Merge branch 'main' into fix-issue-11937

Author: koppor

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -43,7 +43,7 @@ body:
 
   - type: checkboxes
     attributes:
-      label: Checked with the latest development build (copy version output from About dialog)
+      label: Checked with the [latest development build](https://builds.jabref.org/main/) (copy version output from About dialog)
       description: |
         Please always test if the bug is still reproducible in the latest development version. We are constantly improving JabRef and some bugs may already be fixed. If you already use a development version, ensure that you use the latest one.
         You can download the latest development build at: https://builds.jabref.org/main/ . **Please make a backup of your library before you try out this version.**

.github/dependabot.yml

@@ -9,8 +9,7 @@ updates:
     schedule:
       interval: weekly
       day: sunday
-    labels:
-      - "dependencies"
+    labels: [ ]
     ignore:
       - dependency-name: com.microsoft.azure:applicationinsights-core
         versions:
@@ -23,10 +22,17 @@ updates:
     schedule:
       interval: weekly
       day: sunday
-    labels:
-      - "dependencies"
+    labels: [ ]
   - package-ecosystem: "gitsubmodule"
     directory: "/"
     schedule:
       interval: weekly
       day: sunday
+    labels: [ ]
+  - package-ecosystem: "maven"
+    directories:
+      - "jablib-examples/maven3/doi-to-bibtex"
+    schedule:
+      interval: weekly
+      day: sunday
+    labels: [ ]

.github/ghprcomment.yml

@@ -179,19 +179,19 @@
     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 contain "issue <number>"'
-  workflowName: 'PR Format'
+  workflowName: 'Check PR Format'
   always: true
   message: >
     The title of the pull request must not start with "Fix for issue xyz".
     Please use a concise one-line summary that explains what the fix or change actually does.
     Example of a good title: "Prevent crash when importing malformed BibTeX entries".
 - jobName: 'Mandatory Checks present'
-  workflowName: 'PR Format'
+  workflowName: 'Check PR Format'
   always: true
   message: >
     You have removed the "Mandatory Checks" section from your pull request description. Please adhere to our [pull request template](https://github.com/JabRef/jabref/blob/main/.github/PULL_REQUEST_TEMPLATE.md?plain=1#L10).
 - jobName: 'PR checklist OK'
-  workflowName: 'PR Format'
+  workflowName: 'Check PR Format'
   always: true
   message: >
     Note that your PR will not be reviewed/accepted until you have gone through the mandatory checks in the description and marked each of them them exactly in the format of `[x]` (done), `[ ]` (not done yet) or `[/]` (not applicable).

.github/workflows/binaries.yml

@@ -66,70 +66,127 @@ jobs:
           REPO_OWNER: ${{ github.repository_owner }}
         run: |
           if [[ "$GITHUB_WORKFLOW" == *"early access"* && "$REPO_OWNER" != "JabRef" ]]; then
-            echo "🚫 Early access workflow for JabRef disabled for non-JabRef owner"
+            echo "⊘ Early access workflow for JabRef disabled for non-JabRef owner"
+            echo "⊘ Early access workflow for JabRef disabled for non-JabRef owner" >> $GITHUB_STEP_SUMMARY
             echo "should-build=false" >> "$GITHUB_OUTPUT"
             exit 0
           fi
 
           if [[ "$EVENT_NAME" != "labeled" || "$LABEL_NAME" == "automerge"  || "$LABEL_NAME" == "dev: binaries" ]]; then
             echo "📦 build enabled"
+            echo "📦 build enabled" >> $GITHUB_STEP_SUMMARY
             echo "should-build=true" >> "$GITHUB_OUTPUT"
           else
-            echo "🚫 build should be skipped"
+            echo "⊘ build should be skipped"
+            echo "⊘ build should be skipped" >> $GITHUB_STEP_SUMMARY
             echo "should-build=false" >> "$GITHUB_OUTPUT"
             exit 0
           fi
 
           if [ -z "$BUILDJABREFPRIVATEKEY" ]; then
+            echo "⊘ Secret BUILDJABREFPRIVATEKEY not present – skipping upload"
+            echo "⊘ Secret BUILDJABREFPRIVATEKEY not present – skipping upload"
             echo "upload-to-builds-jabref-org=false" >> "$GITHUB_OUTPUT"
             echo "secretspresent=false" >> "$GITHUB_OUTPUT"
-            echo "🚫 Secret BUILDJABREFPRIVATEKEY not present – skipping upload"
             exit 0
           fi
           echo "secretspresent=true" >> "$GITHUB_OUTPUT"
 
