Merge branch 'configurable_external_search_features' of https://github.com/brandon-lau0/jabref into configurable_external_search_features

Author: brandon-lau0

.github/ghprcomment.yml

@@ -141,32 +141,16 @@
   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).
-- jobName: 'Issue number present'
+- jobName: 'Determine issue number'
   always: true
   message: |
-    Your pull request needs to link an issue.
+    Your pull request needs to link an issue correctly.
 
     To ease organizational workflows, please link this pull-request to the issue with syntax as described in <https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue>:
 
     > <h2 id="linking-a-pull-request-to-an-issue-using-a-keyword">Linking a pull request to an issue using a keyword</h2>
     > <p>You can link a pull request to an issue by using a supported keyword
-    > in the pull request's description or in a commit message. The pull
-    > request <strong>must be</strong> on the default branch.</p>
-    > <ul>
-    > <li>close</li>
-    > <li>closes</li>
-    > <li>closed</li>
-    > <li>fix</li>
-    > <li>fixes</li>
-    > <li>fixed</li>
-    > <li>resolve</li>
-    > <li>resolves</li>
-    > <li>resolved</li>
-    > </ul>
-    > <p>If you use a keyword to reference a pull request comment in another
-    > pull request, the pull requests will be linked. Merging the referencing
-    > pull request also closes the referenced pull request.</p>
-    > <p>The syntax for closing keywords depends on whether the issue is in the same repository as the pull request.</p>
+    > in the pull request's description or in a commit message.
 
     ### Examples
 

.github/workflows/binaries-ea.yml

@@ -360,6 +360,10 @@ jobs:
           --resource-dir buildres/mac \
           --file-associations buildres/mac/bibtexAssociations.properties \
           --jlink-options --bind-services \
+          --java-options -XX:+UnlockExperimentalVMOptions \
+          --java-options -XX:+UseCompactObjectHeaders \
+          --java-options -XX:+UseZGC --java-options -XX:+ZUncommit \
+          --java-options -XX:+UseStringDeduplication \
           --java-options --add-exports=javafx.base/com.sun.javafx.event=org.jabref.merged.module \
           --java-options --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module \
           --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref.merged.module \

.github/workflows/binaries.yml

@@ -259,6 +259,10 @@ jobs:
           --resource-dir buildres/mac \
           --file-associations buildres/mac/bibtexAssociations.properties \
           --jlink-options --bind-services \
+          --java-options -XX:+UnlockExperimentalVMOptions \
+          --java-options -XX:+UseCompactObjectHeaders \
+          --java-options -XX:+UseZGC --java-options -XX:+ZUncommit \
+          --java-options -XX:+UseStringDeduplication \
           --java-options --add-exports=javafx.base/com.sun.javafx.event=org.jabref.merged.module \
           --java-options --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module \
           --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref.merged.module \

.github/workflows/cleanup-pr.yml

@@ -6,40 +6,53 @@ on:
 
 jobs:
   cleanup:
-    if: github.repository == 'JabRef/jabref'
+    if: github.event.pull_request.head.repo.full_name == 'JabRef/jabref'
     runs-on: ubuntu-latest
     permissions:
       contents: read
       packages: write
     steps:
-      - name: Cancel deployment run
+      - name: Cancel workflow "binaries" run
         uses: styfle/cancel-workflow-action@0.12.1
         with:
           ignore_sha: true
-          workflow_id: 9813 # workflow "Deployment"
-      - name: Check secrets presence
-        id: checksecrets
-        shell: bash
+          workflow_id: 9160969135
+      - name: Cancel workflow "binaries (ea)" run
+        uses: styfle/cancel-workflow-action@0.12.1
+        with:
+          ignore_sha: true
+          workflow_id: 160969125
+      - name: "Check for 'dev: binaries' label"
+        id: check_label
         run: |
-          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
-            echo "secretspresent=NO" >> $GITHUB_OUTPUT
-            echo "❌ Secret BUILDJABREFPRIVATEKEY not present"
+          labels=$(gh pr view ${{ github.event.pull_request.number }} --json labels -q '.labels[].name')
+          if echo "$labels" | grep -Fxq "dev: binaries"; then
+            echo "has_label_binaries=yes" >> $GITHUB_OUTPUT
           else
-            echo "secretspresent=YES" >> $GITHUB_OUTPUT
-            echo "✔️ Secret BUILDJABREFPRIVATEKEY present"
+            echo "has_label_binaries=no" >> $GITHUB_OUTPUT
           fi
         env:
-          BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - name: Delete folder on builds.jabref.org
-        if: steps.checksecrets.outputs.secretspresent == 'YES'
+        if: steps.check_label.outputs.has_label_binaries == 'yes'
         uses: appleboy/ssh-action@v1.2.2
         with:
           script: rm -rf /var/www/builds.jabref.org/www/pull/${{ github.event.pull_request.number }} || true
           host: build-upload.jabref.org
           port: 9922
           username: jrrsync
           key: ${{ secrets.buildJabRefPrivateKey }}
+      - name: Get changed docker files
+        # in line with dockerimages.yml -> lines 6 and 7
+        id: changed-docker-files
+        uses: tj-actions/changed-files@ed68ef82c095e0d48ec87eccea555d944a631a4c # v46
+        with:
+          # Avoid using single or double quotes for multiline patterns
+          files: |
+            .github/workflows/dockerimages.yml
+            Dockerfile.*
       - name: Remove Docker Tag
+        if: steps.changed-docker-files.outputs.any_changed == 'true'
         # A separate action is needed to delete a tag - see https://github.com/orgs/community/discussions/26267
         uses: rafalkk/remove-dockertag-action@v1
         with:

