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

* upstream/master: (287 commits) Bump junit-vintage-engine from 5.6.1 to 5.6.2 (#6276) Number of items found in ImportEntriesDialog (#6248) Fix dependency label Bump flexmark-ext-gfm-strikethrough from 0.61.0 to 0.61.6 (#6273) Bump unirest-java from 3.7.01 to 3.7.02 (#6275) Bump junit-platform-launcher from 1.6.1 to 1.6.2 (#6279) Bump flexmark-ext-gfm-tasklist from 0.61.0 to 0.61.6 (#6278) Bump junit-jupiter from 5.6.1 to 5.6.2 (#6274) Bump flexmark from 0.61.0 to 0.61.6 (#6280) Bump classgraph from 4.8.68 to 4.8.69 (#6277) Bump org.beryx.jlink from 2.17.4 to 2.17.5 (#6281) Improve performance (#6270) Improve calculation of matched entries upon change (#6268) Fix sort by priority (#6222) (#6265) Squashed 'src/main/resources/csl-styles/' changes from 88726cb..db54e56 Use https everywhere Entry editor: Add more tooltips and wrap tooltips if necessary (#6239) JDK14 switch - and checkstyle skipping (#6250) Bump postgresql from 42.2.11 to 42.2.12 (#6254) Bump unirest-java from 3.7.00 to 3.7.01 (#6253) ...
JabRef · Apr 13, 2020 · 30fec30 · 30fec30
2 parents b24a3a0 + 67b1203
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diff --git a/.dependabot/config.yml b/.dependabot/config.yml
@@ -6,7 +6,7 @@ update_configs:
     directory: "/"
     update_schedule: "weekly"
     default_labels:
-      - "dependencies"
+      - "t: dependencies"
     automerged_updates:
       - match:
          dependency_type: "all"

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,19 +1,18 @@
 <!-- 
 Describe the changes you have made here: what, why, ... 
-Link issues by using the following pattern: #333.
-If you fixed a koppor issue, link it with following pattern: [koppor#47](https://github.com/koppor/jabref/issues/47).
+Link issues that are fixed, e.g. "Fixes #333".
+If you fixed a koppor issue, link it, e.g. "Fixes https://github.com/koppor/jabref/issues/47".
 The title of the PR must not reference an issue, because GitHub does not support autolinking there.
 -->
 
 
 <!-- 
-- All items with `[ ]` are still a TODO.
-- All items checked with `[x]` are done.
-- Remove items not applicable
+- Go through the list below. If a task has been completed, mark it done by using `[x]`.
+- Please don't remove any items, just leave them unchecked if they are not applicable.
 -->
 
 - [ ] Change in CHANGELOG.md described (if applicable)
 - [ ] Tests created for changes (if applicable)
 - [ ] Manually tested changed features in running JabRef (always required)
-- [ ] Screenshots added in PR description (for bigger UI changes)
-- [ ] [Checked documentation](https://docs.jabref.org/): Is the information available and up to date? If not: Issue created at <https://github.com/JabRef/user-documentation/issues>.
+- [ ] Screenshots added in PR description (for UI changes)
+- [ ] [Checked documentation](https://docs.jabref.org/): Is the information available and up to date? If not created an issue at <https://github.com/JabRef/user-documentation/issues> or, even better, submitted a pull request to the documentation repository.
diff --git a/.github/workflows/check-outdated-dependencies.yml b/.github/workflows/check-outdated-dependencies.yml
@@ -1,6 +1,6 @@
 name: Check dependencies
 
-on: 
+on:
   schedule:
     - cron:  '0 0 * * TUE' # Run every Tuesday (after dependabot, which runs Monday)
 
