Merge remote-tracking branch 'upstream/main' into tryToCreateMergedTrustStore

* upstream/main: (295 commits)
  Use OpenRewrite UseStringReplace (#10299)
  Add ReplaceStringBuilderWithString (#10302)
  Apply ShortenFullyQualifiedTypeReferences (#10301)
  Apply StaticMethodNotFinal (#10300)
  Apply exit early pattern (#10297)
  Avoid GH_TOKEN_UPDATE_GRADLE_WRAPPER at refresh-csl-subtrees
  Update snapcraft.yaml
  Fix exception when opening preferences (#10294)
  gnome-42-2204
  use gnome 4.2
  Use gnome
  Update base 22
  Add method for detecting journal abbrev delimiter (#10281)
  Update bug_report.yml
  Fix selection of table sort order (#10250)
  Fix mixup with YAML tags (#10287)
  More guards for upload (#10282)
  Reduced calls to Globals.prefs and Globals.entryTypesManager (#10177)
  Update jmh plugin (#10279)
  Add computer science to protected terms (#10222)
  ...

Author: Siedlerchr

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -12,8 +12,7 @@ body:
     attributes:
       label: JabRef version
       options:
-        - "5.9 (latest release)"
-        - "3.8.2"
+        - "5.10 (latest release)"
         - Latest development branch build (please note build date below)
         - Other (please describe below)
       description: The version as shown in the about dialog.
@@ -42,7 +41,7 @@ body:
 
   - type: checkboxes
     attributes:
-      label: Checked with the latest development build
+      label: Checked with the latest development build (copy version output from About dialog)
       description: |
         Please always test if the bug is still reproducible in the latest development version. We are constantly improving JabRef and some bugs may already be fixed. If you already use a development version, ensure that you use the latest one.
         You can download the latest development build at: https://builds.jabref.org/main/ . **Please make a backup of your library before you try out this version.**

.github/workflows/automerge.yml

@@ -1,34 +1,22 @@
-name: Automerge Pull Requests
-on:
-  pull_request:
-    types:
-      - opened
-      - synchronize
-      - reopened
-      - labeled
+name: Dependabot auto-merge
+on: pull_request
+
+permissions:
+  contents: write
+  pull-requests: write
+
 jobs:
-  automerge:
-    name: Automerge Dependency Updates
+  dependabot:
     runs-on: ubuntu-latest
-    if: github.actor == 'dependabot[bot]' || github.actor == 'dependabot-preview[bot]' || contains(github.event.pull_request.labels.*.name, 'dependencies')
+    if: ${{ github.actor == 'dependabot[bot]' }}
     steps:
-      - name: 'Wait for status checks'
-        id: waitforstatuschecks
-        uses: "WyriHaximus/[email protected]"
-        with:
-          ignoreActions: Automerge Dependabot,Code coverage,Create snapcraft image,Deploy binaries on builds.jabref.org,codecov/project,markdown-link-check
-          checkInterval: 13
+      - name: Approve PR
+        run: gh pr review --approve "$PR_URL"
         env:
-          GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
-      - name: Auto approve
-        uses: hmarr/[email protected]
-        if: steps.waitforstatuschecks.outputs.status == 'success'
-        with:
-          github-token: "${{ secrets.GITHUB_TOKEN }}"
-      - name: Merge pull requests
-        uses: pascalgn/[email protected]
-        if: steps.waitforstatuschecks.outputs.status == 'success'
+          PR_URL: ${{github.event.pull_request.html_url}}
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+      - name: Merge PR
+        run: gh pr merge --auto "$PR_URL"
         env:
-          MERGE_METHOD: "merge"
-          MERGE_LABELS: ""
-          GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+          PR_URL: ${{github.event.pull_request.html_url}}
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}

.github/workflows/cleanup_pr.yml

@@ -26,7 +26,7 @@ jobs:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Delete folder on builds.jabref.org
         if: steps.checksecrets.outputs.secretspresent == 'YES'
-        uses: appleboy/ssh-action@v0.1.10
+        uses: appleboy/ssh-action@v1.0.0
         with:
           script: rm -rf /var/www/builds.jabref.org/www/pull/${{ github.event.pull_request.number }} || true
           host: build-upload.jabref.org

