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

* upstream/master: (468 commits) Fix error prone warnings (#4290) Fix freeze on import into current library (#4299) Upgrade gradle to 4.10 update xmlunit and postgres update xmlunit-matchers from 2.6.0 -> 2.6.1 update gradle build-scan from 1.15.2 -> 1.16 checkstyle execute changes only if disk db present Fix Export to clipbaord action (#4286) fix npe in Merge entries dialog Add minimal height for entry editor (#4283) Fix exceptions when trying to change settings (#4284) Added a comment for the purpose of the class (#4282) Fix NPE when importing from CLI (#4281) Fix display of key patterns convert bibtexkeypatterndlg to javafx as well (#4277) Style preference sections using css Fix a few style issues Changed the behavior of the field formatting dialog (#4275) Fix checkbox display Remove small font size ...
JabRef · Aug 29, 2018 · 03714d1 · 03714d1
2 parents ae2f2ac + ce713ca
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diff --git a/.travis.yml b/.travis.yml
@@ -60,6 +60,7 @@ after_failure:
 branches:
   only:
     - master
+    - maintable-beta
 
 # cache gradle dependencies
 # https://docs.travis-ci.com/user/languages/java#Caching
@@ -70,3 +71,4 @@ cache:
   directories:
     - $HOME/.gradle/caches/
     - $HOME/.gradle/wrapper/
+
diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,7 +1,7 @@
 ## Understanding the basics
 We welcome contributions to JabRef and encourage to create a fork, clone, **create a new branch** (such as `fix-for-issue-121`), **work on the new branch — not master**, and create a pull request.
 Be sure to create a **separate branch** for each improvement you implement.
-Take a look at GitHub's excellent [help documentation] for a detailed explanation and the explanation of [Feature Branch Workflow](https://de.atlassian.com/git/tutorials/comparing-workflows#feature-branch-workflow) for the idea behind this kind of development.
+Take a look at GitHub's excellent overview on the [GitHub flow](https://guides.github.com/introduction/flow/index.html) and their [pull request help documentation](https://help.github.com/articles/about-pull-requests/) for a detailed explanation and the explanation of [Feature Branch Workflow](https://de.atlassian.com/git/tutorials/comparing-workflows#feature-branch-workflow) for the idea behind this kind of development.
 
 We also have [code howtos](https://github.com/JabRef/jabref/wiki/Code-Howtos) and [guidelines for setting up a local workspace](https://github.com/JabRef/jabref/wiki/Guidelines-for-setting-up-a-local-workspace).
 
@@ -118,5 +118,4 @@ You can add the prefix `[WIP]` to indicate that the pull request is not yet comp
 
 
 [commit guidelines section of Pro Git]: http://git-scm.com/book/en/Distributed-Git-Contributing-to-a-Project#Commit-Guidelines
-[good commit message]: http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html
-[help documentation]: https://help.github.com/articles/about-pull-requests/
+[good commit message]: https://github.com/joelparkerhenderson/git_commit_message
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright © 2003-2016 [JabRef Authors](https://github.com/JabRef/jabref/blob/master/AUTHORS)
+Copyright © 2003-2018 [JabRef Authors](https://github.com/JabRef/jabref/blob/master/AUTHORS)
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/build.gradle b/build.gradle
@@ -15,14 +15,14 @@ buildscript {
 }
 
 plugins {
-    id 'com.gradle.build-scan' version '1.11'
-    id 'com.install4j.gradle' version '7.0.4'
-    id 'com.github.johnrengelman.shadow' version '2.0.2'
+    id 'com.gradle.build-scan' version '1.16'
+    id 'com.install4j.gradle' version '7.0.6'
+    id 'com.github.johnrengelman.shadow' version '2.0.4'
     id "de.sebastianboegl.shadow.transformer.log4j" version "2.1.1"
     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'
+    id 'me.champeau.gradle.jmh' version '0.4.7'
+    id 'net.ltgt.errorprone' version '0.0.16'
+    id 'com.github.ben-manes.versions' version '0.20.0'
 }
 
 // use the gradle build scan feature: https://scans.gradle.com/get-started
@@ -44,15 +44,15 @@ apply from: 'localization.gradle'
 apply from: 'xjc.gradle'
 
 group = "org.jabref"
-version = "4.3-dev"
-project.ext.threeDotVersion = "4.2.0.1"
+version = "5.0-dev"
+project.ext.threeDotVersion = "5.0.0.0"
 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"
 
 // These are the Java version requirements we will check on each start of JabRef
-ext.minRequiredJavaVersion = "1.8.0_144"
+ext.minRequiredJavaVersion = "1.8.0_171"
 ext.allowJava9 = false
 
 sourceSets {
@@ -65,6 +65,14 @@ sourceSets {
             srcDirs = ["src/main/java", "src/main/resources"]
         }
     }
+    test{
+        java {
+            srcDirs = ["src/test/java"]
+        }
+        resources {
+            srcDirs = ["src/test/resources"]
+        }
+    }
 }
 
 repositories {
@@ -78,20 +86,22 @@ repositories {
 configurations {
     antlr3
     antlr4
+    errorprone
 }
 
 dependencies {
+    // Include all jar-files in the 'lib' folder as dependencies
     compile fileTree(dir: 'lib', includes: ['*.jar'])
 
     compile 'com.jgoodies:jgoodies-common:1.8.1'
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
 
