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

* upstream/main: (36 commits)
  chore: remove repetitive words (JabRef#11015)
  Fix test names (JabRef#11014)
  Remove obsolete "Comments" tab configuration (JabRef#11011)
  Fix "Other fields" tab respecting custom tabs (JabRef#11012)
  [WIP] Extract PDF References (JabRef#10437)
  Fixed jump to entry from crossref (JabRef#11009)
  fix suggestion provider for crossref field (JabRef#10962)
  Use SequencedSet for required and optional fields (JabRef#11007)
  Bump io.github.classgraph:classgraph from 4.8.165 to 4.8.168 (JabRef#11005)
  Bump org.glassfish.hk2:hk2-api from 3.0.6 to 3.1.0 (JabRef#11006)
  Bump org.apache.logging.log4j:log4j-to-slf4j from 2.23.0 to 2.23.1 (JabRef#11003)
  Bump org.javamodularity.moduleplugin from 1.8.14 to 1.8.15 (JabRef#11002)
  Bump jakarta.xml.bind:jakarta.xml.bind-api from 4.0.1 to 4.0.2 (JabRef#11004)
  Bump softprops/action-gh-release from 1 to 2 (JabRef#11000)
  Bump gittools/actions from 0.13.2 to 0.13.4 (JabRef#11001)
  Update custom-svg-icons.md (JabRef#10999)
  Update Texworks icon (JabRef#10998)
  Use tags editor for auto completion preferences (JabRef#10990)
  Enable auto merge of CHANGELOG.md (JabRef#10986)
  Enhance DOI parser to deal with special characters (JabRef#10989)
  ...

# Conflicts:
#	build.gradle

.gitattributes

@@ -11,5 +11,4 @@ gradlew text eol=lf
 *.java text eol=lf
 *.properties text eol=lf
 
-# disable after a release (otherwise, duplicate CHANGELOG.md entries will be generated)
-# CHANGELOG.md merge=union
+CHANGELOG.md merge=union

.github/workflows/deployment-arm64.yml

@@ -66,12 +66,12 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.11.0
+        uses: gittools/actions/gitversion/setup@v0.13.4
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.11.0
+        uses: gittools/actions/gitversion/execute@v0.13.4
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

.github/workflows/deployment-jdk-ea.yml

@@ -82,18 +82,17 @@ jobs:
           show-progress: 'false'
       - name: Install pigz and cache (linux)
         if: (matrix.os == 'ubuntu-latest') || (matrix.os == 'buildjet-4vcpu-ubuntu-2204-arm')
-        # 1.3.1 works, 1.4.1 does not (https://github.com/awalsh128/cache-apt-pkgs-action/issues/126)
-        uses: koppor/cache-apt-pkgs-action@add-arm64-support
+        uses: awalsh128/cache-apt-pkgs-action@master
         with:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.11.0
+        uses: gittools/actions/gitversion/setup@v0.13.4
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.11.0
+        uses: gittools/actions/gitversion/execute@v0.13.4
       - name: 'Set up JDK ${{ matrix.jdk }}'
         uses: oracle-actions/setup-java@v1
         with:

.github/workflows/deployment.yml

@@ -79,12 +79,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.11.0
+        uses: gittools/actions/gitversion/setup@v0.13.4
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.11.0
+        uses: gittools/actions/gitversion/execute@v0.13.4
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

.github/workflows/upload-release.yml

@@ -18,7 +18,7 @@ jobs:
           cd build
           wget -q -m -r -nH --cut-dirs 2 --no-parent --accept=tar.gz,dmg,pkg,deb,rpm,zip,msi https://builds.jabref.org/tags/
       - name: Release
-        uses: softprops/action-gh-release@v1
+        uses: softprops/action-gh-release@v2
         with:
           draft: true
           files: build/**

CHANGELOG.md

@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We converted the "Custom API key" list to a table to be more accessible. [#10926](https://github.com/JabRef/jabref/issues/10926)
 - We added a "refresh" button for the LaTeX citations tab in the entry editor. [#10584](https://github.com/JabRef/jabref/issues/10584)
 - We added the possibility to show the BibTeX source in the [web search](https://docs.jabref.org/collect/import-using-online-bibliographic-database) import screen. [#560](https://github.com/koppor/jabref/issues/560)
 - We added a fetcher for [ISIDORE](https://isidore.science/), simply paste in the link into the text field or the last 6 digits in the link that identify that paper. [#10423](https://github.com/JabRef/jabref/issues/10423)
@@ -25,6 +26,10 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added the citation key pattern `[camelN]`. Equivalent to the first N words of the `[camel]` pattern.
 - We added importing of static groups and linked files from BibDesk .bib files. [#10381](https://github.com/JabRef/jabref/issues/10381)
 - We added ability to export in CFF (Citation File Format) [#10661](https://github.com/JabRef/jabref/issues/10661).
+- We added ability to push entries to TeXworks. [#3197](https://github.com/JabRef/jabref/issues/3197)
+- We added the ability to zoom in and out in the document viewer using <kbd>Ctrl</kbd> + <kbd>Scroll</kbd>. [#10964](https://github.com/JabRef/jabref/pull/10964)
+- We added a Cleanup for removing non-existent files and grouped the related options [#10929](https://github.com/JabRef/jabref/issues/10929)
+- We added the functionality to parse the bibliography of PDFs using the GROBID online service. [#10200](https://github.com/JabRef/jabref/issues/10200)
 
 ### Changed
 
@@ -39,6 +44,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We made the command "Push to TexShop" more robust to allow cite commands with a character before the first slash. [forum#2699](https://discourse.jabref.org/t/push-to-texshop-mac/2699/17?u=siedlerchr)
 - We only show the notification "Saving library..." if the library contains more than 2000 entries. [#9803](https://github.com/JabRef/jabref/issues/9803)
 - We enhanced the dialog for adding new fields in the content selector with a selection box containing a list of standard fields. [#10912](https://github.com/JabRef/jabref/pull/10912)
+- We store the citation relations in an LRU cache to avoid bloating the memory and out-of-memory exceptions. [#10958](https://github.com/JabRef/jabref/issues/10958)
+- Keywords filed are now displayed as tags. [#10910](https://github.com/JabRef/jabref/pull/10910)
 
 ### Fixed
 
@@ -47,6 +54,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the preview panel showing the wrong entry (an entry that is not selected in the entry table). [#9172](https://github.com/JabRef/jabref/issues/9172)
 - We fixed an issue where HTML-reserved characters like '&' and '<', in addition to HTML entities like '&amp;' were not rendered correctly in entry preview. [#10677](https://github.com/JabRef/jabref/issues/10677)
 - The last page of a PDF is now indexed by the full text search. [#10193](https://github.com/JabRef/jabref/issues/10193)
+- The entry editor respects the configured custom tabs when showing "Other fields". [#11012](https://github.com/JabRef/jabref/pull/11012)
 - The default owner of an entry can be changed again. [#10924](https://github.com/JabRef/jabref/issues/10924)
 - We fixed an issue where the duplicate check did not take umlauts or other LaTeX-encoded characters into account. [#10744](https://github.com/JabRef/jabref/pull/10744)
 - We fixed the colors of the icon on hover for unset special fields. [#10431](https://github.com/JabRef/jabref/issues/10431)
@@ -55,6 +63,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the `CommentsTab` was not properly formatted when the `defaultOwner` contained capital or special letters. [#10870](https://github.com/JabRef/jabref/issues/10870)
 - We fixed an issue where the `File -> Close library` menu item was not disabled when no library was open. [#10948](https://github.com/JabRef/jabref/issues/10948)
 - We fixed an issue where the Document Viewer would show the PDF in only half the window when maximized. [#10934](https://github.com/JabRef/jabref/issues/10934)
+- Clicking on the crossref and related tags in the entry editor jumps to the linked entry. [#5484](https://github.com/JabRef/jabref/issues/5484) [#9369](https://github.com/JabRef/jabref/issues/9369)
 
