp-jvm-sse", "okhttp3.sse")
     module("com.squareup.okio:okio", "okio")
     module("com.squareup.retrofit2:converter-jackson", "retrofit2.converter.jackson")
     module("com.squareup.retrofit2:retrofit", "retrofit2")
@@ -280,7 +282,7 @@ extraJavaModuleInfo {
     module("net.javacrumbs.json-unit:json-unit-core", "net.javacrumbs.jsonunit.core")
     module("com.github.javaparser:javaparser-core", "com.github.javaparser.core")
     module("com.github.javaparser:javaparser-symbol-solver-core", "com.github.javaparser.symbolsolver.core")
-    module("net.sf.jopt-simple:jopt-simple", "net.sf.jopt.simple")
+    module("net.sf.jopt-simple:jopt-simple", "jopt.simple")
 
     module("com.tngtech.archunit:archunit-junit5-api", "com.tngtech.archunit.junit5.api") {
         exportAllPackages()
@@ -361,7 +363,7 @@ extraJavaModuleInfo {
         requires("java.xml")
         requires("jakarta.xml.bind")
     }
-    module("org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2", "jersey.test.provider.grizzly2") {
+    module("org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2", "jersey.test.framework.provider.grizzly2") {
         requireAllDefinedDependencies()
         requires("java.logging")
     }
@@ -581,5 +583,5 @@ extraJavaModuleInfo {
     module("org.openjdk.jmh:jmh-generator-asm", "jmh.generator.asm")
     module("org.openjdk.jmh:jmh-generator-bytecode", "jmh.generator.bytecode")
     module("org.openjdk.jmh:jmh-generator-reflection", "jmh.generator.reflection")
-    module("org.apache.commons:commons-math3", "org.apache.commons.math3")
+    module("org.apache.commons:commons-math3", "commons.math3")
 }

build-logic/src/main/kotlin/org.jabref.gradle.base.targets.gradle.kts

@@ -18,12 +18,12 @@ javaModulePackaging {
     target("ubuntu-22.04") {
         operatingSystem = OperatingSystemFamily.LINUX
         architecture = MachineArchitecture.X86_64
-        packageTypes = listOf("app-image", "deb")
+        packageTypes = listOf("app-image", "deb", "rpm")
     }
     target("ubuntu-22.04-arm") {
         operatingSystem = OperatingSystemFamily.LINUX
         architecture = MachineArchitecture.ARM64
-        packageTypes = listOf("app-image", "deb")
+        packageTypes = listOf("app-image", "deb", "rpm")
     }
     target("macos-13") {
         operatingSystem = OperatingSystemFamily.MACOS