Merge remote-tracking branch 'upstream/master' into udpate-gradle-to-64

* upstream/master: (50 commits)
  Keep group pane size when resizing window (#6180) (#6423)
  Changelog: Fix missing citation for biblatex-mla
  Update AUTHORS
  Check duplicate DOI (#6333)
  Fix missing citation for biblatex-mla
  Change EasyBind dependency (#6480)
  Add testing of latest dev version as mandatory
  Squashed 'src/main/resources/csl-styles/' changes from 5dad23d..586e0b8
  Fix libre office connection and other progress dialogs (#6478)
  Fix clear year and month field when converting to biblatex (#6434)
  Add truncate as a BibTex key modifier (#6427)
  Add new authors (not all - they need more work)
  Remove empty line
  Add simple Unit Tests for #6207 (#6240)
  Enforce LeftCurly rule (#6452)
  Implement task progress indicator (and dialog) in the toolbar (#6443)
  Consider empty brackets
  Changelog update
  Added a test
  Fixed brackets in regular expressions
  ...

.editorconfig

@@ -5,3 +5,6 @@ charset = utf-8
 indent_style = space
 insert_final_newline = true
 trim_trailing_whitespace = true
+
+[*.md]
+trim_trailing_whitespace = false

.github/ISSUE_TEMPLATE/bug_report.md

@@ -20,7 +20,7 @@ JabRef version <!-- version as shown in the about box --> on <!-- Windows 10|Ubu
       Please make a backup of your library before you try out this version.
       If you already use a development version, ensure that you use the latest one.
  -->
-- [ ] I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists
+- [ ] **Mandatory**: I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists
 
 <!-- Add a clear and concise description of what the bug is. -->
 

.github/outdatedDependencies.md

@@ -1,5 +1,5 @@
 ---
 title: Outdated dependencies
-labels: t: dependencies
+labels: type: dependencies
 ---
 [There are outdated dependencies!](https://github.com/JabRef/jabref/actions?query=is%3Afailure+workflow%3A%22Check+dependencies%22) 

.gitignore

@@ -2,6 +2,9 @@
 src/main/gen/
 src/main/generated/
 
+# the journal list cache
+*.mv
+
 # private data
 /buildres/jabref-cert-2016.p12
 

.mailmap

@@ -193,3 +193,10 @@ Christoph Treude <ctreude@gmail.com>
 Goutam Lavudiya <gtam25@gmail.com>
 Shikun Xiong <53288073+ShikunXiong@users.noreply.github.com>
 Fabiani Giovanni <fabiani.giovanni@gmail.com>
+Dimitra Karadima <44123133+dimitra-karadima@users.noreply.github.com>
+Dimitra Karadima <44123133+dimitra-karadima@users.noreply.github.com> <t8170038@aueb.gr>
+Cai Zhichun <54977532+braincident@users.noreply.github.com>
+Gennadiy Stakhovskiy <GennadiyStakhovskiy@gmail.com>
+Mootez Saad <34676841+MootezSaaD@users.noreply.github.com>
+Mootez Saad <34676841+MootezSaaD@users.noreply.github.com> <mootez.saad@medtech.tn>
+Chen Yuheng <pass@chenyuheng.cn>

AUTHORS

@@ -41,6 +41,7 @@ Ayachi Nene
 Bartosz J. Kaczkowski
 Bartłomiej Dach
 Behrouz Javanmardi
+Benedikt Tutzer
 Benjamin Köhler
 Berk Gureken
 Bernd Kalbfuss
@@ -51,15 +52,18 @@ Bherwani Ayush
 Bitor Tonixa Biriato Balença
 Brian Quistorff
 Brian Van Essen
+Cai Zhichun
 captain123
 Carl Christian Snethlage
 carlg0ransson
 Carlos Morales
 Carlos Silla
 Carlos Silva
+Catarina Gomes
 Cerrianne Santos
 Chamod Shehanka
 Chelsey Ong
+Chen Yuheng
 Chris Brown
 Christian Bartsch
 Christian Kopf
@@ -88,6 +92,7 @@ Dennis Tschechlov
 DevSiroukane
 Dilan Coss
 dima
+Dimitra Karadima
 Domenico Cufalo
 Dominik Schrempf
 Dominik Traczyk
@@ -126,15 +131,20 @@ frasca80
 Fred Stevens
 Frédéric Darboux
 Galileo Sartor
+Gennadiy Stakhovskiy
 Geoffrey Taerim Kim
 Gert Renckens
 Goutam Lavudiya
 Gregor Herrmann
+Grzegorz Popiel
 guenesaydin
 Guillaume Gardey
 Hakan Duran
 Hannes Restel
 Harinda Samarasekara
+HifeFish
+hrandrianasolo
+Hussain Arif
 Igor Chernyavsky
 Igor Steinmacher
 Illes Solt
@@ -146,6 +156,7 @@ Jan Schäfer
 Janosch Kutscherauer
 Jason Pickering
 Javier Muñoz Ferrara
+jcampbell11245
 Jeff Kerr
 Jeff Miller
 Jeffrey Kuhn
@@ -158,6 +169,7 @@ John David
 John Relph
 John Zedlewski
 Jonas Lähnemann
+Jonas Moosmann
 Jonathan Powell
 Jong-Ho Shinn
 Jorge Tornero
@@ -173,6 +185,7 @@ Jörg Wegner
 Jörg Zieren
 Jørgen Kvalsvik
 Jürgen Lange
+k3KAW8Pnf7mkmdSMPHz27
 Kai Mindermann
 Kai Takac
 Kaique Komata
@@ -213,6 +226,7 @@ Martin Stolle
 Martina Catizone
 Mathias Walter
 Matthias Geiger
+Matthias Mayr
 Matthias Mueller
 Mattia Bunel
 Mattias Ulbrich
@@ -232,6 +246,7 @@ Michel Krämer
 Mihu
 Mike Smoot
 mohamean
+Mootez Saad
 Morgan Lovato
 Moritz Ringler
 Morten Alver
@@ -312,6 +327,7 @@ Stanley Foerster
 Stefan Feyer
 Stefan Gerzmann
 Stefan Kolb
+Stefan Kufer
 Stefan Robert
 Stefan Scheffel
 Stefano Gariazzo
@@ -360,6 +376,7 @@ Yara Grassi Gouffon
 Yash Kothari
 Yichen Sun
 Yifan Peng
+Yunsheng Luo
 Yurick Honda
 zacmks
 Zeabin

