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

* upstream/master: (40 commits)
  add env var also to mv command
  add branch env var
  move to releases
  somehow the env vars don't get expanded
  fix dirs
  add circle ci config for building gradle jlink
  remove unix again
  crate unix archive
  update install4j to 8.0.1
  add install4j install option for unix installer
  Add MIT license field
  Integrate with system themes
  snap: Add custom gradle plugin avoid committing python cache to git
  Add gtk3 support
  remove desktop gtk3
  add desktop gtk 3
  Update snapcraft to java 11 will require bionic now as base
  Bump jaxb-xjc from 2.2.4-1 to 2.3.2 (#4956)
  Fix/field inheritance (#5282)
  added comments
  ...

Author: Siedlerchr

.circleci/config.yml

@@ -32,6 +32,10 @@ jobs:
       - run: git submodule sync
       - run: git submodule update --init
       - run: ./gradlew -Pdev=true -Pinstall4jDir="install4j8" release --stacktrace
+      - run: ./gradlew jlink
+      - run: mv build/image jabref
+      - run: tar cvzf JabRef-linux-${CIRCLE_BRANCH}-latest.tar.gz jabref
+      - run: mv JabRef-linux-${CIRCLE_BRANCH}-latest.tar.gz build/releases/
       - save_cache:
           key: gradle
           paths:

.dependabot/config.yml

@@ -5,6 +5,8 @@ update_configs:
   - package_manager: "java:gradle"
     directory: "/"
     update_schedule: "weekly"
+    default_labels:
+      - "dependencies"
     automerged_updates:
       - match:
          dependency_type: "all"
@@ -13,6 +15,8 @@ update_configs:
   - package_manager: "submodules"
     directory: "/"
     update_schedule: "weekly"
+    default_labels:
+      - "dependencies"
     automerged_updates:
       - match:
          dependency_type: "all"

.gitignore

@@ -10,6 +10,9 @@ status.md
 # Install4J
 install4j6/
 
+# Python
+__pycache__/
+
 # Snap
 parts/
 stage/

CHANGELOG.md

@@ -13,8 +13,12 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 ### Changed
 
+- We added a short DOI field formatter which shortens DOI to more human readable form. [koppor#343](https://github.com/koppor/jabref/issues/343)
+
 ### Fixed
 
+- Inherit fields from cross-referenced entries as specified by biblatex [#5045](https://github.com/JabRef/jabref/issues/5045)
+
 ### Removed
 
 
@@ -70,7 +74,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [5.0-alpha] – 2019-08-25
 
 ### Changed
-
+- We added eventitle, eventdate and venue fields to @unpublished entry type.
+- We added @software and @dataSet entry type to biblatex.
 - All fields are now properly sorted alphabetically (in the subgroups of required/optional fields) when the entry is written to the bib file.
 - We fixed an issue where some importers used the field `pubstatus` instead of the standard BibTeX field `pubstate`.
 - We changed the latex command removal for docbook exporter. [#3838](https://github.com/JabRef/jabref/issues/3838)

build.gradle

@@ -35,6 +35,8 @@ plugins {
 // use the gradle build scan feature: https://scans.gradle.com/get-started
 buildScan { termsOfServiceUrl = 'https://gradle.com/terms-of-service'; termsOfServiceAgree = 'yes' }
 
+// show stacktrace on error
+gradle.startParameter.showStacktrace = org.gradle.api.logging.configuration.ShowStacktrace.ALWAYS
 
 apply plugin: 'java'
 apply plugin: 'application'
@@ -55,7 +57,7 @@ project.ext.threeDotVersion = "5.0.0.1"
 project.ext.install4jDir = hasProperty("install4jDir") ? getProperty("install4jDir") : (OperatingSystem.current().isWindows() ? 'C:/Program Files/install4j8' : 'install4j8')
 sourceCompatibility = 11
 targetCompatibility = 11
-mainClassName = "org.jabref.JabRefLauncher"
+mainClassName = "$moduleName/org.jabref.JabRefLauncher"
 
 // TODO: Ugly workaround to temporarily ignore build errors to dependencies of latex2unicode
 // These should be removed, as well as the files in the lib folder, as soon as they have valid module names
@@ -204,9 +206,9 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.4.1'
 
     testCompile 'junit:junit:4.12'
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.5.1'
-    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.5.1'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.5.1'
+    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:1.10.1'
     testRuntime 'org.apache.logging.log4j:log4j-core:2.12.0'
@@ -225,7 +227,7 @@ dependencies {
     testCompile "org.testfx:testfx-junit5:4.0.15-alpha"
 
     checkstyle 'com.puppycrawl.tools:checkstyle:8.24'
-    xjc 'com.sun.xml.bind:jaxb-xjc:2.2.4-1'
+    xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.2'
     jython 'org.python:jython-standalone:2.7.1'
 }
 
@@ -351,10 +353,9 @@ task generateEndnoteSource(type: XjcTask) {
     group = 'JabRef'
     description = "Generates java files for the endnote importer."
 
