Merge remote-tracking branch 'upstream/main' into addcustomjdbc

* upstream/main:
  Update latex citations status in JavaFx thread (#11302)
  Remove EnglishStemAnalyzer and use EnglishAnalyzer (#11301)
  Fix comment (#11299)
  Try gradle build speedup (#11300)
  Remove obsolete step (#11295)
  Bump com.fasterxml.jackson.dataformat:jackson-dataformat-yaml (#11290)
  Remove outdated pdf indexed files from Lucene index (#11293)
  Bump src/main/resources/csl-styles from `5338902` to `434df0a` (#11292)
  Bump org.mockito:mockito-core from 5.11.0 to 5.12.0 (#11291)
  Bump com.fasterxml.jackson.datatype:jackson-datatype-jsr310 (#11289)
  Bump com.dlsc.gemsfx:gemsfx from 2.12.0 to 2.16.0 (#11287)
  Bump org.openrewrite.recipe:rewrite-recipe-bom from 2.9.0 to 2.11.0 (#11288)
  Introduce formatter to remove word-enclosing braces (#11253)
  Try parallel tests (#9797)
  Store preview divider pos in entry editor (#11285)

CHANGELOG.md

@@ -16,6 +16,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added value selection (such as for month) for content selectors in custom entry types. [#11109](https://github.com/JabRef/jabref/issues/11109)
 - We added a duplicate checker for the Citation Relations tab. [#10414](https://github.com/JabRef/jabref/issues/10414)
 - We added tooltip on main table cells that shows cell content or cell content and entry preview if set in preferences. [10925](https://github.com/JabRef/jabref/issues/10925)
+- Added a formatter to remove word enclosing braces. [#11222](https://github.com/JabRef/jabref/issues/11222)
 - We added the ability to add a keyword/crossref when typing the separator character (e.g., comma) in the keywords/crossref fields. [#11178](https://github.com/JabRef/jabref/issues/11178)
 - We added an exporter and improved the importer for Endnote XML format. [#11137](https://github.com/JabRef/jabref/issues/11137)
 - We added support for automatically update LaTeX citations when a LaTeX file is created, removed, or modified. [#10585](https://github.com/JabRef/jabref/issues/10585)
@@ -38,6 +39,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where drag and dropping entries created a shallow copy. [#11160](https://github.com/JabRef/jabref/issues/11160)
 - We fixed an issue where imports to a custom group would only work for the first entry [#11085](https://github.com/JabRef/jabref/issues/11085), [#11269](https://github.com/JabRef/jabref/issues/11269)
 - We fixed an issue where a new entry was not added to the selected group [#8933](https://github.com/JabRef/jabref/issues/8933)
+- We fixed an issue where the horizontal position of the Entry Preview inside the entry editor was not remembered across restarts [#11281](https://github.com/JabRef/jabref/issues/11281)
 
 ### Removed
 

build.gradle

@@ -184,8 +184,8 @@ dependencies {
 
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.9.0.202403050737-r'
 
-    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.17.0'
-    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.17.0'
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.17.1'
+    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.17.1'
 
     implementation 'com.fasterxml:aalto-xml:1.3.2'
 
@@ -222,7 +222,7 @@ dependencies {
     }
     implementation 'org.fxmisc.flowless:flowless:0.7.2'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.2'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.12.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.16.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude module: 'commons-lang3'
         exclude group: 'org.openjfx'
@@ -306,7 +306,7 @@ dependencies {
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.2'
 
-    testImplementation 'org.mockito:mockito-core:5.11.0'
+    testImplementation 'org.mockito:mockito-core:5.12.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.10.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.10.0'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.3.0'
@@ -320,7 +320,7 @@ dependencies {
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'
 
-    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.9.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.11.0"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")
@@ -428,6 +428,9 @@ tasks.register('generateCitaviSource', XjcTask) {
 
 tasks.withType(JavaCompile).configureEach {
     options.encoding = 'UTF-8'
+
+    // hint by https://docs.gradle.org/current/userguide/performance.html#run_the_compiler_as_a_separate_process
+    options.fork = true
 }
 
 compileJava {
@@ -529,16 +532,32 @@ testlogger {
     showStackTraces false
 }
 
+tasks.withType(Test) {
+    reports.html.outputLocation.set(file("${reporting.baseDir}/${name}"))
+    // Enable parallel tests. See https://docs.gradle.org/8.1/userguide/performance.html#execute_tests_in_parallel for details.
+    maxParallelForks = Runtime.runtime.availableProcessors() - 1
+}
+
 tasks.register('databaseTest', Test) {
     useJUnitPlatform {
         includeTags 'DatabaseTest'
     }
+
+    testLogging {
+        // set options for log level LIFECYCLE
+        events = ["FAILED"]
+        exceptionFormat "full"
+    }
+
+    maxParallelForks = 1
 }
 
 tasks.register('fetcherTest', Test) {
     useJUnitPlatform {
         includeTags 'FetcherTest'
     }
+
+    maxParallelForks = 1
 }
 
 tasks.register('guiTest', Test) {
@@ -551,6 +570,8 @@ tasks.register('guiTest', Test) {
         events = ["FAILED"]
         exceptionFormat "full"
     }
+
+    maxParallelForks = 1
 }
 