 ### Removed
 

build.gradle

@@ -9,7 +9,7 @@ plugins {
 
     id 'me.champeau.jmh' version '0.7.2'
 
-    id 'org.javamodularity.moduleplugin' version '1.8.13'
+    id 'org.javamodularity.moduleplugin' version '1.8.15'
 
     id 'org.openjfx.javafxplugin' version '0.1.0'
 
@@ -27,7 +27,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.8.2'
+    id 'org.openrewrite.rewrite' version '6.8.4'
 }
 
 // Enable following for debugging
@@ -177,7 +177,7 @@ dependencies {
     implementation('com.tobiasdiez:easybind:2.2.1-SNAPSHOT')
     implementation 'org.fxmisc.flowless:flowless:0.7.2'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.2'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.0.3') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.2.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude group: 'org.apache.logging.log4j'
     }
@@ -196,14 +196,14 @@ dependencies {
     // route all requests to java.util.logging to SLF4J (which in turn routes to tinylog)
     implementation 'org.slf4j:jul-to-slf4j:2.0.9'
     // route all requests to log4j to SLF4J
-    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.23.0'
+    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.23.1'
 
     implementation('de.undercouch:citeproc-java:3.0.0-beta.2') {
         exclude group: 'org.antlr'
     }
 
     // jakarta.activation is already dependency of glassfish
-    implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '4.0.1'
+    implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '4.0.2'
     implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '4.0.3'
 
     implementation ('com.github.tomtung:latex2unicode_2.13:0.3.2') {
@@ -228,7 +228,7 @@ dependencies {
     implementation 'org.glassfish.jersey.core:jersey-server:3.1.5'
     // injection framework
     implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.5'
-    implementation 'org.glassfish.hk2:hk2-api:3.0.6'
+    implementation 'org.glassfish.hk2:hk2-api:3.1.0'
     // testImplementation 'org.glassfish.hk2:hk2-testing:3.0.4'
     // implementation 'org.glassfish.hk2:hk2-testing-jersey:3.0.4'
     // testImplementation 'org.glassfish.hk2:hk2-junitrunner:3.0.4'
@@ -242,13 +242,14 @@ dependencies {
     // Because of GraalVM quirks, we need to ship that. See https://github.com/jspecify/jspecify/issues/389#issuecomment-1661130973 for details
     implementation 'org.jspecify:jspecify:0.3.0'
 
+    // parse plist files
     implementation 'com.googlecode.plist:dd-plist:1.23'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.165'
+    testImplementation 'io.github.classgraph:classgraph:4.8.168'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.2'
 
-    testImplementation 'org.mockito:mockito-core:5.10.0'
+    testImplementation 'org.mockito:mockito-core:5.11.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.1'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.1'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.2.1'
@@ -262,7 +263,7 @@ 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:2.6.4"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.7.1"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")

config/README.md

@@ -20,7 +20,7 @@ Style-checks are done for each pull request and installing this code style confi
 # Eclipse:
 
 The Eclipse code formatter style is stored in the `eclipse.gradle` file and gets imported automatically.
-In case the formatter style needs to be adapted, configure it and export in in eclipse.
+In case the formatter style needs to be adapted, configure it and export in eclipse.
 
 1. Right click on the eclipse project "JabRef"
 2. Select "Export > General > Preferences"

docs/code-howtos/custom-svg-icons.md

@@ -23,7 +23,14 @@ Good icon design requires years of experience and cannot be covered here. Adapti
 
