Merge branch 'main' into fix-for-issue-10423

u7492883 · Dec 26, 2023 · 8e3eb37 · 8e3eb37
2 parents cd6d630 + 6f84663
commit 8e3eb37
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.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.

diff --git a/.github/heylogs.java b/.github/heylogs.java
diff --git a/.github/workflows/check-links.yaml b/.github/workflows/check-links.yaml
diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml
@@ -0,0 +1,35 @@
+name: Check external href links in the documentation
+
+on:
+  push:
+    paths:
+      - '.github/workflows/check-links.yml'
+      - '**/*.md'
+  schedule:
+    # Run on the first of each month at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07)
+    - cron: "0 9 1 * *"
+  workflow_dispatch:
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
+  cancel-in-progress: true
+
+jobs:
+  lychee:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          show-progress: 'false'
+      - name: Restore lychee cache
+        uses: actions/cache@v3
+        with:
+          path: .lycheecache
+          key: cache-lychee-${{ github.sha }}
+          restore-keys: cache-lychee-
+      - name: Link Checker
+        id: lychee
+        uses: lycheeverse/[email protected]
+        with:
+          fail: true
+          args: --max-concurrency 1 --cache --no-progress --exclude-all-private './**/*.md'
diff --git a/.github/workflows/cleanup_pr.yml → .github/workflows/cleanup-pr.yml b/.github/workflows/cleanup_pr.yml → .github/workflows/cleanup-pr.yml
diff --git a/.github/workflows/deployment-arm64.yml b/.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
diff --git a/.github/workflows/deployment.yml b/.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 }}

diff --git a/.github/workflows/gource.yml b/.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/

diff --git a/.github/workflows/pages.yml b/.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
diff --git a/.github/workflows/refresh-journal-lists.yml b/.github/workflows/refresh-journal-lists.yml
@@ -28,11 +28,12 @@ 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

diff --git a/.github/workflows/tests-fetchers.yml b/.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: