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

# By Tobias Diez (10) and others # Via dimitra-karadima (5) and others * upstream/master: (62 commits) Backward compatibility for 4.3.1 (#6296) Fix Export to clipboard Dialog icon (#6345) Refactor EntryEditorPreferences (#6245) Update label names Squashed 'src/main/resources/csl-locales/' changes from d0ee4d13c9..79845b087b Squashed 'src/main/resources/csl-styles/' changes from c1793d2..143464e Cite work by @ayaankazerouni Improve performance for loading files (#6332) Add ADR von JUnit vs. AssertJ (#6335) 'Name' textfield on focus instead of 'OK' button when user clicks on 'Add subgroup' option (#6330) Bump jurt from 6.3.2 to 6.4.3 (#6325) Bump unoil from 6.3.2 to 6.4.3 (#6320) Bump ridl from 6.3.2 to 6.4.3 (#6326) Bump classgraph from 4.8.69 to 4.8.71 (#6322) Bump flexmark from 0.61.6 to 0.61.16 (#6318) Bump richtextfx from 0.10.4 to 0.10.5 (#6319) Bump guava from 28.2-jre to 29.0-jre (#6323) Bump flexmark-ext-gfm-tasklist from 0.61.6 to 0.61.16 (#6327) Bump org.beryx.jlink from 2.17.5 to 2.17.7 (#6324) Improve performance massively by fixing a stupid binding mistake (#6316) ... # Conflicts: # build.gradle
JabRef · Apr 26, 2020 · e692f4b · e692f4b
2 parents 1a01b70 + d7a57b8
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diff --git a/.github/outdatedDependencies.md b/.github/outdatedDependencies.md
@@ -1,5 +1,5 @@
 ---
 title: Outdated dependencies
-labels: code-quality, dependencies
+labels: t: dependencies
 ---
 [There are outdated dependencies!](https://github.com/JabRef/jabref/actions?query=is%3Afailure+workflow%3A%22Check+dependencies%22) 
diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -54,31 +54,10 @@ jobs:
         uses: actions/setup-java@v1
         with:
           java-version: 14
-      - uses: actions/cache@v1
-        name: Restore gradle cache
-        with:
-          path: ~/.gradle/caches
-          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: |
-            ${{ runner.os }}-gradle-cache-
-            Linux-gradle-cache-${{ hashFiles('**/*.gradle') }}
-            Windows-gradle-cache-${{ hashFiles('**/*.gradle') }}
-            macOS-gradle-cache-${{ hashFiles('**/*.gradle') }}
-      - uses: actions/cache@v1
-        name: Cache gradle wrapper
-        with:
-          path: ~/.gradle/wrapper
-          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="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
       - name: Build installer
-        run: ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
+        run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
         shell: bash
       - name: Package application image
         run: ${{ matrix.archivePortable }}

diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml
@@ -0,0 +1,18 @@
+name: Mark stale issues and pull requests
+
+on:
+  schedule:
+  - cron: "0 0 * * *"
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/stale@master
+      with:
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+        stale-issue-message: 'This issue will be closed in 7 days due to inactivity :zzz: Please provide the requested information if the problem persists.'
+        stale-issue-label: 'status: stale'
+        days-before-stale: 30
+        only-labels: 'status: waiting-for-customer-feedback'
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -205,7 +205,7 @@ jobs:
         if: ${{ steps.checksecrets.outputs.secretspresent }}
         run: xvfb-run --auto-servernum ./gradlew jacocoTestReport && bash <(curl -s https://codecov.io/bash);
         env:
-          CI: "false" # we pretend to run locally - even if tests fail on the CI, they count towards test coverage
+          CI: "true"
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
           DBMS: "postgresql"
   # This is https://github.com/marketplace/actions/gradle-wrapper-validation

diff --git a/.idea/runConfigurations/JabRef_Main.xml b/.idea/runConfigurations/JabRef_Main.xml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added tooltips for most fields in the entry editor containing a short description. [#5847](https://github.com/JabRef/jabref/issues/5847)
 - We added support for basic markdown in custom formatted previews [#6194](https://github.com/JabRef/jabref/issues/6194)
 - We now show the number of items found and selected to import in the online search dialog. [#6248](https://github.com/JabRef/jabref/pull/6248)
+- We created a new install screen for macOS. [#5759](https://github.com/JabRef/jabref/issues/5759)
 