           if [[ "$GITHUB_REF" == refs/heads/gh-readonly-queue* ]]; then
+            echo "⊘ merge queue – skipping upload"
+            echo "⊘ merge queue – skipping upload" >> $GITHUB_STEP_SUMMARY
             echo "upload-to-builds-jabref-org=false" >> "$GITHUB_OUTPUT"
-            echo "🚫 merge queue – skipping upload"
             exit 0
           fi
 
           if [[ "${GITHUB_REF}" == refs/tags/* ]]; then
+            echo "⊘ tag bulid" >> $GITHUB_STEP_SUMMARY
             echo "tagbuild=true" >> "$GITHUB_OUTPUT"
           else
+            echo "⊘ no tag bulid" >> $GITHUB_STEP_SUMMARY
             echo "tagbuild=false" >> "$GITHUB_OUTPUT"
           fi
 
           if [[ "${GITHUB_REF}" == refs/tags/* ]] || [[ "${{ inputs.notarization }}" == "true" ]]; then
             # This workflow runs on ubuntu-latest even for notarization for macOS; need to check later if really on macOS
              echo "🧾 macOS notarization"
+             echo "🧾 macOS notarization" >> $GITHUB_STEP_SUMMARY
              echo "should-notarize=true" >> "$GITHUB_OUTPUT"
              echo "☁️ will upload"
+             echo "☁️ will upload" >> $GITHUB_STEP_SUMMARY
              echo "upload-to-builds-jabref-org=true" >> "$GITHUB_OUTPUT"
              exit 0;
           else
-            echo "🚫 no macOS notarization"
+            echo "⊘ no macOS notarization"
+            echo "⊘ no macOS notarization" >> $GITHUB_STEP_SUMMARY
             echo "should-notarize=false" >> "$GITHUB_OUTPUT"
           fi
 
           if [ "${{ github.event_name }}" != "pull_request" ]; then
-            echo "upload-to-builds-jabref-org=true" >> "$GITHUB_OUTPUT"
             echo "☁️ Non-PR event – will upload"
+            echo "☁️ Non-PR event – will upload" >> $GITHUB_STEP_SUMMARY
+            echo "upload-to-builds-jabref-org=true" >> "$GITHUB_OUTPUT"
             exit 0
           fi
 
           LABELS=$(gh api repos/${{ github.repository }}/issues/${{ github.event.pull_request.number }}/labels --jq '.[].name')
 
           if echo "$LABELS" | grep -q "^dev: binaries$"; then
-            echo "upload-to-builds-jabref-org=true" >> "$GITHUB_OUTPUT"
             echo "☁️ Label 'dev: binaries' found – will upload"
+            echo "☁️ Label 'dev: binaries' found – will upload" >> $GITHUB_STEP_SUMMARY
+            echo "upload-to-builds-jabref-org=true" >> "$GITHUB_OUTPUT"
           else
+            echo "⊘ Label 'dev: binaries' not found – skipping upload"
+            echo "⊘ Label 'dev: binaries' not found – skipping upload" >> $GITHUB_STEP_SUMMARY
             echo "upload-to-builds-jabref-org=false" >> "$GITHUB_OUTPUT"
-            echo "🚫 Label 'dev: binaries' not found – skipping upload"
           fi
 