@@ -9,21 +9,18 @@ jobs:
     name: Check dependencies
     runs-on: ubuntu-latest
     steps:
-    - name: Checkout source
-      uses: actions/checkout@v1
-      with:
-        depth: 1
-        submodules: false
-    - name: Set up JDK
-      uses: actions/setup-java@v1
-      with:
-        java-version: 13.0.2
-    - name: Look for outdated dependencies
-      run: ./gradlew -q checkOutdatedDependencies
-    - name: Report issues
-      if: failure()
-      uses: JasonEtco/create-an-issue@master
-      env: 
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      with:
-        filename: .github/outdatedDependencies.md
+      - name: Checkout source
+        uses: actions/checkout@v2
+      - name: Set up JDK
+        uses: actions/setup-java@v1
+        with:
+          java-version: 14
+      - name: Look for outdated dependencies
+        run: ./gradlew -q checkOutdatedDependencies
+      - name: Report issues
+        if: failure()
+        uses: JasonEtco/create-an-issue@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          filename: .github/outdatedDependencies.md
diff --git a/.github/workflows/cleanup_pr.yml b/.github/workflows/cleanup_pr.yml
@@ -9,15 +9,28 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - name: Extract branch name
-      id: extract_branch
-      run: |
-        echo "##[set-output name=branch;]$(echo ${{ github.event.pull_request.head.ref }})"
-    - name: Delete folder on builds.jabref.org
-      uses: appleboy/[email protected]
-      with:
-        script: rm -rf /var/www/builds.jabref.org/www/${{ steps.extract_branch.outputs.branch }}
-        host: build-upload.jabref.org
-        port: 9922
-        username: jrrsync
-        key: ${{ secrets.buildJabRefPrivateKey }}
+      - name: Check secrets presence
+        id: checksecrets
+        shell: bash
+        run: |
+          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
+            echo ::set-output name=secretspresent::false
+          else
+            echo ::set-output name=secretspresent::true
+          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 }})"
+      - name: Delete folder on builds.jabref.org
+        if: ${{ steps.checksecrets.outputs.secretspresent }}
+        uses: appleboy/[email protected]
+        with:
+          script: rm -rf /var/www/builds.jabref.org/www/${{ steps.extract_branch.outputs.branch }} || true
+          host: build-upload.jabref.org
+          port: 9922
+          username: jrrsync
+          key: ${{ secrets.buildJabRefPrivateKey }}
diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - master
+      - master-release
     paths-ignore:
       - 'docs/**'
       - 'src/test/**'
@@ -14,123 +15,77 @@ on:
       - 'src/test/**'
       - 'README.md'
 