CHANGELOG.md

@@ -18,7 +18,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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)
+- We added a new integrity check for duplicate DOIs. [koppor#339](https://github.com/koppor/jabref/issues/339)
 - We implemented an option to download fulltext files while importing. [#6381](https://github.com/JabRef/jabref/pull/6381)
+- We added a progress-indicator showing the average progress of background tasks to the toolbar. Clicking it reveals a pop-over with a list of running background tasks. [6443](https://github.com/JabRef/jabref/pull/6443)
+- We fixed the bug when strike the delete key in the text field. [#6421](https://github.com/JabRef/jabref/issues/6421)
+- We added a BibTex key modifier for truncating strings. [#3915](https://github.com/JabRef/jabref/issues/3915)
+- We added support for jumping to target entry when typing letter/digit after sorting a column in maintable [#6146](https://github.com/JabRef/jabref/issues/6146)
 
 ### Changed
 
@@ -41,6 +46,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where opening a library from the recent libraries menu was not possible. [#5939](https://github.com/JabRef/jabref/issues/5939)
 - 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 the issue that groups panel does not keep size when resizing window. [#6180](https://github.com/JabRef/jabref/issues/6180)
 - We fixed an error that sometimes occurred when using the context menu. [#6085](https://github.com/JabRef/jabref/issues/6085)
 - 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 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)
@@ -50,9 +56,17 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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)
+- We fixed an issue where only the field `abstract` and `comment` were declared as multiline fields. Other fields can now be configured in the preferences using "Do not wrap the following fields when saving" [4373](https://github.com/JabRef/jabref/issues/4373)
 - We fixed an issue where JabRef switched to discrete graphics under macOS [#5935](https://github.com/JabRef/jabref/issues/5935)
 - We fixed an issue where the Preferences entry preview will be unexpected modified leads to Value too long exception [#6198](https://github.com/JabRef/jabref/issues/6198)
 - We fixed an issue where custom jstyles for Open/LibreOffice would only be valid if a layout line for the entry type `default` was at the end of the layout section [#6303](https://github.com/JabRef/jabref/issues/6303)
+- We fixed an issue where long directory names created from patterns could create an exception. [#3915](https://github.com/JabRef/jabref/issues/3915)
+- We fixed an issue where sort on numeric cases was broken. [#6349](https://github.com/JabRef/jabref/issues/6349)
+- We fixed an issue where year and month fields were not cleared when converting to biblatex [#6224](https://github.com/JabRef/jabref/issues/6224)
+- We fixed an issue where an "Not on FX thread" exception occured when saving on linux [#6453](https://github.com/JabRef/jabref/issues/6453)
+- We fixed an issue where the library sort order was lost. [#6091](https://github.com/JabRef/jabref/issues/6091)
+- We fixed an issue where brackets in regular expressions were not working. [6469](https://github.com/JabRef/jabref/pull/6469)
+- We fixed an issue where LaTeX citations for specific commands (\autocites) of biblatex-mla were not recognized. [#6476](https://github.com/JabRef/jabref/issues/6476)
 
 ### Removed
 

README.md

@@ -1,11 +1,5 @@
 # JabRef Bibliography Management
 
-[![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)
-[![Paypal Donate](https://img.shields.io/badge/donate-paypal-00457c.svg?logo=paypal&style=flat-square)](https://paypal.me/JabRef)
-[![Crowdin](https://d322cqt584bo4o.cloudfront.net/jabref/localized.svg)](https://crowdin.com/project/jabref)
-
 JabRef is an open-source, cross-platform citation and reference management tool.
 
