Merge branch 'main' into nativecompile

# Conflicts:
#	build.gradle
#	src/main/java/org/jabref/logic/protectedterms/ProtectedTermsParser.java

.github/workflows/cleanup-pr.yml

@@ -19,8 +19,10 @@ jobs:
  run: |
  if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
  echo "secretspresent=NO" >> $GITHUB_OUTPUT
+ echo "❌ Secret BUILDJABREFPRIVATEKEY not present"
  else
  echo "secretspresent=YES" >> $GITHUB_OUTPUT
+ echo "✔️ Secret BUILDJABREFPRIVATEKEY present"
  fi
  env:
  BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}

.github/workflows/deployment-arm64.yml

@@ -54,8 +54,10 @@ jobs:
  run: |
  if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
  echo "secretspresent=NO" >> $GITHUB_OUTPUT
+ echo "❌ Secret BUILDJABREFPRIVATEKEY not present"
  else
  echo "secretspresent=YES" >> $GITHUB_OUTPUT
+ echo "✔️ Secret BUILDJABREFPRIVATEKEY present"
  fi
  env:
  BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
@@ -66,12 +68,12 @@ jobs:
  submodules: 'true'
  show-progress: 'false'
  - name: Install GitVersion
- uses: gittools/actions/gitversion/setup@v1.1.1
+ uses: gittools/actions/gitversion/setup@v3.0.0
  with:
  versionSpec: "5.x"
  - name: Run GitVersion
  id: gitversion
- uses: gittools/actions/gitversion/execute@v1.1.1
+ uses: gittools/actions/gitversion/execute@v3.0.0
  - name: Setup JDK
  uses: actions/setup-java@v4
  with:
@@ -109,6 +111,7 @@ jobs:
  --module org.jabref/org.jabref.Launcher \
  --module-path ${{env.JAVA_HOME}}/jmods/:build/jlinkbase/jlinkjars \
  --add-modules org.jabref,org.jabref.merged.module \
+ --add-modules jdk.incubator.vector \
  --dest build/distribution \
  --app-content buildres/mac/jabrefHost.py \
  --app-content buildres/mac/native-messaging-host \
@@ -137,7 +140,8 @@ jobs:
  --java-options --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref \
  --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref \
  --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
- --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref
+ --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref \
+ --java-options --add-modules=jdk.incubator.vector
  - name: Build pkg (macOS)
  if: (steps.checksecrets.outputs.secretspresent == 'YES')
  shell: bash
@@ -146,6 +150,7 @@ jobs:
  --module org.jabref/org.jabref.Launcher \
  --module-path ${{env.JAVA_HOME}}/jmods/:build/jlinkbase/jlinkjars \
  --add-modules org.jabref,org.jabref.merged.module \
+ --add-modules jdk.incubator.vector \
  --dest build/distribution \
  --app-content buildres/mac/jabrefHost.py \
  --app-content buildres/mac/native-messaging-host \
@@ -173,7 +178,8 @@ jobs:
  --java-options --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref \
  --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref \
  --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
- --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref
+ --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref \
+ --java-options --add-modules=jdk.incubator.vector
  - name: Rename files with arm64 suffix as well
  if: (steps.checksecrets.outputs.secretspresent == 'YES')
  shell: bash
@@ -225,8 +231,10 @@ jobs:
  run: |
  if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
  echo "secretspresent=NO" >> $GITHUB_OUTPUT
+ echo "❌ Secret BUILDJABREFPRIVATEKEY not present"
  else
  echo "secretspresent=YES" >> $GITHUB_OUTPUT
+ echo "✔️ Secret BUILDJABREFPRIVATEKEY present"
  fi
  env:
  BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}

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

@@ -84,12 +84,12 @@ jobs:
  packages: pigz
  version: 1.0
  - name: Install GitVersion
- uses: gittools/actions/gitversion/setup@v1.1.1
+ uses: gittools/actions/gitversion/setup@v3.0.0
  with:
  versionSpec: "5.x"
  - name: Run GitVersion
  id: gitversion
- uses: gittools/actions/gitversion/execute@v1.1.1
+ uses: gittools/actions/gitversion/execute@v3.0.0
 