+env:
+  SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
+
 jobs:
   build:
     strategy:
-      fail-fast: true
+      fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macOS-latest]
         include:
-         - os: ubuntu-latest
-           displayName: linux
-           jpackageDownload: https://download.java.net/java/early_access/jdk14/34/GPL/openjdk-14-ea+34_linux-x64_bin.tar.gz
-           jdk14Path: /jdk-14
-           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
-           jpackageDownload: https://download.java.net/java/early_access/jdk14/34/GPL/openjdk-14-ea+34_windows-x64_bin.zip
-           jdk14Path: /jdk-14
-           archivePortable: 7z a -r build/distribution/JabRef-portable_windows.zip ./build/distribution/JabRef && rm -R build/distribution/JabRef
-         - os: macOS-latest
-           displayName: macOS
-           jpackageDownload: https://download.java.net/java/early_access/jdk14/34/GPL/openjdk-14-ea+34_osx-x64_bin.tar.gz
-           jdk14Path: /jdk-14.jdk/Contents/Home
-           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
+          - 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
+            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: Checkout source
-        uses: actions/checkout@v2-beta
-        with:
-          fetch-depth: 0
-      - name: Fetch tags and master for GitVersion
-        run: |
-          git fetch --tags origin
-          git rev-parse --verify master
-          if (-not $?) {
-            git branch --force --create-reflog master origin/master
-          }
-        shell: pwsh
+        uses: actions/checkout@v2
+      - name: Fetch all history for all tags and branches
+        run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/setup-gitversion@v0.3
+        uses: gittools/actions/gitversion/setup@v0.9.2
         with:
-            versionSpec: '5.1.2'
+          versionSpec: '5.2.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/execute-gitversion@v0.3
+        uses: gittools/actions/gitversion/execute@v0.9.2
       - name: Set up JDK
         uses: actions/setup-java@v1
         with:
-          java-version: 13.0.2
-      # configuration based on https://github.com/actions/cache/blob/master/examples.md#java---gradle
+          java-version: 14
       - uses: actions/cache@v1
         name: Restore gradle cache
         with:
           path: ~/.gradle/caches
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
+          key: ${{ runner.os }}-gradle-cache-${{ hashFiles('**/*.gradle') }}
+          # in case there is no cache for the current OS, fall back to any other OS
           restore-keys: |
-            ${{ runner.OS }}-gradle-${{ env.cache-name }}-
-            ${{ runner.OS }}-gradle-
-            ${{ runner.OS }}-
+            ${{ runner.os }}-gradle-cache-
+            Linux-gradle-cache-${{ hashFiles('**/*.gradle') }}
+            Windows-gradle-cache-${{ hashFiles('**/*.gradle') }}
+            macOS-gradle-cache-${{ hashFiles('**/*.gradle') }}
       - uses: actions/cache@v1
         name: Cache gradle wrapper
-        # cache at Mac OS X is 2 GB (too large)
-        if: matrix.displayName == 'linux' || matrix.displayName == 'windows'
         with:
           path: ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
-      - name: Download jpackage
-        # We need to download jpackage from https://jdk.java.net/jpackage/
-        run: |
-          import tarfile
-          import zipfile
-          import sys
-          if sys.version_info[0] >= 3:
-            from urllib.request import urlretrieve
-          else:
-            from urllib import urlretrieve
-
-          url = "${{ matrix.jpackageDownload }}"
-          tmpfile, headers = urlretrieve(url)
-          if (url.endswith("tar.gz")):
-            tar = tarfile.open(tmpfile)
-            tar.extractall()
-            tar.close()
-          elif (url.endswith("zip")):
-            zip = zipfile.ZipFile(tmpfile)
-            zip.extractall()
-            zip.close()
-        shell: python
+          key: ${{ runner.os }}-gradle-wrapper-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
+          # in case there is no cache for the current OS, fall back to any other OS
+          restore-keys: |
+            Linux-gradle-wrapper-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
+            Windows-gradle-wrapper-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
+            macOS-gradle-wrapper-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
       - name: Build runtime image
         run: ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
       - name: Build installer
-        run: |
-          export BADASS_JLINK_JPACKAGE_HOME="${GITHUB_WORKSPACE}${{ matrix.jdk14Path }}"
-          ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
+        run: ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
         shell: bash
       - name: Package application image
         run: ${{ matrix.archivePortable }}
         shell: bash
-      - name: Build snap (1) Setup snapcraft
-        uses: jhenstridge/snapcraft-build-action@v1
-        id: snapcraft
-        if: matrix.displayName == 'linux'
-      - name: Build snap (2) Run build
-        run: |
-          mv ${{ steps.snapcraft.outputs.snap }} build/distribution/
-        if: matrix.displayName == 'linux'
-      - name: Build snap (3) Upload snap
-        if: matrix.displayName == 'linux' && github.ref == 'refs/heads/master'
-        env:
-          SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
-        run: |
-            mkdir .snapcraft && echo ${SNAPCRAFT_LOGIN_FILE} | base64 --decode --ignore-garbage > .snapcraft/snapcraft.cfg
-            snapcraft push build/distribution/jabref*.snap --release edge || true
-        shell: bash
       - name: Rename files
         run: |
+          get-childitem -Path build/distribution/*
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.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
@@ -144,25 +99,28 @@ jobs:
     runs-on: ubuntu-latest
     needs: [build]
     steps:
-      - name: Checkout source
-        uses: actions/checkout@v2-beta
-        with:
-          fetch-depth: 0
-      - name: Fetch tags and master for GitVersion
+      - name: Check secrets presence
+        id: checksecrets
+        shell: bash
         run: |
-          git fetch --tags origin
-          git rev-parse --verify master
-          if (-not $?) {
-            git branch --force --create-reflog master origin/master
-          }
-        shell: pwsh
+          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
+            echo ::set-output name=secretspresent::false
+          else
+            echo ::set-output name=secretspresent::true
+          fi
+        env:
+          BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
+      - name: Checkout source
+        uses: actions/checkout@v2
+      - name: Fetch all history for all tags and branches
+        run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/setup-gitversion@v0.3
+        uses: gittools/actions/gitversion/setup@v0.9.2
         with:
-            versionSpec: '5.1.2'
+          versionSpec: '5.2.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/execute-gitversion@v0.3
+        uses: gittools/actions/gitversion/execute@v0.9.2
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:
@@ -180,6 +138,7 @@ jobs:
           path: build/distribution/
       - name: Deploy to builds.jabref.org
         id: deploy
+        if: ${{ steps.checksecrets.outputs.secretspresent }}
         uses: Pendect/[email protected]
         env:
           DEPLOY_KEY: ${{ secrets.buildJabRefPrivateKey }}
@@ -190,3 +149,4 @@ jobs:
           ssh_options: '-p 9922'
           src: 'build/distribution/'
           dest: [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
+
diff --git a/.github/workflows/gradle-wrapper-validation.yml b/.github/workflows/gradle-wrapper-validation.yml
diff --git a/.github/workflows/snap.yml b/.github/workflows/snap.yml
@@ -0,0 +1,41 @@
+name: Snap
+
+on:
+  push:
+    branches:
+      - snapcraft
+  schedule:
+    # run on each day
+    - cron: '33 4 * * *'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    name: Create snapcraft image
+
+    steps:
+      - name: Check secrets presence
+        id: checksecrets
+        shell: bash
+        run: |
+          if [ "SNAPCRAFT_LOGIN_FILE" == "" ]; then
+            echo ::set-output name=secretspresent::false
+          else
+            echo ::set-output name=secretspresent::true
+          fi
+        env:
+          SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
+      - name: Checkout source
+        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
+        uses: jhenstridge/snapcraft-build-action@v1
+        id: snapcraft
+      - name: Build snap (2) Upload snap
+        if: ${{ steps.checksecrets.outputs.secretspresent }}
+        uses: jhenstridge/snapcraft-publish-action@v1
+        with:
+          store_login: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
+          snap: ${{ steps.snapcraft.outputs.snap }}
+          release: edge