Merge branch 'main' into palantir-java-format-auto

# Conflicts:
#	build.gradle

.git-blame-ignore-revs

@@ -0,0 +1,28 @@
+# Automatic code reformatting
+c5bcad738fe6e8dfcb62442a426c2778241515a1
+
+# net.sf.jabref -> org.jabref
+b2ad6eb279f5def38fa21be12cb5dd4545c1ba1a
+dd385f4ad6dc9251bfdb1c0b75ded402f680b32a
+a6e80311c6376c973b5860658f6e4ace7a3fd1f4
+648a4703e80ac0dbe1ff044f354bc0e332e4064d
+ac08c6a2c55e1600bf5072c0ea2e6aac920b915d
+ec863166cf4f38a1a6bcc80a607fd33299b815aa
+8c61577e4377746fc064db2a136bb68968cd4055
+0ef3228f0c1334ff203d4ea5e698e3ad88cb7089
+ce939b4ef19ca856e7ecac08275cf1ca764207b6
+7f1a8069d03737c202bcb7ce352b3755c6a36f5f
+dbd0cfbc8177ada414e89da038cd014657d48ed3
+bc7ea00c8cc3ec9ec8b1a799b0dd96513bc51404
+9a5cff44aa1e0d4b737296a30b97f7f384c8b885
+bf81b595a77f0f7f254872be6f05a063c44528d8
+277b40c9e79e0158d272de33e24fa7fc06af91bf
+662dd326d212ecfd336a00214e969145ec501c5a
+33f040cfbb16111ada117f858e98d606a6bee4fd
+29fe730f64eeb62ff9de10fcb460a63297e24be6
+
+# This commit should not exist
+185d7345946c29a2a4e2726c912be0c4db4810b9
+# Resulted in this problematic merge commits
+7e1645978b3028df5e65af19f0f819ddfd0f24aa
+a31f396765492ac12eaab228e33eb9d22487403b

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -12,7 +12,7 @@ body:
     attributes:
       label: JabRef version
       options:
-        - "5.11 (latest release)"
+        - "5.12 (latest release)"
         - Latest development branch build (please note build date below)
         - Other (please describe below)
       description: The version as shown in the about dialog.

.github/workflows/check-links.yml

@@ -11,7 +11,7 @@ on:
   workflow_dispatch:
 
 concurrency:
-  group: "${{ github.workflow }}-${{ github.head_ref }}"
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
   cancel-in-progress: true
 
 jobs:
@@ -29,7 +29,7 @@ jobs:
           restore-keys: cache-lychee-
       - name: Link Checker
         id: lychee
-        uses: lycheeverse/lychee-action@v1.8.0
+        uses: lycheeverse/lychee-action@v1.9.0
         with:
           fail: true
-          args: --max-concurrency 1 --cache --no-progress --exclude-all-private './**/*.md'
+          args: --accept '200,201,202,203,204,429,500' --max-concurrency 1 --cache --no-progress --exclude-all-private './**/*.md'

.github/workflows/cleanup-pr.yml

@@ -26,7 +26,7 @@ jobs:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Delete folder on builds.jabref.org
         if: steps.checksecrets.outputs.secretspresent == 'YES'
-        uses: appleboy/[email protected].0
+        uses: appleboy/[email protected].3
         with:
           script: rm -rf /var/www/builds.jabref.org/www/pull/${{ github.event.pull_request.number }} || true
           host: build-upload.jabref.org