.github/workflows/dockerimages.yml

@@ -38,6 +38,9 @@ jobs:
             type=edge,branch=main
             type=ref,event=pr
       - name: Login to GitHub Container Registry
+        if: >
+          (github.event_name == 'push' && github.repository == 'JabRef/jabref') || 
+          (github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == 'JabRef/jabref')
         uses: docker/login-action@v3
         with:
           registry: ghcr.io
@@ -50,7 +53,11 @@ jobs:
       - name: Build and push
         uses: docker/build-push-action@v6
         with:
-          push: ${{ github.repository == 'JabRef/jabref' }}
+          push: >
+            ${{ 
+              (github.event_name == 'push' && github.repository == 'JabRef/jabref') || 
+              (github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == 'JabRef/jabref')
+            }}
           platforms: linux/amd64
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}

.github/workflows/merge-upstream.yml

@@ -0,0 +1,20 @@
+name: Sync fork with upstream
+
+on:
+  pull_request:
+    types: [ opened ]
+  schedule:
+    - cron: "0 6 * * *"
+  workflow_dispatch:
+
+jobs:
+  sync-fork:
+    if: ${{ github.repository != 'JabRef/jabref' }}
+    runs-on: ubuntu-latest
+    permissions:
+      actions: write
+      contents: write
+    steps:
+      - uses: thiagokokada/merge-upstream@v1.0.2
+        with:
+          branch: main

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

@@ -6,13 +6,27 @@ on:
        - unassigned
 
 jobs:
-  ensure_column:
+  columns_and_labels:
     if: ${{ github.repository_owner == 'JabRef' }}
     runs-on: ubuntu-latest
     permissions:
       issues: write
+      contents: read
     steps:
+      - name: Check assignees
+        id: check_assignee
+        run: |
+          issue=$(gh issue view ${{ github.event.issue.number }} --json assignees)
+          count=$(echo "$issue" | jq '.assignees | length')
+          if [ "$count" -gt 0 ]; then
+            echo "assigned=yes" >> $GITHUB_OUTPUT
+          else
+            echo "assigned=no" >> $GITHUB_OUTPUT
+          fi
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - name: Move Issue to "Free to take" Column in "Candidates for University Projects"
+        if: steps.check_assignee.outputs.assigned == 'no'
         uses: m7kvqbe1/github-action-move-issues@main
         with:
           github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
@@ -23,6 +37,7 @@ jobs:
           default-column: "Free to take"
           skip-if-not-in-project: true
       - name: Move Issue to "Free to take" Column in "Good First Issues"
+        if: steps.check_assignee.outputs.assigned == 'no'
         uses: m7kvqbe1/github-action-move-issues@main
         with:
           github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
@@ -32,19 +47,16 @@ jobs:
           ignored-columns: ""
           default-column: "Free to take"
           skip-if-not-in-project: true
-  remove_labels:
-    if: ${{ github.repository_owner == 'JabRef' }}
-    runs-on: ubuntu-latest
-    permissions:
-      issues: write
-      contents: read
-    steps:
       - uses: actions/checkout@v4
-      - name: Remove assigned label
-        run: gh issue edit ${{ github.event.issue.number }} --remove-label "📍 Assigned"
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - name: Remove FirstTimeCodeContribution label
-        run: gh issue edit ${{ github.event.issue.number }} --remove-label "FirstTimeCodeContribution"
+        if: steps.check_assignee.outputs.assigned == 'no'
+      - name: Remove labels assigned, reminder-sent, pinned, and "FirstTimeCodeContribution"
+        if: steps.check_assignee.outputs.assigned == 'no'
+        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/on-pr-closed.yml

@@ -86,17 +86,9 @@ jobs:
           gh issue edit ${{ needs.determine_issue_number.outputs.issue_number }} --remove-label "FirstTimeCodeContribution"
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - name: Remove label pinned (to enable automated pinging and unassignment with a message)
-        if: steps.check_assignee.outputs.assigned == 'yes'
-        run: |
-          set -e
-
-          gh issue edit ${{ needs.determine_issue_number.outputs.issue_number }} --remove-label "📌 Pinned"
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - name: Move issue to "Free to take" in "Good First Issues"
         if: steps.check_assignee.outputs.assigned == 'no'
-        uses: m7kvqbe1/github-action-move-issues/@add-issue-parameter
+        uses: m7kvqbe1/github-action-move-issues/@main
         with:
           github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
           project-url: "https://github.com/orgs/JabRef/projects/5"
@@ -108,7 +100,7 @@ jobs:
           skip-if-not-in-project: true
       - name: Move issue to "Free to take" in "Candidates for University Projects"
         if: steps.check_assignee.outputs.assigned == 'no'
-        uses: m7kvqbe1/github-action-move-issues/@add-issue-parameter
+        uses: m7kvqbe1/github-action-move-issues/@main
         with:
           github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
           project-url: "https://github.com/orgs/JabRef/projects/3"

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

@@ -42,7 +42,7 @@ jobs:
           titleRegex: '^#(?<ticketNumber>\d+)'
           branchRegex: '^(?<ticketNumber>\d+)'
           # Matches GitHub's closes/fixes/resolves #{number}, but does not match our example `Closes #12345` in PULL_REQUEST_TEMPLATE
-          bodyRegex: '(?<action>fixes|closes|resolves)\s+(?:https?:\/\/github\.com\/JabRef\/jabref\/issues\/)?#?(?<ticketNumber>(?!12345\b)\d+)'
+          bodyRegex: '(?<action>fixes|closes|resolves|refs)\s+(?:https?:\/\/github\.com\/JabRef\/jabref\/issues\/)?#?(?<ticketNumber>(?!12345\b)\d+)'
           bodyRegexFlags: 'i'
           outputOnly: true
       - run: echo "${{ steps.get_issue_number.outputs.ticketNumber }}"
@@ -52,6 +52,7 @@ jobs:
           echo "No valid ticket number found!"
           exit 1
   move_issue:
+    if: github.repository_owner == 'JabRef'
     name: Mark issue as in progress
     # after determine_issue_number to ensure that there is only one failure because of no ticket number
     needs: determine_issue_number
@@ -60,7 +61,7 @@ jobs:
       issues: write
     steps:
       - name: Move issue to "In Progress" in "Good First Issues"
-        uses: m7kvqbe1/github-action-move-issues/@add-issue-parameter
+        uses: m7kvqbe1/github-action-move-issues/@main
         with:
           github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
           project-url: "https://github.com/orgs/JabRef/projects/5"
@@ -71,7 +72,7 @@ jobs:
           issue-number: ${{ needs.determine_issue_number.outputs.issue_number }}
           skip-if-not-in-project: true
       - name: Move issue to "In Progress" in "Candidates for University Projects"
-        uses: m7kvqbe1/github-action-move-issues/@add-issue-parameter
+        uses: m7kvqbe1/github-action-move-issues/@main
         with:
           github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
           project-url: "https://github.com/orgs/JabRef/projects/3"
@@ -82,6 +83,7 @@ jobs:
           issue-number: ${{ needs.determine_issue_number.outputs.issue_number }}
           skip-if-not-in-project: true
   ensure_assignment:
+    if: github.repository_owner == 'JabRef'
     name: Ensure that contributor is assigned (fails if not commented on issue)
     # after determine_issue_number to ensure that there is only one failure because of no ticket number
     needs: determine_issue_number
@@ -141,6 +143,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   upload-pr-number:
+    if: ${{ github.repository == 'JabRef/jabref' }}
     runs-on: ubuntu-latest
     steps:
       - name: Create pr_number.txt

.github/workflows/unassign-issues.yml

@@ -7,7 +7,7 @@ on:
 
 jobs:
   unassign_issues:
-    if: github.repository == 'JabRef/jabref'
+    if: github.repository_owner == 'JabRef'
     runs-on: ubuntu-latest
     permissions:
       issues: write
@@ -65,7 +65,7 @@ jobs:
         issue_number: ${{ fromJson(needs.unassign_issues.outputs.unassigned_issues) }}
     steps:
       - name: Move issue to "Free to take" in "Good First Issues"
-        uses: m7kvqbe1/github-action-move-issues/@add-issue-parameter
+        uses: m7kvqbe1/github-action-move-issues/@main
         with:
           github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
           project-url: "https://github.com/orgs/JabRef/projects/5"
@@ -76,7 +76,7 @@ jobs:
           issue-number: ${{ matrix.issue_number }}
           skip-if-not-in-project: true
       - name: Move issue to "Free to take" in "Candidates for University Projects"
-        uses: m7kvqbe1/github-action-move-issues/@add-issue-parameter
+        uses: m7kvqbe1/github-action-move-issues/@main
         with:
           github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
           project-url: "https://github.com/orgs/JabRef/projects/3"