+  disk-space-check:
+    needs: conditions
+    runs-on: ubuntu-latest
+    outputs:
+      available: ${{ steps.diskspace.outputs.available }}
+    steps:
+      - name: No upload
+        if: needs.conditions.outputs.upload-to-builds-jabref-org == 'false'
+        shell: bash
+        run: |
+          echo "⊘ no upload – skipping upload"
+          echo "⊘ no upload – skipping upload" >> $GITHUB_STEP_SUMMARY
+          echo "available=false" >> "$GITHUB_OUTPUT"
+      - name: Setup SSH key
+        if: needs.conditions.outputs.upload-to-builds-jabref-org == 'true'
+        run: |
+          echo "${{ secrets.buildJabRefPrivateKey }}" > sshkey
+          chmod 600 sshkey
+      - name: Check disk space on builds.jabref.org
+        if: needs.conditions.outputs.upload-to-builds-jabref-org == 'true'
+        id: diskspace
+        shell: bash
+        run: |
+          USAGE=$(ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no jrrsync@build-upload.jabref.org \
+            "df --output=pcent /var/www/builds.jabref.org | tail -n1 | tr -dc '0-9'")
+          echo "Remote usage: ${USAGE}%"
+          echo "Remote usage: ${USAGE}%" >> $GITHUB_STEP_SUMMARY
+
+          if [ "$USAGE" -lt 80 ]; then
+            echo "☁️ enough disk space available – will upload"
+            echo "☁️ enough disk space available – will upload" >> $GITHUB_STEP_SUMMARY
+            echo "available=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "⛔ not enough disk space – skipping upload"
+            echo "⛔ not enough disk space – skipping upload" >> $GITHUB_STEP_SUMMARY
+            echo "available=false" >> "$GITHUB_OUTPUT"
+          fi
+      - name: Output URL
+        if: steps.diskspace.outputs.available == 'true'
+        shell: bash
+        run: |
+          echo "Link: https://builds.jabref.org/pull/${{ github.event.pull_request.number }}/merge"
+          echo "Link: <https://builds.jabref.org/pull/${{ github.event.pull_request.number }}/merge>" >> $GITHUB_STEP_SUMMARY
+
   build:
-    needs: [conditions]
+    needs: [conditions, disk-space-check]
     if: ${{ needs.conditions.outputs.should-build == 'true' }}
     strategy:
       fail-fast: false
@@ -238,6 +295,10 @@ jobs:
       - name: Build runtime image and installer
         shell: bash
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" :jabgui:jpackage
+      - name: Smoke test JabGui
+        shell: bash
+        run: |
+          ./gradlew :jabgui:run --args="--help"
       - name: Package JabGui application image
         shell: bash
         run: |
@@ -261,9 +322,18 @@ jobs:
           rm debian-binary control.tar.* data.tar.*
           mv -f jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}${{ matrix.suffix }}${{ matrix.archForDebianRepack }}_repackaged.deb jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}${{ matrix.suffix }}.deb
 
+      - name: Smoke test JabSrv-CLI
+        shell: bash
+        run: |
+          ./gradlew :jabsrv-cli:run --args="--help"
+
       - name: Build JabKit
         shell: bash
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" :jabkit:jpackage
+      - name: Smoke test JabKit
+        shell: bash
+        run: |
+          ./gradlew :jabkit:run --args="--help"
       - name: Package JabKit application image
         shell: bash
         run: |
@@ -273,6 +343,10 @@ jobs:
       - name: Build JabLS-CLI
         shell: bash
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" :jabls-cli:jpackage
+      - name: Smoke test JabLs-CLI
+        shell: bash
+        run: |
+          ./gradlew :jabls-cli:run --args="--help"
       - name: Package JabLS-CLI application image
         shell: bash
         run: |
@@ -281,62 +355,49 @@ jobs:
 