 ## Step 2. Packing the icons into a font
 
-Use the [IcoMoon](https://icomoon.io) tool for packing the icons. Create a new set and import _all_ icons. Rearrange them so that they have the same order as in `org.jabref.gui.JabRefMaterialDesignIcon`. This will avoid that you have to change the code points for the existing glyphs. In the settings for your icon set, set the _Grid_ to 24. This is important to get the correct spacing. The name of the font is `JabRefMaterialDesign`. When your icon-set is ready, select all of them and download the font-package.
+Use the [IcoMoon](https://icomoon.io) tool for packing the icons.
+
+1. Create a new set by importing the json file
+2. Next to the icons, click on the hamburger menu, chose "Import to Set" to add a new icon (it will be added to the front)
+Rearrange them so that they have the same order as in `org.jabref.gui.JabRefMaterialDesignIcon`. This will avoid that you have to change the code points for the existing glyphs. In the settings for your icon set, set the _Grid_ to 24. This is important to get the correct spacing. The name of the font is `JabRefMaterialDesign`.
+3. Next to the icons, click on the hamburger menu and click "Select all".
+4. Proceed with the font creating, set the font property name to `JabRefMaterialDesign`
+When your icon-set is ready, select all of them and download the font-package.
 
 ## Step 3. Replace the existing `JabRefMaterialDesign.ttf`
 

src/main/java/org/jabref/gui/JabRefFrame.java

@@ -574,9 +574,11 @@ public void init() {
         EasyBind.subscribe(tabbedPane.getSelectionModel().selectedItemProperty(), selectedTab -> {
             if (selectedTab instanceof LibraryTab libraryTab) {
                 stateManager.setActiveDatabase(libraryTab.getBibDatabaseContext());
+                stateManager.activeTabProperty().set(Optional.of(libraryTab));
             } else if (selectedTab == null) {
                 // All databases are closed
                 stateManager.setActiveDatabase(null);
+                stateManager.activeTabProperty().set(Optional.empty());
             }
         });
 

src/main/java/org/jabref/gui/LibraryTab.java

@@ -282,8 +282,9 @@ private void setDatabaseContext(BibDatabaseContext bibDatabaseContext) {
             return;
         }
         if (tabPane.getSelectionModel().selectedItemProperty().get().equals(this)) {
-            LOGGER.debug("This case should not happen.");
+            LOGGER.warn("This case should not happen.");
             stateManager.setActiveDatabase(bibDatabaseContext);
+            stateManager.activeTabProperty().set(Optional.of(this));
         }
 
         // Remove existing dummy BibDatabaseContext and add correct BibDatabaseContext from ParserResult to trigger changes in the openDatabases list in the stateManager
@@ -597,8 +598,8 @@ private void setupAutoCompletion() {
         if (autoCompletePreferences.shouldAutoComplete()) {
             suggestionProviders = new SuggestionProviders(getDatabase(), Globals.journalAbbreviationRepository, autoCompletePreferences);
         } else {
-            // Create suggestion providers with database for crossref if auto-completion is deactivated
-            suggestionProviders = new SuggestionProviders(getDatabase());
+            // Create empty suggestion providers if auto-completion is deactivated
+            suggestionProviders = new SuggestionProviders();
         }
         searchAutoCompleter = new PersonNameSuggestionProvider(FieldFactory.getPersonNameFields(), getDatabase());
     }

src/main/java/org/jabref/gui/StateManager.java

@@ -54,6 +54,7 @@ public class StateManager {
     private final CustomLocalDragboard localDragboard = new CustomLocalDragboard();
     private final ObservableList<BibDatabaseContext> openDatabases = FXCollections.observableArrayList();
     private final OptionalObjectProperty<BibDatabaseContext> activeDatabase = OptionalObjectProperty.empty();
+    private final OptionalObjectProperty<LibraryTab> activeTab = OptionalObjectProperty.empty();
     private final ReadOnlyListWrapper<GroupTreeNode> activeGroups = new ReadOnlyListWrapper<>(FXCollections.observableArrayList());
     private final ObservableList<BibEntry> selectedEntries = FXCollections.observableArrayList();
     private final ObservableMap<BibDatabaseContext, ObservableList<GroupTreeNode>> selectedGroups = FXCollections.observableHashMap();
@@ -91,6 +92,10 @@ public OptionalObjectProperty<BibDatabaseContext> activeDatabaseProperty() {
         return activeDatabase;
     }
 
