Merge branch 'main' into fix-for-issue-8888

Author: Siedlerchr

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -14,7 +14,7 @@ body:
       label: JabRef version
       options:
         - "5.15 (latest release)"
-        - "6.0-alpha2"
+        - "6.0-alpha.3"
         - Latest development branch build (please note build date below)
         - Other (please describe below)
       description: The version as shown in the about dialog.

.github/workflows/binaries.yml

@@ -147,7 +147,7 @@ jobs:
             displayName: linux-arm
             archivePortable: tar -c -C jabgui/build/packages/ubuntu-22.04-arm JabRef | pigz --rsyncable > jabgui/build/packages/ubuntu-22.04-arm/JabRef-portable_linux_arm64.tar.gz && rm -R jabgui/build/packages/ubuntu-22.04-arm/JabRef
             archivePortableJabKit: tar -c -C jabkit/build/packages/ubuntu-22.04-arm jabkit | pigz --rsyncable > jabkit/build/packages/ubuntu-22.04-arm/jabkit-portable_linux_arm64.tar.gz && rm -R jabkit/build/packages/ubuntu-22.04-arm/jabkit
-            archivePortableJabLS: tar -c -C jabls-cli/build/packages/ubuntu-22.04-arm jabls | pigz --rsyncable > jabls-cli/build/packages/ubuntu-22.04-arm/jabls-cli-portable_linux_arm64.tar.gz && rm -R jabls-cli/build/packages/ubuntu-22.04-arm/jabls
+            archivePortableJabLS: tar -c -C jabls-cli/build/packages/ubuntu-22.04-arm jabls | pigz --rsyncable > jabls-cli/build/packages/ubuntu-22.04-arm/jabls-portable_linux_arm64.tar.gz && rm -R jabls-cli/build/packages/ubuntu-22.04-arm/jabls
             suffix: '_arm64'
             archForDebianRepack: '_arm64'
           - os: windows-latest
@@ -168,7 +168,7 @@ jobs:
             displayName: macOS-arm
             archivePortable: 7z a -r jabgui/build/packages/macos-15/JabRef-portable_macos-arm.zip ./jabgui/build/packages/macos-15/JabRef.app && rm -R jabgui/build/packages/macos-15/JabRef.app
             archivePortableJabKit: 7z a -r jabkit/build/packages/macos-15/jabkit-portable_macos-arm.zip ./jabkit/build/packages/macos-15/jabkit.app && rm -R jabkit/build/packages/macos-15/jabkit.app
-            archivePortableJabLS: 7z a -r jabls-cli/build/packages/macos-15/jabls-portable_macos-arm.zip ./jabls-cli/build/packages/macos-15/jabkit.app && rm -R jabls-cli/build/packages/macos-15/jabls.app
+            archivePortableJabLS: 7z a -r jabls-cli/build/packages/macos-15/jabls-portable_macos-arm.zip ./jabls-cli/build/packages/macos-15/jabls.app && rm -R jabls-cli/build/packages/macos-15/jabls.app
             suffix: '_arm64'
             archForDebianRepack: ''
     runs-on: ${{ matrix.os }}
@@ -326,7 +326,7 @@ jobs:
         run: |
           rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'C:\ProgramData\chocolatey\lib\rsync\tools\bin\ssh.exe -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabls-cli/build/packages/${{ matrix.os }}/ [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
       - name: Upload jabgui to builds.jabref.org (linux, macOS)
-        if: ${{ (steps.diskspace.outputs.available == 'true') && (startsWith(matrix.os, 'macos') || startsWith(matrix.os, 'ubuntu')) }}
+        if: ${{ (steps.diskspace.outputs.available == 'true') && ((startsWith(matrix.os, 'macos') && (needs.conditions.outputs.should-notarize != 'true')) || startsWith(matrix.os, 'ubuntu')) }}
         shell: bash
         run: |
           rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabgui/build/packages/${{ matrix.os }}/ [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
@@ -342,7 +342,7 @@ jobs:
           rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabls-cli/build/packages/${{ matrix.os }}/ [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
       - name: Upload to GitHub workflow artifacts store (macOS)
         if: ${{ (startsWith(matrix.os, 'macos')) && (needs.conditions.outputs.should-notarize == 'true') }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           # tbn = to-be-notarized
           name: JabRef-${{ matrix.os }}-tbn
@@ -375,12 +375,16 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: echo PR data
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          PR_URL: ${{ github.event.pull_request.html_url }}
+          PR_BODY: ${{ github.event.pull_request.body }}
         run: |
-          echo "PR Number: ${{ github.event.pull_request.number }}"
-          echo "PR URL: ${{ github.event.pull_request.html_url }}"
+          echo "PR Number: $PR_NUMBER"
+          echo "PR URL: $PR_URL"
           cat <<EOF
           PR Body:
-          ${{ github.event.pull_request.body }}
+          $PR_BODY
           EOF
       - name: Determine issue number
         id: get_issue_number
@@ -421,14 +425,10 @@ jobs:
         include:
           - os: macos-15
             displayName: macOS (ARM64)
-            suffix: '_arm64'
-          - os: macos-15-intel  # intel image
-            displayName: macOS
-            suffix: ''
     runs-on: ${{ matrix.os }}
     steps:
       - name: Download from GitHub workflow artifacts store (macOS)
-        uses: actions/download-artifact@v5
+        uses: actions/download-artifact@v6
         with:
           name: JabRef-${{ matrix.os }}-tbn
       - name: Notarize dmg
@@ -437,15 +437,15 @@ jobs:
           cd jabgui
           find . -type f
           xcrun notarytool store-credentials "notarytool-profile" --apple-id "[email protected]" --team-id "6792V39SK3" --password "${{ secrets.OSX_NOTARIZATION_APP_PWD }}"
-          xcrun notarytool submit packages/${{ matrix.os }}/JabRef-${{ needs.build.outputs.major }}.${{ needs.build.outputs.minor }}${{ matrix.suffix}}.dmg --keychain-profile "notarytool-profile" --wait
-          xcrun stapler staple packages/${{ matrix.os }}/JabRef-${{ needs.build.outputs.major }}.${{ needs.build.outputs.minor }}${{ matrix.suffix}}.dmg
+          xcrun notarytool submit build/packages/${{ matrix.os }}/JabRef-${{ needs.build.outputs.major }}.${{ needs.build.outputs.minor }}${{ matrix.suffix}}.dmg --keychain-profile "notarytool-profile" --wait
+          xcrun stapler staple build/packages/${{ matrix.os }}/JabRef-${{ needs.build.outputs.major }}.${{ needs.build.outputs.minor }}${{ matrix.suffix}}.dmg
       - name: Notarize pkg
         shell: bash
         run: |
           cd jabgui
           xcrun notarytool store-credentials "notarytool-profile" --apple-id "[email protected]" --team-id "6792V39SK3" --password "${{ secrets.OSX_NOTARIZATION_APP_PWD }}"
-          xcrun notarytool submit packages/${{ matrix.os }}/JabRef-${{ needs.build.outputs.major }}.${{ needs.build.outputs.minor }}${{ matrix.suffix}}.pkg --keychain-profile "notarytool-profile" --wait
-          xcrun stapler staple packages/${{ matrix.os }}/JabRef-${{ needs.build.outputs.major }}.${{ needs.build.outputs.minor }}${{ matrix.suffix}}.pkg
+          xcrun notarytool submit build/packages/${{ matrix.os }}/JabRef-${{ needs.build.outputs.major }}.${{ needs.build.outputs.minor }}${{ matrix.suffix}}.pkg --keychain-profile "notarytool-profile" --wait
+          xcrun stapler staple build/packages/${{ matrix.os }}/JabRef-${{ needs.build.outputs.major }}.${{ needs.build.outputs.minor }}${{ matrix.suffix}}.pkg
       - name: Upload to builds.jabref.org
         shell: bash
         run: |

