Merge branch 'main' into fix

JabRef · Dec 15, 2022 · 29380b5 · 29380b5
2 parents 3f92780 + 513d3aa
commit 29380b5
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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/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.yml b/.github/workflows/deployment.yml
@@ -31,21 +31,20 @@ concurrency:
   group: ${{ github.ref }}
   cancel-in-progress: true
 
-
 jobs:
   build:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macOS-latest]
+        os: [ubuntu-latest, windows-latest, macos-latest]
         include:
           - os: ubuntu-latest
             displayName: linux
             archivePortable: tar -c -C build/distribution JabRef | pigz --rsyncable > build/distribution/JabRef-portable_linux.tar.gz && rm -R build/distribution/JabRef
           - os: windows-latest
             displayName: windows
             archivePortable: 7z a -r build/distribution/JabRef-portable_windows.zip ./build/distribution/JabRef && rm -R build/distribution/JabRef
-          - os: macOS-latest
+          - 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
     runs-on: ${{ matrix.os }}
@@ -56,9 +55,9 @@ jobs:
         shell: bash
         run: |
           if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
-            echo ::set-output name=secretspresent::false
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
           else
-            echo ::set-output name=secretspresent::true
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
           fi
         env:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
@@ -67,42 +66,42 @@ jobs:
         with:
           fetch-depth: 0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.9.14
+        uses: gittools/actions/gitversion/setup@v0.9.15
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.14
+        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: Setup OSX key chain on OSX
-        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
+        if: (matrix.os == 'macos-latest') && (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') && steps.checksecrets.outputs.secretspresent
+        if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
         uses: apple-actions/import-codesign-certs@v1
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT_APPLICATION }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}
           create-keychain: false
           keychain-password: jabref
       - name: Build runtime image
-        if: (matrix.os != 'macos-latest') || steps.checksecrets.outputs.secretspresent
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
       - name: Build installer
-        if: (matrix.os != 'macos-latest') || steps.checksecrets.outputs.secretspresent
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
         shell: bash
       - name: Resign app image for OSX and build dmg
-        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
+        if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: |
           codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: JabRef e.V. (6792V39SK3)" build/distribution/JabRef.app/Contents/runtime/Contents/MacOS/libjli.dylib
@@ -113,7 +112,7 @@ jobs:
           jpackage --type pkg --dest build/distribution --name JabRef --mac-package-identifier JabRef --app-version "${{ 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 }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
       - name: Notarize dmg and pkg installer
-        if: (matrix.os == 'macos-latest') && startsWith(github.ref, 'refs/tags/') && steps.checksecrets.outputs.secretspresent
+        if: (matrix.os == 'macos-latest') && startsWith(github.ref, 'refs/tags/') && (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: |
           REQUEST_UUID_DMG=$(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 $3}')
@@ -134,15 +133,17 @@ jobs:
           rm "build/distribution/JabRef-${{ 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') || (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: ${{ matrix.archivePortable }}
       - name: Rename files
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: pwsh
         run: |
-          get-childitem -Path build/distribution/*
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.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: Upload to GitHub workflow artifacts store
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
         uses: actions/upload-artifact@v3
         with:
           name: JabRef-${{ matrix.displayName }}
@@ -159,42 +160,49 @@ jobs:
         shell: bash
         run: |
           if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
-            echo ::set-output name=secretspresent::false
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
           else
-            echo ::set-output name=secretspresent::true
+            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
-        uses: gittools/actions/gitversion/setup@v0.9.14
+        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@v0.9.14
+        uses: gittools/actions/gitversion/execute@v0.9.15
       - name: Get linux binaries
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: actions/download-artifact@master
         with:
           name: JabRef-linux
           path: build/distribution
       - name: Get windows binaries
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: actions/download-artifact@master
         with:
           name: JabRef-windows
           path: build/distribution
       - name: Get macOS binaries
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: actions/download-artifact@master
         with:
           name: JabRef-macOS
           path: build/distribution/
       - name: Deploy to builds.jabref.org
         id: deploy
-        if: ${{ steps.checksecrets.outputs.secretspresent }}
-        uses: Pendect/action-rsyncer@v1.1.0
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
+        uses: Pendect/action-rsyncer@v2.0.0
         env:
           DEPLOY_KEY: ${{ secrets.buildJabRefPrivateKey }}
           BRANCH: ${{ steps.gitversion.outputs.branchName }}

