Merge remote-tracking branch 'upstream/maintable-beta' into fixdragandrop

* upstream/maintable-beta: (174 commits)
  Fix ACM fetcher import of entries (#4019)
  Reimplement tooltips for file and identifier columns (#4011)
  Add button-icon for union/intersection in the groups side panel (#3954)
  Update Dependencies (#4012)
  set look and feel to windows, aqua or nimbus for swing in case
  fix import
  remove look and feel
  New translations JabRef_en.properties (French) (#4009)
  Fix Look and Feel related issues (#4002)
  Fix statement in changelog
  [WIP] Add Text File Export for "Find Unlinked Files" (#3979)
  Fix IEEE preview does not display month  (#3983)
  Activate context menu on key press (#4004)
  Improve code layout
  Fix concurrent modification exception when adding entries to groups
  Fix build
  Typo
  Add fix
  Rename test
  Fix #3994 Duplicate unmodifiable list for sorting (#3996)
  ...

# Conflicts:
#	src/main/java/org/jabref/gui/actions/CleanupAction.java
#	src/main/java/org/jabref/gui/maintable/MainTable.java

Author: Siedlerchr

.mailmap

@@ -117,7 +117,7 @@ Daniel Mair <[email protected]> <[email protected]>
 Sven Jäger <[email protected]>
 Tim van Rossum <[email protected]>
 Saulius Gražulis <[email protected]>
-Rolf Starre <[email protected]> <[email protected]>
+Rolf Starre <[email protected]>
 Owen Huang <[email protected]>
 Anita Armbruster <[email protected]>
 Fabian Bauer <[email protected]>
@@ -140,3 +140,6 @@ Mattia Bunel <[email protected]>
 Waida Fan <[email protected]>
 Johannes Manner <[email protected]>
 Dominik Traczyk <[email protected]>
+Cerrianne Santos <[email protected]>
+Stefan Scheffel <[email protected]>
+Stefan Gerzmann <[email protected]>

.travis.yml

@@ -17,8 +17,8 @@ env:
   global:
     - GRADLE_OPTS=-Dorg.gradle.daemon=false
   matrix:
-    - TEST_SUITE=checkstyle
     - TEST_SUITE=check OPTIONS=modernizer
+    - TEST_SUITE=checkstyle
     - TEST_SUITE=fetcherTest
     - TEST_SUITE=databaseTest
     - TEST_SUITE=guiTest
@@ -50,7 +50,7 @@ script:
   - if [ "$TEST_SUITE" != "guiTest" ] && [ "$TEST_SUITE" != "checkstyle" ] && [ "$TEST_SUITE" != "codecov" ]; then ./gradlew $TEST_SUITE $OPTIONS --scan; fi
   - if [ "$TEST_SUITE" == "checkstyle" ]; then ./gradlew checkstyleMain checkstyleTest checkstyleJmh; fi
   - if [ "$TEST_SUITE" == "guiTest" ]; then ./buildres/gui-tests.sh; fi
-  - if [ "$TEST_SUITE" == "codecov" ]; then ./gradlew jacocoJunit5TestReport; bash <(curl -s https://codecov.io/bash); fi
+  - if [ "$TEST_SUITE" == "codecov" ]; then ./gradlew jacocoTestReport; bash <(curl -s https://codecov.io/bash); fi
   - if [ "$DEPENDENCY_UPDATES" == "check" ]; then ./gradlew -q checkOutdatedDependencies; fi
 
 after_failure:

