Merge remote-tracking branch 'upstream/main' into fix-for-issue-8729

* upstream/main: (145 commits) Enable groups drag'n'drop to new library (JabRef#9460) Update MacOS jabrefHost.py to find local installs (JabRef#9487) Fix remember last open valid library with empty new one (JabRef#9489) Observable Preferences R (CitationKeyPatternPreferences) (JabRef#9486) Fixed ZBMathTest and extracted keyWordSeparator (JabRef#9485) New Crowdin updates (JabRef#9483) Add log for ignored excepton (JabRef#9302) Select Library to import into (JabRef#9402) Bump org.eclipse.jgit from 6.3.0.202209071007-r to 6.4.0.202211300538-r (JabRef#9476) Bump com.github.andygoossens.modernizer from 1.6.2 to 1.7.0 (JabRef#9478) Bump mockito-core from 4.9.0 to 4.10.0 (JabRef#9479) Bump checkstyle from 10.4 to 10.5.0 (JabRef#9477) Bump slf4j-api from 2.0.5 to 2.0.6 in /buildSrc (JabRef#9480) Bibtex month not deprecated (JabRef#9404) Show development information\n\n+semver: major Release v5.8 Update external libraries add afterburner fx jabref add jakarta inject fix display name for artifact store Prepare CHANGELOG for release Also trigger on branch arm64mac-release ... # Conflicts: # CHANGELOG.md # src/main/java/org/jabref/preferences/JabRefPreferences.java
shafinkamal · Dec 21, 2022 · f95130c · f95130c
2 parents b0716f7 + 41c8b48
commit f95130c
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -12,7 +12,7 @@ body:
     attributes:
       label: JabRef version
       options:
-        - "5.7 (latest release)"
+        - "5.8 (latest release)"
         - "3.8.2"
         - Latest development branch build (please note build date below)
         - Other (please describe below)

diff --git a/.github/workflows/check-links.yaml b/.github/workflows/check-links.yaml
@@ -4,6 +4,8 @@ on:
   push:
     paths:
       - '**.md'
+    paths-ignore:
+      - 'CHANGELOG.md'
   schedule:
     # Run on the first of each month at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07)
     - cron: "0 9 1 * *"

diff --git a/.github/workflows/cleanup_pr.yml b/.github/workflows/cleanup_pr.yml
@@ -13,21 +13,21 @@ jobs:
         id: checksecrets
         shell: bash
         run: |
-          if [ -z "$BUILDJABREFPRIVATEKEY" ]; then
-            echo ::set-output name=secretspresent::false
+          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
           else
-            echo ::set-output name=secretspresent::true
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
           fi
         env:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Extract branch name
         id: extract_branch
         if: ${{ steps.checksecrets.outputs.secretspresent }}
         run: |
-          echo "##[set-output name=branch;]$(echo ${{ github.event.pull_request.head.ref }})"
+          echo "branch=${{ github.event.pull_request.head.ref }}" >> $GITHUB_OUTPUT
       - name: Delete folder on builds.jabref.org
-        if: ${{ steps.checksecrets.outputs.secretspresent }}
-        uses: appleboy/ssh-action@v0.1.5
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
+        uses: appleboy/ssh-action@v0.1.6
         with:
           script: rm -rf /var/www/builds.jabref.org/www/${{ steps.extract_branch.outputs.branch }} || true
           host: build-upload.jabref.org

