Merge branch 'main' into fix/copy-linked-files-on-entry-transfer

Author: UmutAkbayin

.github/ghprcomment.yml

@@ -102,7 +102,7 @@
     [Markdown lint's rules](https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md#rules) help to keep our Markdown files consistent within this repository and consistent with the Markdown files outside here.
 
 
-    You can check the detailed error output by navigating to your pull request, selecting the tab "Checks", section "Tests" (on the left), subsection "CHANGELOG.md".
+    You can check the detailed error output by navigating to your pull request, selecting the tab "Checks", section "Source Code Tests" (on the left), subsection "CHANGELOG.md".
 - jobName: Markdown
   workflowName: 'Source Code Tests'
   message: >
@@ -111,7 +111,7 @@
     [Markdown lint's rules](https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md#rules) help to keep our Markdown files consistent within this repository and consistent with the Markdown files outside here.
 
 
-    You can check the detailed error output by navigating to your pull request, selecting the tab "Checks", section "Tests" (on the left), subsection "Markdown".
+    You can check the detailed error output by navigating to your pull request, selecting the tab "Checks", section "Source Code Tests" (on the left), subsection "Markdown".
 
 
 # Submodules and branches

.github/workflows/binaries.yml

@@ -208,7 +208,6 @@ jobs:
       - name: Use cache
         uses: actions/cache@v4
         with:
-          lookup-only: true
           path: ~/.jbang
           key: ${{ steps.cache-key.outputs.cache_key }}
           restore-keys:

.github/workflows/on-issue-unlabeled.yml

@@ -42,3 +42,13 @@ jobs:
           done
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Remove labels assigned, reminder-sent, pinned, and "FirstTimeCodeContribution"
+        run: |
+          set -e
+
+          gh issue edit ${{ github.event.issue.number }} --remove-label "📍 Assigned"
+          gh issue edit ${{ github.event.issue.number }} --remove-label "🔔 reminder-sent"
+          gh issue edit ${{ github.event.issue.number }} --remove-label "📌 Pinned"
+          gh issue edit ${{ github.event.issue.number }} --remove-label "FirstTimeCodeContribution"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/publish.yml

@@ -13,6 +13,12 @@ on:
     # run on each Monday
     - cron: '2 3 * * 1'
   workflow_dispatch:
+    inputs:
+      tagbuild:
+        description: 'Trigger a full maven central release'
+        required: false
+        default: false
+        type: boolean
 
 permissions:
   actions: write
@@ -62,7 +68,6 @@ jobs:
       - name: Use cache
         uses: actions/cache@v4
         with:
-          lookup-only: true
           path: ~/.jbang
           key: ${{ steps.cache-key.outputs.cache_key }}
           restore-keys:
@@ -97,5 +102,13 @@ jobs:
           file ${{ steps.secring.outputs.filePath }}
           md5sum ${{ steps.secring.outputs.filePath }}
       - name: publishAllPublicationsToMavenCentralRepository
-        run: ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" -Ptagbuild="${{ steps.istagbuild.outputs.tagbuild }}" :jablib:publishAllPublicationsToMavenCentralRepository
+        # Different version at maven centrl: 6.0-SNAPSHOT - and not 6.0.23234-SNAPSHOT
+        # We need to manually trigger a full maven central release - to avoid 6.0-alpha3 being published as 6.0 on maven central.
+        run: |
+          if [[ "${{ github.event.inputs.tagbuild }}" == "true" ]]; then
+            tagbuild="true"
+          else
+            tagbuild="false"
+          fi
+          ./gradlew -PprojVersion="${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" -Ptagbuild="$tagbuild" :jablib:publishAllPublicationsToMavenCentralRepository
       # endregion

.github/workflows/run-openrewrite.yml

@@ -45,7 +45,6 @@ jobs:
       - name: Use cache
         uses: actions/cache@v4
         with:
-          lookup-only: true
           path: ~/.jbang
           key: ${{ steps.cache-key.outputs.cache_key }}
           restore-keys:

.github/workflows/tests-code.yml

@@ -57,6 +57,20 @@ jobs:
           checkstyle_config: 'config/checkstyle/checkstyle_reviewdog.xml'
       - 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:
+          path: ~/.jbang
+          key: ${{ steps.cache-key.outputs.cache_key }}
+          restore-keys:
+            jbang-
+      - name: Setup JBang
+        uses: jbangdev/setup-jbang@main
       - name: Run checkstyle using gradle
         run: ./gradlew checkstyleMain checkstyleTest checkstyleJmh
 
