Merge branch 'fix-issue-11937' of https://github.com/tejjgv/jabref into fix-issue-11937

Author: tejjgv

.github/workflows/cleanup-pr.yml

@@ -36,7 +36,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - name: Delete folder on builds.jabref.org
         if: steps.check_label.outputs.has_label_binaries == 'yes'
-        uses: appleboy/ssh-action@v1.2.2
+        uses: appleboy/ssh-action@v1.2.3
         with:
           script: rm -rf /var/www/builds.jabref.org/www/pull/${{ github.event.pull_request.number }} || true
           host: build-upload.jabref.org

.github/workflows/on-pr-changes-requested-move-labels.yml

@@ -10,9 +10,9 @@ jobs:
     if: ${{ github.event.workflow_run.conclusion == 'success' }}
     runs-on: ubuntu-latest
     permissions:
-      issues: write
       actions: read
       contents: read
+      pull-requests: write
     steps:
       - name: Download artifact from triggering run
         uses: actions/download-artifact@v6

.github/workflows/on-pr-opened-updated.yml renamed to .github/workflows/on-pr-opened-updated-check.yml

@@ -1,4 +1,4 @@
-name: On PR opened/updated
+name: On PR opened/updated (Check)
 
 on:
   # _target is required
@@ -10,6 +10,9 @@ jobs:
     if: github.repository == 'JabRef/jabref'
     name: Conflicts with target branch
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      actions: write
     steps:
       - uses: actions/checkout@v5
         with:

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

@@ -2,17 +2,17 @@ name: On PR opened/updated (Labels)
 
 on:
   workflow_run:
-    workflows: ["On PR opened/updated"]
+    workflows: ["On PR opened/updated (Check)"]
     types: [completed]
 
 jobs:
    apply-labels:
     if: ${{ github.event.workflow_run.conclusion == 'success' }}
     runs-on: ubuntu-latest
     permissions:
-      issues: write
       actions: read
       contents: read
+      pull-requests: write
     steps:
       - name: Download artifact from triggering run
         uses: actions/download-artifact@v6

.github/workflows/tests-code.yml

@@ -92,7 +92,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v5
         with:
-          java-version: 24
+          java-version: 25
           distribution: 'corretto'
           check-latest: true
       - name: Setup Gradle
@@ -206,17 +206,24 @@ jobs:
       - name: Lint CHANGELOG.md
         run: |
           # run heylogs verification
-          jbang com.github.nbbrd.heylogs:heylogs-cli:0.11.1:bin check CHANGELOG.md > heylogs.txt || true
+          jbang com.github.nbbrd.heylogs:heylogs-cli:0.14.1:bin check CHANGELOG.md > heylogs.txt || true
 
-          # improve output
-          sed -i 's/all-h2-contain-a-version/all-h2-contain-a-version (ignored)/' heylogs.txt
+          # ignore some errors
+          grep -v no-empty-headings < heylogs.txt | grep -v all-h2-contain-a-version | tee heylogs.txt
 
-          cat heylogs.txt
+          # exit 1 in case of an error
+          remaining=$(
+              grep -E " error " heylogx.txt \
+              | wc -l
+            )
 
-          # exit 1 in case of error
-          # We have 1 "valid" issue in CHANGELOG.md
-          grep -q "1 problem" heylogs.txt || exit 1
+          echo "Remaining errors: $remaining"
 
+          # We have on acceptable error
+          if [ "$remaining" -gt 1 ]; then
+            echo "Failing because of $remaining remaining error(s)."
+            exit 1
+          fi
   changelog-unreleased-only:
     if: github.event_name == 'pull_request'
     name: CHANGELOG.md - only unreleased touched
@@ -462,6 +469,7 @@ jobs:
         run: |
           echo "cache_key=jbang-$(date +%F)" >> $GITHUB_OUTPUT
       - name: Use cache
+        if: steps.changed-jablib-files.outputs.any_changed != 'true'
         uses: actions/cache@v4
         with:
           path: ~/.jbang
@@ -473,17 +481,17 @@ jobs:
         uses: jbangdev/setup-jbang@main
 
       # Build all JBang scripts
-      - run: jbang build .jbang/CheckoutPR.java
-        if: steps.changed-jablib-files.outputs.any_changed != 'true'
-      - run: jbang build .jbang/CloneJabRef.java
-        if: steps.changed-jablib-files.outputs.any_changed != 'true'
-      - run: jbang build --fresh .jbang/JabKitLauncher.java
-        if: steps.changed-jablib-files.outputs.any_changed != 'true'
-      - run: jbang build --fresh .jbang/JabLsLauncher.java
-        if: steps.changed-jablib-files.outputs.any_changed != 'true'
-      - run: jbang build --fresh .jbang/JabSrvLauncher.java
+      - run: |
+          for f in .jbang/*.java; do
+            echo "Building $f..."
+            jbang build --fresh "$f"
+          done
         if: steps.changed-jablib-files.outputs.any_changed != 'true'
-      - run: jbang build --fresh jablib-examples/*.java
+      - run: |
+          for f in jablib-examples/*.java; do
+            echo "Building $f..."
+            jbang build --fresh "$f"
+          done
         if: steps.changed-jablib-files.outputs.any_changed != 'true'
 