       # region Upload to builds.jabref.org / GitHub artifacts store
       - name: Setup SSH key
-        if: (needs.conditions.outputs.upload-to-builds-jabref-org == 'true')
+        if: ${{ needs.disk-space-check.outputs.available == 'true' }}
         run: |
           echo "${{ secrets.buildJabRefPrivateKey }}" > sshkey
           chmod 600 sshkey
-      - name: Check disk space on builds.jabref.org
-        if: (needs.conditions.outputs.upload-to-builds-jabref-org == 'true')
-        id: diskspace
-        shell: bash
-        run: |
-          USAGE=$(ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no jrrsync@build-upload.jabref.org \
-            "df --output=pcent /var/www/builds.jabref.org | tail -n1 | tr -dc '0-9'")
-          echo "Remote usage: $USAGE%"
-          if [ "$USAGE" -lt 90 ]; then
-            echo "available=true" >> "$GITHUB_OUTPUT"
-          else
-            echo "available=false" >> "$GITHUB_OUTPUT"
-          fi
       - name: Setup rsync (macOS)
-        if: ${{ (steps.diskspace.outputs.available == 'true') && (startsWith(matrix.os, 'macos') && (needs.conditions.outputs.upload-to-builds-jabref-org == 'true')) }}
+        if: ${{ (needs.disk-space-check.outputs.available == 'true') && (startsWith(matrix.os, 'macos') && (needs.conditions.outputs.upload-to-builds-jabref-org == 'true')) }}
         run: brew install rsync
       - name: Setup rsync (Windows)
-        if: ${{ (steps.diskspace.outputs.available == 'true') && (matrix.os == 'windows-latest') }}
+        if: ${{ (needs.disk-space-check.outputs.available == 'true') && (matrix.os == 'windows-latest') }}
         # We want to have rsync available at this place to avoid uploading and downloading from GitHub artifact store (taking > 5 minutes in total)
         # We cannot use "action-rsyncer", because that requires Docker which is unavailable on Windows
         # We cannot use "setup-rsync", because that does not work on Windows
         # We do not use egor-tensin/setup-cygwin@v4, because it replaces the default shell
         # We need to use v6.4.4 as v6.4.5 misses "lib\rsync\tools\bin\ssh.exe"
         run: choco install rsync --version=6.4.4
       - name: Upload jabgui to builds.jabref.org (Windows)
-        if: ${{ (steps.diskspace.outputs.available == 'true') && (matrix.os == 'windows-latest') }}
+        if: ${{ (needs.disk-space-check.outputs.available == 'true') && (matrix.os == 'windows-latest') }}
         shell: cmd
         # for rsync installed by chocolatey, we need the ssh.exe delivered with that installation
         run: |
           rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'C:\ProgramData\chocolatey\lib\rsync\tools\bin\ssh.exe -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabgui/build/packages/${{ matrix.os }}/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
       - name: Upload jabkkit to builds.jabref.org (Windows)
-        if: ${{ (steps.diskspace.outputs.available == 'true') && (matrix.os == 'windows-latest') }}
+        if: ${{ (needs.disk-space-check.outputs.available == 'true') && (matrix.os == 'windows-latest') }}
         shell: cmd
         run: |
           rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'C:\ProgramData\chocolatey\lib\rsync\tools\bin\ssh.exe -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabkit/build/packages/${{ matrix.os }}/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
       - name: Upload jabls-cli to builds.jabref.org (Windows)
-        if: ${{ (steps.diskspace.outputs.available == 'true') && (matrix.os == 'windows-latest') }}
+        if: ${{ (needs.disk-space-check.outputs.available == 'true') && (matrix.os == 'windows-latest') }}
         shell: cmd
         run: |
           rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ 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/${{ matrix.os }}/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
       - name: Upload jabgui to builds.jabref.org (linux, macOS)
-        if: ${{ (steps.diskspace.outputs.available == 'true') && ((startsWith(matrix.os, 'macos') && (needs.conditions.outputs.should-notarize != 'true')) || startsWith(matrix.os, 'ubuntu')) }}
+        if: ${{ (needs.disk-space-check.outputs.available == 'true') && ((startsWith(matrix.os, 'macos') && (needs.conditions.outputs.should-notarize != 'true')) || startsWith(matrix.os, 'ubuntu')) }}
         shell: bash
         run: |
           rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabgui/build/packages/${{ matrix.os }}/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
       - name: Upload jabkit to builds.jabref.org (linux, macOS)
-        if: ${{ (steps.diskspace.outputs.available == 'true') && (startsWith(matrix.os, 'macos') || startsWith(matrix.os, 'ubuntu')) }}
+        if: ${{ (needs.disk-space-check.outputs.available == 'true') && (startsWith(matrix.os, 'macos') || startsWith(matrix.os, 'ubuntu')) }}
         shell: bash
         run: |
           rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabkit/build/packages/${{ matrix.os }}/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
       - name: Upload jabls-cli to builds.jabref.org (linux, macOS)
-        if: ${{ (steps.diskspace.outputs.available == 'true') && (startsWith(matrix.os, 'macos') || startsWith(matrix.os, 'ubuntu')) }}
+        if: ${{ (needs.disk-space-check.outputs.available == 'true') && (startsWith(matrix.os, 'macos') || startsWith(matrix.os, 'ubuntu')) }}
         shell: bash
         run: |
           rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabls-cli/build/packages/${{ matrix.os }}/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true

.github/workflows/on-pr-labeled-update-pr-status.yml

@@ -0,0 +1,45 @@
+name: Adapt PR status
+
+on:
+  workflow_run:
+    workflows: ["On PR labeled"]
+    types: [completed]
+
+jobs:
+   apply-labels:
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      pull-requests: write
+    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" >> "$GITHUB_OUTPUT"
+          fi
+      - name: Mark PR ready for review
+        if: steps.check.outputs.continue == 'true'
+        run: |
+          LABELS=$(gh api repos/${{ github.repository }}/issues/${{ steps.check.outputs.pr_number }}/labels --jq '.[].name')
+
+          if echo "$LABELS" | grep -q "^status: ready-for-review$"; then
+            echo "✅ label ready-for-review found"
+            gh pr ready --repo ${{ github.repository }} ${{ steps.check.outputs.pr_number }}
+          else
+            echo "⊘ label ready-for-review not found"
+          fi;
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/on-pr-labeled.yml

@@ -24,3 +24,15 @@ jobs:
         env:
           PR_URL: ${{github.event.pull_request.html_url}}
           GITHUB_TOKEN: ${{secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER}}
+  upload-pr-nnumber:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      actions: write
+    steps:
+      - name: Create pr_number.txt
+        run: echo "${{ github.event.pull_request.number }}" > pr_number.txt
+      - uses: actions/upload-artifact@v5
+        with:
+          name: pr_number
+          path: pr_number.txt