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

* upstream/main: (354 commits)
  Fix ScienceDirect fetcher (#7684)
  Refactor NoBibTexFieldCheckerTest to increase mutation coverage (#7697)
  Update Gradle from 6.8.3 to 7.0 (#7619)
  Fixes #7305: the RFC fetcher is not compatible with the draftFix for issue 7305 (#7674)
  Refactoring existing unit tests (#7693)
  cover boundary cases & add more unit tests (#7694)
  Bump classgraph from 4.8.104 to 4.8.105 (#7688)
  Bump java-diff-utils from 4.9 to 4.10 (#7692)
  Fix arXiv fetcher tests (#7686)
  Make key for ScienceDirect configurable (#7683)
  migration of timestamp (#7671)
  Fix CCSB and DOAJ (#7426)
  [Bot] Update CSL styles (#7680)
  MS Office XML: Export month name (#7677)
  linkfix (#7678)
  readd fix (#7675)
  Fix threading cleanup in performSearch (#7672)
  add missing changelog
  delete bug fix (#7580)
  Add more unit tests to three gui classes  (#7636)
  ...

# Conflicts:
#	build.gradle

.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: ''
 
 ---
 
@@ -16,11 +19,11 @@ JabRef version <!-- version as shown in the about box --> on <!-- Windows 10|Ubu
 <!-- 
       Please always test if the bug is still reproducible in the latest development version.
       We are constantly improving JabRef and some bugs may already be fixed.
-      You can download the development version at: http://builds.jabref.org/master/
+      You can download the development version at: http://builds.jabref.org/main
       Please make a backup of your library before you try out this version.
       If you already use a development version, ensure that you use the latest one.
  -->
-- [ ] **Mandatory**: I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists
+- [ ] **Mandatory**: I have tested the latest development version from http://builds.jabref.org/main and the problem persists
 
 <!-- Add a clear and concise description of what the bug is. -->
 

.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

@@ -3,22 +3,27 @@ on: [pull_request]
 
 jobs:
   automerge:
-    name: Automerge Dependabot
+    name: Automerge Dependency Updates
     runs-on: ubuntu-latest
-    if: github.actor == 'dependabot[bot]'
+    if: github.actor == 'dependabot[bot]' || github.actor == 'dependabot-preview[bot]' || contains(github.event.pull_request.labels.*.name, 'dependencies')
     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@v0.12.0
+        uses: pascalgn/automerge-action@v0.13.1
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
-          MERGE_METHOD: "squash"
+          MERGE_METHOD: "merge"
           MERGE_LABELS: ""
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/check-outdated-dependencies.yml

@@ -12,9 +12,10 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v2
       - name: Set up JDK
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
           java-version: 14
+          distribution: 'adopt'
       - name: Look for outdated dependencies
         run: ./gradlew -q checkOutdatedDependencies
       - name: Report issues

.github/workflows/deployment.yml

@@ -1,10 +1,11 @@
 name: Deployment
 
 on:
+  workflow_dispatch:
   push:
     branches:
-      - master
-      - master-release
+      - main
+      - main-release
     paths-ignore:
       - 'docs/**'
       - 'src/test/**'
@@ -20,6 +21,7 @@ env:
   AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
   IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
   OSXCERT: ${{ secrets.OSX_SIGNING_CERT }}
+  GRADLE_OPTS: -Dorg.gradle.daemon=false -Dorg.gradle.vfs.watch=false
 
 jobs:
   build:
@@ -41,37 +43,41 @@ 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@0.9.0
         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
+        uses: actions/setup-java@v2
         with:
           java-version: 15
+          distribution: 'adopt'
         if: matrix.os != 'windows-latest'
       - name: Set up JDK 14 for windows
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
           java-version: 14
+          distribution: 'adopt'
         if: matrix.os == 'windows-latest'
       - name: Restore gradle cache
-        uses: actions/cache@master
+        uses: actions/cache@v2
         with:
-          path: ~/.gradle/caches
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*') }}
+          path: |
+            ~/.gradle/caches
+            ~/.gradle/wrapper
+          key: ${{ runner.os }}-gradle7x-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
           restore-keys: |
-            ${{ runner.os }}-gradle-
+            ${{ runner.os }}-gradle7x-
       - name: Setup OSX key chain on OSX
         if: matrix.os == 'macos-latest'
         uses: apple-actions/import-codesign-certs@v1
@@ -96,18 +102,18 @@ jobs:
         if: matrix.os == 'macos-latest'
         shell: bash
         run: |
-          codesign --entitlements buildres/mac/myapp.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app/Contents/runtime/Contents/MacOS/libjli.dylib
-          codesign --entitlements buildres/mac/myapp.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app/Contents/MacOS/JabRef
-          codesign --entitlements buildres/mac/myapp.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app
+          codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: JabRef e.V. (6792V39SK3)" build/distribution/JabRef.app/Contents/runtime/Contents/MacOS/libjli.dylib
+          codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: JabRef e.V. (6792V39SK3)" build/distribution/JabRef.app/Contents/MacOS/JabRef
+          codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: JabRef e.V. (6792V39SK3)" build/distribution/JabRef.app
           jpackage --type pkg --dest build/distribution --name JabRef --app-version "${{ 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 }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
-          codesign -s "Developer ID Application: Tobias Diez (W2PU6LW5U5)" --options runtime --entitlements buildres/mac/myapp.entitlements -vvvv --deep "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
+          codesign -s "Developer ID Application: JabRef e.V. (6792V39SK3)" --options runtime --entitlements buildres/mac/jabref.entitlements -vvvv --deep "build/distribution/JabRef-${{ 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 }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
-          productsign --sign "Developer ID Installer: Tobias Diez (W2PU6LW5U5)" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
+          productsign --sign "Developer ID Installer: JabRef e.V. (6792V39SK3)" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
       - name: Notarize dmg and pkg installer
-        if: matrix.os == 'macos-latest' && github.ref == 'refs/heads/master'
+        if: matrix.os == 'macos-latest' && github.ref == 'refs/heads/main'
         shell: bash
         run: |
-          REQUEST_UUID_DMG=$(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 $3}')
+          REQUEST_UUID_DMG=$(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  ${{ secrets.OSX_NOTARIZATION_APP_PWD }} | grep "Status: in progress" > /dev/null; do
             echo "Verification in progress..."
             sleep 30
@@ -116,7 +122,7 @@ jobs:
           spctl -vvv --assess --type exec build/distribution/JabRef.app
           codesign -vvv --deep --strict "build/distribution/JabRef-${{ 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 $3}')
+          REQUEST_UUID_PKG=$(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
@@ -161,12 +167,12 @@ 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:
@@ -14,30 +15,37 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v2
         with:
-          ref: master
+          ref: main
           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 checkout main
           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/
+          git add .
+          git commit -m"Refresh example styles" || true
       - 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
+          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/
+          git add .
+          git commit -m"Refresh example styles" || true
+      - uses: peter-evans/create-pull-request@v3
         with:
-          filename: .github/failure-csl-update.md
+          token: ${{ secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER }}
+          branch: refresh-csl
+          commit-message: Update CSL styles
+          title: "[Bot] Update CSL styles"
+          labels: dependencies