AUTHORS

@@ -11,6 +11,7 @@ Alex Montgomery
 Alexis Gallagher
 Alexsandro Lauber
 Ali Ayan
+Alick Zhao
 Ambrogio Oliva
 Andreas Amann
 Andreas Buhr
@@ -29,8 +30,8 @@ Bernd Kalbfuss
 Bernhard Tempel
 Brian Quistorff
 Brian Van Essen
-captain123
 Carlos Silla
+Cerrianne Santos
 Christian Bartsch
 Christian Kopf
 Christoph Braun
@@ -67,11 +68,11 @@ Felix Berger
 Felix Langner
 Felix Wilke
 Fernando Santagata
+Florian Beetz
 Florian Straßer
 Foivos Christoulakis
 Francois Charette
 Frank Steimle
-Fred
 Frédéric Darboux
 Gert Renckens
 Gregor Herrmann
@@ -128,9 +129,7 @@ Mathias Walter
 Matthias Geiger
 Mattia Bunel
 Mattias Ulbrich
-mcmoody
 Meltem Demirköprü
-Michael
 Michael Beckmann
 Michael Falkenthal
 Michael Lass
@@ -145,18 +144,15 @@ Nadeem Mahmood
 Nathan Dunn
 Nathan Sheffield
 Nicolas Pavillon
-nikmilpv
 Niv Ierushalmi
 Nizar N. Batada
-noravanq
 Olaf Lenz
 Oliver Beckmann
 Oliver Kopp
 Oscar Gustafsson
 Owen Huang
 Patrick Scheibe
 Paul Martin
-payload
 Peter Ansell
 Philip Johnson
 Predrag Milanovic
@@ -181,16 +177,15 @@ Seb Wills
 Shitikanth
 Simon Harrer
 Simon Rutishauser
-speed9
 Stefan Feyer
+Stefan Gerzmann
 Stefan Kolb
 Stefan Robert
 Stefano Gariazzo
 Stephan Lau
 Stephan Rave
 Stéphane Curet
 Sven Jäger
-The Gitter Badger
 Thiago Toledo
 Thomas Arildsen
 Thomas Ilsche
@@ -201,10 +196,7 @@ Tobias Boceck
 Tobias Bouschen
 Tobias Denkinger
 Tobias Diez
-tokkot
-Tony K
 Toralf Senger
-uid112001
 Ulrich Stärk
 Ulrik Stervbo
 Uwe Kuehn
@@ -213,9 +205,7 @@ Waida Fan
 Waluyo Adi Siswanto
 Ward Poelmans
 Wenbo Yang
-wuw
 Yang Zongze
 Yara Grassi Gouffon
 Yifan Peng
-zacmks
 Zhang Liang

CHANGELOG.md

@@ -12,17 +12,14 @@ buildscript {
             url 'https://oss.sonatype.org/content/groups/public'
         }
     }
-    dependencies {
-        classpath 'org.junit.platform:junit-platform-gradle-plugin:1.1.0'
-    }
 }
 
 plugins {
     id 'com.gradle.build-scan' version '1.11'
-    id 'com.install4j.gradle' version '7.0.3'
+    id 'com.install4j.gradle' version '7.0.4'
     id 'com.github.johnrengelman.shadow' version '2.0.2'
     id "de.sebastianboegl.shadow.transformer.log4j" version "2.1.1"
-    id "com.simonharrer.modernizer" version '1.5.0-1'
+    id "com.simonharrer.modernizer" version '1.6.0-1'
     id 'me.champeau.gradle.jmh' version '0.4.3'
     id 'net.ltgt.errorprone' version '0.0.13'
     id 'com.github.ben-manes.versions' version '0.17.0'
@@ -41,16 +38,15 @@ apply plugin: 'jacoco'
 apply plugin: 'install4j'
 apply plugin: 'me.champeau.gradle.jmh'
 apply plugin: 'checkstyle'
-apply plugin: 'org.junit.platform.gradle.plugin'
 
 apply from: 'eclipse.gradle'
 apply from: 'localization.gradle'
 apply from: 'xjc.gradle'
 
 group = "org.jabref"
-version = "4.2-dev"
-project.ext.threeDotVersion = "4.1.0.1"
-project.ext.install4jDir = hasProperty("install4jDir") ? getProperty("install4jDir") : (OperatingSystem.current().isWindows() ? 'C:/Program Files/install4j6' : 'install4j6')
+version = "4.3-dev"
+project.ext.threeDotVersion = "4.2.0.1"
+project.ext.install4jDir = hasProperty("install4jDir") ? getProperty("install4jDir") : (OperatingSystem.current().isWindows() ? 'C:/Program Files/install4j7' : 'install4j7')
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
 mainClassName = "org.jabref.JabRefMain"
@@ -91,9 +87,9 @@ dependencies {
     compile 'com.jgoodies:jgoodies-common:1.8.1'
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
 