-    schemaFile = "src/main/resources/xjc/endnote/RSXML.dtd"
+    schemaFile = "src/main/resources/xjc/endnote/endnote.xsd"
     outputDirectory = "src/main/gen/"
     javaPackage = "org.jabref.logic.importer.fileformat.endnote"
-    arguments = '-dtd'
 }
 
 task generateModsSource(type: XjcTask) {

config/checkstyle/checkstyle.xml

@@ -8,16 +8,30 @@
         <property name="header" value=""/>
     </module>
 
+    <module name="SuppressionFilter">
+        <property name="file" value="${config_loc}/suppressions.xml"/>
+    </module>
+
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="module\-info\.java$"/>
+    </module>
+
     <module name="TreeWalker">
+        <!-- Checks for Javadoc comments: https://checkstyle.org/config_javadoc.html -->
+        <module name="InvalidJavadocPosition"/>
+        <module name="JavadocMethod">
+            <property name="allowUndeclaredRTE" value="true"/>
+            <property name="allowMissingParamTags" value="true"/>
+            <property name="allowMissingThrowsTags" value="true"/>
+            <property name="allowMissingReturnTag" value="true"/>
+            <property name="validateThrows" value="true"/>
+        </module>
 
+        <!-- Checks for imports: https://checkstyle.org/config_import.html -->
         <module name="UnusedImports"/>
-
         <module name="RedundantImport"/>
-
         <module name="AvoidStarImport"/>
-
         <module name="IllegalImport"/>
-
         <module name="ImportOrder">
             <property name="groups" value="java,javax,javafx,org.jabref,*"/>
             <property name="ordered" value="true"/>
@@ -26,17 +40,18 @@
             <property name="sortStaticImportsAlphabetically" value="true"/>
         </module>
 
+        <!-- Checks for common coding problems: https://checkstyle.org/config_coding.html -->
+        <module name="DeclarationOrder"/>
+
+        <!-- Checks for whitespace: https://checkstyle.org/config_whitespace.html -->
         <module name="EmptyLineSeparator">
             <property name="tokens"
                       value="IMPORT, CLASS_DEF, INTERFACE_DEF, ENUM_DEF, STATIC_INIT, INSTANCE_INIT, METHOD_DEF"/>
             <property name="allowMultipleEmptyLines" value="false"/>
             <property name="allowMultipleEmptyLinesInsideClassMembers" value="false"/>
         </module>
-
-        <module name="DeclarationOrder"/>
-
-        <!-- RCULRY causes issues if classes are nested within arrays, therefore not activated -->
         <module name="WhitespaceAround">
+            <!-- RCULRY causes issues if classes are nested within arrays, therefore not activated -->
             <property name="tokens"
                       value="ASSIGN, BAND, BAND_ASSIGN, BOR, BOR_ASSIGN, BSR, BSR_ASSIGN, BXOR, BXOR_ASSIGN, COLON, DIV,
                       DIV_ASSIGN, DO_WHILE, EQUAL, GE, GT, LAND, LCURLY, LE, LITERAL_CATCH, LITERAL_DO, LITERAL_ELSE,
@@ -46,18 +61,12 @@
                       SL, SLIST, SL_ASSIGN, SR, SR_ASSIGN, STAR, STAR_ASSIGN, LITERAL_ASSERT, TYPE_EXTENSION_AND"/>
         </module>
 
+        <!-- Checks for Naming Conventions: https://checkstyle.org/config_naming.html -->
         <module name="ConstantName">
             <property name="format" value="^log(ger)?|[A-Z][A-Z0-9]*(_[A-Z0-9]+)*$"/>
         </module>
-            
-        <module name="NeedBraces"/>
-    </module>
 
-    <module name="SuppressionFilter">
-        <property name="file" value="${config_loc}/suppressions.xml"/>
-    </module>
-
-    <module name="BeforeExecutionExclusionFileFilter">
-        <property name="fileNamePattern" value="module\-info\.java$"/>
+        <!-- Checks for blocks: https://checkstyle.org/config_blocks.html -->
+        <module name="NeedBraces"/>
     </module>
 </module>

scripts/prepare-install4j.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
-wget --quiet -nc --show-progress https://download-gcdn.ej-technologies.com/install4j/install4j_unix_8_0.tar.gz
-tar -xf install4j_unix_8_0.tar.gz
-mv install4j8.0 install4j8
+wget --quiet -nc --show-progress https://download-gcdn.ej-technologies.com/install4j/install4j_unix_8_0_1.tar.gz
+tar -xf install4j_unix_8_0_1.tar.gz
+mv install4j8.0.1 install4j8