Merge remote-tracking branch 'origin/main' into just-jdk25

Author: koppor

.github/ghprcomment.yml

@@ -88,8 +88,8 @@
 
 # CHANGELOG.md and *.md
 
-- jobName: 'CHANGELOG.md needs to be modified'
-  workflowName: 'PR Tests'
+- jobName: 'CHANGELOG.md needs to be modified if indicated'
+  workflowName: 'Check PR CHANGELOG.md'
   message: >
     You ticked that you modified `CHANGELOG.md`, but no new entry was found there.
 
@@ -127,14 +127,14 @@
 # Submodules and branches
 
 - jobName: 'Submodules not modified'
-  workflowName: 'PR Tests'
+  workflowName: 'Check PR Modifications'
   message: >
     Your pull request modified git submodules.
 
 
     Please follow our [FAQ on submodules](https://devdocs.jabref.org/code-howtos/faq.html#submodules) to fix.
 - jobName: no-force-push
-  workflowName: 'PR Tests'
+  workflowName: 'Check PR Modifications'
   always: true
   message: >
     Hey, we noticed that you **force-pushed** your changes.
@@ -156,7 +156,7 @@
     Please [merge `upstream/main`](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork#syncing-a-fork-branch-from-the-command-line) with your code.
     For a step-by-step guide to resolve merge conflicts, see <https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/addressing-merge-conflicts/resolving-a-merge-conflict-using-the-command-line>.
 - jobName: 'Source branch is other than "main"'
-  workflowName: 'PR Tests'
+  workflowName: 'Check PR Modifications'
   message: >
     You committed your code on the `main` brach of your fork. This is a bad practice.
     The right way is to branch out from `main`, work on your patch/feature in that new branch, and then get that branch merged via the pull request (see [GitHub flow](https://docs.github.com/en/get-started/using-github/github-flow)).

.github/workflows/delete-old-runs-automatically.yml

@@ -15,14 +15,17 @@ jobs:
       - uses: plbstl/first-contribution@v4
         with:
           labels: first contrib
-          pr-opened-msg: |
+          pr-opened-msg: >
             ### Hey @{fc-author}!
 
+
             Thank you for contributing to JabRef! Your help is truly appreciated :heart:.
 
+
             We have automatic checks in place, based on which you will soon get automated feedback if any of them are failing.
             We also use [TragBot](https://usetrag.com/) with custom rules that scans your changes and provides some preliminary comments, before a maintainer takes a look.
             TragBot is still learning, and may not always be accurate.
             In the "Files changed" tab, you can go through its comments and just click on "Resolve conversation" if you are sure that it is incorrect, or comment on the conversation if you are doubtful.
 
+
             Please re-check our [contribution guide](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md) in case of any other doubts related to our contribution workflow.

.github/workflows/on-pr-opened.yml

@@ -44,9 +44,11 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added support for using Medline/Pubmed fetcher with an API key. [#11296](https://github.com/JabRef/jabref/issues/11296#issuecomment-3289005011)
 - We added support for using OpenAlex fetcher. [#13940](https://github.com/JabRef/jabref/issues/13940)
 - We added an option to choose the group during import of the entry(s). [#9191](https://github.com/JabRef/jabref/issues/9191)
+- We added an option to search and filter the fields and formatters in the Clean up entries dialog. [#13890](https://github.com/JabRef/jabref/issues/13890)
 
 ### Changed
 
+- We merged `Citation information` and `Citation relations` into a singular tab. [#13618](https://github.com/JabRef/jabref/issues/13618)
 - We changed `ISSNCleanup` into `NormalizeIssn` a `ISSN` formatter. [#13748](https://github.com/JabRef/jabref/issues/13748)
 - We changed Citation Relations tab and gave tab panes more descriptive titles and tooltips. [#13619](https://github.com/JabRef/jabref/issues/13619)
 - We changed the name from Open AI Provider to Open AI (or API compatible). [#13585](https://github.com/JabRef/jabref/issues/13585)
@@ -103,8 +105,9 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Fixed
 
