Merge branch 'main' into hotfix/11674-deprecated-api-usages

* main:
  Rename ghprcomment.yaml to ghprcomment.yml
  Add commenting functionality (JabRef#11672)
  Bump io.github.classgraph:classgraph from 4.8.174 to 4.8.175 (JabRef#11676)
  Bump io.github.stefanbratanov:jvm-openai from 0.9.3 to 0.10.0 (JabRef#11680)
  Bump com.puppycrawl.tools:checkstyle from 10.17.0 to 10.18.0 (JabRef#11679)
  Bump com.h2database:h2-mvstore from 2.3.230 to 2.3.232 (JabRef#11678)
  Bump org.postgresql:postgresql from 42.7.3 to 42.7.4 (JabRef#11677)
  Bump src/main/resources/csl-styles from `d9989a2` to `35ac18d` (JabRef#11675)

Author: viktorkrimstein

.github/ghprcomment.yml

@@ -0,0 +1,36 @@
+- jobName: Checkstyle
+  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.
+- jobName: OpenRewrite
+  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".
+- jobName: Modernizer
+  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".
+- jobName: Markdown
+  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".
+- jobName: CHANGELOG.md
+  message: |
+    While the PR was in progress, a new version of JabRef has been released.
+    You have to merge `upstream/main` and move your entry in `CHANGELOG.md` up to the section `## [Unreleased]`.

.github/workflows/pr-comment.yml

@@ -0,0 +1,52 @@
+# Description: This workflow is triggered when the "Check" workflow completes.
+# Since this pull request has write permissions on the target repo, we should **NOT** execute any untrusted code.
+# https://securitylab.github.com/research/github-actions-preventing-pwn-requests/
+# Based on https://github.com/spring-projects/spring-security/pull/15477/files
+---
+name: Comment on PR
+
+on:
+  workflow_run:
+    workflows: ["Tests"]
+    types:
+      - completed
+
+jobs:
+  comment:
+    # https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#running-a-workflow-based-on-the-conclusion-of-another-workflow
+    if: ${{ github.event.workflow_run.conclusion == 'failure' }}
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      pull-requests: write
+    timeout-minutes: 10
+    steps:
+      - name: Download PR number
+        uses: actions/download-artifact@v4
+        with:
+          name: pr_number
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          run-id: ${{ github.event.workflow_run.id }}
+      - name: Read pr_number.txt
+        id: read-pr_number
+        run: |
+          PR_NUMBER=$(cat pr_number.txt)
+          echo "Read PR number $PR_NUMBER"
+          echo "pr_number=$PR_NUMBER" >> $GITHUB_OUTPUT
+      - name: Checkout
+        if: ${{ steps.read-pr_number.outputs.pr_number != '' }}
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: '0'
+          show-progress: 'false'
+          token: ${{ secrets.GITHUB_TOKEN }}
+      - name: jbang
+        if: ${{ steps.read-pr_number.outputs.pr_number != '' }}
+        uses: jbangdev/jbang-action@v0.117.1
+        with:
+          script: ghprcomment@koppor/ghprcomment
+          scriptargs: "-r koppor/workflow-comment-test -p ${{ steps.read-pr_number.outputs.pr_number }} -w ${{ github.event.workflow_run.id }}"
+          trust: https://github.com/koppor/ghprcomment/
+        env:
+          GITHUB_OAUTH: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/tests.yml

@@ -363,3 +363,13 @@ jobs:
         with:
           script: |
               core.setFailed('Pull requests should come from a branch other than "main"\n\n👉 Please read https://devdocs.jabref.org/contributing again carefully. 👈')
+
+  upload-pr-number:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Create pr_number.txt
+        run: echo "${{ github.event.number }}" > pr_number.txt
+      - uses: actions/upload-artifact@v4
+        with:
+          name: pr_number
+          path: pr_number.txt

build.gradle

@@ -175,7 +175,7 @@ dependencies {
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.16.0'
     implementation group: 'org.apache.commons', name: 'commons-text', version: '1.12.0'
     implementation 'commons-logging:commons-logging:1.3.3'
-    implementation 'com.h2database:h2-mvstore:2.3.230'
+    implementation 'com.h2database:h2-mvstore:2.3.232'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     implementation 'org.bouncycastle:bcprov-jdk18on:1.78.1'
@@ -205,7 +205,7 @@ dependencies {
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.9'
 
-    implementation 'org.postgresql:postgresql:42.7.3'
+    implementation 'org.postgresql:postgresql:42.7.4'
 
     // Support unix socket connection types
     implementation 'com.kohlschutter.junixsocket:junixsocket-core:2.10.0'
@@ -334,7 +334,7 @@ dependencies {
     implementation 'ai.djl:api:0.29.0'
     implementation 'ai.djl.pytorch:pytorch-model-zoo:0.29.0'
     implementation 'ai.djl.huggingface:tokenizers:0.29.0'
-    implementation 'io.github.stefanbratanov:jvm-openai:0.9.3'
+    implementation 'io.github.stefanbratanov:jvm-openai:0.10.0'
     // openai depends on okhttp, which needs kotlin - see https://github.com/square/okhttp/issues/5299 for details
     implementation ('com.squareup.okhttp3:okhttp:4.12.0') {
         exclude group: 'org.jetbrains.kotlin', module: 'kotlin-stdlib-jdk8'
@@ -344,7 +344,7 @@ dependencies {
 
     implementation 'commons-io:commons-io:2.16.1'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.174'
+    testImplementation 'io.github.classgraph:classgraph:4.8.175'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.11.0'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.3'
 
@@ -357,7 +357,7 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:3.0"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.17.0'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.18.0'
     // 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'