diff --git a/.github/workflows/gource.yml b/.github/workflows/gource.yml
@@ -19,9 +19,9 @@ jobs:
       - name: Determine dates
         id: dates
         run: |
-          echo ::set-output name=start_date::`date -d "$(date +%Y-%m-01) -3 months" +%Y-%m-%d`
-          echo ::set-output name=stop_date::`date -d "$(date +%Y-%m-01) -1 day" +%Y-%m-%d`
-          echo ::set-output name=quarter::`date -d "$(date +%Y-%m-01) -1 day" +%Y`-Q$(( ((`date -d "$(date +%Y-%m-01) -1 day" +%m`)-1)/3+1 ))
+          echo "start_date=`date -d "$(date +%Y-%m-01) -3 months" +%Y-%m-%d`" >> $GITHUB_STATE
+          echo "stop_date=`date -d "$(date +%Y-%m-01) -1 day" +%Y-%m-%d`" >> $GITHUB_STATE
+          echo "quarter=`date -d "$(date +%Y-%m-01) -1 day" +%Y`-Q$(( ((`date -d "$(date +%Y-%m-01) -1 day" +%m`)-1)/3+1 ))" >> $GITHUB_STATE
       - name: 'Development history of last quarter'
         uses: nbprojekt/gource-action@v1
         with:

diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
@@ -1,6 +1,10 @@
 name: Deploy Jekyll site to Pages
 
 on:
+  pull_request:
+    paths:
+      - 'docs/**'
+      - '.github/workflows/pages.yml'
   push:
     paths:
       - 'docs/**'
@@ -27,19 +31,21 @@ jobs:
       - name: Setup Ruby
         uses: ruby/setup-ruby@v1
         with:
-          ruby-version: '3.0' # Not needed with a .ruby-version file
+          ruby-version: '2.7' # Not needed with a .ruby-version file
           bundler-cache: true # runs 'bundle install' and caches installed gems automatically
-          cache-version: 0 # Increment this number if you need to re-download cached gems
+          cache-version: 1 # Increment this number if you need to re-download cached gems
+          working-directory: docs/
       - name: Setup Pages
         id: pages
         uses: actions/configure-pages@v2
       - name: Build with Jekyll
-        uses: actions/jekyll-build-pages@v1
-        with:
-          source: docs/
-          destination: ./_site
+        run: |
+          cd docs
+          bundle exec jekyll build
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v1
+        with:
+          path: docs/_site/
 
   deploy:
     if: github.ref == 'refs/heads/main'

diff --git a/.github/workflows/snap.yml b/.github/workflows/snap.yml
@@ -22,10 +22,10 @@ jobs:
         id: checksecrets
         shell: bash
         run: |
-          if [ "SNAPCRAFT_LOGIN_FILE" == "" ]; then
-            echo ::set-output name=secretspresent::false
+          if [ "$SNAPCRAFT_LOGIN_FILE" == "" ]; then
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
           else
-            echo ::set-output name=secretspresent::true
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
           fi
         env:
           SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
@@ -39,7 +39,7 @@ jobs:
         with:
           snapcraft-args: "--debug"
       - name: Upload snap
-        if: ${{ steps.checksecrets.outputs.secretspresent }}
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: snapcore/action-publish@v1
         with:
           store_login: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -149,10 +149,10 @@ jobs:
         id: checksecrets
         shell: bash
         run: |
-          if [ "CODECOV_TOKEN" == "" ]; then
-            echo ::set-output name=secretspresent::false
+          if [ "$CODECOV_TOKEN" == "" ]; then
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
           else
-            echo ::set-output name=secretspresent::true
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
           fi
         env:
           SNAPCRAFT_LOGIN_FILE: ${{ secrets.CODECOV_TOKEN }}
@@ -165,7 +165,7 @@ jobs:
           distribution: 'temurin'
           cache: 'gradle'
       - name: Update test coverage metrics
-        if: ${{ steps.checksecrets.outputs.secretspresent }}
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         run: xvfb-run --auto-servernum ./gradlew jacocoTestReport && bash <(curl -s https://codecov.io/bash);
         env:
           CI: "true"

diff --git a/.idea/runConfigurations/JabRef_Main.xml b/.idea/runConfigurations/JabRef_Main.xml