+    public OptionalObjectProperty<LibraryTab> activeTabProperty() {
+        return activeTab;
+    }
+
     public OptionalObjectProperty<SearchQuery> activeSearchQueryProperty() {
         return activeSearchQuery;
     }

src/main/java/org/jabref/gui/actions/StandardActions.java

@@ -32,6 +32,7 @@ public enum StandardActions implements Action {
     REBUILD_FULLTEXT_SEARCH_INDEX(Localization.lang("Rebuild fulltext search index"), IconTheme.JabRefIcons.FILE),
     REDOWNLOAD_MISSING_FILES(Localization.lang("Redownload missing files"), IconTheme.JabRefIcons.DOWNLOAD),
     OPEN_EXTERNAL_FILE(Localization.lang("Open file"), IconTheme.JabRefIcons.FILE, KeyBinding.OPEN_FILE),
+    EXTRACT_FILE_REFERENCES(Localization.lang("Extract references from file"), IconTheme.JabRefIcons.FILE_STAR),
     OPEN_URL(Localization.lang("Open URL or DOI"), IconTheme.JabRefIcons.WWW, KeyBinding.OPEN_URL_OR_DOI),
     SEARCH_SHORTSCIENCE(Localization.lang("Search ShortScience")),
     MERGE_WITH_FETCHED_ENTRY(Localization.lang("Get bibliographic data from %0", "DOI/ISBN/...")),

src/main/java/org/jabref/gui/autocompleter/AutoCompletePreferences.java

@@ -10,7 +10,6 @@
 import javafx.collections.ObservableSet;
 
 import org.jabref.model.entry.field.Field;
-import org.jabref.model.entry.field.FieldFactory;
 
 public class AutoCompletePreferences {
 
@@ -80,8 +79,4 @@ public void setNameFormat(NameFormat nameFormat) {
     public ObservableSet<Field> getCompleteFields() {
         return completeFields;
     }
-
-    public String getCompleteNamesAsString() {
-        return FieldFactory.serializeFieldsList(completeFields);
-    }
 }

src/main/java/org/jabref/gui/autocompleter/ContentSelectorSuggestionProvider.java

@@ -1,7 +1,6 @@
 package org.jabref.gui.autocompleter;
 
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.List;
 import java.util.stream.Stream;
 
@@ -26,7 +25,7 @@ public Stream<String> getSource() {
     }
 
     @Override
-    public Collection<String> getPossibleSuggestions() {
+    public List<String> getPossibleSuggestions() {
         List<String> suggestions = new ArrayList<>();
         if (suggestionProvider != null) {
             suggestions.addAll(suggestionProvider.getPossibleSuggestions());

src/main/java/org/jabref/gui/autocompleter/SuggestionProvider.java

@@ -29,6 +29,7 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Comparator;
+import java.util.List;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
@@ -60,7 +61,7 @@ public final Collection<T> provideSuggestions(ISuggestionRequest request) {
 
     protected abstract Equivalence<T> getEquivalence();
 
-    public Collection<T> getPossibleSuggestions() {
+    public List<T> getPossibleSuggestions() {
         Comparator<T> comparator = getComparator().reversed();
         Equivalence<T> equivalence = getEquivalence();
         return getSource().map(equivalence::wrap) // Need to do a bit of acrobatic as there is no distinctBy method

src/main/java/org/jabref/gui/autocompleter/SuggestionProviders.java

@@ -22,21 +22,12 @@ public SuggestionProviders(BibDatabase database, JournalAbbreviationRepository a
         this.isEmpty = false;
     }
 
-    public SuggestionProviders(BibDatabase database) {
-        this.database = database;
-        this.isEmpty = true;
-    }
-
     public SuggestionProviders() {
         this.isEmpty = true;
     }
 
     public SuggestionProvider<?> getForField(Field field) {
         if (isEmpty || !autoCompletePreferences.getCompleteFields().contains(field)) {
-            Set<FieldProperty> fieldProperties = field.getProperties();
-            if (fieldProperties.contains(FieldProperty.SINGLE_ENTRY_LINK)) {
-                return new BibEntrySuggestionProvider(database);
-            }
             return new EmptySuggestionProvider();
         }