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

* upstream/master:
  Fix eclipse classpath build file
  New translations JabRef_en.properties (French) (#5709)
  Check for existing master branch
  Disable failing MathSciNet test due to missing subscription
  Try to force creating reflog
  Change travis to github in Readme
  Use GitVersion to increment build numbers (#5682)
  New Crowdin translations (#5687)
  Bump checkstyle from 8.26 to 8.27 (#5694)
  Bump byte-buddy-parent from 1.10.3 to 1.10.4
  Bump classgraph from 4.8.54 to 4.8.58
  Bump unirest-java from 3.1.04 to 3.2.00
  Bump richtextfx from 0.10.2 to 0.10.3
  Bump mockito-core from 3.1.0 to 3.2.0
  Update JavaFX (#5690)
  Run outdated dependency check after dpendabot
  Update outdatedDependencies.md

.github/outdatedDependencies.md

@@ -2,5 +2,4 @@
 title: Outdated dependencies
 labels: code-quality, dependencies
 ---
-There are outdated dependencies! 
-See https://github.com/JabRef/jabref/actions?query=is%3Afailure for details.
+[There are outdated dependencies!](https://github.com/JabRef/jabref/actions?query=is%3Afailure+workflow%3A%22Check+dependencies%22) 

.github/workflows/check-outdated-dependencies.yml

@@ -2,7 +2,7 @@ name: Check dependencies
 
 on: 
   schedule:
-    - cron:  '0 0 * * 0' # Run every Sunday
+    - cron:  '0 0 * * TUE' # Run every Tuesday (after dependabot, which runs Monday)
 
 jobs:
   checkDependencies:

.github/workflows/deployment.yml

@@ -30,18 +30,24 @@ jobs:
 
     steps:
     - name: Checkout source
-      uses: actions/checkout@v1
+      uses: actions/checkout@v2-beta
       with:
-        depth: 1
-        submodules: false
-    - name: Extract branch name
-      shell: bash
+        fetch-depth: 0
+    - name: Fetch tags and master for GitVersion
       run: |
-         ref=${GITHUB_REF#refs/heads/}
-         ref=${ref#refs/pull/}
-         ref=${ref%/merge}
-         echo "##[set-output name=branch;]${ref}"
-      id: extract_branch
+        git fetch --tags origin
+        git rev-parse --verify master
+        if (-not $?) {
+          git branch --force --create-reflog master origin/master
+        }
+      shell: pwsh
+    - name: Install GitVersion
+      uses: gittools/actions/setup-gitversion@v0.3
+      with:
+          versionSpec: '5.1.2'
+    - name: Run GitVersion
+      id: gitversion
+      uses: gittools/actions/execute-gitversion@v0.3
     - name: Set up JDK
       uses: actions/setup-java@v1
       with:
@@ -82,11 +88,11 @@ jobs:
           zip.close()
       shell: python
     - name: Build runtime image
-      run: ./gradlew -Pdev=true jlinkZip
+      run: ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
     - name: Build installer
       run: |
         export BADASS_JLINK_JPACKAGE_HOME="${GITHUB_WORKSPACE}${{ matrix.jdk14Path }}"
-        ./gradlew -Pdev=true jpackage
+        ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
       shell: bash
     - name: Add installer as artifact
       uses: actions/upload-artifact@master
@@ -97,18 +103,23 @@ jobs:
       run: ${{ matrix.archivePortable }}
       shell: bash
     - name: Build and publish snap
-      if: matrix.os == 'ubuntu-latest' && steps.extract_branch.outputs.branch == 'master'
+      if: matrix.os == 'ubuntu-latest' && steps.gitversion.outputs.branchName == 'master'
       env:
         SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
       run: |
           mkdir .snapcraft && echo ${SNAPCRAFT_LOGIN_FILE} | base64 --decode --ignore-garbage > .snapcraft/snapcraft.cfg
           docker run -v $(pwd):$(pwd) -t lyzardking/snapcraft-bionic sh -c "apt update -qq && cd $(pwd) && snapcraft && mv jabref*.snap build/distribution/ && snapcraft push build/distribution/jabref*.snap --release edge || true"
       shell: bash
+    - name: Rename files
+      run: |
+        get-childitem -Path build/distribution/* | rename-item -NewName {$_.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 builds.jabref.org
       uses: garygrossgarten/github-action-scp@release
       with:
         local: build/distribution
-        remote: www/${{ steps.extract_branch.outputs.branch }}
+        remote: www/${{ steps.gitversion.outputs.branchName }}
         host: builds.jabref.org
         username: builds_jabref_org
         privateKey: ${{ secrets.buildJabRefPrivateKey }}

