Merge branch 'main' into fix/12351-area-of-preview-hover

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -13,6 +13,7 @@ body:
       label: JabRef version
       options:
         - "5.15 (latest release)"
+        - "6.0-alpha"
         - Latest development branch build (please note build date below)
         - Other (please describe below)
       description: The version as shown in the about dialog.

.github/workflows/deployment-arm64.yml

@@ -69,12 +69,12 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v3.0.3
+        uses: gittools/actions/gitversion/setup@v3.1.1
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v3.0.3
+        uses: gittools/actions/gitversion/execute@v3.1.1
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

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

@@ -85,12 +85,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v3.0.3
+        uses: gittools/actions/gitversion/setup@v3.1.1
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v3.0.3
+        uses: gittools/actions/gitversion/execute@v3.1.1
 
       # JDK
       - name: 'Set up JDK ${{ matrix.jdk }}'

.github/workflows/deployment.yml

@@ -81,12 +81,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v3.0.3
+        uses: gittools/actions/gitversion/setup@v3.1.1
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v3.0.3
+        uses: gittools/actions/gitversion/execute@v3.1.1
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

.github/workflows/gource.yml

@@ -26,7 +26,7 @@ jobs:
       - name: 'Development history of current build'
         uses: BoundfoxStudios/action-gource@v2
         with:
-          gource_title: 'JabRef v5.16 (in development) | more information at contribute.jabref.org'
+          gource_title: 'JabRef v6.0 (in development) | more information at contribute.jabref.org'
           logo_url: 'https://www.jabref.org/img/JabRef-icon-256.png'
           avatars_auto_fetch: true
           # 5s * 365 / 4 = 7.5min
@@ -36,7 +36,7 @@ jobs:
       - name: 'Store video'
         run: |
           mkdir gource-videos
-          mv ./gource/gource.mp4 ./gource-videos/jabref-v5.16-dev.mp4
+          mv ./gource/gource.mp4 ./gource-videos/jabref-v6.0-dev.mp4
       - name: 'Development history of last release'
         uses: BoundfoxStudios/action-gource@v2
         with:

CHANGELOG.md

@@ -11,6 +11,20 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+### Changed
+
+- We improved the offline parsing of BibTeX data from PDF-documents. [#12278](https://github.com/JabRef/jabref/issues/12278)
+
+### Fixed
+
+- We fixed an issue where a bib file with UFF-8 charset was wrongly loaded with a different charset [forum#5369](https://discourse.jabref.org/t/jabref-5-15-opens-bib-files-with-shift-jis-encoding-instead-of-utf-8/5369/)
+
+### Removed
+
+## [6.0-alpha] – 2024-12-23
+
+### Added
+
 - We added a Markdown export layout. [#12220](https://github.com/JabRef/jabref/pull/12220)
 - We added a "view as BibTeX" option before importing an entry from the citation relation tab. [#11826](https://github.com/JabRef/jabref/issues/11826)
 - We added support finding LaTeX-encoded special characters based on plain Unicode and vice versa. [#11542](https://github.com/JabRef/jabref/pull/11542)
@@ -82,6 +96,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - The CitationKey column is now a default shown column for the entry table. [#10510](https://github.com/JabRef/jabref/issues/10510)
 - We disabled the actions "Open Terminal here" and "Reveal in file explorer" for unsaved libraries. [#11920](https://github.com/JabRef/jabref/issues/11920)
 - JabRef now opens the corresponding directory in the library properties when "Browse" is clicked. [#12223](https://github.com/JabRef/jabref/pull/12223)
+- We changed the icon for macOS to be more consistent with Apple's Guidelines [#8443](https://github.com/JabRef/jabref/issues/8443)
 
 ### Fixed
 
@@ -126,19 +141,15 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where identifier paste couldn't work with Unicode REPLACEMENT CHARACTER. [#11986](https://github.com/JabRef/jabref/issues/11986)
 - We fixed an issue when click on entry at "Check Integrity" wasn't properly focusing the entry and field. [#11997](https://github.com/JabRef/jabref/issues/11997)
 - We fixed an issue with the ui not scaling when changing the font size [#11219](https://github.com/JabRef/jabref/issues/11219)
+- We fixed an issue where a custom application for external file types would not be saved [#112311](https://github.com/JabRef/jabref/issues/12311)
+- We fixed an issue where a file that no longer exists could not be deleted from an entry using keyboard shortcut [#9731](https://github.com/JabRef/jabref/issues/9731)
 
 ### Removed
 
 - We removed the description of search strings. [#11542](https://github.com/JabRef/jabref/pull/11542)
 - We removed support for importing using the SilverPlatterImporter (`Record INSPEC`). [#11576](https://github.com/JabRef/jabref/pull/11576)
 - We removed support for automatically generating file links using the CLI (`--automaticallySetFileLinks`).
 
-
-
-
-
-
-
 ## [5.15] – 2024-07-10
 
 ### Added
@@ -1485,7 +1496,8 @@ The changelog of JabRef 4.x is available at the [v4.3.1 tag](https://github.com/
 The changelog of JabRef 3.x is available at the [v3.8.2 tag](https://github.com/JabRef/jabref/blob/v3.8.2/CHANGELOG.md).
 The changelog of JabRef 2.11 and all previous versions is available as [text file in the v2.11.1 tag](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG).
 
-[Unreleased]: https://github.com/JabRef/jabref/compare/v5.15...HEAD
+[Unreleased]: https://github.com/JabRef/jabref/compare/v6.0-alpha...HEAD
+[6.0-alpha]: https://github.com/JabRef/jabref/compare/v5.15...v6.0-alpha
 [5.15]: https://github.com/JabRef/jabref/compare/v5.14...v5.15
 [5.14]: https://github.com/JabRef/jabref/compare/v5.13...v5.14
 [5.13]: https://github.com/JabRef/jabref/compare/v5.12...v5.13

GitVersion.yml

@@ -5,5 +5,5 @@ mode: ContinuousDeployment
 branches:
   main:
     regex: ^main
-    tag: ''
-    pre-release-weight: 0  # 0 after stable release, 15000 before alpha release, 30000 before beta release, 50000 before stable release
+    tag: 'alpha'
+    pre-release-weight: 15000 # 0 after stable release, 15000 before alpha release, 30000 before beta release, 50000 before stable release

build.gradle

@@ -29,7 +29,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.27.2'
+    id 'org.openrewrite.rewrite' version '6.29.3'
 
     id "org.itsallcode.openfasttrace" version "3.0.1"
 }
@@ -172,7 +172,7 @@ dependencies {
         exclude group: 'commons-logging'
     }
 
-    def luceneVersion = "10.0.0"
+    def luceneVersion = "10.1.0"
     implementation "org.apache.lucene:lucene-core:$luceneVersion"
     implementation "org.apache.lucene:lucene-queryparser:$luceneVersion"
     implementation "org.apache.lucene:lucene-queries:$luceneVersion"
@@ -181,7 +181,7 @@ dependencies {
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.12.0'
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.17.0'
-    implementation group: 'org.apache.commons', name: 'commons-text', version: '1.12.0'
+    implementation group: 'org.apache.commons', name: 'commons-text', version: '1.13.0'
     implementation 'commons-logging:commons-logging:1.3.4'
     implementation 'com.h2database:h2-mvstore:2.3.232'
 
@@ -204,10 +204,10 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.13.2'
     implementation 'org.antlr:antlr4-runtime:4.13.2'
 
-    implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '7.0.0.202409031743-r'
+    implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '7.1.0.202411261347-r'
 
-    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.18.1'
-    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.18.1'
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.18.2'
+    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.18.2'
 
     implementation 'com.fasterxml:aalto-xml:1.3.3'
 
@@ -243,8 +243,8 @@ dependencies {
         exclude group: 'org.openjfx'
     }
     implementation 'org.fxmisc.flowless:flowless:0.7.3'
-    implementation 'org.fxmisc.richtext:richtextfx:0.11.3'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.64.0') {
+    implementation 'org.fxmisc.richtext:richtextfx:0.11.4'
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.80.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude module: 'commons-lang3'
         exclude group: 'org.apache.commons.validator'
@@ -265,7 +265,7 @@ dependencies {
     implementation 'org.controlsfx:controlsfx:11.2.1'
 
     // region HTTP clients
-    implementation 'org.jsoup:jsoup:1.18.1'
+    implementation 'org.jsoup:jsoup:1.18.3'
     implementation 'com.konghq:unirest-java-core:4.4.5'
     implementation 'com.konghq:unirest-modules-gson:4.4.5'
     implementation 'org.apache.httpcomponents.client5:httpclient5:5.4.1'
@@ -279,9 +279,9 @@ dependencies {
     // route all requests to java.util.logging to SLF4J (which in turn routes to tinylog)
     implementation 'org.slf4j:jul-to-slf4j:2.0.16'
     // route all requests to log4j to SLF4J
-    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.24.2'
+    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.24.3'
 
-    implementation('de.undercouch:citeproc-java:3.1.0') {
+    implementation('de.undercouch:citeproc-java:3.2.0') {
         exclude group: 'org.antlr'
     }
 
@@ -335,7 +335,7 @@ dependencies {
     implementation 'org.yaml:snakeyaml:2.3'
 
     // region AI
-    implementation 'dev.langchain4j:langchain4j:0.36.0'
+    implementation 'dev.langchain4j:langchain4j:0.36.2'
     // Even though we use jvm-openai for LLM connection, we still need this package for tokenization.
     implementation('dev.langchain4j:langchain4j-open-ai:0.36.2') {
         exclude group: 'com.squareup.okhttp3'
@@ -358,7 +358,7 @@ dependencies {
     }
 
     implementation 'org.apache.velocity:velocity-engine-core:2.4.1'
-    implementation platform('ai.djl:bom:0.30.0')
+    implementation platform('ai.djl:bom:0.31.1')
     implementation 'ai.djl:api'
     implementation 'ai.djl.huggingface:tokenizers'
     implementation 'ai.djl.pytorch:pytorch-model-zoo'
@@ -380,8 +380,8 @@ dependencies {
     implementation enforcedPlatform('io.zonky.test.postgres:embedded-postgres-binaries-bom:17.2.0')
 
     testImplementation 'io.github.classgraph:classgraph:4.8.179'
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.11.3'
-    testImplementation 'org.junit.platform:junit-platform-launcher:1.11.3'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.11.4'
+    testImplementation 'org.junit.platform:junit-platform-launcher:1.11.4'
 
     testImplementation 'org.mockito:mockito-core:5.14.2'
     testImplementation 'org.xmlunit:xmlunit-core:2.10.0'
@@ -394,14 +394,14 @@ dependencies {
     testImplementation "com.github.javaparser:javaparser-symbol-solver-core:3.26.2"
 
     // recommended by https://github.com/wiremock/wiremock/issues/2149#issuecomment-1835775954
-    testImplementation 'org.wiremock:wiremock-standalone:3.9.2'
+    testImplementation 'org.wiremock:wiremock-standalone:3.10.0'
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.20.1'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.21.1'
     // xjc needs the runtime as well for the ant task, otherwise it fails
     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:2.22.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.23.2"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")
@@ -594,7 +594,8 @@ javadoc {
         version = false
         author = false
         addMultilineStringsOption("-add-exports").setValue([
-            'javafx.controls/com.sun.javafx.scene.control=org.jabref'
+            'javafx.controls/com.sun.javafx.scene.control=org.jabref',
+            'org.controlsfx.controls/impl.org.controlsfx.skin=org.jabref'
         ])
     }
 }