-    compile 'org.apache.pdfbox:pdfbox:2.0.8'
-    compile 'org.apache.pdfbox:fontbox:2.0.8'
-    compile 'org.apache.pdfbox:xmpbox:2.0.8'
+    compile 'org.apache.pdfbox:pdfbox:2.0.9'
+    compile 'org.apache.pdfbox:fontbox:2.0.9'
+    compile 'org.apache.pdfbox:xmpbox:2.0.9'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     compile 'org.bouncycastle:bcprov-jdk15on:1.59'
@@ -121,24 +117,23 @@ dependencies {
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:24.1-jre'
+    compile 'com.google.guava:guava:25.0-jre'
 
     // JavaFX stuff
     compile 'de.codecentric.centerdevice:javafxsvg:1.3.0'
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
     compile 'de.saxsys:mvvmfx-validation:1.7.0'
     compile 'de.saxsys:mvvmfx:1.7.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
-    compile 'org.fxmisc.flowless:flowless:0.6'
-    compile 'org.fxmisc.richtext:richtextfx:0.8.2'
+    compile 'org.fxmisc.flowless:flowless:0.6.1'
+    compile 'org.fxmisc.richtext:richtextfx:0.9.0'
     compile 'com.sibvisions.external.jvxfx:dndtabpane:0.1'
     compile 'javax.inject:javax.inject:1'
 
-
     // Cannot be updated to 9.*.* until Jabref works with Java 9
     compile 'org.controlsfx:controlsfx:8.40.15-SNAPSHOT'
 
-    compile 'org.jsoup:jsoup:1.11.2'
+    compile 'org.jsoup:jsoup:1.11.3'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
     // >1.8.0-beta is required for java 9 compatibility
@@ -155,31 +150,31 @@ dependencies {
 
     compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'
 
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.0.1'
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.0.1'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.1.0'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.1.0'
 
-    testCompile 'org.junit.jupiter:junit-jupiter-api:5.1.0'
-    testCompile 'org.junit.jupiter:junit-jupiter-params:5.1.0'
-    testRuntime 'org.junit.jupiter:junit-jupiter-engine:5.1.0'
-    testRuntime 'org.junit.vintage:junit-vintage-engine:5.1.0'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.1.0'
+    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.2.0'
+    testCompile 'org.junit.jupiter:junit-jupiter-params:5.2.0'
+    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.2.0'
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.2.0'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.2.0'
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.0'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.0'
-    testCompile 'org.mockito:mockito-core:2.16.0'
-    testCompile 'com.github.tomakehurst:wiremock:2.15.0'
+    testCompile 'org.mockito:mockito-core:2.18.3'
+    testCompile 'com.github.tomakehurst:wiremock:2.17.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
-    testCompile 'org.xmlunit:xmlunit-core:2.5.1'
-    testCompile 'org.xmlunit:xmlunit-matchers:2.5.1'
+    testCompile 'org.xmlunit:xmlunit-core:2.6.0'
+    testCompile 'org.xmlunit:xmlunit-matchers:2.6.0'
     testCompile 'com.tngtech.archunit:archunit-junit:0.5.0'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.8'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.10'
 }
 
 jacoco {
-    toolVersion = '0.8.0'
+    toolVersion = '0.8.1'
 }
 
 dependencyUpdates {
@@ -205,12 +200,12 @@ dependencyUpdates.resolutionStrategy = {
             }
         }
         withModule("org.jacoco:org.jacoco.agent") { ComponentSelection selection ->
-            if (selection.candidate.version.equals("0.8.0")) {
+            if (selection.candidate.version ==~ /0.8.*/) {
                 selection.reject("As a native plugin we cannot control the actual version of jacoco. This dependency should be hidden.")
             }
         }
         withModule("org.jacoco:org.jacoco.ant") { ComponentSelection selection ->
-            if (selection.candidate.version.equals("0.8.0")) {
+            if (selection.candidate.version ==~ /0.8.*/) {
                 selection.reject("As a native plugin we cannot control the actual version of jacoco. This dependency should be hidden.")
             }
         }
@@ -315,14 +310,16 @@ javadoc {
 }
 
