Merge branch 'main' of github.com:JabRef/jabref

* 'main' of github.com:JabRef/jabref: (26 commits)
  Change Open AI to Open AI  (or API Compatible)  (#13608)
  Remove all assignment tracking labels
  Updated architecture and components link in CONTRIBUTING.md (#13606)
  #13301 Fix/unicode reference marks (#13590)
  Show fetch exception at citation relation (#13549)
  More jbang caching
  Sequential run for moving issues
  Update CSL Styles (#13601)
  Fix gradle issues (#13603)
  Add System.exit (#13510)
  New Crowdin updates (#13600)
  Automatic lookup DOI at citation information. (#13596)
  Update heylogs from 0.10.0 to 0.11.1 (#13594)
  add fallback and reenable defaultcomeslast (#13593)
  Fix debian vagrant image (#13589)
  Fix: Replace string "Tests" with "Source Code Tests" in PR Comment (#13587)
  Fix version for SNAPSHOT (#13581)
  Update JDK and JavaFX (#13580)
  Add icon (#13579)
  Fixes link I broke in PR 13568 (#13577)
  ...

Author: Siedlerchr

.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/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/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
 

.jbang/JabSrvLauncher.java

@@ -14,40 +14,44 @@
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/dto/GsonFactory.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/dto/LinkedPdfFileDTO.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/JabrefMediaType.java
-//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/CAYWResource.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/JabRefSrvStateManager.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/SrvStateManager.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/CAYWQueryParams.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/CAYWResource.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/format/BibLatexFormatter.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/format/CAYWFormatter.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/format/FormatterService.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/format/SimpleJsonFormatter.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/gui/CAYWEntry.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/gui/SearchDialog.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/gui/SearchField.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/gui/SearchResultContainer.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/gui/SelectedItemsContainer.java
-//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/format/BibLatexFormatter.java
-//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/format/CAYWFormatter.java
-//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/format/FormatterService.java
-//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/format/SimpleJsonFormatter.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/command/Command.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/command/CommandResource.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/command/SelectEntriesCommand.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/CORSFilter.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/LibrariesResource.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/LibraryResource.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/PreferencesFactory.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/RootResource.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/Server.java
-//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/services/ContextsToServe.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/services/FilesToServe.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/services/ServerUtils.java
 
 // 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
 //DEPS org.jspecify:jspecify:1.0.0

.sdkmanrc

@@ -1,2 +1,2 @@
-java=24.0.1-amzn
+java=24.0.2-amzn
 #visualvm=2.1.10