 // Test result tasks
@@ -560,10 +581,6 @@ tasks.register('copyTestResources', Copy) {
 }
 processTestResources.dependsOn copyTestResources
 
-tasks.withType(Test) {
-    reports.html.outputLocation.set(file("${reporting.baseDir}/${name}"))
-}
-
 tasks.register('jacocoPrepare') {
     doFirst {
         // Ignore failures of tests

docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.md

@@ -32,12 +32,6 @@ After clicking "Download", IntelliJ installs Eclipse Temurin:
 ![IntelliJ installs Eclipse Temurin](guidelines-intellij-installs-temurin.png)
 {% endfigure %}
 
-Open the module settings: Right click on "JabRef" and select "Open Module Settings":
-
-{% figure caption:"Open IntelliJ Module Settings" %}
-![IntelliJ Module Settings](guidelines-intellij-open-module-settings.png)
-{% endfigure %}
-
 Navigate to **Project Settings > Project** and ensure that the projects' SDK is Java 21.
 
 {% figure caption:"Project SDK is pinned to the downloaded SDK (showing JDK 21 as example)" %}

gradle.properties

@@ -1,2 +1,12 @@
 org.gradle.vs.watch=true
+
+# hint by https://docs.gradle.org/current/userguide/performance.html#increase_the_heap_size
 org.gradle.jvmargs=-Xmx4096M
+
+# hint by https://docs.gradle.org/current/userguide/performance.html#enable_configuration_cache
+# Does not work:
+# - Task `:compileJava` of type `org.gradle.api.tasks.compile.JavaCompile`: cannot serialize object of type 'org.gradle.api.internal.project.DefaultProject', a subtype of 'org.gradle.api.Project', as these are not supported with the configuration cache.
+# org.gradle.configuration-cache=false
+
+# hint by https://docs.gradle.org/current/userguide/performance.html#enable_the_build_cache
+org.gradle.caching=true

src/main/java/org/jabref/gui/entryeditor/EntryEditorPreferences.java

@@ -49,6 +49,7 @@ public static JournalPopupEnabled fromString(String status) {
     private final ObjectProperty<JournalPopupEnabled> enablementStatus;
     private final BooleanProperty shouldShowSciteTab;
     private final BooleanProperty showUserCommentsFields;
+    private final DoubleProperty previewWidthDividerPosition;
 
     public EntryEditorPreferences(Map<String, Set<Field>> entryEditorTabList,
                                   Map<String, Set<Field>> defaultEntryEditorTabList,
@@ -62,7 +63,8 @@ public EntryEditorPreferences(Map<String, Set<Field>> entryEditorTabList,
                                   boolean autolinkFilesEnabled,
                                   JournalPopupEnabled journalPopupEnabled,
                                   boolean showSciteTab,
-                                  boolean showUserCommentsFields) {
+                                  boolean showUserCommentsFields,
+                                  double previewWidthDividerPosition) {
 
         this.entryEditorTabList = new SimpleMapProperty<>(FXCollections.observableMap(entryEditorTabList));
         this.defaultEntryEditorTabList = new SimpleMapProperty<>(FXCollections.observableMap(defaultEntryEditorTabList));
@@ -77,6 +79,7 @@ public EntryEditorPreferences(Map<String, Set<Field>> entryEditorTabList,
         this.enablementStatus = new SimpleObjectProperty<>(journalPopupEnabled);
         this.shouldShowSciteTab = new SimpleBooleanProperty(showSciteTab);
         this.showUserCommentsFields = new SimpleBooleanProperty(showUserCommentsFields);
+        this.previewWidthDividerPosition = new SimpleDoubleProperty(previewWidthDividerPosition);
     }
 
     public ObservableMap<String, Set<Field>> getEntryEditorTabs() {
@@ -226,4 +229,19 @@ public BooleanProperty showUserCommentsFieldsProperty() {
     public void setShowUserCommentsFields(boolean showUserCommentsFields) {
         this.showUserCommentsFields.set(showUserCommentsFields);
     }
+
+    public void setPreviewWidthDividerPosition(double previewWidthDividerPosition) {
+        this.previewWidthDividerPosition.set(previewWidthDividerPosition);
+    }
+
+    /**
+     * Holds the horizontal divider position when the Preview is shown in the entry editor
+     */
+    public DoubleProperty previewWidthDividerPositionProperty() {
+        return previewWidthDividerPosition;
+    }
+
+    public Double getPreviewWidthDividerPosition() {
+        return previewWidthDividerPosition.get();
+    }
 }

src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java

@@ -41,6 +41,7 @@
 import org.jabref.preferences.PreferencesService;
 
 import com.tobiasdiez.easybind.EasyBind;
+import com.tobiasdiez.easybind.Subscription;
 