.github/workflows/deployment-arm64.yml

@@ -5,11 +5,12 @@ on:
     inputs:
       notarization:
         type: boolean
-        required: false
-        default: false
+        required: true
+        default: true
   push:
    branches:
     - arm64mac-release
+    - updateArm64Notarization
 
 env:
   SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
@@ -34,7 +35,6 @@ jobs:
           - os: self-hosted
             displayName: macOS (Arm64)
             suffix: '_arm64'
-            archivePortable: tar -c -C build/distribution JabRef.app | pigz --rsyncable > build/distribution/JabRef-portable_macos_arm64.tar.gz && rm -R build/distribution/JabRef.app
     runs-on: ${{ matrix.os }}
     name: Create installer and portable version for ${{ matrix.displayName }}
     steps:
@@ -78,7 +78,7 @@ jobs:
             sed -i'.bak' -e "s/JavaLanguageVersion.of(20)/JavaLanguageVersion.of(21)/" build.gradle
       - name: Clean up keychain
         run: |
-         security delete-keychain signing_temp.keychain || true
+         security delete-keychain signing_temp.keychain ${{runner.temp}}/keychain/notarization.keychain || true
       - name: Setup OSX key chain on OSX
         uses: apple-actions/import-codesign-certs@v2
         with:
@@ -92,8 +92,13 @@ jobs:
           p12-password: ${{ secrets.OSX_CERT_PWD }}
           create-keychain: false
           keychain-password: jabref
+      - name: Create notarization keychain
+        run: |
+          mkdir ${{runner.temp}}/keychain
+          security create-keychain -p jabref ${{runner.temp}}/keychain/notarization.keychain
+          security set-keychain-settings ${{runner.temp}}/keychain/notarization.keychain
       - name: Prepare merged jars and modules dir (macos)
-        run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" prepareModulesDir   
+        run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" prepareModulesDir
       - name: Build dmg (macos)
         shell: bash
         run: |
@@ -138,40 +143,38 @@ jobs:
           --resource-dir buildres/mac \
           --file-associations buildres/mac/bibtexAssociations.properties \
           --jlink-options --bind-services
-      - name: Rename files
-        shell: pwsh
+      - name: Rename files with arm64 suffix as well
+        shell: bash
         run: |
-          get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "${{ steps.gitversion.outputs.AssemblySemVer }}","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}"}
-          get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "portable","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-portable"}
+          mv build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg  build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-arm64.dmg
+          mv build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg  build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-arm64.pkg
       - name: Notarize dmg
         if: (startsWith(github.ref, 'refs/tags/') || (${{ inputs.notarization }}))
         shell: bash
         run: |
-          xcrun notarytool store-credentials "notarytool-profile" --apple-id "[email protected]" --team-id "6792V39SK3" --password "${{ secrets.OSX_NOTARIZATION_APP_PWD }}"
-          xcrun notarytool submit build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg --keychain-profile "notarytool-profile" --wait
-          xcrun stapler staple build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg
+          xcrun notarytool store-credentials "notarytool-profile" --apple-id "[email protected]" --team-id "6792V39SK3" --password "${{ secrets.OSX_NOTARIZATION_APP_PWD }}" --keychain ${{runner.temp}}/keychain/notarization.keychain
+          xcrun notarytool submit build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-arm64.dmg --keychain-profile "notarytool-profile" --keychain ${{runner.temp}}/keychain/notarization.keychain --wait
+          xcrun stapler staple build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-arm64.dmg
       - name: Notarize pkg
         if: (startsWith(github.ref, 'refs/tags/') || (${{ inputs.notarization }}))
         shell: bash
         run: |
-          xcrun notarytool store-credentials "notarytool-profile" --apple-id "[email protected]" --team-id "6792V39SK3" --password "${{ secrets.OSX_NOTARIZATION_APP_PWD }}"
-          xcrun notarytool submit build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg --keychain-profile "notarytool-profile" --wait
-          xcrun stapler staple build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg
-      - name: Package application image
+          xcrun notarytool store-credentials "notarytool-profile" --apple-id "[email protected]" --team-id "6792V39SK3" --password "${{ secrets.OSX_NOTARIZATION_APP_PWD }}" --keychain ${{runner.temp}}/keychain/notarization.keychain
+          xcrun notarytool submit build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-arm64.pkg --keychain-profile "notarytool-profile" --keychain ${{runner.temp}}/keychain/notarization.keychain --wait
+          xcrun stapler staple build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-arm64.pkg
+      - name: Upload with rsync
+        if: ${{ !startsWith(github.ref, 'refs/heads/gh-readonly-queue') }}
         shell: bash
-        run: ${{ matrix.archivePortable }}
+        run: |
+          mkdir ${{runner.temp}}/sshkey
+          if [[ -z "${{ secrets.buildJabRefPrivateKey }}" ]]; then
+            echo "buildJabRefPrivateKey is empty, exiting"
+            exit 1
+          fi
+          rsync -Pavz --itemize-changes --stats --partial-dir=/tmp/partial --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i ~/.ssh/id_rsa' build/distribution/ [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
       - name: Upload to GitHub workflow artifacts store
+        if: ${{ !startsWith(github.ref, 'refs/heads/gh-readonly-queue') }}
         uses: actions/upload-artifact@v3
         with:
           name: JabRef-${{ matrix.displayName }}
           path: build/distribution
-      - name: Upload to builds.jabref.org (TODO - won't run on Mac, because Dockerized action)
-        uses: Pendect/[email protected]
-        env:
-          DEPLOY_KEY: ${{ secrets.buildJabRefPrivateKey }}
-        with:
-          flags: -vaz --itemize-changes --stats --partial-dir=/tmp/partial --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync"
-          options: ''
-          ssh_options: '-p 9922'
-          src: 'build/distribution/'
-          dest: [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/