  # JDK
  - name: 'Set up JDK ${{ matrix.jdk }}'

.github/workflows/deployment.yml

@@ -99,8 +99,10 @@ jobs:
  run: |
  if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
  echo "secretspresent=NO" >> $GITHUB_OUTPUT
+ echo "❌ Secret BUILDJABREFPRIVATEKEY not present"
  else
  echo "secretspresent=YES" >> $GITHUB_OUTPUT
+ echo "✔️ Secret BUILDJABREFPRIVATEKEY present"
  fi
  env:
  BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
@@ -117,12 +119,12 @@ jobs:
  packages: pigz
  version: 1.0
  - name: Install GitVersion
- uses: gittools/actions/gitversion/setup@v1.1.1
+ uses: gittools/actions/gitversion/setup@v3.0.0
  with:
  versionSpec: "5.x"
  - name: Run GitVersion
  id: gitversion
- uses: gittools/actions/gitversion/execute@v1.1.1
+ uses: gittools/actions/gitversion/execute@v3.0.0
  - name: Setup JDK
  uses: actions/setup-java@v4
  with:
@@ -159,6 +161,7 @@ jobs:
  --module org.jabref/org.jabref.Launcher \
  --module-path ${{env.JAVA_HOME}}/jmods/:build/jlinkbase/jlinkjars \
  --add-modules org.jabref,org.jabref.merged.module \
+ --add-modules jdk.incubator.vector \
  --dest build/distribution \
  --app-content buildres/mac/jabrefHost.py \
  --app-content buildres/mac/native-messaging-host \
@@ -187,7 +190,8 @@ jobs:
  --java-options --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref \
  --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref \
  --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
- --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref
+ --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref \
+ --java-options --add-modules=jdk.incubator.vector
  - name: Build pkg (macOS)
  if: (matrix.os == 'macos-13') && (steps.checksecrets.outputs.secretspresent == 'YES')
  shell: bash
@@ -196,6 +200,7 @@ jobs:
  --module org.jabref/org.jabref.Launcher \
  --module-path ${{env.JAVA_HOME}}/jmods/:build/jlinkbase/jlinkjars \
  --add-modules org.jabref,org.jabref.merged.module \
+ --add-modules jdk.incubator.vector \
  --dest build/distribution \
  --app-content buildres/mac/jabrefHost.py \
  --app-content buildres/mac/native-messaging-host \
@@ -224,7 +229,8 @@ jobs:
  --java-options --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref \
  --java-options --add-opens=javafx.graphics/javafx.scene=org.jabref \
  --java-options --add-opens=javafx.controls/javafx.scene.control=org.jabref \
- --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref
+ --java-options --add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref \
+ --java-options --add-modules=jdk.incubator.vector
  - name: Build runtime image and installer (linux, Windows)
  if: (matrix.os != 'macos-13') && (steps.checksecrets.outputs.secretspresent == 'YES')
  shell: bash
@@ -306,8 +312,10 @@ jobs:
  run: |
  if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
  echo "secretspresent=NO" >> $GITHUB_OUTPUT
+ echo "❌ Secret BUILDJABREFPRIVATEKEY not present"
  else
  echo "secretspresent=YES" >> $GITHUB_OUTPUT
+ echo "✔️ Secret BUILDJABREFPRIVATEKEY present"
  fi
  env:
  BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
@@ -331,8 +339,10 @@ jobs:
  run: |
  if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
  echo "secretspresent=NO" >> $GITHUB_OUTPUT
+ echo "❌ Secret BUILDJABREFPRIVATEKEY not present"
  else
  echo "secretspresent=YES" >> $GITHUB_OUTPUT
+ echo "✔️ Secret BUILDJABREFPRIVATEKEY present"
  fi
  env:
  BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}

.github/workflows/gource.yml

@@ -75,8 +75,10 @@ jobs:
  run: |
  if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
  echo "secretspresent=NO" >> $GITHUB_OUTPUT
+ echo "❌ Secret BUILDJABREFPRIVATEKEY not present"
  else
  echo "secretspresent=YES" >> $GITHUB_OUTPUT
+ echo "✔️ Secret BUILDJABREFPRIVATEKEY present"
  fi
  env:
  BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}

.github/workflows/tests.yml

@@ -5,9 +5,10 @@ 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 }}
@@ -51,6 +52,21 @@ 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
@@ -72,6 +88,20 @@ 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
  runs-on: ubuntu-latest
@@ -95,6 +125,19 @@ 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
  runs-on: ubuntu-latest
@@ -110,6 +153,19 @@ 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
  runs-on: ubuntu-latest
@@ -136,6 +192,7 @@ jobs:
  # exit 1 in case of error
  # We have 1 "valid" issue in CHANGELOG.md
  grep -q "1 problem" heylogs.txt || exit 1
+
  changelog-unreleased-only:
  name: CHANGELOG.md - only unreleased touched
  runs-on: ubuntu-latest
@@ -156,6 +213,15 @@ 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: ${{ failure() }}
+ uses: thollander/actions-comment-pull-request@v2
+ with:
+ message: >
+ While the PR was in progress, JabRef released a new version.
+ You have to merge `upstream/main` and move your entry in `CHANGELOG.md` up to the section `## [Unreleased]`.
+ comment_tag: automated-test-feedback
+
  tests:
  name: Unit tests
  runs-on: ubuntu-latest
@@ -187,6 +253,7 @@ jobs:
  - name: Format failed test results
  if: failure()
  run: scripts/after-failure.sh
+
  databasetests:
  name: Database tests
  runs-on: ubuntu-latest
@@ -238,6 +305,7 @@ jobs:
  env:
  CI: "true"
  DBMS: "mysql"
+
  guitests:
  name: GUI tests
  runs-on: ubuntu-latest
@@ -260,6 +328,7 @@ jobs:
  run: xvfb-run --auto-servernum ./gradlew guiTest
  env:
  CI: "true"
+
  codecoverage:
  name: Code coverage
  runs-on: ubuntu-latest
@@ -282,8 +351,10 @@ jobs:
  run: |
  if [ "$CODECOV_TOKEN" == "" ]; then
  echo "secretspresent=NO" >> $GITHUB_OUTPUT
+ echo "❌ Secret CODECOV_TOKEN not present"
  else
  echo "secretspresent=YES" >> $GITHUB_OUTPUT
+ echo "✔️ Secret CODECOV_TOKEN present"
  fi
  env:
  CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
@@ -319,6 +390,7 @@ jobs:
  run: bash <(curl -Ls https://coverage.codacy.com/get.sh)
  env:
  CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
+
  # This is https://github.com/marketplace/actions/gradle-wrapper-validation
  # It ensures that the jar file is from gradle and not by a strange third party.
  gradlevalidation:
@@ -329,6 +401,7 @@ jobs:
  with:
  show-progress: 'false'
  - uses: gradle/actions/wrapper-validation@v3
+
  # This ensures that no git merge conflict markers (<<<, ...) are contained
  merge_conflict_job:
  name: Find merge conflicts
@@ -339,6 +412,7 @@ jobs:
  show-progress: 'false'
  - name: Merge Conflict finder
  uses: olivernybroe/action-conflict-finder@v4.0
+
  other_than_main:
  name: Source branch is other than "main"
  runs-on: ubuntu-latest