Merge remote-tracking branch 'upstream/master' into writebackupToTemp

* upstream/master: (191 commits)
  Fix for issue 7416: font size of the preferences dialog does not update with the rest of the GUI. (#7509)
  Fix school/instituation is printed twice (#7574)
  Dsiable notarisation until we hae an account for JabRef e.V. (#7572)
  Fix citation keys unintentionally being overwritten on import (#7443)
  Fix AuthentificationPlugin not declared in mergedModule (#7570)
  Suggestions for changes in caching latex free authors (#7301)
  Add simple Unit Tests (#7542)
  Fix drag and drop into empty library (#7555)
  Bump richtextfx from 0.10.4 to 0.10.6 (#7563)
  Bump pdfbox from 2.0.22 to 2.0.23 (#7561)
  Bump org.eclipse.jgit (#7560)
  Bump fontbox from 2.0.22 to 2.0.23 (#7562)
  Bump guava from 30.1-jre to 30.1.1-jre (#7564)
  Bump xmpbox from 2.0.22 to 2.0.23 (#7565)
  Bump hmarr/auto-approve-action from v2.0.0 to v2.1.0 (#7566)
  Add gource (#7193)
  UI: Fix for group icon (#7552)
  Fix for issue 6487: Opening BibTex file (doubleclick) from Folder with spaces not working (#7551)
  add ability to insert arxivId (#7549)
  Fixed missing trigger for linked file operations (#7548)
  ...

.gitattributes

@@ -5,9 +5,6 @@ gradlew text eol=lf
 # windows line endings at windows files
 *.bat text eol=crlf
 
-# required for proper releasing
-AUTHORS text eol=lf
-
 # ensure that line endings of *.java, and *.properties are normalized
 *.java text
 *.properties text

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,6 +1,9 @@
 ---
 name: Bug report
 about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
 
 ---
 

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Help
+    url: https://discourse.jabref.org/c/help/
+    about: Questions and requests for help are handled at https://discourse.jabref.org
+  - name: Feature requests
+    url: https://discourse.jabref.org/c/features/
+    about: If you are missing an important feature? Let us know!

.github/ISSUE_TEMPLATE/suggestion-for-improvement.md

@@ -1,6 +1,9 @@
 ---
 name: Suggestion for improvement
 about: Suggest an enhancement
+title: ''
+labels: ''
+assignees: ''
 
 ---
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -11,7 +11,7 @@ The title of the PR must not reference an issue, because GitHub does not support
 - Please don't remove any items, just leave them unchecked if they are not applicable.
 -->
 
-- [ ] Change in CHANGELOG.md described (if applicable)
+- [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if applicable)
 - [ ] Tests created for changes (if applicable)
 - [ ] Manually tested changed features in running JabRef (always required)
 - [ ] Screenshots added in PR description (for UI changes)

.github/workflows/automerge.yml

@@ -5,18 +5,23 @@ jobs:
   automerge:
     name: Automerge Dependabot
     runs-on: ubuntu-latest
-    if: github.actor == 'dependabot[bot]'
+    if: github.actor == 'dependabot[bot]' || github.actor == 'dependabot-preview[bot]'
     steps:
       - name: 'Wait for status checks'
         id: waitforstatuschecks
-        uses: "WyriHaximus/github-action-wait-for-status@v1.2"
+        uses: "WyriHaximus/github-action-wait-for-status@v1.3"
         with:
-          ignoreActions: Automerge Dependabot
+          ignoreActions: Automerge Dependabot,Code coverage,Create snapcraft image,Deploy binaries on builds.jabref.org,codecov/project,markdown-link-check
           checkInterval: 13
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+      - name: Auto approve
+        uses: hmarr/auto-approve-action@v2.1.0
+        if: steps.waitforstatuschecks.outputs.status == 'success'
+        with:
+          github-token: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/automerge-action@v0.13.0
+        uses: pascalgn/automerge-action@v0.13.1
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "squash"