+- We fixed an issue where search results would show stale entries after deleting entries from search results. [#13984](https://github.com/JabRef/jabref/issues/13984)
 - When filename pattern is missing for linked files, pattern handling has been introduced to avoid suggesting meaningless filenames like "-". [#13735](https://github.com/JabRef/jabref/issues/13735)
-- We fixed an issue where "Specify Bib(La)TeX" tab was not focused when Bib(La)TeX was in the clipboard [#13597](https://github.com/JabRef/jabref/issues/13597)
+- We fixed an issue where "Specify Bib(La)TeX" tab was not focused when Bib(La)TeX was in the clipboard. [#13597](https://github.com/JabRef/jabref/issues/13597)
 - We fixed an issue whereby the 'About' dialog was not honouring the user's configured font preferences. [#13558](https://github.com/JabRef/jabref/issues/13558)
 - We fixed an issue where the Pagetotal column was sorting the values alphabetically instead of numerically. [#12533](https://github.com/JabRef/jabref/issues/12533)
 - We fixed an issue where URLs starting with "www." (without a protocol) in file fields caused an `IllegalArgumentException: URI is not absolute` error. [#12186](https://github.com/JabRef/jabref/issues/12186)
@@ -145,7 +148,10 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where hierarchical keywords would only show the parent keyword in the entry editor. [#11390](https://github.com/JabRef/jabref/issues/11390)
 - We fixed an issue where some file choosers regarding LaTeX-aux files did not open in the directory of the last selected file. [#13861](https://github.com/JabRef/jabref/pull/13861)
 - We fixed an issue where the LaTeX file directory was not stored correctly in combination with the usage of groups from aux files. [#8344](https://github.com/JabRef/jabref/issues/8344)
+- We prevented a brief flash of the default JavaFX (Modena) theme on startup. [#13877](https://github.com/JabRef/jabref/pull/13877)
+- We fixed an issue where button-bar buttons truncated long text with ellipsis. [#13877](https://github.com/JabRef/jabref/pull/13877)
 - We fixed an issue where ignoring of subdirectories via `.gitingore` patterns did not work in the "Find unlinked files dialog". [forum#5425](https://discourse.jabref.org/t/set-list-of-ignored-folders-paths/5425/6)
+- We fixed an issue where the "Applications to push entries to" list in the preferences was not sorted alphabetically. [#14058](https://github.com/JabRef/jabref/issues/14058)
 
 ### Removed
 

CHANGELOG.md

@@ -1,5 +1,3 @@
-import org.gradle.api.internal.artifacts.dsl.dependencies.DependenciesExtensionModule.module
-
 plugins {
     id("org.gradlex.extra-java-module-info")
     id("org.gradlex.jvm-dependency-conflict-resolution")
@@ -662,4 +660,25 @@ extraJavaModuleInfo {
     module("org.openjdk.jmh:jmh-generator-bytecode", "jmh.generator.bytecode")
     module("org.openjdk.jmh:jmh-generator-reflection", "jmh.generator.reflection")
     module("org.apache.commons:commons-math3", "commons.math3")
+
+    // We need to transform this, because the java modules plugin touches all Java paths
+    // Otherwise, one gets following errormessage
+    // configuration ':jablib:annotationProcessor'.
+
+    module("javax.inject:javax.inject", "javax.inject")
+    module("com.google.auto.value:auto-value-annotations", "auto.value.annotations")
+    module("io.github.eisop:dataflow-errorprone", "org.checkerframework.dataflow")
+    module("com.google.googlejavaformat:google-java-format", "com.google.googlejavaformat")
+    module("com.google.errorprone:error_prone_core", "com.google.errorprone.core")
+    module("com.google.errorprone:error_prone_check_api", "com.google.errorprone.check.api")
+    module("com.google.errorprone:error_prone_annotation", "com.google.errorprone.annotation")
+    module("com.google.auto:auto-common", "auto.common")
+    module("com.google.auto.service:auto-service-annotations", "com.google.auto.service")
+    module("com.google.protobuf:protobuf-java", "com.google.protobuf")
+    module("com.github.kevinstern:software-and-algorithms", "software.and.algorithms")
+
+    module("com.uber.nullaway:nullaway", "nullaway")
+    module("org.checkerframework:dataflow-nullaway", "org.checkerframework.dataflow") {
+        exportAllPackages()
+    }
 }

build-logic/src/main/kotlin/org.jabref.gradle.base.dependency-rules.gradle.kts

@@ -1,8 +1,6 @@
 ---
-title: Adopt JSpecify nullness annotations for compile-time null safety
-nav_order: 51
+nav_order: 52
 parent: Decision Records
-status: pending
 ---
 
 # Adopt JSpecify nullness annotations for compile-time null safety
@@ -28,7 +26,7 @@ We want to detect null-safety issues earlier at compile time and improve API cla
 
 ## Decision Outcome
 
-Chosen option: "Adopt JSpecify annotations" because comes out best (see below).
+Chosen option: "Adopt JSpecify annotations" because it comes out best (see below).
 
 ## Consequences
 

…sions/0051-jspecify-nullable-annotations …ns/0052-jspecify-nullable-annotations.mddocs/decisions/0051-jspecify-nullable-annotations renamed to docs/decisions/0052-jspecify-nullable-annotations.md docs/decisions/0051-jspecify-nullable-annotations renamed to docs/decisions/0052-jspecify-nullable-annotations.md

