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

* upstream/main: (244 commits) Use Set instead of List for custom journal abbreviations (JabRef#9515) Delete snap.yml (JabRef#9526) New Crowdin updates (JabRef#9523) Fix not on fx thread error when downloading file (JabRef#9522) Fix downloading in case of circular redirect (JabRef#9519) Typo: sucess -> success (JabRef#9520) New Crowdin updates (JabRef#9517) Add CHANGELOG.md entry for 9472 Fix journal abbbrev checker for curly braces (JabRef#9504) Remove journal_abbreviations_ieee_strings.csv from journal lists (JabRef#9511) Bump mockito-core from 4.10.0 to 4.11.0 (JabRef#9513) Bump lucene-core from 9.4.1 to 9.4.2 (JabRef#9512) Bump checkstyle from 10.5.0 to 10.6.0 (JabRef#9514) Create a better solution for define multi line fields (JabRef#9456) Check links once a month Really ignore CHANGELOG.md in link check Fix spaces Add missing dots Squashed 'buildres/csl/csl-styles/' changes from 84dba23..43566f2 try to repack deb file (JabRef#9506) ...
JabRef · Jan 5, 2023 · 4638d77 · 4638d77
2 parents 698e88f + 06771c8
commit 4638d77
Show file tree

Hide file tree

Showing 637 changed files with 22,441 additions and 7,051 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
@@ -0,0 +1,22 @@
+name: GreetingFirstTimeCodeContribution
+
+on: 
+  issues:
+     types:
+       - labeled
+
+jobs:
+  GreetingFirstTimeCodeContribution:
+    if: ${{ github.event.label.name == 'FirstTimeCodeContribution' }}
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+    - name: GreetingFirstTimeCodeContribution
+      uses: peter-evans/create-or-update-comment@v2
+      with:
+        issue-number: ${{ github.event.issue.number }}
+        body: |
+            As a general advice for newcomers: check out [Contributing](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md) for a start. Also, [guidelines for setting up a local workspace](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace) is worth having a look at.
+            
+            Feel free to ask here at GitHub, if you have any issue related questions. If you have questions about how to setup your workspace use JabRef's [Gitter](https://gitter.im/JabRef/jabref) chat. Try to open a (draft) pull-request early on, so that people can see you are working on the issue and so that they can see the direction the pull request is heading towards. This way, you will likely receive valuable feedback.
diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -16,12 +16,12 @@ jobs:
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Auto approve
-        uses: hmarr/auto-approve-action@v2.4.0
+        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
@@ -1,9 +1,6 @@
 name: Check external href links in the documentation
 
 on:
-  push:
-    paths:
-      - '**.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 * *"
@@ -20,4 +17,4 @@ jobs:
           use-verbose-mode: 'no'
           config-file: 'mlc_config.json'
           folder-path: 'docs/'
-          file-path: './CHANGELOG.md, ./README.md'
+          file-path: './README.md'
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 }}/