.github/workflows/deployment.yml

@@ -42,20 +42,20 @@ jobs:
     name: Create installer and portable version for ${{ matrix.displayName }}
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.6.0
+        uses: styfle/cancel-workflow-action@0.8.0
         with:
           access_token: ${{ github.token }}
       - name: Fetch all history for all tags and branches
         uses: actions/checkout@v2
         with:
           fetch-depth: 0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.9.7
+        uses: gittools/actions/gitversion/setup@v0.9.9
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.7
+        uses: gittools/actions/gitversion/execute@v0.9.9
       - name: Set up JDK 15 for linux and mac
         uses: actions/setup-java@v1
         with:
@@ -97,34 +97,35 @@ jobs:
         if: matrix.os == 'macos-latest'
         shell: bash
         run: |
-          codesign --entitlements buildres/mac/myapp.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app/Contents/runtime/Contents/MacOS/libjli.dylib
-          codesign --entitlements buildres/mac/myapp.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app/Contents/MacOS/JabRef
-          codesign --entitlements buildres/mac/myapp.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app
+          codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app/Contents/runtime/Contents/MacOS/libjli.dylib
+          codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app/Contents/MacOS/JabRef
+          codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" 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 }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
-          codesign -s "Developer ID Application: Tobias Diez (W2PU6LW5U5)" --options runtime --entitlements buildres/mac/myapp.entitlements -vvvv --deep "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
+          codesign -s "Developer ID Application: Tobias Diez (W2PU6LW5U5)" --options runtime --entitlements buildres/mac/jabref.entitlements -vvvv --deep "build/distribution/JabRef-${{ 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 }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
           productsign --sign "Developer ID Installer: Tobias Diez (W2PU6LW5U5)" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
-      - name: Notarize dmg and pkg installer
-        if: matrix.os == 'macos-latest' && github.ref == 'refs/heads/master'
-        shell: bash
-        run: |
-          REQUEST_UUID_DMG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "W2PU6LW5U5" --file "build/distribution/JabRef-${{ 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 ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "W2PU6LW5U5" --file "build/distribution/JabRef-${{ 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 }}.${{ steps.gitversion.outputs.Minor }}.pkg"
+      # DISABLED UNTIL WE HAVE A NEW APPLE DEVELOPER ACCOUNT
+      # - name: Notarize dmg and pkg installer
+      #   if: matrix.os == 'macos-latest' && github.ref == 'refs/heads/master'
+      #   shell: bash
+      #   run: |
+      #     REQUEST_UUID_DMG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "W2PU6LW5U5" --file "build/distribution/JabRef-${{ 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 ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "W2PU6LW5U5" --file "build/distribution/JabRef-${{ 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"
       - name: Package application image
         shell: bash
         run: ${{ matrix.archivePortable }}
@@ -162,12 +163,12 @@ jobs:
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.9.7
+        uses: gittools/actions/gitversion/setup@v0.9.9
         with:
           versionSpec: '5.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.7
+        uses: gittools/actions/gitversion/execute@v0.9.9
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:

.github/workflows/gource.yml

@@ -0,0 +1,55 @@
+name: Gource
+
+on:
+  push:
+    branches:
+      - gource
+  schedule:
+    - cron:  '15 3 1 1,4,7,10 *'
+
+jobs:
+  action:
+    runs-on: ubuntu-latest
+    steps:
+      - name: 'Checkout'
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - 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 ))
+      - name: 'Development history of last quarter'
+        uses: nbprojekt/gource-action@v1
+        with:
+          gource_title: 'JabRef | more information at contribute.jabref.org'
+          logo_url: 'https://www.jabref.org/img/JabRef-icon-256.png'
+          # 5s * 365 / 4 = 7.5min
+          gource_seconds_per_day: 5
+          gource_start_date: ${{ steps.dates.outputs.start_date }}
+          gource_stop_date: ${{ steps.dates.outputs.stop_date }}
+          gource_file_filter: csl$
+      - name: 'Store video'
+        run: |
+          mkdir gource-videos
+          mv ./gource/gource.mp4 ./gource-videos/jabref-${{ steps.dates.outputs.quarter }}.mp4
+      - name: 'Complete development history'
+        uses: nbprojekt/gource-action@v1
+        with:
+          gource_title: 'JabRef | more information at contribute.jabref.org'
+          logo_url: 'https://www.jabref.org/img/JabRef-icon-256.png'
+          # 0.01 leads to a 45 second video for the complete history until end of 2020
+          # 0.1 leads to a 8 minute video
+          gource_seconds_per_day: 0.1
+          gource_file_filter: csl$
+      - name: 'Store video'
+        run: |
+          mv gource/gource.mp4 gource-videos/jabref-complete.mp4
+      - name: 'Upload gource video'
+        uses: actions/upload-artifact@v2
+        with:
+          name: Gource
+          path: ./gource-videos/
+          retention-days: 80

