Merge branch 'main' into fix/add-buttons

Author: Yubo-Cao

.github/workflows/tests-code.yml

@@ -483,6 +483,8 @@ jobs:
         with:
           files: |
             jablib/src/main/java/**/*.java
+          files_ignore: |
+            jablib/src/main/java/**/*-*.java
 
       - name: Build ${{ matrix.launcher }} launcher including changed classes
         shell: bash

CHANGELOG.md

@@ -28,6 +28,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a new ID based fetcher for [EuropePMC](https://europepmc.org/). [#13389](https://github.com/JabRef/jabref/pull/13389)
 - We added quick settings for welcome tab. [#12664](https://github.com/JabRef/jabref/issues/12664)
 - We added an initial [cite as you write](https://retorque.re/zotero-better-bibtex/citing/cayw/) endpoint. [#13187](https://github.com/JabRef/jabref/issues/13187)
+- We added pagination support for the web search entries dialog, improving navigation for large search results. [#5507](https://github.com/JabRef/jabref/issues/5507)
 - We added "copy preview as markdown" feature. [#12552](https://github.com/JabRef/jabref/issues/12552)
 - In case no citation relation information can be fetched, we show the data providers reason. [#13549](https://github.com/JabRef/jabref/pull/13549)
 - When relativizing file names, symlinks are now taken into account. [#12995](https://github.com/JabRef/jabref/issues/12995)
@@ -83,6 +84,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - The Welcome tab now has a responsive layout. [#12664](https://github.com/JabRef/jabref/issues/12664)
 - We introduced a donation prompt in the Welcome tab. [#12664](https://github.com/JabRef/jabref/issues/12664)
 - We changed to syntax for the websearch to the one of the main search bar. [#13607](https://github.com/JabRef/jabref/issues/13607)
+- We improved the for the web search tab in the preferences dialog [#13791](https://github.com/JabRef/jabref/pull/13791)
+- We improved the event viewer for debugging [#13783](https://github.com/JabRef/jabref/pull/13783).
 
 ### Fixed
 
@@ -118,6 +121,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the groups were still displayed after closing all libraries. [#13382](https://github.com/JabRef/jabref/issues/13382)
 - Enhanced field selection logic in the Merge Entries dialog when fetching from DOI to prefer valid years and entry types. [#12549](https://github.com/JabRef/jabref/issues/12549)
 - We improved consistency in the Add Buttons. [#13791](https://github.com/JabRef/jabref/pull/13791)
+- We fixed an issue where theme or font size are not respected for all dialogs [#13558](https://github.com/JabRef/jabref/issues/13558)
+- We removed unnecessary spacing and margin in the AutomaticFieldEditor. [#13792](https://github.com/JabRef/jabref/pull/13792)
 
 ### Removed
 

build-logic/build.gradle.kts

@@ -10,7 +10,7 @@ repositories {
 
 dependencies {
     implementation("com.adarshr:gradle-test-logger-plugin:4.0.0")
-    implementation("com.autonomousapps:dependency-analysis-gradle-plugin:3.0.0")
+    implementation("com.autonomousapps:dependency-analysis-gradle-plugin:3.0.1")
     implementation("com.github.andygoossens:gradle-modernizer-plugin:1.11.0")
     implementation("org.gradlex:extra-java-module-info:1.13")
     implementation("org.gradlex:java-module-dependencies:1.9.2")

build.gradle.kts

@@ -9,7 +9,7 @@ plugins {
 // This is the behavior when applied in the root project (https://docs.openrewrite.org/reference/gradle-plugin-configuration#multi-module-gradle-projects)
 
 dependencies {
-    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:3.13.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:3.14.0"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")

docs/code-howtos/fetchers.md

@@ -12,7 +12,7 @@ Fetchers are the implementation of the [search using online services](https://do
 | [SAO/NASA Astrophysics Data System](https://docs.jabref.org/collect/import-using-online-bibliographic-database#sao-nasa-astrophysics-data-system) | [ADS UI](https://ui.adsabs.harvard.edu/user/settings/token)                                                    | `AstrophysicsDataSystemAPIKey` | 5000 calls/day                   |
 | [ScienceDirect](https://www.sciencedirect.com)                                                                                                    |                                                                                                                | `ScienceDirectApiKey`          |                                  |
 | [SemanticScholar](https://www.semanticscholar.org/)                                                                                               | <https://www.semanticscholar.org/product/api#api-key-form>                                                     | `SemanticScholarApiKey`        |                                  |
-| [Springer Nature](https://docs.jabref.org/collect/import-using-online-bibliographic-database#springer)                                            | [Springer Nature API Portal](https://dev.springernature.com)                                                   | `SpringerNatureAPIKey`         | 5000 calls/day                   |
+| [Springer Nature](https://docs.jabref.org/collect/import-using-online-bibliographic-database#springer)                                            | [Springer Nature API Portal](https://dev.springernature.com). Use the "Meta API" API key.                      | `SpringerNatureAPIKey`         | 5000 calls/day                   |
 | [Zentralblatt Math](https://www.zbmath.org)                                                                                                       | (none)                                                                                                         | (none)                         | Depending on the current network |
 | [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/)                                                                             | [Biodiversitylibrary](https://about.biodiversitylibrary.org/tools-and-services/developer-and-data-tools/#APIs) | `BiodiversityHeritageApiKey`   | -                                |
 

jabgui/src/main/java/org/jabref/gui/consistency/ConsistencyCheckDialogViewModel.java

