Merge remote-tracking branch 'upstream/main' into Add-log-for-ignored…

…-excepton * upstream/main: (184 commits) 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 Only arm64 m+ Update deployment-arm64.yml add deployment with arm as well Revert "Test self hosted runner" remove self hosted from normal deployment fix unit test for slr Refine do not put under drive letter Update journal abbrev list (JabRef#9469) ... # Conflicts: # src/main/java/org/jabref/logic/remote/server/RemoteListenerServer.java
VernonKwa · Dec 19, 2022 · fcea58d · fcea58d
2 parents 1bd2d07 + 1c9a6c5
commit fcea58d
Show file tree

Hide file tree

Showing 396 changed files with 13,008 additions and 3,793 deletions.
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/GreetingFirstTimeCodeContribution.yml b/.github/workflows/GreetingFirstTimeCodeContribution.yml
@@ -15,7 +15,6 @@ jobs:
     - name: GreetingFirstTimeCodeContribution
       uses: peter-evans/create-or-update-comment@v2
       with:
-        repo-token: ${{ secrets.GITHUB_TOKEN }}
         issue-number: ${{ github.event.issue.number }}
         body: |
             As a general advice for newcomers: check out [Contributing](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md) for a start. Also, [guidelines for setting up a local workspace](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace) is worth having a look at.

diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -16,12 +16,12 @@ jobs:
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Auto approve
-        uses: hmarr/auto-approve-action@v3.0.0
+        uses: hmarr/auto-approve-action@v3.1.0
         if: steps.waitforstatuschecks.outputs.status == 'success'
         with:
           github-token: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/automerge-action@v0.15.3
+        uses: pascalgn/automerge-action@v0.15.5
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "merge"

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 }}/