Merge branch 'main' into fix-for-issue-11512

.github/workflows/deployment-arm64.yml

@@ -98,7 +98,7 @@ jobs:
           create-keychain: false
           keychain-password: jabref
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Prepare merged jars and modules dir (macOS)
@@ -141,6 +141,8 @@ jobs:
           --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref \
           --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
           --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref \
+          --java-options --add-opens=javafx.base/javafx.collections=org.jabref \
+          --java-options --add-opens=javafx.base/javafx.collections.transformation=org.jabref \
           --java-options --add-modules=jdk.incubator.vector
       - name: Build pkg (macOS)
         if: (steps.checksecrets.outputs.secretspresent == 'YES')
@@ -179,6 +181,8 @@ jobs:
           --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref \
           --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
           --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref \
+          --java-options --add-opens=javafx.base/javafx.collections=org.jabref \
+          --java-options --add-opens=javafx.base/javafx.collections.transformation=org.jabref \
           --java-options --add-modules=jdk.incubator.vector
       - name: Rename files with arm64 suffix as well
         if: (steps.checksecrets.outputs.secretspresent == 'YES')

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

@@ -191,7 +191,7 @@ jobs:
           java-version: 21
           distribution: 'temurin'
       - name: Set up Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Prepare merged jars and modules dir

.github/workflows/deployment.yml

@@ -93,7 +93,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Prepare merged jars and modules dir (macOS)
@@ -153,6 +153,8 @@ jobs:
           --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref \
           --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
           --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref \
+          --java-options --add-opens=javafx.base/javafx.collections=org.jabref \
+          --java-options --add-opens=javafx.base/javafx.collections.transformation=org.jabref \
           --java-options --add-modules=jdk.incubator.vector
       - name: Build pkg (macOS)
         if: (matrix.os == 'macos-13') && (steps.checksecrets.outputs.secretspresent == 'YES')
@@ -192,6 +194,8 @@ jobs:
           --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref \
           --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
           --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref \
+          --java-options --add-opens=javafx.base/javafx.collections=org.jabref \
+          --java-options --add-opens=javafx.base/javafx.collections.transformation=org.jabref \
           --java-options --add-modules=jdk.incubator.vector
       - name: Build runtime image and installer (linux, Windows)
         if: (matrix.os != 'macos-13') && (steps.checksecrets.outputs.secretspresent == 'YES')

.github/workflows/tests-fetchers.yml

@@ -51,7 +51,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Run fetcher tests

.github/workflows/tests.yml

@@ -47,7 +47,7 @@ jobs:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           checkstyle_config: 'config/checkstyle/checkstyle_reviewdog.xml'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Run checkstyle using gradle
@@ -82,7 +82,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Run OpenRewrite
@@ -117,7 +117,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Run modernizer
@@ -237,7 +237,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Run tests
@@ -280,7 +280,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Run tests on PostgreSQL
@@ -321,7 +321,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Run GUI tests
@@ -371,7 +371,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Update test coverage metrics
@@ -400,7 +400,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           show-progress: 'false'
-      - uses: gradle/actions/wrapper-validation@v3
+      - uses: gradle/actions/wrapper-validation@v4
 