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

@@ -4,6 +4,7 @@ on:
   schedule:
     # run on 1st and 15th of each month
     - cron: '1 2 1,15 * *'
+  workflow_dispatch:
 
 jobs:
   publish:
@@ -16,28 +17,31 @@ jobs:
         with:
           ref: master
           fetch-depth: 0
-      - name: Add csl-styles remote
-        run: git remote add -f csl-styles https://github.com/citation-style-language/styles.git
-      - name: Update csl-styles
+      - name: Initialize git
         run: |
           git checkout master
           git config --local core.editor /usr/bin/cat
           git config user.name "github actions"
           git config user.email "jabrefmail+webfeedback@gmail.com"
-          git subtree pull --prefix src/main/resources/csl-styles csl-styles master --squash
+      - name: Add csl-styles remote
+        run: git remote add -f csl-styles https://github.com/citation-style-language/styles.git
+      - name: Update csl-styles
+        run: |
+          git subtree pull --prefix buildres/csl/csl-styles csl-styles master --squash || true
+          cp buildres/csl/csl-styles/acm-siggraph.csl src/main/resources/csl-styles/
+          cp buildres/csl/csl-styles/ieee.csl src/main/resources/csl-styles/
+          cp buildres/csl/csl-styles/turabian-author-date.csl src/main/resources/csl-styles/
       - name: Add csl-locales remote
         run: git remote add -f csl-locales https://github.com/citation-style-language/locales.git
       - name: Update csl-locales
         run: |
-          git subtree pull --prefix src/main/resources/csl-locales csl-locales master --squash
-      - uses: ad-m/github-push-action@master
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          branch: master
-      - name: Report issues
-        if: failure()
-        uses: JasonEtco/create-an-issue@master
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          git subtree pull --prefix buildres/csl/csl-locales csl-locales master --squash || true
+          git subtree pull --prefix buildres/csl/csl-locales csl-locales master --squash
+          cp buildres/csl/csl-locales/locales.json src/main/resources/csl-locales/
+          cp buildres/csl/csl-locales/locales-en-US.xml src/main/resources/csl-locales/
+      - uses: peter-evans/create-pull-request@v3
         with:
-          filename: .github/failure-csl-update.md
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: refresh-csl
+          commit-message: Update CSL styles
+          title: "[Bot] Update CSL styles"

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

@@ -47,10 +47,9 @@ jobs:
           cd $GITHUB_WORKSPACE
           ./gradlew generateJournalAbbreviationList
 
-          # git commit
-          git config user.email "jabrefmail+webfeedback@gmail.com"
-          git config user.name "JabRef refresh journal lists [bot]"
-          git add . && git commit -m"Update journalList.mv"
-      - uses: ad-m/github-push-action@master
+      - uses: peter-evans/create-pull-request@v3
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: update-journallist
+          title: "[Bot] Update Journal abbrev list"
+          commit-message: Update journal abbrev list

.github/workflows/snap.yml

@@ -1,6 +1,7 @@
 name: Snap
 
 on:
+  workflow_dispatch:
   push:
     branches:
       - snapcraft
@@ -28,12 +29,12 @@ jobs:
         uses: actions/checkout@v2
       # The image relies on https://builds.jabref.org/master/JabRef-5.0-portable_linux.tar.gz^
       # See snap/snapcraft.yml for details
-      - name: Build snap (1) Run build
+      - name: Run snapcraft build
         uses: snapcore/action-build@v1
         id: snapcraft
         with:
           snapcraft-args: "--debug"
-      - name: Build snap (2) Upload snap
+      - name: Upload snap
         if: ${{ steps.checksecrets.outputs.secretspresent }}
         uses: snapcore/action-publish@v1
         with:

.github/workflows/tests-fetchers.yml

@@ -38,7 +38,7 @@ jobs:
         with:
           java-version: 14
       - uses: actions/cache@v1
-        name: Restore gradle chache
+        name: Restore gradle cache
         with:
           path: ~/.gradle/caches
           key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}