 /**
  * A single tab displayed in the EntryEditor holding several FieldEditors.
@@ -61,6 +62,7 @@ abstract class FieldsEditorTab extends EntryEditorTab {
     private PreviewPanel previewPanel;
     private final UndoManager undoManager;
     private Collection<Field> fields = new ArrayList<>();
+    private Subscription dividerPositionSubscription;
 
     public FieldsEditorTab(boolean compressed,
                            BibDatabaseContext databaseContext,
@@ -258,9 +260,22 @@ private void initPanel() {
                     container.getItems().remove(previewPanel);
                 } else {
                     container.getItems().add(1, previewPanel);
+                    container.setDividerPositions(preferences.getEntryEditorPreferences().getPreviewWidthDividerPosition());
                 }
             });
+
+            // save position
+            dividerPositionSubscription = EasyBind.valueAt(container.getDividers(), 0)
+                                                  .mapObservable(SplitPane.Divider::positionProperty)
+                                                  .subscribeToValues(this::savePreviewWidthDividerPosition);
             setContent(container);
         }
     }
+
+    private void savePreviewWidthDividerPosition(Number position) {
+        if (!preferences.getPreviewPreferences().shouldShowPreviewAsExtraTab()) {
+            preferences.getEntryEditorPreferences().setPreviewWidthDividerPosition(position.doubleValue());
+        }
+    }
 }
+

src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java

@@ -92,7 +92,7 @@ private FileAlterationListener getListener() {
             @Override
             public void onStart(FileAlterationObserver observer) {
                 if (!updateStatusOnCreate.get()) {
-                    status.set(Status.IN_PROGRESS);
+                    DefaultTaskExecutor.runInJavaFXThread(() -> status.set(Status.IN_PROGRESS));
                 }
             }
 

src/main/java/org/jabref/logic/formatter/Formatters.java

@@ -25,7 +25,8 @@
 import org.jabref.logic.formatter.bibtexfields.NormalizeUnicodeFormatter;
 import org.jabref.logic.formatter.bibtexfields.OrdinalsToSuperscriptFormatter;
 import org.jabref.logic.formatter.bibtexfields.RegexFormatter;
-import org.jabref.logic.formatter.bibtexfields.RemoveBracesFormatter;
+import org.jabref.logic.formatter.bibtexfields.RemoveEnclosingBracesFormatter;
+import org.jabref.logic.formatter.bibtexfields.RemoveWordEnclosingAndOuterEnclosingBracesFormatter;
 import org.jabref.logic.formatter.bibtexfields.ShortenDOIFormatter;
 import org.jabref.logic.formatter.bibtexfields.UnicodeToLatexFormatter;
 import org.jabref.logic.formatter.bibtexfields.UnitsToLatexFormatter;
@@ -82,7 +83,8 @@ public static List<Formatter> getOthers() {
                 new NormalizeNamesFormatter(),
                 new NormalizePagesFormatter(),
                 new OrdinalsToSuperscriptFormatter(),
-                new RemoveBracesFormatter(),
+                new RemoveEnclosingBracesFormatter(),
+                new RemoveWordEnclosingAndOuterEnclosingBracesFormatter(),
                 new UnitsToLatexFormatter(),
                 new EscapeUnderscoresFormatter(),
                 new EscapeAmpersandsFormatter(),

src/main/java/org/jabref/logic/formatter/bibtexfields/RemoveBracesFormatter.java → src/main/java/org/jabref/logic/formatter/bibtexfields/RemoveEnclosingBracesFormatter.java

@@ -6,7 +6,7 @@
 import org.jspecify.annotations.NullMarked;
 
 @NullMarked
-public class RemoveBracesFormatter extends Formatter {
+public class RemoveEnclosingBracesFormatter extends Formatter {
 
     @Override
     public String getName() {
@@ -18,6 +18,16 @@ public String getKey() {
         return "remove_braces";
     }
 
+    @Override
+    public String getDescription() {
+        return Localization.lang("Removes braces encapsulating the complete field content.");
+    }
+
+    @Override
+    public String getExampleInput() {
+        return "{In CDMA}";
+    }
+
     @Override
     public String format(String value) {
         String formatted = value;
@@ -37,16 +47,6 @@ public String format(String value) {
         return formatted;
     }
 
-    @Override
-    public String getDescription() {
-        return Localization.lang("Removes braces encapsulating the complete field content.");
-    }
-
-    @Override
-    public String getExampleInput() {
-        return "{In CDMA}";
-    }
-
     /**
      * Check if a string at any point has had more ending } braces than opening { ones.
      * Will e.g. return true for the string "DNA} text {EPA"