 ### Changed
 
@@ -34,8 +35,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue with inconsistent capitalization of file extensions when downloading files. [#6115](https://github.com/JabRef/jabref/issues/6115)
 - We fixed the display of language and encoding in the preferences dialog. [#6130](https://github.com/JabRef/jabref/pull/6130)
 - We fixed an issue where search full-text documents downloaded files with same name, overwriting existing files. [#6174](https://github.com/JabRef/jabref/pull/6174)
-- We fixe an issue where custom jstyles for Open/LibreOffice where not saved correctly. [#6170](https://github.com/JabRef/jabref/issues/6170)
-
+- We fixed an issue when importing into current library an erroneous message "import cancelled" is displayed even though import is successful. [#6266](https://github.com/JabRef/jabref/issues/6266)
+- We fixed an issue where custom jstyles for Open/LibreOffice where not saved correctly. [#6170](https://github.com/JabRef/jabref/issues/6170)
+- We fixed an issue where the INSPIRE fetcher was no longer working [#6229](https://github.com/JabRef/jabref/issues/6229)
+- We fixed the display of icon both in the main table and linked file editor. [#6169](https://github.com/JabRef/jabref/issues/6169)
+- We fixed the paste entry command in the menu and toolbar, that did not do anything. [#6293](https://github.com/JabRef/jabref/issues/6293)
+- We fixed an issue where the windows installer did not create an entry in the start menu [bug report in the forum](https://discourse.jabref.org/t/error-while-fetching-from-doi/2018/3)
 
 ### Removed
 
@@ -84,6 +89,9 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where citation styles except the default "Preview" could not be used. [#56220](https://github.com/JabRef/jabref/issues/5622)
 - We fixed an issue where a warning was displayed when the title content is made up of two sentences. [#5832](https://github.com/JabRef/jabref/issues/5832)
 - We fixed an issue where an exception was thrown when adding a save action without a selected formatter in the library properties [#6069](https://github.com/JabRef/jabref/issues/6069)
+- We fixed an issue where JabRef's icon was missing in the Export to clipboard Dialog. [#6286](https://github.com/JabRef/jabref/issues/6286)
+- We fixed an issue when an "Abstract field" was duplicating text, when importing from RIS file (Neurons) [#6065](https://github.com/JabRef/jabref/issues/6065)
+
 
 ### Removed
 
@@ -240,6 +248,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added a 'LaTeX citations' tab to the entry editor, to search for citations to the active entry in the LaTeX file directory. It can be disabled in the preferences dialog.
 - We added an option in preferences to allow for integers in field "edition" when running database in bibtex mode. [#4680](https://github.com/JabRef/jabref/issues/4680)
 - We added the ability to use negation in export filter layouts. [#5138](https://github.com/JabRef/jabref/pull/5138)
+- Focus on Name Area instead of 'OK' button whenever user presses 'Add subgroup'. [#6307](https://github.com/JabRef/jabref/issues/6307)
 
 ### Fixed
 

diff --git a/JabRef-downgrade-regpatch.reg b/JabRef-downgrade-regpatch.reg
diff --git a/README.md b/README.md
@@ -23,7 +23,7 @@ JabRef supports you in every step of your research work.
 - Easily retrieve and link full-text articles
 - Fetch complete bibliographic information based on ISBN, DOI, PubMed-ID and arXiv-ID
 - Extract metadata from PDFs
-- [JabFox Firefox Add-on](https://addons.mozilla.org/en-US/firefox/addon/jabfox/) lets you import new references directly from the browser with one click
+- Import new references directly from the browser with one click using the [official browser extension](https://github.com/JabRef/JabRef-Browser-Extension) for [Firefox](https://addons.mozilla.org/en-US/firefox/addon/jabref/?src=external-github),  [Chrome](https://chrome.google.com/webstore/detail/jabref-browser-extension/bifehkofibaamoeaopjglfkddgkijdlh), [Edge](https://microsoftedge.microsoft.com/addons/detail/pgkajmkfgbehiomipedjhoddkejohfna) and [Vivaldi](https://chrome.google.com/webstore/detail/jabref-browser-extension/bifehkofibaamoeaopjglfkddgkijdlh)
 
 ### Organize
 
@@ -88,7 +88,7 @@ We view pull requests as a collaborative process.
 Submit a pull request early to get feedback from the team on work in progress.
 We will discuss improvements with you and agree to merge them once the [developers](https://github.com/JabRef/jabref/blob/master/DEVELOPERS) approve.
 
-If you want a step-by-step walk-through on how to set-up your workspace, please check [this guideline](https://devdocs.jabref.org/guidelines-for-setting-up-a-local-workspace/).
+If you want a step-by-step walk-through on how to set-up your workspace, please check [this guideline](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace).
 