.github/workflows/deployment.yml

@@ -22,6 +22,7 @@ on:
       - 'docs/**'
       - 'src/test/**'
       - 'README.md'
+  merge_group:
 
 env:
   SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
@@ -54,7 +55,6 @@ jobs:
             eaJDK: https://files.jabref.org/jdks/jdk-windows-x64.zip
           - os: macos-latest
             displayName: macOS
-            archivePortable: brew install pigz && tar -c -C build/distribution JabRef.app | pigz --rsyncable > build/distribution/JabRef-portable_macos.tar.gz && rm -R build/distribution/JabRef.app
             eaJDK: https://files.jabref.org/jdks/jdk-macos-x64.tar.gz
     runs-on: ${{ matrix.os }}
     name: Create installer and portable version for ${{ matrix.displayName }}
@@ -74,6 +74,12 @@ jobs:
         uses: actions/checkout@v3
         with:
           fetch-depth: 0
+      - name: Install pigz and cache (linux)
+        if: (matrix.os == 'ubuntu-latest')
+        uses: awalsh128/cache-apt-pkgs-action@latest
+        with:
+          packages: pigz
+          version: 1.0
       - name: Install GitVersion
         uses: gittools/actions/gitversion/[email protected]
         with:
@@ -223,7 +229,7 @@ jobs:
           rm debian-binary control.tar.* data.tar.*
           mv -f jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}_amd64_repackaged.deb  jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}_amd64.deb
       - name: Upload to builds.jabref.org (ubuntu)
-        if: (matrix.os == 'ubuntu-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        if: (matrix.os == 'ubuntu-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
         uses: Pendect/[email protected]
         env:
           DEPLOY_KEY: ${{ secrets.buildJabRefPrivateKey }}
@@ -234,13 +240,13 @@ jobs:
           src: 'build/distribution/'
           dest: [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
       - name: Upload to GitHub workflow artifacts store (windows)
-        if: (matrix.os == 'windows-latest')
+        if: (matrix.os == 'windows-latest') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
         uses: actions/upload-artifact@v3
         with:
           name: JabRef-${{ matrix.displayName }}
           path: build/distribution
       - name: Upload to GitHub workflow artifacts store (macos)
-        if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
         uses: actions/upload-artifact@v3
         with:
           # tbn = to-be-notarized
@@ -283,25 +289,25 @@ jobs:
           name: JabRef-macOS-tbn
           path: build/distribution/
       - name: Notarize dmg
-        if: (steps.checksecrets.outputs.secretspresent == 'YES') && ((startsWith(github.ref, 'refs/tags/') || (${{ inputs.notarization }}))
+        if: (steps.checksecrets.outputs.secretspresent == 'YES') && (startsWith(github.ref, 'refs/tags/') ||  inputs.notarization == true)
         shell: bash
         run: |
           xcrun notarytool store-credentials "notarytool-profile" --apple-id "[email protected]" --team-id "6792V39SK3" --password "${{ secrets.OSX_NOTARIZATION_APP_PWD }}"
           xcrun notarytool submit build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg --keychain-profile "notarytool-profile" --wait
           xcrun stapler staple build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg
       - name: Notarize pkg
-        if: (steps.checksecrets.outputs.secretspresent == 'YES') && ((startsWith(github.ref, 'refs/tags/') || (${{ inputs.notarization }}))
+        if: (steps.checksecrets.outputs.secretspresent == 'YES') && (startsWith(github.ref, 'refs/tags/') ||  inputs.notarization == true)
         shell: bash
         run: |
           xcrun notarytool store-credentials "notarytool-profile" --apple-id "[email protected]" --team-id "6792V39SK3" --password "${{ secrets.OSX_NOTARIZATION_APP_PWD }}"
           xcrun notarytool submit build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg --keychain-profile "notarytool-profile" --wait
           xcrun stapler staple build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg
       - name: Package application image
-        if: (steps.checksecrets.outputs.secretspresent == 'YES')
+        if: (steps.checksecrets.outputs.secretspresent == 'YES') && (matrix.os != 'macos-latest')
         shell: bash
         run: ${{ matrix.archivePortable }}
       - name: Upload to GitHub workflow artifacts store
-        if: (steps.checksecrets.outputs.secretspresent == 'YES')
+        if: (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
         uses: actions/upload-artifact@v3
         with:
           name: JabRef-macOS
@@ -312,6 +318,7 @@ jobs:
     name: Upload binaries on builds.jabref.org
     runs-on: ubuntu-latest
     needs: [build, notarize]
+    if: ${{ !startsWith(github.ref, 'refs/heads/gh-readonly-queue') }}
     steps:
       - name: Check secrets presence
         id: checksecrets
@@ -346,13 +353,13 @@ jobs:
           name: JabRef-windows
           path: build/distribution
       - name: Get macOS binaries unsigned
-        if: (steps.checksecrets.outputs.secretspresent == 'YES') && ! (${{ inputs.notarization }})) && ! (startsWith(github.ref, 'refs/tags/')
+        if: (steps.checksecrets.outputs.secretspresent == 'YES') && (inputs.notarization == false && !startsWith(github.ref, 'refs/tags/'))
         uses: actions/download-artifact@master
         with:
           name: JabRef-macOS-tbn
           path: build/distribution/
       - name: Get macOS binaries notarized
-        if: (steps.checksecrets.outputs.secretspresent == 'YES') && ((${{ inputs.notarization }})) || (startsWith(github.ref, 'refs/tags/'))
+        if: (steps.checksecrets.outputs.secretspresent == 'YES') && (inputs.notarization == true || startsWith(github.ref, 'refs/tags/'))
         uses: actions/download-artifact@master
         with:
           name: JabRef-macOS