.github/workflows/gource.yml

@@ -21,9 +21,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - title: 'JabRef v6.0 (in development) | more information at contribute.jabref.org'
-            # Last alpha release 2025-04-27, but want to have some seconds before
-            start: '2025-04-15'
+          - title: 'JabRef v6.0 (since alpha.3) | more information at contribute.jabref.org'
+            # Last alpha release 2025-10-30, but want to have some seconds before
+            start: '2025-10-29'
             end: ''
             file: 'jabref-v6.0-dev.mp4'
 #          - title: 'JabRef v6.0-alpha2 | more information at contribute.jabref.org'
@@ -73,7 +73,7 @@ jobs:
           mv ./gource/gource.mp4 ${{ matrix.file }}
 
       - name: Upload gource video
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: Gource-${{ matrix.file }}
           path: ${{ matrix.file }}

.github/workflows/latex.yml

@@ -99,7 +99,7 @@ jobs:
         working-directory: ${{ matrix.directory }}
 
       - name: Upload build result
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: PDF-${{ matrix.tex }}
           path: |

.github/workflows/link-issue.yml

@@ -26,12 +26,16 @@ jobs:
       issue_number: ${{ steps.get_issue_number.outputs.ticketNumber }}
     steps:
       - name: echo PR data
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          PR_URL: ${{ github.event.pull_request.html_url }}
+          PR_BODY: ${{ github.event.pull_request.body }}
         run: |
-          echo "PR Number: ${{ github.event.pull_request.number }}"
-          echo "PR URL: ${{ github.event.pull_request.html_url }}"
+          echo "PR Number: $PR_NUMBER"
+          echo "PR URL: $PR_URL"
           cat <<EOF
           PR Body:
-          ${{ github.event.pull_request.body }}
+          $PR_BODY
           EOF
       - name: Determine issue number
         id: get_issue_number

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

@@ -20,16 +20,25 @@ jobs:
           # If this is updated, also update the number at unassign-issues.yml
           days_until_unassign: 21
           maintainers: 'koppor,Siedlerchr,ThiloteE,calixtus,HoussemNasri,subhramit,InAnYan,LinusDietz'
-          assigned_comment: |
+          assigned_comment: >
             👋 Hey @{{ handle }}, thank you for your interest in this issue! 🎉
 
-            We're excited to have you on board. Start by exploring our [Contributing](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md) guidelines, and don't forget to check out our [workspace setup guidelines](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace) to get started smoothly.
 