@@ -0,0 +1,57 @@
+---
+nav_order: 53
+parent: Decision Records
+---
+
+# Null Checking Framework Selection
+
+## Context and Problem Statement
+
+Null pointer exceptions are a pervasive source of bugs in Java. To alleviate this, we want a compile-time null‐checking / nullness analysis framework. Two major contenders are Checker Framework and Error Prone (with NullAway). We also want our solution to align with modern nullness specification efforts such as JSpecify.
+
+## Decision Drivers
+
+* Static prevention of null dereference errors.
+* Developer experience: low friction, good IDE, and build integration.
+* Scalability to our codebase.
+* Interoperability with JSpecify and future ecosystem alignment.
+* Incremental adoption: we should not be forced to annotate everything at once.
+
+## Considered Options
+
+* Error Prone + NullAway
+* Checker Framework
+* No nullness analysis (status quo)
+
+## Decision Outcome
+
+Chosen option: "Error Prone + NullAway" because it comes out best (see below).
+
+## Consequences
+
+* We will annotate public APIs (interfaces, service endpoints, widely used modules) using JSpecify `@Nullable` / `@NonNull` (or `@NullMarked` scoping) progressively.
+* We enable NullAway in CI builds; thus violations break the build.
+* NullAway may not check some corner cases (especially around generics); therefore, manual reviews need to keep that in mind.
+* Developers must be trained on JSpecify and on how NullAway behaves.
+* Over time, we gradually annotate more of the codebase; initially non-annotated code will be treated as “unspecified nullness” until annotated.
+
+## Pros and Cons of the Options
+
+### Checker Framework
+
+* Good, because it supports advanced nullness contracts, refinement, and pluggability.
+* Bad, because compile times increase significantly.
+* Bad, because it lacks support for JSpecify’s `@NullMarked` / `@NullUnmarked` scopes.
+
+## Error Prone + NullAway
+
+* Good, because it is lightweight, fast, and has a low overhead.
+* Good, because support for JSpecify is built-in.
+* Good, because it fully supports JSpecify annotations.
+* Good, because it is [endorsed by JUnit 6](https://github.com/junit-team/junit-framework/wiki/Upgrading-to-JUnit-6.0#null-safety).
+* Bad, because it lacks support for advanced nullness contracts, refinement, and pluggability, and misses some edge cases.
+
+## No Nullness Framework
+
+* Good, because zero overhead or tooling complexity.
+* Bad, because we suffer from null pointer exceptions at runtime.

docs/decisions/0053-nullness-checking-framework.md

@@ -292,7 +292,7 @@ private void openWindow() {
         Scene scene = new Scene(JabRefGUI.mainFrame);
 
         LOGGER.debug("installing CSS");
-        themeManager.installCss(scene);
+        themeManager.installCssImmediately(scene);
 
         LOGGER.debug("Handle TextEditor key bindings");
         scene.addEventFilter(KeyEvent.KEY_PRESSED, event -> {

jabgui/src/main/java/org/jabref/gui/JabRefGUI.java

@@ -6,7 +6,6 @@
 import javafx.beans.value.ObservableValue;
 import javafx.fxml.FXML;
 import javafx.scene.control.CheckBox;
-import javafx.scene.control.ComboBox;
 import javafx.scene.control.SelectionMode;
 import javafx.scene.control.TableColumn;
 import javafx.scene.control.TableView;
@@ -27,6 +26,7 @@
 
 import com.airhacks.afterburner.views.ViewLoader;
 import jakarta.inject.Inject;
+import org.controlsfx.control.SearchableComboBox;
 
 public class FieldFormatterCleanupsPanel extends VBox {
 
@@ -35,8 +35,8 @@ public class FieldFormatterCleanupsPanel extends VBox {
     @FXML private TableColumn<FieldFormatterCleanup, Field> fieldColumn;
     @FXML private TableColumn<FieldFormatterCleanup, Formatter> formatterColumn;
     @FXML private TableColumn<FieldFormatterCleanup, Field> actionsColumn;
-    @FXML private ComboBox<Field> addableFields;
-    @FXML private ComboBox<Formatter> addableFormatters;
+    @FXML private SearchableComboBox<Field> addableFields;
+    @FXML private SearchableComboBox<Formatter> addableFormatters;
 
     @Inject private StateManager stateManager;
 

jabgui/src/main/java/org/jabref/gui/commonfxcontrols/FieldFormatterCleanupsPanel.java

@@ -324,7 +324,6 @@ private List<EntryEditorTab> createTabs() {
 
         tabs.add(new MathSciNetTab());
         tabs.add(new FileAnnotationTab(stateManager, preferences));
-        tabs.add(new SciteTab(preferences, taskExecutor, dialogService));
         tabs.add(new CitationRelationsTab(
                 dialogService,
                 undoManager,
@@ -376,7 +375,6 @@ private Map<String, Set<Field>> getAdditionalUserConfiguredTabs() {
         // Same order as in org.jabref.gui.entryeditor.EntryEditor.createTabs after the call of getAdditionalUserConfiguredTabs
         entryEditorTabList.remove(MathSciNetTab.NAME);
         entryEditorTabList.remove(FileAnnotationTab.NAME);
-        entryEditorTabList.remove(SciteTab.NAME);
         entryEditorTabList.remove(CitationRelationsTab.NAME);
         entryEditorTabList.remove(RelatedArticlesTab.NAME);
         // SourceTab is not listed, because it has different names for BibTeX and biblatex mode