Merge branch 'main' into JUnit5BestPractices

.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:

.github/workflows/tests.yml

@@ -18,7 +18,7 @@ env:
   JAVA_OPTS: -Xmx4g
 
 concurrency:
-  group: tests-${{ github.head_ref }}
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
   cancel-in-progress: true
 
 permissions:
@@ -35,18 +35,19 @@ 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: Run checkstyle reporter
         uses: nikitasavinov/checkstyle-action@master
         with:
           reporter: github-pr-review
           github_token: ${{ secrets.GITHUB_TOKEN }}
           checkstyle_config: 'config/checkstyle/checkstyle_reviewdog.xml'
           checkstyle_version: '10.3'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run checkstyle using gradle
         run: ./gradlew checkstyleMain checkstyleTest checkstyleJmh
   openrewrite:
@@ -59,11 +60,12 @@ 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 OpenRewrite
         run: |
           ./gradlew rewriteDryRun
@@ -77,11 +79,12 @@ 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 modernizer
         run: |
           # enable failing of this task if modernizer complains
@@ -97,7 +100,7 @@ jobs:
           submodules: 'false'
           show-progress: 'false'
       - name: markdownlint-cli2-action
-        uses: DavidAnson/markdownlint-cli2-action@v13
+        uses: DavidAnson/markdownlint-cli2-action@v14
         with:
           globs: |
             *.md
@@ -158,11 +161,12 @@ 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 tests
         run: xvfb-run --auto-servernum ./gradlew check -x checkstyleJmh -x checkstyleMain -x checkstyleTest -x modernizer
         env:
@@ -193,11 +197,12 @@ 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 tests on PostgreSQL
         run: ./gradlew databaseTest --rerun-tasks
         env:
@@ -230,11 +235,12 @@ 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 GUI tests
         run: xvfb-run --auto-servernum ./gradlew guiTest
         env:
@@ -274,11 +280,12 @@ jobs:
           show-progress: 'false'
       - name: Set up JDK
         if: github.ref == 'refs/heads/main'
-        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: Update test coverage metrics
         if: (github.ref == 'refs/heads/main') && (steps.checksecrets.outputs.secretspresent == 'YES')
         run: xvfb-run --auto-servernum ./gradlew jacocoTestReport

.github/workflows/update-gradle-wrapper.yml

@@ -8,9 +8,14 @@ on:
 jobs:
   update-gradle-wrapper:
     runs-on: ubuntu-latest
-
+   
     steps:
       - uses: actions/checkout@v4
+      - name: Setup JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: 21.0.1
+          distribution: 'liberica'
 
       - name: Update Gradle Wrapper
         uses: gradle-update/update-gradle-wrapper-action@v1

.gitmodules

@@ -1,9 +1,15 @@
-[submodule "buildres/abbrv.jabref.org"]
+[submodule "abbrv.jabref.org"]
   path = buildres/abbrv.jabref.org
   url = https://github.com/JabRef/abbrv.jabref.org.git
-[submodule "buildres/csl-styles"]
+  ignore = all
+  shallow = true
+[submodule "csl-styles"]
   path = src/main/resources/csl-styles
   url = https://github.com/citation-style-language/styles.git
-[submodule "buildres/csl-locales"]
+  ignore = all
+  shallow = true
+[submodule "csl-locales"]
   path = src/main/resources/csl-locales
   url = https://github.com/citation-style-language/locales.git
+  ignore = all
+  shallow = true

.lycheeignore

@@ -2,6 +2,7 @@ https://arxiv.org/
 https://contribute.jabref.org/
 https://donations.jabref.org/
 https://pubs.acs.org/
+https://scholar.archive.org/
 https://web.archive.org/
 https://www.researchgate.net/privacy-policy
 https://www.sciencedirect.com/