-    compile 'org.apache.pdfbox:pdfbox:2.0.9'
-    compile 'org.apache.pdfbox:fontbox:2.0.9'
-    compile 'org.apache.pdfbox:xmpbox:2.0.9'
+    compile 'org.apache.pdfbox:pdfbox:2.0.11'
+    compile 'org.apache.pdfbox:fontbox:2.0.11'
+    compile 'org.apache.pdfbox:xmpbox:2.0.11'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    compile 'org.bouncycastle:bcprov-jdk15on:1.59'
+    compile 'org.bouncycastle:bcprov-jdk15on:1.60'
 
     compile 'commons-cli:commons-cli:1.4'
 
@@ -100,7 +110,7 @@ dependencies {
     compile "org.libreoffice:ridl:5.4.2"
     compile "org.libreoffice:unoil:5.4.2"
 
-    compile 'com.github.bkromhout:java-diff-utils:2.1.1'
+    compile 'io.github.java-diff-utils:java-diff-utils:2.2.0'
     compile 'info.debatty:java-string-similarity:1.1.0'
 
     antlr3 'org.antlr:antlr:3.5.2'
@@ -109,23 +119,23 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.7.1'
     compile 'org.antlr:antlr4-runtime:4.7.1'
 
-    // VersionEye states that 6.0.5 is the most recent version, but http://dev.mysql.com/downloads/connector/j/ shows that as "Development Release"
-    compile 'mysql:mysql-connector-java:5.1.46'
+    compile 'mysql:mysql-connector-java:8.0.12'
 
-    compile 'com.impossibl.pgjdbc-ng:pgjdbc-ng:0.7.1'
+    compile 'org.postgresql:postgresql:42.2.5'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:25.0-jre'
+    compile 'com.google.guava:guava:26.0-jre'
 
     // JavaFX stuff
-    compile 'com.airhacks:afterburner.fx:1.7.0'
-    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:0.6.1'
-    compile 'org.fxmisc.richtext:richtextfx:0.9.0'
+    compile 'org.fxmisc.richtext:richtextfx:0.9.1'
+    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'
@@ -135,10 +145,10 @@ dependencies {
 
     // >1.8.0-beta is required for java 9 compatibility
     compile 'org.slf4j:slf4j-api:1.8.0-beta2'
-    compile 'org.apache.logging.log4j:log4j-slf4j-impl:2.11.0'
-    compile 'org.apache.logging.log4j:log4j-jcl:2.11.0'
-    compile 'org.apache.logging.log4j:log4j-api:2.11.0'
-    compile 'org.apache.logging.log4j:log4j-core:2.11.0'
+    compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.11.1'
+    compile 'org.apache.logging.log4j:log4j-jcl:2.11.1'
+    compile 'org.apache.logging.log4j:log4j-api:2.11.1'
+    compile 'org.apache.logging.log4j:log4j-core:2.11.1'
 
     // need to use snapshots as the stable version is from 2013 and doesn't support v1.0.1 CitationStyles
     compile 'org.citationstyles:styles:1.0.1-SNAPSHOT'
@@ -147,27 +157,30 @@ dependencies {
 
     compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'
 
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.0.2'
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.0.2'
-
-    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.2.0-RC1'
-    testCompile 'org.junit.jupiter:junit-jupiter-params:5.2.0-RC1'
-    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.2.0-RC1'
-    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.2.0-RC1'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.2.0-RC1'
-    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:2.18.3'
-    testCompile 'com.github.tomakehurst:wiremock:2.17.0'
+    errorprone 'com.google.errorprone:error_prone_core:2.3.1'
+
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.1.2'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.1.2'
+
+    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.3.0-RC1'
+    testCompile 'org.junit.jupiter:junit-jupiter-params:5.3.0-RC1'
+    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.3.0-RC1'
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.3.0-RC1'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.3.0-RC1'
+    testCompile 'org.junit-pioneer:junit-pioneer:0.1.2'
+    testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
+    testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.1'
+    testCompile 'org.mockito:mockito-core:2.21.0'
+    testCompile 'com.github.tomakehurst:wiremock:2.18.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
-    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.xmlunit:xmlunit-core:2.6.2'
+    testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
+    testCompile 'com.tngtech.archunit:archunit-junit:0.8.3'
     testCompile "org.testfx:testfx-core:4.0.+"
-    testCompile "org.testfx:testfx-junit:4.0.+"
+    testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.9'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.12'
 }
 
 jacoco {
@@ -178,32 +191,30 @@ dependencyUpdates {
     outputFormatter = "json"
 }
 