   # This ensures that no git merge conflict markers (<<<, ...) are contained
   merge_conflict_job:

CHANGELOG.md

@@ -14,9 +14,14 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added support for selecting and using CSL Styles in JabRef's OpenOffice/LibreOffice integration for inserting bibliographic and in-text citations into a document. [#2146](https://github.com/JabRef/jabref/issues/2146), [#8893](https://github.com/JabRef/jabref/issues/8893)
 - We added Tools > New library based on references in PDF file... to create a new library based on the references section in a PDF file. [#11522](https://github.com/JabRef/jabref/pull/11522)
 - When converting the references section of a paper (PDF file), more than the last page is treated. [#11522](https://github.com/JabRef/jabref/pull/11522)
+- Added the functionality to invoke offline reference parsing explicitly. [#11565](https://github.com/JabRef/jabref/pull/11565)
+- The dialog for [adding an entry using reference text](https://docs.jabref.org/collect/newentryfromplaintext) is now filled with the clipboard contents as default. [#11565](https://github.com/JabRef/jabref/pull/11565)
 - Added minimal support for [biblatex data annotation](https://mirrors.ctan.org/macros/latex/contrib/biblatex/doc/biblatex.pdf#subsection.3.7) fields in `.layout` files. [#11505](https://github.com/JabRef/jabref/issues/11505)
 - Added saving of selected options in the [Lookup -> Search for unlinked local files dialog](https://docs.jabref.org/collect/findunlinkedfiles#link-the-pdfs-to-your-bib-library). [#11439](https://github.com/JabRef/jabref/issues/11439)
 - We fixed black text in Dark mode inside "Citation information" [#11512](https://github.com/JabRef/jabref/issues/11512)
+- We added a toggle button to invert the selected groups. [#9073](https://github.com/JabRef/jabref/issues/9073)
+- We reintroduced the floating search in the main table. [#4237](https://github.com/JabRef/jabref/issues/4237)
+- We fixed an issue where the selection of an entry in the table lost after searching for a group. [#3176](https://github.com/JabRef/jabref/issues/3176)
 
 ### Changed
 
@@ -25,11 +30,13 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - JabRef respects the [configuration for storing files relative to the .bib file](https://docs.jabref.org/finding-sorting-and-cleaning-entries/filelinks#directories-for-files) in more cases. [#11492](https://github.com/JabRef/jabref/pull/11492)
 - JabRef does not show finished background tasks in the status bar popup. [#11574](https://github.com/JabRef/jabref/pull/11574)
 - We enhanced the indexing speed. [#11502](https://github.com/JabRef/jabref/pull/11502)
+- ⚠️ Renamed command line parameters `embeddBibfileInPdf` to `embedBibFileInPdf`, `writeMetadatatoPdf` to `writeMetadataToPdf`, and `writeXMPtoPdf` to `writeXmpToPdf`. [#11575](https://github.com/JabRef/jabref/pull/11575)
 
 ### Fixed
 
 - We fixed an issue where the "Check for updates" preference was not saved. [#11485](https://github.com/JabRef/jabref/pull/11485)
 - We fixed an issue where an exception was thrown after changing "show preview as a tab" in the preferences. [#11515](https://github.com/JabRef/jabref/pull/11515)
+- We fixed an issue that online and offline mode for new library creation were handled incorrectly. [#11565](https://github.com/JabRef/jabref/pull/11565)
 - We fixed an issue with colors in the search bar when dark theme is enabled. [#11569](https://github.com/JabRef/jabref/issues/11569)
 - We fixed an issue where a new unsaved library was not marked with an asterisk. [#11519](https://github.com/JabRef/jabref/pull/11519)
 - We fixed an issue where JabRef starts without window decorations. [#11440](https://github.com/JabRef/jabref/pull/11440)

build.gradle

@@ -29,7 +29,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.16.4'
+    id 'org.openrewrite.rewrite' version '6.17.1'
 }
 
 // Enable following for debugging
@@ -89,7 +89,10 @@ application {
         '--add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref',
         '--add-opens=javafx.graphics/javafx.scene=org.jabref',
         '--add-opens=javafx.controls/javafx.scene.control=org.jabref',
-        '--add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref'
+        '--add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref',
+
+        '--add-opens=javafx.base/javafx.collections=org.jabref',
+        '--add-opens=javafx.base/javafx.collections.transformation=org.jabref'
     ]
 }
 
@@ -184,7 +187,7 @@ dependencies {
     implementation 'com.github.javakeyring:java-keyring:1.0.4'
 
     antlr4 'org.antlr:antlr4:4.13.1'
-    implementation 'org.antlr:antlr4-runtime:4.13.1'
+    implementation 'org.antlr:antlr4-runtime:4.13.2'
 
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.10.0.202406032230-r'
 
@@ -291,8 +294,8 @@ dependencies {
     // testImplementation 'org.glassfish.hk2:hk2-junitrunner:3.0.4'
     // HTTP server
     // implementation 'org.glassfish.jersey.containers:jersey-container-netty-http:3.1.1'
-    implementation 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.7'
-    testImplementation 'org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:3.1.7'
+    implementation 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.8'
+    testImplementation 'org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:3.1.8'
     // Allow objects "magically" to be mapped to JSON using GSON
     // implementation 'org.glassfish.jersey.media:jersey-media-json-gson:3.1.1'
 