 To compile JabRef from source, you need a Java Development Kit 14 and `JAVA_HOME` pointing to this JDK.
 To run it, just execute `gradlew run`.

diff --git a/build.gradle b/build.gradle
@@ -22,7 +22,7 @@ plugins {
     id 'com.github.ben-manes.versions' version '0.28.0'
     id 'org.javamodularity.moduleplugin' version '1.5.0'
     id 'org.openjfx.javafxplugin' version '0.0.8'
-    id 'org.beryx.jlink' version '2.17.5'
+    id 'org.beryx.jlink' version '2.17.7'
 
     // nicer test outputs during running and completion
     id 'com.adarshr.test-logger' version '2.0.0'
@@ -128,10 +128,10 @@ dependencies {
     // See https://bugs.documentfoundation.org/show_bug.cgi?id=117331#c8 for background information
     // Use the task bundleLibreOffice to update the bundled jar
     // DO NOT CHANGE THE libreoffice PREFIX
-    libreoffice 'org.libreoffice:juh:6.3.2'
-    libreoffice 'org.libreoffice:jurt:6.3.2'
-    libreoffice 'org.libreoffice:ridl:6.3.2'
-    libreoffice 'org.libreoffice:unoil:6.3.2'
+    libreoffice 'org.libreoffice:juh:6.4.3'
+    libreoffice 'org.libreoffice:jurt:6.4.3'
+    libreoffice 'org.libreoffice:ridl:6.4.3'
+    libreoffice 'org.libreoffice:unoil:6.4.3'
 
     implementation 'io.github.java-diff-utils:java-diff-utils:4.5'
     implementation 'info.debatty:java-string-similarity:1.2.1'
@@ -151,7 +151,7 @@ dependencies {
         exclude module: 'oraclepki'
     }
 
-    implementation ('com.google.guava:guava:28.2-jre') {
+    implementation ('com.google.guava:guava:29.0-jre') {
         // TODO: Remove this as soon as https://github.com/google/guava/issues/2960 is fixed
         exclude module: "jsr305"
     }
@@ -165,7 +165,7 @@ dependencies {
     implementation 'de.saxsys:mvvmfx:1.8.0'
     implementation 'org.fxmisc.easybind:easybind:1.0.3'
     implementation 'org.fxmisc.flowless:flowless:0.6.1'
-    implementation 'org.fxmisc.richtext:richtextfx:0.10.4'
+    implementation 'org.fxmisc.richtext:richtextfx:0.10.5'
     implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
     implementation 'com.jfoenix:jfoenix:9.0.9'
     implementation 'org.controlsfx:controlsfx:11.0.1'
@@ -196,11 +196,11 @@ dependencies {
         exclude module: "log4j-core"
     }
 
-    implementation 'com.vladsch.flexmark:flexmark:0.61.6'
+    implementation 'com.vladsch.flexmark:flexmark:0.61.16'
     implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.61.6'
-    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.61.6'
+    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.61.16'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.69'
+    testImplementation 'io.github.classgraph:classgraph:4.8.71'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.6.2'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.6.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.6.2'
@@ -648,9 +648,11 @@ jlink {
             installerOptions = [
                     '--vendor', 'JabRef',
                     '--app-version', "${project.version}",
+                    '--verbose',
                     '--win-upgrade-uuid', 'd636b4ee-6f10-451e-bf57-c89656780e36',
                     '--win-dir-chooser',
                     '--win-shortcut',
+                    '--win-menu',
                     '--temp', "$buildDir/installer",
                     '--resource-dir', "${projectDir}/buildres/windows",
                     '--file-associations', "${projectDir}/buildres/windows/bibtexAssociations.properties"
@@ -662,6 +664,7 @@ jlink {
                     '--icon', "${projectDir}/src/main/resources/icons/JabRef-icon-64.png",
             ]
             installerOptions = [
+                    '--verbose',
                     '--vendor', 'JabRef',
                     '--app-version', "${project.version}",
                     // '--temp', "$buildDir/installer",
@@ -681,10 +684,11 @@ jlink {
                     '--resource-dir', "${projectDir}/buildres/mac"
             ]
             installerOptions = [
+                    '--verbose',
                     '--vendor', 'JabRef',
                     '--app-version', "${project.version}",
-                    '--resource-dir', "${projectDir}/buildres/mac",
-                    '--file-associations', "${projectDir}/buildres/mac/bibtexAssociations.properties"
+                    '--file-associations', "${projectDir}/buildres/mac/bibtexAssociations.properties",
+                    '--resource-dir', "${projectDir}/buildres/mac"
             ]
         }
     }

diff --git a/buildres/mac/JabRef-background.tiff b/buildres/mac/JabRef-background.tiff
diff --git a/config/checkstyle/checkstyle.xml b/config/checkstyle/checkstyle.xml
@@ -4,13 +4,15 @@
         "http://www.checkstyle.org/dtds/configuration_1_3.dtd">
 