GitVersion.yml

@@ -0,0 +1,2 @@
+assembly-versioning-format: '{major}.{minor}.{buildmetadata}'
+assembly-informational-format: '{major}.{minor}{PreReleaseTagWithDash}--{CommitDate}--{ShortSha}'

README.md

@@ -1,6 +1,7 @@
 # JabRef Bibliography Management
 
-[![Build Status](https://travis-ci.org/JabRef/jabref.svg?branch=master)](https://travis-ci.org/JabRef/jabref)
+[![Deployment Status](https://github.com/JabRef/jabref/workflows/Deployment/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ADeployment)
+[![Build Status](https://github.com/JabRef/jabref/workflows/Tests/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ATests)
 [![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=master)
 [![Donation](https://img.shields.io/badge/donate%20to-jabref-orange.svg)](https://donations.jabref.org)
 [![Crowdin](https://d322cqt584bo4o.cloudfront.net/jabref/localized.svg)](https://crowdin.com/project/jabref)
@@ -94,7 +95,7 @@ When you want to develop, it is necessary to generate additional sources using `
 and then generate the Eclipse `gradlew eclipse`.
 For IntelliJ IDEA, just import the project via a Gradle Import by pointing at the `build.gradle`.
 
-`gradlew test` executes all tests. We use [Travis CI](https://travis-ci.org/) for executing the tests after each commit. For developing, it is sufficient to locally only run the associated test for the classes you changed. Travis will report any other failure.
+`gradlew test` executes all tests. We use [Github Actions](https://github.com/JabRef/jabref/actions) for executing the tests after each commit. For developing, it is sufficient to locally only run the associated test for the classes you changed. Github will report any other failure.
 
   [BibTeX]: https://www.ctan.org/pkg/bibtex
   [Biblatex]: https://www.ctan.org/pkg/biblatex

build.gradle

@@ -44,7 +44,7 @@ apply plugin: LocalizationPlugin
 apply from: 'eclipse.gradle'
 
 group = "org.jabref"
-version = "5.0.0"
+version = project.findProperty('projVersion') ?: '100.0.0'
 
 sourceCompatibility = 13
 targetCompatibility = 13
@@ -102,7 +102,7 @@ configurations {
 }
 
 javafx {
-    version = "13"
+    version = "13.0.1"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
 }
 
@@ -163,13 +163,13 @@ dependencies {
     compile 'de.saxsys:mvvmfx:1.8.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
     compile 'org.fxmisc.flowless:flowless:0.6.1'
-    compile 'org.fxmisc.richtext:richtextfx:0.10.2'
+    compile 'org.fxmisc.richtext:richtextfx:0.10.3'
     compile group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
     compile 'com.jfoenix:jfoenix:9.0.9'
     compile 'org.controlsfx:controlsfx:11.0.0'
 
     compile 'org.jsoup:jsoup:1.12.1'
-    compile 'com.konghq:unirest-java:3.1.04'
+    compile 'com.konghq:unirest-java:3.2.00'
 
     compile 'org.slf4j:slf4j-api:2.0.0-alpha1'
     compile group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'
@@ -206,15 +206,15 @@ dependencies {
     }
 
 
-    testCompile 'io.github.classgraph:classgraph:4.8.54'
+    testCompile 'io.github.classgraph:classgraph:4.8.58'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.5.2'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.5.2'
     testCompile 'org.junit.platform:junit-platform-launcher:1.5.2'
 
-    testCompile 'net.bytebuddy:byte-buddy-parent:1.10.3'
+    testCompile 'net.bytebuddy:byte-buddy-parent:1.10.4'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
-    testCompile 'org.mockito:mockito-core:3.1.0'
+    testCompile 'org.mockito:mockito-core:3.2.0'
     //testCompile 'com.github.tomakehurst:wiremock:2.24.1'
     testCompile 'org.xmlunit:xmlunit-core:2.6.3'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.3'
@@ -225,7 +225,7 @@ dependencies {
     testCompile "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
     testCompile "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.26'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.27'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.2'
     jython 'org.python:jython-standalone:2.7.1'
 }
@@ -283,7 +283,7 @@ processResources {
     filteringCharset = 'UTF-8'
 