@@ -84,7 +98,6 @@ jobs:
       - name: Use cache
         uses: actions/cache@v4
         with:
-          lookup-only: true
           path: ~/.jbang
           key: ${{ steps.cache-key.outputs.cache_key }}
           restore-keys:
@@ -111,6 +124,20 @@ jobs:
           distribution: 'zulu'
       - name: Setup Gradle
         uses: gradle/actions/setup-gradle@v4
+      - name: Generate JBang cache key
+        id: cache-key
+        shell: bash
+        run: |
+          echo "cache_key=jbang-$(date +%F)" >> $GITHUB_OUTPUT
+      - name: Use cache
+        uses: actions/cache@v4
+        with:
+          path: ~/.jbang
+          key: ${{ steps.cache-key.outputs.cache_key }}
+          restore-keys:
+            jbang-
+      - name: Setup JBang
+        uses: jbangdev/setup-jbang@main
       - name: Run modernizer
         run: |
           # enable failing of this task if modernizer complains
@@ -146,21 +173,20 @@ jobs:
         id: cache-key
         shell: bash
         run: |
-          echo "cache_key=jbang-$(date +%F)" >> $GITHUB_OUTPUT
+          echo "cache_key=jbang-heylogs-$(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-
+            jbang-heylogs-
       - name: Setup JBang
         uses: jbangdev/setup-jbang@main
       - name: Lint CHANGELOG.md
         run: |
           # run heylogs verification
-          jbang com.github.nbbrd.heylogs:heylogs-cli:0.10.0:bin check CHANGELOG.md > heylogs.txt || true
+          jbang com.github.nbbrd.heylogs:heylogs-cli:0.11.1:bin check CHANGELOG.md > heylogs.txt || true
 
           # improve output
           sed -i 's/all-h2-contain-a-version/all-h2-contain-a-version (ignored)/' heylogs.txt
@@ -215,6 +241,20 @@ jobs:
           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:
+          path: ~/.jbang
+          key: ${{ steps.cache-key.outputs.cache_key }}
+          restore-keys:
+            jbang-
+      - name: Setup JBang
+        uses: jbangdev/setup-jbang@main
       - run: ./gradlew javadoc
 
   tests:
@@ -242,7 +282,6 @@ jobs:
       - name: Use cache
         uses: actions/cache@v4
         with:
-          lookup-only: true
           path: ~/.jbang
           key: ${{ steps.cache-key.outputs.cache_key }}
           restore-keys:
@@ -285,6 +324,20 @@ jobs:
           distribution: 'zulu'
       - name: Setup Gradle
         uses: gradle/actions/setup-gradle@v4
+      - name: Generate JBang cache key
+        id: cache-key
+        shell: bash
+        run: |
+          echo "cache_key=jbang-$(date +%F)" >> $GITHUB_OUTPUT
+      - name: Use cache
+        uses: actions/cache@v4
+        with:
+          path: ~/.jbang
+          key: ${{ steps.cache-key.outputs.cache_key }}
+          restore-keys:
+            jbang-
+      - name: Setup JBang
+        uses: jbangdev/setup-jbang@main
       - name: Run ${{ matrix.module }} tests
         run: ./gradlew :${{ matrix.module }}:check -x checkstyleJmh -x checkstyleMain -x checkstyleTest -x modernizer
         env:
@@ -320,6 +373,20 @@ jobs:
           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:
+          path: ~/.jbang
+          key: ${{ steps.cache-key.outputs.cache_key }}
+          restore-keys:
+            jbang-
+      - name: Setup JBang
+        uses: jbangdev/setup-jbang@main
       - name: Run tests on PostgreSQL
         run: ./gradlew :jablib:databaseTest --rerun-tasks
         env:
@@ -350,7 +417,6 @@ jobs:
       - name: Use cache
         uses: actions/cache@v4
         with:
-          lookup-only: true
           path: ~/.jbang
           key: ${{ steps.cache-key.outputs.cache_key }}
           restore-keys:
@@ -406,6 +472,20 @@ jobs:
           distribution: 'zulu'
       - name: Setup Gradle
         uses: gradle/actions/setup-gradle@v4
+      - name: Generate JBang cache key
+        id: cache-key
+        shell: bash
+        run: |
+          echo "cache_key=jbang-$(date +%F)" >> $GITHUB_OUTPUT
+      - name: Use cache
+        uses: actions/cache@v4
+        with:
+          path: ~/.jbang
+          key: ${{ steps.cache-key.outputs.cache_key }}
+          restore-keys:
+            jbang-
+      - name: Setup JBang
+        uses: jbangdev/setup-jbang@main
       - name: Update test coverage metrics
         if: (github.ref == 'refs/heads/main') && (steps.checksecrets.outputs.secretspresent == 'YES')
         run: xvfb-run --auto-servernum ./gradlew jacocoTestReport