@@ -8,7 +8,6 @@
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Comparator;
-import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
@@ -46,15 +45,13 @@
 public class ConsistencyCheckDialogViewModel extends AbstractViewModel {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(ConsistencyCheckDialogViewModel.class);
-    private static final int EXTRA_COLUMNS_COUNT = 2;
 
     private final BibliographyConsistencyCheck.Result result;
     private final DialogService dialogService;
     private final GuiPreferences preferences;
     private final BibEntryTypesManager entryTypesManager;
 
     private final List<Field> allReportedFields;
-    private final int columnCount;
     private final ObservableList<ConsistencyMessage> tableData = FXCollections.observableArrayList();
     private final StringProperty selectedEntryType = new SimpleStringProperty();
 
@@ -72,7 +69,6 @@ public ConsistencyCheckDialogViewModel(DialogService dialogService,
                                   .sorted(Comparator.comparing(Field::getName))
                                   .distinct()
                                   .toList();
-        this.columnCount = getColumnNames().size();
 
         result.entryTypeToResultMap().entrySet().stream()
               .sorted(Comparator.comparing(entry -> entry.getKey().getName()))
@@ -93,8 +89,8 @@ public ObservableList<ConsistencyMessage> getTableData() {
         return tableData;
     }
 
-    public Set<String> getColumnNames() {
-        Set<String> result = LinkedHashSet.newLinkedHashSet(columnCount + EXTRA_COLUMNS_COUNT);
+    public List<String> getColumnNames() {
+        List<String> result = new ArrayList<>(allReportedFields.size() + 2); // there are two extra columns
         result.add("Entry Type");
         result.add("CitationKey");
         allReportedFields.forEach(field-> result.add(field.getDisplayName().trim()));
@@ -138,7 +134,7 @@ private void writeBibEntry(BibEntry bibEntry, String entryType, Set<Field> requi
     }
 
     private List<String> getFindingsAsList(BibEntry bibEntry, String entryType, Set<Field> requiredFields, Set<Field> optionalFields) {
-        List<String> result = new ArrayList<>(columnCount + EXTRA_COLUMNS_COUNT);
+        List<String> result = new ArrayList<>(allReportedFields.size() + 2);
         result.add(entryType);
         result.add(bibEntry.getCitationKey().orElse(""));
         allReportedFields.forEach(field ->

jabgui/src/main/java/org/jabref/gui/edit/automaticfiededitor/AbstractAutomaticFieldEditorTabView.java

@@ -1,11 +1,11 @@
 package org.jabref.gui.edit.automaticfiededitor;
 
-import javafx.scene.layout.AnchorPane;
+import javafx.scene.layout.VBox;
 
-public abstract class AbstractAutomaticFieldEditorTabView extends AnchorPane implements AutomaticFieldEditorTab {
+public abstract class AbstractAutomaticFieldEditorTabView extends VBox implements AutomaticFieldEditorTab {
 
     @Override
-    public AnchorPane getContent() {
+    public VBox getContent() {
         return this;
     }
 }

jabgui/src/main/java/org/jabref/gui/edit/automaticfiededitor/AutomaticFieldEditorDialog.java

@@ -60,17 +60,11 @@ public AutomaticFieldEditorDialog(StateManager stateManager, UndoManager undoMan
             }
             return "";
         });
-
-        // This will prevent all dialog buttons from having the same size
-        // Read more: https://stackoverflow.com/questions/45866249/javafx-8-alert-different-button-sizes
-        getDialogPane().getButtonTypes().stream()
-            .map(getDialogPane()::lookupButton)
-            .forEach(btn -> ButtonBar.setButtonUniformSize(btn, false));
     }
 
     @FXML
     public void initialize() {
-        viewModel = new AutomaticFieldEditorViewModel(selectedEntries, database, undoManager, stateManager);
+        viewModel = new AutomaticFieldEditorViewModel(database, undoManager, stateManager);
 
         for (AutomaticFieldEditorTab tabModel : viewModel.getFieldEditorTabs()) {
             NotificationPaneAdapter notificationPane = new NotificationPaneAdapter(tabModel.getContent());

jabgui/src/main/java/org/jabref/gui/edit/automaticfiededitor/AutomaticFieldEditorViewModel.java

@@ -1,7 +1,5 @@
 package org.jabref.gui.edit.automaticfiededitor;
 
-import java.util.List;
-
 import javax.swing.undo.UndoManager;
 
 import javafx.collections.FXCollections;
@@ -14,7 +12,6 @@
 import org.jabref.gui.edit.automaticfiededitor.renamefield.RenameFieldTabView;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.model.database.BibDatabase;
-import org.jabref.model.entry.BibEntry;
 
 public class AutomaticFieldEditorViewModel extends AbstractViewModel {
     public static final String NAMED_COMPOUND_EDITS = "EDIT_FIELDS";
@@ -23,7 +20,7 @@ public class AutomaticFieldEditorViewModel extends AbstractViewModel {
 
     private final UndoManager undoManager;
 
-    public AutomaticFieldEditorViewModel(List<BibEntry> selectedEntries, BibDatabase database, UndoManager undoManager, StateManager stateManager) {
+    public AutomaticFieldEditorViewModel(BibDatabase database, UndoManager undoManager, StateManager stateManager) {
         this.undoManager = undoManager;
         fieldEditorTabs.addAll(
                 new EditFieldContentTabView(database, stateManager),