Merge branch 'main' into fix/786

Author: Siedlerchr

.github/PULL_REQUEST_TEMPLATE.md

@@ -11,7 +11,7 @@ Closes _____
 <!-- You can add screenshots or videos (using Loom - https://www.loom.com or by just adding .mp4 files). -->
 <!-- (REPLACE THIS PARAGRAPH) -->
 
-<!-- YOU HAVE TO MODIFY THE ABOVE TEXT FIT YOUR PR. OTHERWISE, YOUR PR WILL BE CLOSED WITHOUT FURTHER COMMENT. -->
+<!-- YOU HAVE TO MODIFY THE ABOVE TEXT TO FIT YOUR PR. OTHERWISE, YOUR PR WILL BE CLOSED WITHOUT FURTHER COMMENT. -->
 
 ### Mandatory checks
 

.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/binaries.yml

@@ -154,16 +154,16 @@ jobs:
             archivePortableJabKit: 7z a -r jabkit/build/packages/windows-latest/jabkit-portable_windows.zip ./jabkit/build/packages/windows-latest/jabkit && rm -R jabkit/build/packages/windows-latest/jabkit
             suffix: ''
             archForDebianRepack: ''
-          - os: macos-13  # intel image
+          - os: macos-15-intel  # intel image
             displayName: macOS
-            archivePortable: 7z a -r jabgui/build/packages/macos-13/JabRef-portable_macos.zip ./jabgui/build/packages/macos-13/JabRef.app && rm -R jabgui/build/packages/macos-13/JabRef.app
-            archivePortableJabKit: 7z a -r jabkit/build/packages/macos-13/jabkit-portable_macos.zip ./jabkit/build/packages/macos-13/jabkit.app && rm -R jabkit/build/packages/macos-13/jabkit.app
+            archivePortable: 7z a -r jabgui/build/packages/macos-15-intel/JabRef-portable_macos.zip ./jabgui/build/packages/macos-15-intel/JabRef.app && rm -R jabgui/build/packages/macos-15-intel/JabRef.app
+            archivePortableJabKit: 7z a -r jabkit/build/packages/macos-15-intel/jabkit-portable_macos.zip ./jabkit/build/packages/macos-15-intel/jabkit.app && rm -R jabkit/build/packages/macos-15-intel/jabkit.app
             suffix: ''
             archForDebianRepack: ''
-          - os: macos-14
+          - os: macos-15
             displayName: macOS-arm
-            archivePortable: 7z a -r jabgui/build/packages/macos-14/JabRef-portable_macos-arm.zip ./jabgui/build/packages/macos-14/JabRef.app && rm -R jabgui/build/packages/macos-14/JabRef.app
-            archivePortableJabKit: 7z a -r jabkit/build/packages/macos-14/jabkit-portable_macos-arm.zip ./jabkit/build/packages/macos-14/jabkit.app && rm -R jabkit/build/packages/macos-14/jabkit.app
+            archivePortable: 7z a -r jabgui/build/packages/macos-15/JabRef-portable_macos-arm.zip ./jabgui/build/packages/macos-15/JabRef.app && rm -R jabgui/build/packages/macos-15/JabRef.app
+            archivePortableJabKit: 7z a -r jabkit/build/packages/macos-15/jabkit-portable_macos-arm.zip ./jabkit/build/packages/macos-15/jabkit.app && rm -R jabkit/build/packages/macos-15/jabkit.app
             suffix: '_arm64'
             archForDebianRepack: ''
     runs-on: ${{ matrix.os }}
@@ -396,10 +396,10 @@ jobs:
       max-parallel: 1
       matrix:
         include:
-          - os: macos-14
+          - os: macos-15
             displayName: macOS (ARM64)
             suffix: '_arm64'
-          - os: macos-13  # intel image
+          - os: macos-15-intel  # intel image
             displayName: macOS
             suffix: ''
     runs-on: ${{ matrix.os }}

.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

@@ -18,6 +18,12 @@
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticBuilder.java
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java
+//SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/LspLinkHandler.java
+//SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/LspParserHandler.java
+//SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/LspRangeUtil.java
+//SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/DefinitionProvider.java
+//SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/DefinitionProviderFactory.java
+//SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/MarkdownDefinitionProvider.java
 
 // REPOS mavencentral,snapshots=https://central.sonatype.com/repository/maven-snapshots/
 // REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,s01oss=https://s01.oss.sonatype.org/content/repositories/snapshots/,oss=https://oss.sonatype.org/content/repositories,jitpack=https://jitpack.io,oss2=https://oss.sonatype.org/content/groups/public,ossrh=https://oss.sonatype.org/content/repositories/snapshots

.jbang/JabLsLauncher.java

@@ -85,7 +85,7 @@
 //DEPS com.konghq:unirest-modules-gson:4.5.1
 //DEPS com.google.guava:guava:33.5.0-jre
 //DEPS org.jabref:afterburner.fx:2.0.0
-//DEPS net.harawata:appdirs:1.4.0
+//DEPS net.harawata:appdirs:1.5.0
 //DEPS de.undercouch:citeproc-java:3.3.0
 
 /// This class is required for [jbang](https://www.jbang.dev/)

.jbang/JabSrvLauncher.java

@@ -44,9 +44,12 @@ 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)
+- We added support for managing multiple linked files via the entry context menu. [#12567](https://github.com/JabRef/jabref/issues/12567)
 
 ### 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)
@@ -70,6 +73,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added support for import of a Refer/BibIX file format. [#13069](https://github.com/JabRef/jabref/issues/13069)
 - We added markdown rendering and copy capabilities to AI chat responses. [#12234](https://github.com/JabRef/jabref/issues/12234)
 - We added a new `jabkit` command `pseudonymize` to pseudonymize the library. [#13109](https://github.com/JabRef/jabref/issues/13109)
+- We moved the clear fields mechanic in the Automatic Field Editor from the edit content tab to a separate tab. [#13780](https://github.com/JabRef/jabref/issues/13780)
 - We added functionality to focus running instance when trying to start a second instance. [#13129](https://github.com/JabRef/jabref/issues/13129)
 - We added a "Copy Field Content" submenu to the entry context menu, allowing users to quickly copy specific field contents including Author, Journal, Date, Keywords, and Abstract fields from selected entries. [#13280](https://github.com/JabRef/jabref/pull/13280)
 - We added a highlighted diff regarding changes to the Group Tree Structure of a bib file, made outside JabRef. [#11221](https://github.com/JabRef/jabref/issues/11221)
@@ -103,8 +107,9 @@ 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 +150,13 @@ 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 CTRL+W does not close the current tab [#12530](https://github.com/JabRef/jabref/issues/12530)
+- 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)
+- We fixed an issue where notice text in AI chat was not automatically refreshed when the user changed preferences.[#13855](https://github.com/JabRef/jabref/issues/13855)
+- We fixed an issue where the user could add custom entry types with spaces in their names. [#14088](https://github.com/JabRef/jabref/issues/14088)
 
 ### Removed
 

CHANGELOG.md

@@ -8,10 +8,10 @@ repositories {
 
 dependencies {
     implementation("com.adarshr:gradle-test-logger-plugin:4.0.0")
-    implementation("com.autonomousapps:dependency-analysis-gradle-plugin:3.0.4")
+    implementation("com.autonomousapps:dependency-analysis-gradle-plugin:3.1.0")
     implementation("com.github.andygoossens:gradle-modernizer-plugin:1.12.0")
     implementation("org.gradlex:extra-java-module-info:1.13.1")
-    implementation("org.gradlex:java-module-dependencies:1.10")
+    implementation("org.gradlex:java-module-dependencies:1.11")
     implementation("org.gradlex:java-module-packaging:1.1") // required for platform-specific packaging of JavaFX dependencies
     implementation("org.gradlex:java-module-testing:1.7")
     implementation("org.gradlex:jvm-dependency-conflict-resolution:2.4")

build-logic/build.gradle.kts

@@ -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()
+    }
 }