+//We have to use this as long as junit-pioneer has no official release
+dependencyUpdates.revision = 'integration'
+
 // We have some dependencies which cannot be updated due to various reasons.
 dependencyUpdates.resolutionStrategy = {
-    componentSelection {
-        withModule("org.controlsfx:controlsfx") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /9.*/) { // Reject version 9 or higher
-                selection.reject("Cannot be updated to 9.*.* until Jabref works with Java 9")
-            }
-        }
-        withModule("de.jensd:fontawesomefx-materialdesignfont") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /2.*/) {
-                selection.reject("Cannot be upgraded to version 2")
+    componentSelection { rules ->
+        rules.all { ComponentSelection selection ->
+            if ( selection.candidate.module!="javax.inject"  && selection.candidate.version ==~ /[0-9].*SNAPSHOT/ ) {
+                selection.reject("Ignore SNAPSHOT releases")
             }
         }
-        withModule("mysql:mysql-connector-java") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /[6-9].*/) {
-                selection.reject("http://dev.mysql.com/downloads/connector/j/ lists the version 5.* as last stable version.")
+        rules.withModule("org.controlsfx:controlsfx") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /9.*/) { // Reject version 9 or higher
+                selection.reject("Cannot be updated to 9.*.* until Jabref works with Java 9")
             }
         }
-        withModule("org.jacoco:org.jacoco.agent") { ComponentSelection selection ->
-            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.")
+        rules.withModule("com.github.tomtung:latex2unicode_2.12") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /0.2.2/) { // Reject version higher than 2.0.2
+                selection.reject("Cannot be updated to 0.2.4 until JabRef is prepared for it")
             }
         }
-        withModule("org.jacoco:org.jacoco.ant") { ComponentSelection selection ->
-            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.")
+        rules.withModule("de.jensd:fontawesomefx-materialdesignfont") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /2.*/) {
+                selection.reject("Cannot be upgraded to version 2")
             }
         }
     }
@@ -311,7 +322,7 @@ 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"
@@ -372,7 +383,7 @@ 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 = []
 }
@@ -484,3 +495,19 @@ jmh {
     iterations = 10
     fork = 2
 }
+
+// Source: https://stackoverflow.com/a/44168582/873282
+task downloadDependencies {
+    description "Pre-downloads *most* dependencies"
+    doLast {
+        configurations.getAsMap().each { name, config ->
+            println "Retrieving dependencies for $name"
+            try {
+                config.files
+            } catch (e) {
+                // some cannot be resolved, just log them
+                project.logger.info e.message
+            }
+        }
+    }
+}
diff --git a/circle.yml b/circle.yml
@@ -13,19 +13,14 @@ dependencies:
     - install4j7/bin/install4jc --verbose --license=$INSTALL4J_KEY 
     #--win-keystore-password $CERTIFICATE_PW --mac-keystore-password $CERTIFICATE_PW
   override:
-    # We do this to decrease build time by using CircleCI's cache. See https://discuss.circleci.com/t/effective-caching-for-gradle/540 for a longer motivation.
-    - ./gradlew compileJava
+    - ./gradlew downloadDependencies
   cache_directories:
     - "~/.install4j7"
     - "~/downloads"
 
 test:
   override:
-    - ./gradlew -Pdev=true -Pinstall4jDir="install4j7" release --stacktrace
-  post:
-    # save test reports as build artifacts
-    - mkdir -p $CIRCLE_TEST_REPORTS/junit/
-    - find . -type f -regex ".*/build/test-results/.*xml" -exec cp {} $CIRCLE_TEST_REPORTS/junit/ \;
+    - "true"
 
 deployment:
   release:
@@ -34,18 +29,19 @@ deployment:
    commands:
       # we have to do a clean build as changing gradle's "project.version" does not lead to a rebuild of resources (mirroring project.version)
       - ./gradlew -Pinstall4jDir="install4j7" clean release --stacktrace
-      # upload at all circumstances
-      - scripts/upload-to-builds.jabref.org.sh
+      # if upload fails, it is accepted; CircleCI provides deep links to the binaries as fallback.
+      - timeout 580 scripts/upload-to-builds.jabref.org.sh || exit 0
+      # generate dependency information. This is not published on our buid server, but can be collected as logged in user at CircleCI
       - ./gradlew dependencyUpdates -Drevision=release -DoutputFormatter=json -DoutputDir=build/releases
   development:
      # match all branches; this is executed, if "release" is not matched - see https://circleci.com/docs/configuration/
     branch: /.*/
     commands:
+      # generate binaries
+      - ./gradlew -Pdev=true -Pinstall4jDir="install4j7" release --stacktrace
       # if upload fails, it is accepted; CircleCI provides deep links to the binaries as fallback
       - timeout 580 scripts/upload-to-builds.jabref.org.sh || exit 0
 
-
-
 general:
   artifacts:
     - "build/releases"