@@ -328,7 +331,7 @@ 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:2.15.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.16.0"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")
@@ -495,7 +498,10 @@ run {
                 'org.controlsfx.controls/org.controlsfx.control.textfield' : 'org.jabref',
 
                 'javafx.controls/javafx.scene.control.skin' : 'org.controlsfx.controls',
-                'javafx.graphics/javafx.scene' : 'org.controlsfx.controls'
+                'javafx.graphics/javafx.scene' : 'org.controlsfx.controls',
+
+                'javafx.base/javafx.collections' : 'org.jabref',
+                'javafx.base/javafx.collections.transformation' : 'org.jabref'
         ]
 
         addModules = [

src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -239,22 +239,22 @@ public void processArguments() {
             automaticallySetFileLinks(loaded);
         }
 
-        if ((cli.isWriteXMPtoPdf() && cli.isEmbeddBibfileInPdf()) || (cli.isWriteMetadatatoPdf() && (cli.isWriteXMPtoPdf() || cli.isEmbeddBibfileInPdf()))) {
-            System.err.println("Give only one of [writeXMPtoPdf, embeddBibfileInPdf, writeMetadatatoPdf]");
+        if ((cli.isWriteXmpToPdf() && cli.isEmbedBibFileInPdf()) || (cli.isWriteMetadataToPdf() && (cli.isWriteXmpToPdf() || cli.isEmbedBibFileInPdf()))) {
+            System.err.println("Give only one of [writeXmpToPdf, embedBibFileInPdf, writeMetadataToPdf]");
         }
 
-        if (cli.isWriteMetadatatoPdf() || cli.isWriteXMPtoPdf() || cli.isEmbeddBibfileInPdf()) {
+        if (cli.isWriteMetadataToPdf() || cli.isWriteXmpToPdf() || cli.isEmbedBibFileInPdf()) {
             if (!loaded.isEmpty()) {
                 writeMetadataToPdf(loaded,
-                        cli.getWriteMetadatatoPdf(),
+                        cli.getWriteMetadataToPdf(),
                         preferencesService.getXmpPreferences(),
                         preferencesService.getFilePreferences(),
                         preferencesService.getLibraryPreferences().getDefaultBibDatabaseMode(),
                         Injector.instantiateModelOrService(BibEntryTypesManager.class),
                         preferencesService.getFieldPreferences(),
                         Injector.instantiateModelOrService(JournalAbbreviationRepository.class),
-                        cli.isWriteXMPtoPdf() || cli.isWriteMetadatatoPdf(),
-                        cli.isEmbeddBibfileInPdf() || cli.isWriteMetadatatoPdf());
+                        cli.isWriteXmpToPdf() || cli.isWriteMetadataToPdf(),
+                        cli.isEmbedBibFileInPdf() || cli.isWriteMetadataToPdf());
             }
         }
 
@@ -379,7 +379,7 @@ private void writeMetadataToPDFsOfEntry(BibDatabaseContext databaseContext,
                 if (embeddedBibFilePdfExporter.exportToAllFilesOfEntry(databaseContext, filePreferences, entry, List.of(entry), abbreviationRepository)) {
                     System.out.printf("Successfully embedded metadata on at least one linked file of %s%n", citeKey);
                 } else {
-                    System.out.printf("Cannot embedd metadata on any linked files of %s. Make sure there is at least one linked file and the path is correct.%n", citeKey);
+                    System.out.printf("Cannot embed metadata on any linked files of %s. Make sure there is at least one linked file and the path is correct.%n", citeKey);
                 }
             }
         } catch (Exception e) {

src/main/java/org/jabref/cli/JabRefCLI.java

@@ -33,7 +33,6 @@ public class JabRefCLI {
 
     public JabRefCLI(String[] args) throws ParseException {
         Options options = getOptions();
-
         this.cl = new DefaultParser().parse(options, args, true);
         this.leftOver = cl.getArgList();
     }
@@ -153,21 +152,21 @@ public boolean isAutomaticallySetFileLinks() {
         return cl.hasOption("automaticallySetFileLinks");
     }
 