.github/workflows/tests-pr.yml

@@ -22,7 +22,7 @@ jobs:
           path: pr_number.txt
 
   check_title_format:
-    name: PR title must not start with "Fix for issue <number>"
+    name: PR title must not contain "issue <number>"
     if: github.actor != 'dependabot[bot]' && github.event.pull_request.head.repo.full_name != 'JabRef/jabref'
     runs-on: ubuntu-latest
     steps:
@@ -36,13 +36,8 @@ jobs:
           TITLE=$(gh pr view "${{ github.event.number }}" --json title --template '{{.title}}')
           echo "Title: $TITLE"
 
-          if echo "$TITLE" | grep -Eiq '^Fix for issue #?[0-9]+'; then
-            echo "❌ Title starts with 'Fix for issue <number>' — not allowed."
-            exit 1
-          fi
-
-          if echo "$TITLE" | grep -Eiq '^Fixed the issue'; then
-            echo "❌ Title starts with 'Fixed the issue' — not allowed."
+          if echo "$TITLE" | grep -Eiq 'issue ?#?[0-9]+.+'; then
+            echo "❌ Title contains 'issue <number>' — not allowed."
             exit 1
           fi
 

.github/workflows/unassign-issues.yml

@@ -64,6 +64,8 @@ jobs:
     if: ${{ needs.unassign_issues.outputs.unassigned_issues != '[]' }}
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
+      max-parallel: 1
       matrix:
         issue_number: ${{ fromJson(needs.unassign_issues.outputs.unassigned_issues) }}
     steps:

.jbang/CheckoutPR.java

@@ -20,7 +20,7 @@
 //JAVA 21+
 //RUNTIME_OPTIONS --enable-native-access=ALL-UNNAMED
 
-//DEPS org.kohsuke:github-api:2.0-rc.3
+//DEPS org.kohsuke:github-api:2.0-rc.4
 //DEPS org.eclipse.jgit:org.eclipse.jgit.pgm:7.3.0.202506031305-r
 
 public class CheckoutPR {

.jbang/JabKitLauncher.java

@@ -21,18 +21,18 @@
 //FILES tinylog.properties=../jabkit/src/main/resources/tinylog.properties
 
 // REPOS mavencentral,snapshots=https://central.sonatype.com/repository/maven-snapshots/
-//REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,s01oss=https://s01.oss.sonatype.org/content/repositories/snapshots/,oss=https://oss.sonatype.org/content/repositories,jitpack=https://jitpack.io,oss2=https://oss.sonatype.org/content/groups/public,ossrh=https://oss.sonatype.org/content/repositories/snapshots
-// REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,s01oss=https://s01.oss.sonatype.org/content/repositories/snapshots/,oss=https://oss.sonatype.org/content/repositories,jitpack=https://jitpack.io,oss2=https://oss.sonatype.org/content/groups/public,ossrh=https://oss.sonatype.org/content/repositories/snapshots,raw=https://raw.githubusercontent.com/JabRef/jabref/refs/heads/main/jablib/lib/
+// REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,s01oss=https://s01.oss.sonatype.org/content/repositories/snapshots/,oss=https://oss.sonatype.org/content/repositories,jitpack=https://jitpack.io,oss2=https://oss.sonatype.org/content/groups/public,ossrh=https://oss.sonatype.org/content/repositories/snapshots
+//REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,s01oss=https://s01.oss.sonatype.org/content/repositories/snapshots/,oss=https://oss.sonatype.org/content/repositories,jitpack=https://jitpack.io,oss2=https://oss.sonatype.org/content/groups/public,ossrh=https://oss.sonatype.org/content/repositories/snapshots,raw=https://raw.githubusercontent.com/JabRef/jabref/refs/heads/main/jablib/lib/
 // REPOS mavencentral,jitpack=https://jitpack.io
 
 // TODO: ASCII things won't work, but we accept for now to keep things going
 //DEPS com.ibm.icu:icu4j:77.1
 
 // Choose one - both should work
 // https://central.sonatype.com/service/rest/repository/browse/maven-snapshots/org/jabref/jablib/
-// DEPS org.jabref:jablib:6.+
+//DEPS org.jabref:jablib:6.0-SNAPSHOT
 // https://jitpack.io/#jabref/jabref/main-SNAPSHOT
-//DEPS com.github.jabref:jabref:main-SNAPSHOT
+// DEPS com.github.jabref:jabref:main-SNAPSHOT
 
 //DEPS info.picocli:picocli:4.7.7