-            For questions on JabRef functionality and the code base, you can consult the [JabRef Guru](https://gurubase.io/g/jabref) or ask on our Gitter chat.
+            We're excited to have you on board.
+            Start by exploring our [Contributing guidelines](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md), and set up your local development workspace by following the steps in our [workspace setup guidelines](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace) to get started smoothly.
+
+
+            For questions on JabRef functionality, you can consult the [JabRef Guru](https://gurubase.io/g/jabref).
+            For questions related to the codebase, please start using [DeepWiki](https://deepwiki.com/JabRef/jabref).
+
 
             In case you encounter failing tests during development, please check our [developer FAQs](https://devdocs.jabref.org/code-howtos/faq.html)!
 
-            Having any questions or issues? Feel free to ask here on GitHub. Need help setting up your local workspace? Join the conversation on [JabRef's Gitter chat](https://gitter.im/JabRef/jabref). And don't hesitate to open a (draft) pull request early on to show the direction it is heading towards. This way, you will receive valuable feedback.
+
+            Still facing issues or having more questions?
+            Feel free to ask here on GitHub or on [JabRef's Gitter chat](https://gitter.im/JabRef/jabref).
+            Please don't hesitate to open a (draft) pull request early on to show the direction you are heading towards if unsure.
+
 
             Happy coding! 🚀
           assignment_suggestion_comment: >

.github/workflows/on-pr-changes-requested-check.yml

@@ -0,0 +1,20 @@
+name: Adapt PR status labels (Check)
+
+on:
+  pull_request_review:
+    types: [submitted]
+
+jobs:
+  label-changes-required:
+    if: github.event.review.state == 'changes_requested'
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      actions: write
+    steps:
+      - name: Create pr_number.txt
+        run: echo "${{ github.event.pull_request.number }}" > pr_number.txt
+      - uses: actions/upload-artifact@v5
+        with:
+          name: pr_number
+          path: pr_number.txt

.github/workflows/on-pr-changes-requested-move-labels.yml

@@ -0,0 +1,40 @@
+name: Adapt PR status labels (Move)
+
+on:
+  workflow_run:
+    workflows: ["Adapt PR status labels (Check)"]
+    types: [completed]
+
+jobs:
+   apply-labels:
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      actions: read
+      contents: read
+    steps:
+      - name: Download artifact from triggering run
+        uses: actions/download-artifact@v6
+        with:
+          run-id: ${{ github.event.workflow_run.id }}
+          name: pr_number
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+        continue-on-error: true
+      - name: Check for pr_number.txt
+        id: check
+        run: |
+          if [ -f pr_number.txt ]; then
+            echo "continue=true" >> "$GITHUB_OUTPUT"
+            echo "pr_number=$(cat pr_number.txt)" >> "$GITHUB_OUTPUT"
+          else
+            echo "continue=false" >> "$GITHUB_OUTPUT"
+          fi
+      - name: Apply label operations
+        if: steps.check.outputs.continue == 'true'
+        run: |
+          gh issue --repo ${{ github.repository }} edit ${{ steps.check.outputs.pr_number }} --remove-label "status: ready-for-review"
+          gh issue --repo ${{ github.repository }} edit ${{ steps.check.outputs.pr_number }} --remove-label "status: awaiting-second-review"
+          gh issue --repo ${{ github.repository }} edit ${{ steps.check.outputs.pr_number }} --add-label "status: changes-required"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/on-pr-changes-requested.yml

@@ -25,12 +25,16 @@ jobs:
       issue_number: ${{ steps.get_issue_number.outputs.ticketNumber }}
     steps:
       - name: echo PR data
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          PR_URL: ${{ github.event.pull_request.html_url }}
+          PR_BODY: ${{ github.event.pull_request.body }}
         run: |
-          echo "PR Number: ${{ github.event.pull_request.number }}"
-          echo "PR URL: ${{ github.event.pull_request.html_url }}"
+          echo "PR Number: $PR_NUMBER"
+          echo "PR URL: $PR_URL"
           cat <<EOF
           PR Body:
-          ${{ github.event.pull_request.body }}
+          $PR_BODY
           EOF
       - name: Determine issue number
         id: get_issue_number