 // Test tasks
-junitPlatform {
-    filters {
-        tags {
-            exclude 'DatabaseTest', 'FetcherTest', 'GUITest', 'org.jabref.testutils.category.FetcherTest', 'org.jabref.testutils.category.GUITest'
-        }
+test {
+    useJUnitPlatform {
+        excludeTags 'DatabaseTest', 'FetcherTest', 'GUITest', 'org.jabref.testutils.category.FetcherTest', 'org.jabref.testutils.category.GUITest'
+    }
+    
+    testLogging {
+        // set options for log level LIFECYCLE
+        events "failed"
+        exceptionFormat "full"
     }
-
-    logManager 'org.apache.logging.log4j.jul.LogManager'
 }
 
 task databaseTest(type: Test) {
@@ -359,8 +356,8 @@ tasks.withType(Test) {
 }
 
 task jacocoMerge(type: JacocoMerge) {
-    executionData file("$buildDir/jacoco/junitPlatformTest.exec"), file("$buildDir/jacoco/databaseTest.exec"), file("$buildDir/jacoco/fetcherTest.exec")
-    dependsOn junitPlatformTest, databaseTest, fetcherTest
+    executionData file("$buildDir/jacoco/test.exec"), file("$buildDir/jacoco/databaseTest.exec"), file("$buildDir/jacoco/fetcherTest.exec")
+    dependsOn test, databaseTest, fetcherTest
 }
 
 jacocoTestReport {
@@ -373,37 +370,16 @@ jacocoTestReport {
     }
 }
 
-afterEvaluate {
-    def junitPlatformTest = tasks.junitPlatformTest
-
-    jacoco {
-        applyTo(junitPlatformTest)
-    }
-
-    task jacocoJunit5TestReport(type: JacocoReport) {
-        executionData jacocoMerge.destinationFile
-        dependsOn jacocoMerge
-        sourceSets sourceSets.main
-        sourceDirectories = files(sourceSets.main.allSource.srcDirs)
-        classDirectories = files(sourceSets.main.output)
-
-        reports {
-            xml.enabled true
-            html.enabled true
-        }
-    }
-}
-
 // Code quality tasks
 checkstyle {
     // do not use other packages for checkstyle, excluding gen(erated) sources
     checkstyleMain.source = "src/main/java"
     toolVersion = '8.5'
+    
+    // do not perform checkstyle checks by default
+    sourceSets = []
 }
 
-checkstyleMain.shouldRunAfter test
-checkstyleTest.shouldRunAfter test
-
 modernizer {
     // We have more than 20 issues, which are not fixed yet. Nevertheless, we produce the modernizer output.
     // See https://github.com/andrewgaul/modernizer-maven-plugin for more information on modernizer
@@ -452,8 +428,16 @@ install4j {
     installDir = file(project.ext.install4jDir)
 }
 
+task generateFinalJabRefPS1File(type: Copy) {
+    from('buildres') {
+        include 'JabRef.ps1'
+    }
+    into 'build'
+    filter(org.apache.tools.ant.filters.ReplaceTokens, tokens: [jabRefJarFileName: jar.archiveName])
+}
+
 // has to be defined AFTER 'dev' things to have the correct project.version
-task media(type: com.install4j.gradle.Install4jTask, dependsOn: "releaseJar") {
+task media(type: com.install4j.gradle.Install4jTask, dependsOn: ["releaseJar", "generateFinalJabRefPS1File"]) {
     projectFile = file('jabref.install4j')
     release = project.version
     winKeystorePassword = System.getenv('CERTIFICATE_PW')

build.gradle

@@ -0,0 +1,3 @@
+@echo off
+pushd %~dp0
+@powershell.exe -ExecutionPolicy Bypass -NoLogo -NonInteractive -NoProfile -WindowStyle Hidden -File ".\JabRef.ps1"