 <module name="Checker">
+    <property name="charset" value="UTF-8"/>
+
     <module name="Header">
         <property name="header" value=""/>
     </module>
 
     <!-- BeforeExecutionFileFilters is required for sources that are based on java14 -->
     <module name="BeforeExecutionExclusionFileFilter">
-      <property name="fileNamePattern" value="AuthorAndsReplacer.java|Ordinal.java" />
+      <property name="fileNamePattern" value="AuthorAndsReplacer.java|Ordinal.java|EntryTypeView.java" />
     </module>
 
     <module name="SuppressionFilter">
@@ -21,6 +23,9 @@
         <property name="fileNamePattern" value="module\-info\.java$"/>
     </module>
 
+    <module name="FileTabCharacter"/>
+    <module name="NewlineAtEndOfFile"/>
+
     <module name="TreeWalker">
         <!-- Checks for Javadoc comments: https://checkstyle.org/config_javadoc.html -->
         <module name="InvalidJavadocPosition"/>
@@ -42,16 +47,27 @@
             <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="EmptyForInitializerPad"/>
         <module name="EmptyLineSeparator">
+            <!-- check all except variable declarations -->
             <property name="tokens"
-                      value="IMPORT, CLASS_DEF, INTERFACE_DEF, ENUM_DEF, STATIC_INIT, INSTANCE_INIT, METHOD_DEF"/>
+                      value="IMPORT, STATIC_IMPORT, CLASS_DEF, INTERFACE_DEF, ENUM_DEF, STATIC_INIT, INSTANCE_INIT, METHOD_DEF, CTOR_DEF"/>
             <property name="allowMultipleEmptyLines" value="false"/>
             <property name="allowMultipleEmptyLinesInsideClassMembers" value="false"/>
         </module>
+        <module name="GenericWhitespace"/>
+        <module name="MethodParamPad"/>
+        <module name="NoLineWrap"/>
+        <module name="NoWhitespaceAfter"/>
+        <module name="NoWhitespaceBefore"/>
+        <module name="ParenPad"/>
+        <module name="SeparatorWrap">
+            <property name="tokens" value="COMMA, SEMI, ELLIPSIS, ARRAY_DECLARATOR, RBRACK, METHOD_REF"/>
+        </module>
+        <module name="SingleSpaceSeparator"/>
+        <module name="WhitespaceAfter"/>
         <module name="WhitespaceAround">
             <!-- RCULRY causes issues if classes are nested within arrays, therefore not activated -->
             <property name="tokens"
@@ -70,5 +86,44 @@
 
         <!-- Checks for blocks: https://checkstyle.org/config_blocks.html -->
         <module name="NeedBraces"/>
+
+        <module name="EmptyBlock">
+            <property name="option" value="text"/>
+        </module>
+
+        <!-- Disallows empty catch blocks (not even having a comment): https://checkstyle.sourceforge.io/config_blocks.html#EmptyCatchBlock -->
+        <module name="EmptyCatchBlock"/>
+
+        <!--
+            following rule enforces that there are no one line statements such as
+
+              public String getTabName() { return Localization.lang("XMP metadata"); }
+
+            Since it is too much effort to reformat all code, it is currently not enabled -->
+        <!-- <module name="LeftCurly"/> -->
+
+        <module name="RightCurly"/>
+        <!-- coding - https://checkstyle.sourceforge.io/config_coding.html -->
+
+        <module name="AvoidDoubleBraceInitialization"/>
+
+        <module name="CovariantEquals"/>
+
+        <!-- Checks for common coding problems: https://checkstyle.org/config_coding.html -->
+
+        <module name="DeclarationOrder"/>
+        <module name="EmptyStatement"/>
+
+        <module name="EqualsHashCode"/>
+
+        <!-- force a space after // for comments -->
+        <module name="TodoComment">
+            <property name="id" value="commentStartWithSpace"/>
+            <property name="format" value="^([^\s\/*])"/>
+            <message key="todo.match" value="Comment text should start with space."/>
+        </module>
+
+        <module name="MissingDeprecated"/>
+
     </module>
 </module>