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

* upstream/master: (120 commits) Follow up fix for copy paste (#6820) Add CSS Customisation (#6725) Separate signing and notarizing (#6822) Remove checkstyle hack. 8.36 got released (#6816) Feature/enable lucene query parsing (#6799) New release cycle Bump WyriHaximus/github-action-wait-for-status from v1.1.2 to v1.2 (#6814) Bump mockito-core from 3.5.5 to 3.5.7 (#6813) Bump classgraph from 4.8.87 to 4.8.89 (#6812) Bump me.champeau.gradle.jmh from 0.5.0 to 0.5.1 (#6811) Bump checkstyle from 8.35 to 8.36 (#6810) Improve Changelog Refactor edit action (#6808) Fixed typo in BuildInfo (#6807) disable checkstyle for generated fix checkstyle Simplify check-links.yaml (markdown-link-check) (#6720) Rename /gen to /generate (#6800) Disable CSL refresh on push (#6803) New Crowdin updates (#6804) ... # Conflicts: # src/main/java/org/jabref/gui/JabRefFrame.java
JabRef · Aug 31, 2020 · 548fac1 · 548fac1
2 parents 021012f + a2fbb3a
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diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -9,14 +9,14 @@ jobs:
     steps:
       - name: 'Wait for status checks'
         id: waitforstatuschecks
-        uses: "WyriHaximus/github-action-wait-for-status@0.1.0"
+        uses: "WyriHaximus/github-action-wait-for-status@v1.2"
         with:
           ignoreActions: automerge
           checkInterval: 13
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/automerge-action@v0.8.4
+        uses: pascalgn/automerge-action@v0.9.0
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "squash"

diff --git a/.github/workflows/check-links.yaml b/.github/workflows/check-links.yaml
@@ -1,6 +1,9 @@
 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 * *"
@@ -10,11 +13,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Prepare markdown-link-check
-        run: mkdir docs/ROOT && cp CHANGELOG.md README.md docs/ROOT
       - uses: gaurav-nelson/github-action-markdown-link-check@v1
         with:
           use-quiet-mode: 'yes'
           use-verbose-mode: 'no'
           config-file: 'mlc_config.json'
           folder-path: 'docs/'
+          file-path: './CHANGELOG.md, ./README.md'
diff --git a/.github/workflows/cleanup_pr.yml b/.github/workflows/cleanup_pr.yml
@@ -13,7 +13,7 @@ jobs:
         id: checksecrets
         shell: bash
         run: |
-          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
+          if [ -z "$BUILDJABREFPRIVATEKEY" ]; then
             echo ::set-output name=secretspresent::false
           else
             echo ::set-output name=secretspresent::true
@@ -27,7 +27,7 @@ jobs:
           echo "##[set-output name=branch;]$(echo ${{ github.event.pull_request.head.ref }})"
       - name: Delete folder on builds.jabref.org
         if: ${{ steps.checksecrets.outputs.secretspresent }}
-        uses: appleboy/ssh-action@v0.1.2
+        uses: appleboy/ssh-action@v0.1.3
         with:
           script: rm -rf /var/www/builds.jabref.org/www/${{ steps.extract_branch.outputs.branch }} || true
           host: build-upload.jabref.org

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -19,6 +19,7 @@ env:
   SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
   AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
   IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
+  OSXCERT: ${{ secrets.OSX_SIGNING_CERT }}
 
 jobs:
   build:
@@ -36,53 +37,108 @@ jobs:
           - 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 }}
     name: Create installer and portable version for ${{ matrix.displayName }}
-
     steps:
       - 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@v0.9.3
+        uses: gittools/actions/gitversion/setup@v0.9.4
         with:
-          versionSpec: '5.2.x'
+          versionSpec: "5.3.7"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.3
-      - name: Set up JDK
+        uses: gittools/actions/gitversion/execute@v0.9.4
+      - name: Set up Adotptopen JDK mac
+        uses: joschi/setup-jdk@v2
+        with:
+          # reason: https://bugs.openjdk.java.net/browse/JDK-8238184
+          java-version: 15
+          release_type: ea
+        if: matrix.os == 'macos-latest'
+      - name: Set up JDK for linux and windows
         uses: actions/setup-java@v1
         with:
           java-version: 14
+        if: matrix.os != 'macos-latest'
       - name: Restore gradle cache
         uses: actions/cache@master
         with:
           path: ~/.gradle/caches
           key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*') }}
           restore-keys: |
             ${{ runner.os }}-gradle-
+      - name: Setup OSX key chain on OSX
+        if: matrix.os == 'macos-latest'
+        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'
+        uses: apple-actions/import-codesign-certs@v1
+        with:
+          p12-file-base64: ${{ secrets.OSX_SIGNING_CERT_APPLICATION }}
+          p12-password: ${{ secrets.OSX_CERT_PWD }}
+          create-keychain: false
+          keychain-password: jabref
       - name: Build runtime image
         run: ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
       - name: Build installer
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
         shell: bash
+      - name: Resign app image for OSX and build dmg
+        if: matrix.os == 'macos-latest'
+        shell: bash
+        run: |
+          codesign --entitlements buildres/mac/myapp.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app/Contents/runtime/Contents/MacOS/libjli.dylib
+          codesign --entitlements buildres/mac/myapp.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app/Contents/MacOS/JabRef
+          codesign --entitlements buildres/mac/myapp.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app
+          jpackage --type pkg --dest build/distribution --name JabRef --app-version "${{ 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 }}.${{ steps.gitversion.outputs.Minor }}.dmg"
+          jpackage --type pkg --dest build/distribution --name JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --app-image build/distribution/JabRef.app --verbose --type pkg --vendor JabRef --app-version "${{ 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 }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
+      - name: Notarize dmg and pkg installer
+        if: matrix.os == 'macos-latest' && github.ref == 'refs/heads/master'
+        shell: bash
+        run: |
+          REQUEST_UUID=$(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" -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 }}.${{ steps.gitversion.outputs.Minor }}.dmg"
+          REQUEST_UUID=$(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" -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
-        run: ${{ matrix.archivePortable }}
         shell: bash
+        run: ${{ matrix.archivePortable }}
       - name: Rename files
+        shell: pwsh
         run: |
           get-childitem -Path build/distribution/*
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.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"}
-        shell: pwsh
       - name: Upload to GitHub workflow artifacts store
         uses: actions/upload-artifact@master
         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]
@@ -103,12 +159,12 @@ jobs:
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.9.3
+        uses: gittools/actions/gitversion/setup@v0.9.4
         with:
           versionSpec: '5.2.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.3
+        uses: gittools/actions/gitversion/execute@v0.9.4
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:

diff --git a/.github/workflows/refresh-csl-subtrees.yml b/.github/workflows/refresh-csl-subtrees.yml
@@ -1,10 +1,6 @@
 name: Refresh Citation Style Language Files
 
 on:
-  push:
-    paths:
-      - '.github/workflows/refresh-csl-subtrees.yml'
-      - 'src/main/resources/csl-locales/**'
   schedule:
     # run on 1st and 15th of each month
     - cron: '1 2 1,15 * *'
@@ -13,6 +9,7 @@ jobs:
   publish:
     name: Refresh Citation Style Language Files
     runs-on: ubuntu-latest
+    if: github.repository == 'JabRef/jabref'
     steps:
       - name: Checkout source
         uses: actions/checkout@v2

diff --git a/.github/workflows/tests-fetchers.yml b/.github/workflows/tests-fetchers.yml
@@ -22,9 +22,9 @@ on:
     - cron: '2 3 * * 3'
 
 env:
-  SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
-  AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
-  IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
+  SpringerNatureAPIKey: ${{ secrets.SPRINGERNATUREAPIKEY_FOR_TESTS }}
+  AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey_FOR_TESTS }}
+  IEEEAPIKey: ${{ secrets.IEEEAPIKey_FOR_TESTS }}
 
 jobs:
   fetchertests:

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -223,3 +223,37 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: gradle/wrapper-validation-action@v1
+  checkauthors:
+    name: "Validate AUTHORS"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          # full checkout needed for authors generation
+          fetch-depth: 0
+      - name: "Check AUTHORS"
+        id: authors_check
+        shell: bash
+        run: |
+          git config user.name "JabRef Author Checker [bot]"
+          git config user.email "noreply@jabref.org"
+          ./scripts/generate-authors.sh
+          set +o pipefail
+          added=$(git diff HEAD --no-ext-diff --unified=0 -a --no-prefix | egrep "^\+[^+]" | sed "s/^\+//")
+          if [ -z "$added" ]; then
+            echo "::set-output name=newauthor::false"
+            echo "No authors added"
+            exit 0
+          fi
+          message="The JabRef maintainers will add the following name to the [AUTHORS file](https://github.com/JabRef/jabref/blob/master/CONTRIBUTING.md#author-credits). In case you want to use a different one, please comment here and [adjust your name in your git configuration](https://docs.github.com/en/github/using-git/setting-your-username-in-git) for future commits.%0A%0A\`\`\`%0A${added//$'\n'/'%0A'}%0A\`\`\`%0A"
+          echo "::set-output name=message::$message"
+          echo "::set-output name=newauthor::true"
+          echo "New authors found"
+      - name: Comment PR
+        uses: unsplash/comment-on-pr@master
+        if: steps.authors_check.outputs.newauthor == 'true'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          msg: "${{ steps.authors_check.outputs.message }}"
+          check_for_duplicate_msg: true
diff --git a/.mailmap b/.mailmap
@@ -202,3 +202,12 @@ Mootez Saad <34676841+MootezSaaD@users.noreply.github.com> <mootez.saad@medtech.
 Chen Yuheng <pass@chenyuheng.cn>
 Dominik Voigt <43381984+DominikVoigt@users.noreply.github.com>
 Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com> <cc.snethlage@gmail.com>
+Daniel Price <64694785+daniel-price@users.noreply.github.com>
+Cai Zhichun <54977532+braincident@users.noreply.github.com> <569120128@qq.com>
+Hollyqqqqq <55199983+Hollyqqqqq@users.noreply.github.com> <11712639@mail.sustech.edu.cn>
+Grzegorz Popiel <grzegorz.popiel@yahoo.com>
+Tianjian Lei <185049857@qq.com>
+Tianjian Lei <185049857@qq.com> <leitianjian@outlook.com>
+Muhammad Arsalan Badar <arsalan_badar@intuit.com>
+ZhouSky <11711923@mail.sustech.edu.cn>
+Vincent Gagnon <vincentgagnon53@gmail.com>