       # *Launcher.java should support "--help"
@@ -515,6 +523,7 @@ jobs:
         with:
           files: |
             .jbang/*.java
+            jabkit/src/main/java/**/*.java
             jablib/src/main/java/**/*.java
             jablib-examples/**/*.java
           files_ignore: |
@@ -546,7 +555,20 @@ jobs:
           # We modify the JBang scripts directly to avoid issues with relative paths
           for f in ${{ steps.changed-jablib-files.outputs.all_changed_files }}; do
             case "$f" in
-              jablib-examples/*) continue ;; # skip scripts
+              .jbang/*)
+                # skip scripts
+                continue
+                ;;
+              jablib-examples/*)
+                # skip scripts
+                continue
+                ;;
+              jabkit/*)
+                # only JabKit needs its modified sources if jabkit was modified
+                if [ "${{ matrix.script }}" != ".jbang/JabKitLauncher.java" ]; then
+                  continue
+                fi
+                ;;
             esac
             echo "//SOURCES ../$f" >> "${{ matrix.script }}"
           done

.gitignore

@@ -16,7 +16,7 @@ jablib/src/main/resources/csl-locales
 
 javafx/
 
-# genreated by gg.cmd
+# generated by gg.cmd
 m2
 gg.cmd
 

.jbang/JabKitLauncher.java

@@ -5,20 +5,21 @@
 //JAVA 24
 //RUNTIME_OPTIONS --enable-native-access=ALL-UNNAMED
 
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/converter/CygWinPathConverter.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/ArgumentProcessor.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/CheckConsistency.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/CheckIntegrity.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/Convert.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/Fetch.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/GenerateBibFromAux.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/GenerateCitationKeys.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/Pdf.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/PdfUpdate.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/Preferences.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/Pseudonymize.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/Search.java
-//SOURCES ../jabkit/src/main/java/org/jabref/JabKit.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/converter/CygWinPathConverter.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/ArgumentProcessor.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/CheckConsistency.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/CheckIntegrity.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/Convert.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/DoiToBibtex.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/Fetch.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/GenerateBibFromAux.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/GenerateCitationKeys.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/Pdf.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/PdfUpdate.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/Preferences.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/Pseudonymize.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/Search.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/JabKit.java
 //FILES tinylog.properties=../jabkit/src/main/resources/tinylog.properties
 
 // REPOS mavencentral,snapshots=https://central.sonatype.com/repository/maven-snapshots/
@@ -38,11 +39,9 @@
 //DEPS info.picocli:picocli:4.7.7
 //DEPS com.github.ben-manes.caffeine:caffeine:3.2.3
 
-import org.jabref.JabKit;
-
 /// This class is required for [jbang](https://www.jbang.dev/)
 public class JabKitLauncher {
     public static void main(String[] args) {
-        org.jabref.JabKit.main(args);
+        org.jabref.toolkit.JabKit.main(args);
     }
 }

.jbang/JabLsLauncher.java

@@ -23,6 +23,7 @@
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/LspRangeUtil.java
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/DefinitionProvider.java
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/DefinitionProviderFactory.java
+//SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/LatexDefinitionProvider.java
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/MarkdownDefinitionProvider.java
 
 // REPOS mavencentral,snapshots=https://central.sonatype.com/repository/maven-snapshots/

CHANGELOG.md

@@ -13,10 +13,13 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 - We added "IEEE" as another option for parsing plain text citations. [#14233](github.com/JabRef/jabref/pull/14233)
 - We added automatic date-based groups that create year/month/day subgroups from an entry’s date fields. [#10822](https://github.com/JabRef/jabref/issues/10822)
+- We added `doi-to-bibtex` to `JabKit`. [#14244](https://github.com/JabRef/jabref/pull/14244)
 
 ### Changed
 
-- Changed: <kbd>Ctrl</kbd> + <kbd>Shift</kbd> + <kbd>L</kbd> now opens the terminal in the active library directory (#14130)
+- We separated the "Clean up entries" dialog into three tabs for clarity [#13819](https://github.com/JabRef/jabref/issues/13819)
+- `JabKit`: `--porcelain` does not output any logs to the console anymore. [#14244](https://github.com/JabRef/jabref/pull/14244)
+- <kbd>Ctrl</kbd> + <kbd>Shift</kbd> + <kbd>L</kbd> now opens the terminal in the active library directory. [#14130](https://github.com/JabRef/jabref/issues/14130)
 
 ### Fixed
 

build-logic/build.gradle.kts

@@ -13,7 +13,7 @@ dependencies {
     implementation("org.gradlex:extra-java-module-info:1.13.1")
     implementation("org.gradlex:java-module-dependencies:1.11")
     implementation("org.gradlex:java-module-packaging:1.1") // required for platform-specific packaging of JavaFX dependencies
-    implementation("org.gradlex:java-module-testing:1.7")
+    implementation("org.gradlex:java-module-testing:1.8")
     implementation("org.gradlex:jvm-dependency-conflict-resolution:2.4")
     implementation("org.gradle.toolchains:foojay-resolver:1.0.0")
 }