.github/workflows/deployment-arm64.yml

@@ -22,7 +22,7 @@ env:
   JAVA_OPTS: -Xmx4g
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
   cancel-in-progress: true
 
 jobs:
@@ -59,11 +59,10 @@ jobs:
         id: gitversion
         uses: gittools/actions/gitversion/[email protected]
       - name: Setup JDK
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
       - name: Clean up keychain
         run: |
          security delete-keychain signing_temp.keychain ${{runner.temp}}/keychain/notarization.keychain || true
@@ -85,6 +84,8 @@ jobs:
           mkdir ${{runner.temp}}/keychain
           security create-keychain -p jabref ${{runner.temp}}/keychain/notarization.keychain
           security set-keychain-settings ${{runner.temp}}/keychain/notarization.keychain
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Prepare merged jars and modules dir (macOS)
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" prepareModulesDir
       - name: Build dmg (macOS)
@@ -161,7 +162,7 @@ jobs:
           rsync -Pavz --itemize-changes --stats --partial-dir=/tmp/partial --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i ~/.ssh/id_rsa' build/distribution/ [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
       - name: Upload to GitHub workflow artifacts store
         if: ${{ !startsWith(github.ref, 'refs/heads/gh-readonly-queue') }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: JabRef-${{ matrix.displayName }}
           path: build/distribution

.github/workflows/deployment.yml

@@ -31,7 +31,7 @@ env:
   JDK21: ""
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
   cancel-in-progress: true
 
 jobs:
@@ -90,11 +90,12 @@ jobs:
         id: gitversion
         uses: gittools/actions/gitversion/[email protected]
       - name: Setup JDK
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Prepare merged jars and modules dir (macOS)
         if: (matrix.os == 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'NO')
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" prepareModulesDir
@@ -219,14 +220,14 @@ 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/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' build/distribution/ [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
       - name: Upload to GitHub workflow artifacts store (macOS)
         if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (startsWith(github.ref, 'refs/tags/') || inputs.notarization == true)
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           # tbn = to-be-notarized
           name: JabRef-macOS-tbn
           path: build/distribution
       - name: Upload to GitHub workflow artifacts store
         if: (steps.checksecrets.outputs.secretspresent != 'YES')
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           # tbn = to-be-notarized
           name: JabRef-${{ matrix.os }}

.github/workflows/gource.yml

@@ -64,7 +64,7 @@ jobs:
         run: |
           mv gource/gource.mp4 gource-videos/jabref-complete.mp4
       - name: 'Upload gource video'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: Gource
           path: gource-videos/

.github/workflows/pages.yml

@@ -39,13 +39,13 @@ jobs:
           working-directory: docs/
       - name: Setup Pages
         id: pages
-        uses: actions/configure-pages@v3
+        uses: actions/configure-pages@v4
       - name: Build with Jekyll
         run: |
           cd docs
           bundle exec jekyll build
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v2
+        uses: actions/upload-pages-artifact@v3
         with:
           path: docs/_site/
 
@@ -59,4 +59,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v2
+        uses: actions/deploy-pages@v4

.github/workflows/refresh-csl-subtrees.yml

@@ -31,6 +31,11 @@ jobs:
           cd src/main/resources/csl-locales
           git checkout master
           git pull
+      - name: Persist changes
+        run: |
+          git add -f src/main/resources/csl-styles
+          git add -f src/main/resources/csl-locales
+          git diff-index --quiet HEAD || git commit -m 'Update CSL styles'
       - uses: peter-evans/create-pull-request@v5
         with:
           token: ${{ secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER }}

.github/workflows/refresh-journal-lists.yml

@@ -28,14 +28,19 @@ jobs:
           git checkout main
           git pull
       - name: Set up JDK
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Check whether journal-list.mv can be generated (the "real" generation is done inside JabRef's build process)
         run: |
           ./gradlew generateJournalListMV
+      - name: Persist changes
+        run: |
+          git add -f buildres/abbrv.jabref.org
+          git diff-index --quiet HEAD || git commit -m 'Update journal abbreviation lists'
       - uses: peter-evans/create-pull-request@v5
         with:
           token: ${{ secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER }}

.github/workflows/tests-fetchers.yml

@@ -29,7 +29,7 @@ env:
   BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey_FOR_TESTS}}
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
   cancel-in-progress: true
 
 permissions:
@@ -46,11 +46,12 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Set up JDK
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run fetcher tests
         run: ./gradlew fetcherTest
         env: