Merge remote-tracking branch 'upstream/ai-pr-1' into ai-pr-1

.github/workflows/tests.yml

@@ -5,10 +5,9 @@ on:
     branches:
       - main
       - main-release
+  pull_request:
   merge_group:
   workflow_dispatch:
-  # The checkers should write comments on the PR if something fails. For this, we need to have a proper GITHUB_TOKEN. This is enabled by ..._target.
-  pull_request_target:
 
 env:
   SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
@@ -52,21 +51,8 @@ jobs:
           gradle-home-cache-cleanup: true
       - name: Run checkstyle using gradle
         run: ./gradlew checkstyleMain checkstyleTest checkstyleJmh
-      - name: Add comment on pull request
-        if: ${{ failure() }}
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: >
-              Your code currently does not meet [JabRef's code guidelines](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html).
-              We use [Checkstyle](https://checkstyle.sourceforge.io/) to identify issues.
-              The tool reviewdog already placed comments on GitHub to indicate the places. See the tab "Files" in you PR.
-              Please carefully follow [the setup guide for the codestyle](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html).
-              Afterwards, please [run checkstyle locally](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html#run-checkstyle) and fix the issues.
 
 
-              You can check review dog's comments at the tab "Files changed" of your pull request.
-          comment_tag: automated-test-feedback
-
   openrewrite:
     name: OpenRewrite
     runs-on: ubuntu-latest
@@ -88,19 +74,6 @@ jobs:
       - name: Run OpenRewrite
         run: |
           ./gradlew rewriteDryRun
-      - name: Add comment on pull request
-        if: ${{ failure() }}
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: >
-              Your code currently does not meet JabRef's code guidelines.
-              We use [OpenRewrite](https://docs.openrewrite.org/) to ensure "modern" Java coding practices.
-              The issues found can be **automatically fixed**.
-              Please execute the gradle task *`rewriteRun`*, check the results, commit, and push.
-
-
-              You can check the detailed error output by navigating to your pull request, selecting the tab "Checks", section "Tests" (on the left), subsection "OpenRewrite".
-          comment_tag: automated-test-feedback
 
   modernizer:
     name: Modernizer
@@ -125,18 +98,6 @@ jobs:
           # enable failing of this task if modernizer complains
           sed -i "s/failOnViolations = false/failOnViolations = true/" build.gradle
           ./gradlew modernizer
-      - name: Add comment on pull request
-        if: ${{ failure() }}
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: >
-              Your code currently does not meet JabRef's code guidelines.
-              We use [Gradle Modernizer Plugin](https://github.com/andygoossens/gradle-modernizer-plugin#gradle-modernizer-plugin) to ensure "modern" Java coding practices.
-              Please fix the detected errors, commit, and push.
-
-
-              You can check the detailed error output by navigating to your pull request, selecting the tab "Checks", section "Tests" (on the left), subsection "Modernizer".
-          comment_tag: automated-test-feedback
 
   markdown:
     name: Markdown
@@ -153,18 +114,6 @@ jobs:
           globs: |
             *.md
             docs/**/*.md
-      - name: Add comment on pull request
-        if: ${{ failure() }}
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: >
-              You modified Markdown (`*.md`) files and did not meet JabRef's rules for consistently formatted Markdown files.
-              To ensure consistent styling, we have [markdown-lint](https://github.com/DavidAnson/markdownlint) in place.
-              [Markdown lint's rules](https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md#rules) help to keep our Markdown files consistent within this repository and consistent with the Markdown files outside here.
-
-
-              You can check the detailed error output by navigating to your pull request, selecting the tab "Checks", section "Tests" (on the left), subsection "Markdown".
-          comment_tag: automated-test-feedback
 
   changelog:
     name: CHANGELOG.md
@@ -213,14 +162,6 @@ jobs:
           diff \
             <(git show origin/main:CHANGELOG.md | clparse --format=json --separator=– - | jq '.releases[] | select(.version != null)') \
             <(git show HEAD:CHANGELOG.md | clparse --format=json --separator=– - | jq '.releases[] | select(.version != null)')
-      - name: Add comment on pull request
-        if: ${{ failure() }}
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: >
-              While the PR was in progress, JabRef released a new version.
-              You have to merge `upstream/main` and move your entry in `CHANGELOG.md` up to the section `## [Unreleased]`.
-          comment_tag: automated-test-feedback
 
   tests:
     name: Unit tests

PRIVACY.md

@@ -49,18 +49,21 @@ These third-party services are the following:
 | [Collection of Computer Science Bibliographies](https://en.wikipedia.org/wiki/Collection_of_Computer_Science_Bibliographies) | **currently unavailable**, offline  |
 | [CrossRef](https://www.crossref.org/)                                                                                        | <https://www.crossref.org/operations-and-sustainability/privacy/> |
 | [dblp](https://dblp.uni-trier.de/)                                                                                           | <https://dblp.uni-trier.de/db/about/privacy.html> |
+| [DJL (Deep Java Library)](https://djl.ai/)                                                                                   | <https://github.com/deepjavalibrary/djl/discussions/3370#discussioncomment-10233632> |
 | [Directory of Open Access Books](https://www.doabooks.org/)                                                                  | <https://www.doabooks.org/en/resources/accessibility> |
 | [Digitala Vetenskapliga Arkivet](https://www.diva-portal.org/)                                                               | <https://www.uu.se/en/about-uu/data-protection-policy/> |
 | [DOI Foundation](https://www.doi.org/)                                                                                       | <https://www.doi.org/privacy-policy/> |
 | [Elsevier](https://www.elsevier.com/)                                                                                        | <https://www.elsevier.com/legal/privacy-policy> |
 | [Google Scholar](https://scholar.google.com/)                                                                                | <https://policies.google.com/privacy> |
 | [Gemeinsamer Verbundkatalog](https://www.gbv.de/)                                                                            | <https://www.gbv.de/datenschutz> |
+| [Hugging Face](https://huggingface.co/)                                                                                      | <https://huggingface.co/privacy> |
 | [IACR](https://www.iacr.org/)                                                                                                | <https://www.iacr.org/privacy.html> |
 | [IEEEXplore](https://ieeexplore.ieee.org/Xplore/home.jsp)                                                                    | <https://www.ieee.org/security-privacy.html> |
 | [INSPIRE](https://inspirehep.net/)                                                                                           | <https://cern.service-now.com/service-portal?id=privacy_policy&se=INSPIRE-Online&notice=main> |
 | [ISIDORE](https://isidore.science/)                                                                                          | <https://isidore.science/credit> |
 | [JSTOR](https://www.jstor.org/)                                                                                              | <https://www.ithaka.org/privacypolicy/> |
 | [Library of Congress](https://lccn.loc.gov/)                                                                                 | <https://www.loc.gov/legal/> |
+| [Mistral AI](https://mistral.ai/)                                                                                            | <https://mistral.ai/terms/#privacy-policy> |
 | [National Library of Medicine](https://www.ncbi.nlm.nih.gov/)                                                                | <https://www.nlm.nih.gov/web_policies.html> |
 | [MathSciNet](http://www.ams.org/mathscinet)                                                                                  | <https://www.ams.org/about-us/privacy> |
 | [mEDRA](https://www.medra.org/)                                                                                              | <https://www.medra.org/stdoc/en/Servizio_DOI_Informativa_ENG.pdf> |

build.gradle

@@ -152,7 +152,7 @@ dependencies {
     // Include all jar-files in the 'lib' folder as dependencies
     implementation fileTree(dir: 'lib', includes: ['*.jar'])
 
-    def pdfbox = "3.0.2"
+    def pdfbox = "3.0.3"
     implementation ("org.apache.pdfbox:pdfbox:$pdfbox") {
         exclude group: 'commons-logging'
     }
@@ -182,8 +182,12 @@ dependencies {
 
     implementation 'commons-cli:commons-cli:1.8.0'
 
+    // region: LibreOffice
     implementation 'org.libreoffice:unoloader:24.2.3'
     implementation 'org.libreoffice:libreoffice:24.2.3'
+    // Required for ID generation
+    implementation 'io.github.thibaultmeyer:cuid:2.0.3'
+    // endregion
 
     implementation 'io.github.java-diff-utils:java-diff-utils:4.12'
     implementation 'info.debatty:java-string-similarity:2.0.0'
@@ -256,7 +260,7 @@ dependencies {
     implementation 'com.konghq:unirest-modules-gson:4.4.4'
     implementation 'org.apache.httpcomponents.client5:httpclient5:5.3.1'
 
-    implementation 'org.slf4j:slf4j-api:2.0.13'
+    implementation 'org.slf4j:slf4j-api:2.0.16'
     implementation 'org.tinylog:tinylog-api:2.7.0'
     implementation 'org.tinylog:slf4j-tinylog:2.7.0'
     implementation 'org.tinylog:tinylog-impl:2.7.0'
@@ -295,7 +299,7 @@ dependencies {
     // Implementation of the API
     implementation 'org.glassfish.jersey.core:jersey-server:3.1.7'
     // injection framework
-    implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.7'
+    implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.8'
     implementation 'org.glassfish.hk2:hk2-api:3.1.1'
     // testImplementation 'org.glassfish.hk2:hk2-testing:3.0.4'
     // implementation 'org.glassfish.hk2:hk2-testing-jersey:3.0.4'
@@ -351,7 +355,7 @@ dependencies {
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:1.3.0'
     testImplementation "org.testfx:testfx-core:4.0.16-alpha"
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
-    testImplementation "org.hamcrest:hamcrest-library:2.2"
+    testImplementation "org.hamcrest:hamcrest-library:3.0"
 
     checkstyle 'com.puppycrawl.tools:checkstyle:10.17.0'
     // xjc needs the runtime as well for the ant task, otherwise it fails

src/main/java/module-info.java

@@ -174,6 +174,7 @@
     requires transitive org.jspecify;
 
     // region: other libraries (alphabetically)
+    requires cuid;
     requires dd.plist;
     // required by okhttp and some AI library
     requires kotlin.stdlib;

src/main/java/org/jabref/gui/icon/IconTheme.java

@@ -359,7 +359,8 @@ public enum JabRefIcons implements JabRefIcon {
         REMOVE_TAGS(MaterialDesignC.CLOSE),
         ACCEPT_LEFT(MaterialDesignS.SUBDIRECTORY_ARROW_LEFT),
         ACCEPT_RIGHT(MaterialDesignS.SUBDIRECTORY_ARROW_RIGHT),
-        MERGE_GROUPS(MaterialDesignS.SOURCE_MERGE);
+        MERGE_GROUPS(MaterialDesignS.SOURCE_MERGE),
+        ADD_OR_MAKE_BIBLIOGRAPHY(JabRefMaterialDesignIcon.BIBLIOGRAPHY);
 
         private final JabRefIcon icon;
 

src/main/java/org/jabref/gui/icon/JabRefMaterialDesignIcon.java

@@ -32,7 +32,8 @@ public enum JabRefMaterialDesignIcon implements Ikon {
     CANCEL("jab-cancel", '\ue90e'),
     SUBLIME_TEXT("jab-sublime-text", '\ue90f'),
     TEXSHOP("jab-texshop", '\ue910'),
-    TEXWORKS("jab-texworks", '\ue911');
+    TEXWORKS("jab-texworks", '\ue911'),
+    BIBLIOGRAPHY("jab-bibliography", '\ue912');
 
     private String description;
     private int code;