     filesMatching("build.properties") {
-        expand(version: createVersionString(),
+        expand(version: project.findProperty('projVersionInfo') ?: '100.0.0',
                 "year": String.valueOf(Calendar.getInstance().get(Calendar.YEAR)),
                 "authors": new File('AUTHORS').readLines().findAll { !it.startsWith("#") }.join(", "),
                 "developers": new File('DEVELOPERS').readLines().findAll { !it.startsWith("#") }.join(", "),
@@ -723,35 +723,3 @@ task bundleLibreOffice(type: Jar) {
     destinationDir = file('lib')
     archiveName = 'libreoffice.jar'
 }
-
-// Returns the value of project.version in production and a string of the format VERSION-dev--DATE--BRANCH--GIT_HASH for development versions
-def createVersionString() {
-    if (hasProperty('dev')) {
-        String command = "git log --pretty=format:%cd--%h -n 1 --date=short"
-        String commitInfo
-        if (OperatingSystem.current().isWindows()) {
-            commitInfo = "cmd /c $command".execute().in.text
-        } else {
-            commitInfo = command.execute().in.text
-        }
-
-        // determine branch
-        command = "git symbolic-ref -q --short HEAD"
-        String branchName
-        if (OperatingSystem.current().isWindows()) {
-            branchName = "cmd /c $command".execute().in.text
-        } else {
-            branchName = command.execute().in.text
-        }
-        // A newline is returned. Remove it. (trim())
-        // In the context of github, the branch name could be something like "pull/277"
-        // "/" is an illegal character. To be safe, all illegal filename characters are replaced by "_"
-        // http://stackoverflow.com/a/15075907/873282 describes the used pattern.
-        branchName = branchName.trim().replaceAll("[^a-zA-Z0-9.-]", "_")
-
-        // first the date (%cd), then the branch name, and finally the commit id (%h)
-        return project.version + "-dev--" + commitInfo.substring(0, 10) + "--" + branchName + "--" + commitInfo.substring(12)
-    } else {
-        return project.version
-    }
-}

eclipse.gradle

@@ -28,6 +28,9 @@ eclipse {
                 javafxcontrols.entryAttributes['add-exports'] = 'javafx.controls/com.sun.javafx.scene.control=org.jabref:javafx.controls/com.sun.javafx.scene.control.behavior=org.jabref:javafx.controls/javafx.scene.control=org.jabref';
                 javafxcontrols.entryAttributes['add-opens'] = 'javafx.controls/com.sun.javafx.scene.control=org.jabref:javafx.controls/com.sun.javafx.scene.control.behavior=org.jabref:javafx.controls/javafx.scene.control=org.jabref';
 
+                def javafxgraphics = entries.find { isJavafxGraphics(it) };
+                javafxgraphics.entryAttributes['add-opens'] = 'javafx.graphics/javafx.scene=org.controlsfx.controls';
+
                 def graaltruffle = entries.find{ isTruffleGraal(it) } ;
                 graaltruffle.entryAttributes['add-exports'] = 'com.oracle.truffle.regex/com.oracle.truffle.regex=org.graalvm.truffle';
 
@@ -56,6 +59,8 @@ boolean isControlsfx(entry) { return entry.properties.path.contains('controlsfx'
 
 boolean isJavafxControls(entry) { return entry.properties.path.contains('javafx-controls'); }
 
+boolean isJavafxGraphics(entry) { return entry.properties.path.contains('javafx-graphics'); }
+
 boolean isTruffleGraal(entry)  {return entry.properties.path.contains('org.graalvm.regex'); }
 
 // add formatter and cleanup settings to Eclipse settings

src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java

@@ -49,9 +49,6 @@ public BracketedPattern() {
         this.pattern = null;
     }
 
-    /**
-     * @param bibentry
-     */
     public BracketedPattern(String pattern) {
         this.pattern = pattern;
     }

src/main/java/org/jabref/logic/bst/BibtexTextPrefix.java

@@ -20,14 +20,9 @@ private BibtexTextPrefix() {
     }
 
     /**
-     *
-     * @param numOfChars
-     * @param toPrefix
      * @param warn may-be-null
-     * @return
      */
     public static String textPrefix(int inNumOfChars, String toPrefix, Warn warn) {
-
         int numOfChars = inNumOfChars;
         StringBuilder sb = new StringBuilder();
 

src/main/java/org/jabref/logic/openoffice/OOBibStyle.java

@@ -343,7 +343,6 @@ public boolean isValid() {
      * Parse a line providing bibliography structure information for an entry type.
      *
      * @param line The string containing the structure description.
-     * @throws IOException
      */
     private void handleStructureLine(String line) {
         int index = line.indexOf('=');
@@ -369,7 +368,6 @@ private void handleStructureLine(String line) {
      * Parse a line providing a property name and value.
      *
      * @param line The line containing the formatter names.
-     * @throws IOException
      */
     private void handlePropertiesLine(String line, Map<String, Object> map) {
         int index = line.indexOf('=');
@@ -393,9 +391,6 @@ private void handlePropertiesLine(String line, Map<String, Object> map) {
 
     /**
      * Parse a line providing a journal name for which this style is valid.
-     *
-     * @param line
-     * @throws IOException
      */
     private void handleJournalsLine(String line) {
         if (!line.trim().isEmpty()) {