diff --git a/.github/workflows/deployment-arm64.yml b/.github/workflows/deployment-arm64.yml
@@ -0,0 +1,196 @@
+name: Deployment Release for ARM64 - Run manually!
+
+on:
+  workflow_dispatch:
+  push:
+   branches:
+    - arm64mac-release
+
+
+env:
+  SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
+  AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
+  IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
+  BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey}}
+  OSXCERT: ${{ secrets.OSX_SIGNING_CERT }}
+  GRADLE_OPTS: -Xmx4g -Dorg.gradle.daemon=false -Dorg.gradle.vfs.watch=false
+  JAVA_OPTS: -Xmx4g
+
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [self-hosted]
+        include:
+          - 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 ${{ matrix.displayName }}
+    steps:
+      - name: Check secrets presence
+        id: checksecrets
+        shell: bash
+        run: |
+          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
+          else
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
+          fi
+        env:
+          BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
+      - name: Fetch all history for all tags and branches
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Install GitVersion
+        uses: gittools/actions/gitversion/setup@v0.9.15
+        with:
+          versionSpec: "5.x"
+      - name: Run GitVersion
+        id: gitversion
+        uses: gittools/actions/gitversion/execute@v0.9.15
+      - name: Set up JDK
+        uses: actions/setup-java@v3
+        with:
+          java-version: 18
+          distribution: 'temurin'
+          cache: 'gradle'
+      - name: Clean up keychain
+        if: (matrix.os == 'self-hosted') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        run: |
+         security delete-keychain signing_temp.keychain   
+      - name: Setup OSX key chain on OSX
+        if: (matrix.os == 'macos-latest' || matrix.os == 'self-hosted') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        uses: apple-actions/import-codesign-certs@v1
+        with:
+          p12-file-base64: ${{ secrets.OSX_SIGNING_CERT }}
+          p12-password: ${{ secrets.OSX_CERT_PWD }}
+          keychain-password: jabref
+      - name: Setup OSX key chain on OSX for app id cert
+        if: (matrix.os == 'macos-latest' || matrix.os == 'self-hosted') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        uses: apple-actions/import-codesign-certs@v1
+        with:
+          p12-file-base64: ${{ secrets.OSX_SIGNING_CERT_APPLICATION }}
+          p12-password: ${{ secrets.OSX_CERT_PWD }}
+          create-keychain: false
+          keychain-password: jabref
+      - name: Build runtime image
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
+        run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
+      - name: Build installer
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
+        run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
+        shell: bash
+      - name: Resign app image for OSX and build dmg
+        if: (matrix.os == 'macos-latest' || matrix.os == 'self-hosted') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        shell: bash
+        run: |
+          codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: JabRef e.V. (6792V39SK3)" build/distribution/JabRef.app/Contents/runtime/Contents/MacOS/libjli.dylib
+          codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: JabRef e.V. (6792V39SK3)" build/distribution/JabRef.app/Contents/MacOS/JabRef
+          codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: JabRef e.V. (6792V39SK3)" build/distribution/JabRef.app
+          jpackage --type pkg --dest build/distribution --name JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --app-image build/distribution/JabRef.app --verbose --type dmg --vendor JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
+          codesign -s "Developer ID Application: JabRef e.V. (6792V39SK3)" --options runtime --entitlements buildres/mac/jabref.entitlements -vvvv --deep "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
+          jpackage --type pkg --dest build/distribution --name JabRef --mac-package-identifier JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --app-image build/distribution/JabRef.app --verbose --type pkg --vendor JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
+          productsign --sign "Developer ID Installer: JabRef e.V. (6792V39SK3)" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
+      - name: Notarize dmg and pkg installer
+        if: (matrix.os == 'macos-latest' || matrix.os == 'self-hosted' ) && startsWith(github.ref, 'refs/tags/') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        shell: bash
+        run: |
+          REQUEST_UUID_DMG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "6792V39SK3" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg" | grep RequestUUID | awk '{print $3}')
+          while xcrun altool --notarization-info "$REQUEST_UUID_DMG" -u ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} -p  ${{ secrets.OSX_NOTARIZATION_APP_PWD }} | grep "Status: in progress" > /dev/null; do
+            echo "Verification in progress..."
+            sleep 30
+          done
+          xcrun stapler staple "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
+          spctl -vvv --assess --type exec build/distribution/JabRef.app
+          codesign -vvv --deep --strict "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
+          codesign -dvv "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
+          REQUEST_UUID_PKG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "6792V39SK3" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg" | grep RequestUUID | awk '{print $3}')
+          while xcrun altool --notarization-info "$REQUEST_UUID_PKG" -u ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} -p  ${{ secrets.OSX_NOTARIZATION_APP_PWD }} | grep "Status: in progress" > /dev/null; do
+            echo "Verification in progress..."
+            sleep 30
+          done
+          xcrun stapler staple "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
+          rm "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg"
+          mv "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg"
+      - name: Package application image
+        if: (matrix.os != 'macos-latest' && matrix.os != 'self-hosted') || (steps.checksecrets.outputs.secretspresent == 'YES')
+        shell: bash
+        run: ${{ matrix.archivePortable }}
+      - name: Rename files (non-macos)
+        if: (matrix.os != 'macos-latest' && matrix.os != 'self-hosted')
+        shell: pwsh
+        run: |
+          get-childitem -Path build/distribution/* | rename-item -NewName {$_.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"}
+      - name: Rename files (arm64)
+        if: (matrix.os == 'self-hosted') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        shell: pwsh
+        run: |
+          get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace ".dmg", ".${{ matrix.suffix }}.dmg"}
+          get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace ".pkg", ".${{ matrix.suffix }}.pkg"}
+      - name: Upload to GitHub workflow artifacts store
+        if: (matrix.os != 'macos-latest' && matrix.os !='self-hosted') || (steps.checksecrets.outputs.secretspresent == 'YES')
+        uses: actions/upload-artifact@v3
+        with:
+          name: JabRef-${{ matrix.displayName }}
+          path: build/distribution
+  deploy:
+    strategy:
+      fail-fast: false
+    name: Deploy binaries on builds.jabref.org
+    runs-on: ubuntu-latest
+    needs: [build]
+    steps:
+      - name: Check secrets presence
+        id: checksecrets
+        shell: bash
+        run: |
+          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
+          else
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
+          fi
+        env:
+          BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
+      - name: Checkout source
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
+        uses: actions/checkout@v3
+      - name: Fetch all history for all tags and branches
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
+        run: git fetch --prune --unshallow
+      - name: Install GitVersion
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
+        uses: gittools/actions/gitversion/setup@v0.9.15
+        with:
+          versionSpec: '5.x'
+      - name: Run GitVersion
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
+        id: gitversion
+        uses: gittools/actions/gitversion/execute@v0.9.15
+      - name: Get macOSArm64 binaries
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
+        uses: actions/download-artifact@master
+        with:
+          name: JabRef-macOS (Arm64)
+          path: build/distribution/    
+      - name: Deploy to builds.jabref.org
+        id: deploy
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
+        uses: Pendect/action-rsyncer@v2.0.0
+        env:
+          DEPLOY_KEY: ${{ secrets.buildJabRefPrivateKey }}
+          BRANCH: ${{ steps.gitversion.outputs.branchName }}
+        with:
+          flags: -vaz --itemize-changes --stats --partial-dir=/tmp/partial --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync"
+          options: ''
+          ssh_options: '-p 9922'
+          src: 'build/distribution/'
+          dest: jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/