-    public boolean isWriteXMPtoPdf() {
-        return cl.hasOption("writeXMPtoPdf");
+    public boolean isWriteXmpToPdf() {
+        return cl.hasOption("writeXmpToPdf");
     }
 
-    public boolean isEmbeddBibfileInPdf() {
-        return cl.hasOption("embeddBibfileInPdf");
+    public boolean isEmbedBibFileInPdf() {
+        return cl.hasOption("embedBibFileInPdf");
     }
 
-    public boolean isWriteMetadatatoPdf() {
-        return cl.hasOption("writeMetadatatoPdf");
+    public boolean isWriteMetadataToPdf() {
+        return cl.hasOption("writeMetadataToPdf");
     }
 
-    public String getWriteMetadatatoPdf() {
-        return cl.hasOption("writeMetadatatoPdf") ? cl.getOptionValue("writeMetadatatoPdf") :
-                cl.hasOption("writeXMPtoPdf") ? cl.getOptionValue("writeXMPtoPdf") :
+    public String getWriteMetadataToPdf() {
+        return cl.hasOption("writeMetadatatoPdf") ? cl.getOptionValue("writeMetadataToPdf") :
+                cl.hasOption("writeXMPtoPdf") ? cl.getOptionValue("writeXmpToPdf") :
                         cl.hasOption("embeddBibfileInPdf") ? cl.getOptionValue("embeddBibfileInPdf") : null;
     }
 
@@ -273,24 +272,24 @@ private static Options getOptions() {
 
         options.addOption(Option
                 .builder()
-                .longOpt("writeXMPtoPdf")
-                .desc("%s: '%s'".formatted(Localization.lang("Write BibTeXEntry as XMP metadata to PDF."), "-w pathToMyOwnPaper.pdf"))
+                .longOpt("writeXmpToPdf")
+                .desc("%s: '%s'".formatted(Localization.lang("Write BibTeX as XMP metadata to PDF."), "-w pathToMyOwnPaper.pdf"))
                 .hasArg()
                 .argName("CITEKEY1[,CITEKEY2][,CITEKEYn] | PDF1[,PDF2][,PDFn] | all")
                 .build());
 
         options.addOption(Option
                 .builder()
-                .longOpt("embeddBibfileInPdf")
+                .longOpt("embedBibFileInPdf")
                 .desc("%s: '%s'".formatted(Localization.lang("Embed BibTeX as attached file in PDF."), "-w pathToMyOwnPaper.pdf"))
                 .hasArg()
                 .argName("CITEKEY1[,CITEKEY2][,CITEKEYn] | PDF1[,PDF2][,PDFn] | all")
                 .build());
 
         options.addOption(Option
                 .builder("w")
-                .longOpt("writeMetadatatoPdf")
-                .desc("%s: '%s'".formatted(Localization.lang("Write BibTeXEntry as metadata to PDF."), "-w pathToMyOwnPaper.pdf"))
+                .longOpt("writeMetadataToPdf")
+                .desc("%s: '%s'".formatted(Localization.lang("Write BibTeX to PDF (XMP and embedded)"), "-w pathToMyOwnPaper.pdf"))
                 .hasArg()
                 .argName("CITEKEY1[,CITEKEY2][,CITEKEYn] | PDF1[,PDF2][,PDFn] | all")
                 .build());

src/main/java/org/jabref/gui/Base.css

@@ -648,6 +648,22 @@ TextFlow > .tooltip-text-monospaced {
     -fx-padding: 0 .5 0 .5;
 }
 
+.table-row-cell:matching-search-and-groups {
+    -fx-background-color: white;
+}
+
+.table-row-cell:matching-search-not-groups {
+    -fx-background-color: rgba(180, 180, 180, 0.86);
+}
+
+.table-row-cell:matching-groups-not-search {
+    -fx-background-color: rgba(140, 140, 140, 0.86);
+}
+
+.table-row-cell:not-matching-search-and-groups {
+    -fx-opacity: 60%;
+}
+
 .table-row-cell:hover,
 .tree-table-row-cell:hover {
     -fx-background-color: -jr-hover;