.github/workflows/refresh-csl-subtrees.yml

@@ -13,19 +13,22 @@ jobs:
   publish:
     name: Refresh Citation Style Language Files
     runs-on: ubuntu-latest
-    if: github.repository == 'JabRef/jabref'
+    permissions:
+      contents: write  # for peter-evans/create-pull-request to create branch
+      pull-requests: write  # for peter-evans/create-pull-request to create a PR
+    if: (github.repository == 'JabRef/jabref' || github.repository == 'koppor/jabref')
     steps:
-      - name: Checkout source
-        uses: actions/checkout@v3
+      - uses: actions/checkout@v3
         with:
+          persist-credentials: true
           ref: main
           fetch-depth: 0
       - name: Initialize git
         run: |
           git checkout main
           git config --local core.editor /usr/bin/cat
-          git config user.name "github actions"
-          git config user.email "jabrefmail+webfeedback@gmail.com"
+          git config user.name 'github-actions[bot]'
+          git config user.email 'github-actions[bot]@users.noreply.github.com'
       - name: Add csl-styles remote
         run: git remote add -f csl-styles https://github.com/citation-style-language/styles.git
       - name: Update csl-styles
@@ -48,8 +51,8 @@ jobs:
           git commit -m"Refresh example styles" || true
       - uses: peter-evans/create-pull-request@v5
         with:
-          token: ${{ secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER }}
+          token: ${{ secrets.GITHUB_TOKEN }}
           branch: refresh-csl
-          commit-message: Update CSL styles
           title: "[Bot] Update CSL styles"
+          commit-message: Update CSL styles
           labels: dependencies

.github/workflows/refresh-journal-lists.yml

@@ -58,17 +58,8 @@ jobs:
           cd $GITHUB_WORKSPACE
           ./gradlew generateJournalAbbreviationList
       - uses: peter-evans/create-pull-request@v5
-        if: github.ref == 'refs/heads/main'
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           branch: update-journallist
           title: "[Bot] Update journal abbreviation lists"
           commit-message: Update journal abbreviation lists
-      - name: Commit and push changes
-        uses: EndBug/add-and-commit@v9
-        if: github.ref != 'refs/heads/main'
-        with:
-          message: 'Update journal abbreviation lists'
-          committer_email: [email protected]
-          fetch: false
-          push: true

.github/workflows/tests.yml

@@ -7,6 +7,7 @@ on:
       - main-release
   pull_request:
     # always run on pull requests
+  merge_group:
   workflow_dispatch:
 
 env:
@@ -201,3 +202,11 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - uses: gradle/wrapper-validation-action@v1
+  # This ensures that no git merge conflict markers (<<<, ...) are contained
+  merge_conflict_job:
+    name: Find merge conflicts
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Merge Conflict finder
+        uses: olivernybroe/[email protected]