 Stay on top of your literature: JabRef helps you to collect and organize sources, find the paper you need and discover the latest research.
@@ -62,6 +56,7 @@ The [latest stable release is available at FossHub](https://www.fosshub.com/JabR
 ## Bug Reports, Suggestions, Other Feedback
 
 [![Donation](https://img.shields.io/badge/donate%20to-jabref-orange.svg)](https://donations.jabref.org)
+[![Paypal Donate](https://img.shields.io/badge/donate-paypal-00457c.svg?logo=paypal&style=flat-square)](https://paypal.me/JabRef)
 
 We are thankful for any bug reports or other feedback.
 If you have ideas for new features you want to be included in JabRef, [tell us in our forum](http://discourse.jabref.org/c/features)!
@@ -72,14 +67,19 @@ An explanation of donation possibilities and usage of donations is available at
 
 ## Contributing
 
+[![dev-docs](https://img.shields.io/badge/dev-docs-blue)](https://devdocs.jabref.org/)
 [![Help Contribute to Open Source](https://www.codetriage.com/jabref/jabref/badges/users.svg)](https://www.codetriage.com/jabref/jabref)
 [![Join the chat at https://gitter.im/JabRef/jabref](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/JabRef/jabref?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 [![OpenHub](https://www.openhub.net/p/jabref/widgets/project_thin_badge.gif)](https://www.openhub.net/p/jabref)
+[![Deployment Status](https://github.com/JabRef/jabref/workflows/Deployment/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ADeployment)
+[![Test 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)
 
-> Not a programmer? [Learn how to help.](https://contribute.jabref.org)
-
-Want to be part of a free and open-source project that tens of thousands of scientists use every day? Check out the ways you can contribute, below:
+Want to be part of a free and open-source project that tens of thousands of scientists use every day?
+Check out the ways you can contribute, below:
 
+- Not a programmer? Help translating JabRef at [Crowdin](https://crowdin.com/project/jabref) or learn how to help at [contribute.jabref.org](https://contribute.jabref.org)
+- Quick overview on the architecture needed? Look at our [high-level documentation](https://devdocs.jabref.org/getting-into-the-code/high-level-documentation)
 - For details on how to contribute, have a look at our [guidelines for contributing](CONTRIBUTING.md).
 - You are welcome to contribute new features. To get your code included into JabRef, just [fork](https://help.github.com/en/articles/fork-a-repo) the JabRef repository, make your changes, and create a [pull request](https://help.github.com/en/articles/about-pull-requests).
 - To work on existing JabRef issues, check out our [issue tracker](https://github.com/JabRef/jabref/issues). New to open source contributing? Look for issues with the ["good first issue"](https://github.com/JabRef/jabref/labels/good%20first%20issue) label to get started.
@@ -98,8 +98,8 @@ For IntelliJ IDEA, just import the project via a Gradle Import by pointing at th
 
 `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
-  [install4j]: https://www.ej-technologies.com/products/install4j/overview.html
-  [JabRef]: https://www.jabref.org
-  [JavaFX]: https://en.wikipedia.org/wiki/JavaFX
+[BibTeX]: https://www.ctan.org/pkg/bibtex
+[Biblatex]: https://www.ctan.org/pkg/biblatex
+[install4j]: https://www.ej-technologies.com/products/install4j/overview.html
+[JabRef]: https://www.jabref.org
+[JavaFX]: https://en.wikipedia.org/wiki/JavaFX

build.gradle

@@ -16,7 +16,7 @@ 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 '2.18.0'
+    id 'org.beryx.jlink' version '2.19.0'
 
     // nicer test outputs during running and completion
     id 'com.adarshr.test-logger' version '2.0.0'
@@ -81,6 +81,7 @@ sourceSets {
 }
 
 repositories {
+    mavenLocal()
     jcenter()
     maven { url 'https://oss.sonatype.org/content/groups/public' }
     maven { url 'https://repository.apache.org/snapshots' }
@@ -158,7 +159,7 @@ dependencies {
     implementation 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-11'
     implementation 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT'
     implementation 'de.saxsys:mvvmfx:1.8.0'
-    implementation 'org.fxmisc.easybind:easybind:1.0.3'
+    implementation 'com.tobiasdiez:easybind:2.0.0-SNAPSHOT'
     implementation 'org.fxmisc.flowless:flowless:0.6.1'
     implementation 'org.fxmisc.richtext:richtextfx:0.10.5'
     implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
@@ -191,9 +192,9 @@ dependencies {
         exclude module: "log4j-core"
     }
 
-    implementation 'com.vladsch.flexmark:flexmark:0.61.24'
-    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.61.24'
-    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.61.24'
+    implementation 'com.vladsch.flexmark:flexmark:0.61.26'
+    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.61.26'
+    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.61.26'
 
     testImplementation 'io.github.classgraph:classgraph:4.8.78'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.6.2'
@@ -543,7 +544,7 @@ task deleteInstallerTemp(type: Delete) {
 
 jpackage.dependsOn deleteInstallerTemp
 jlink {
-    options = ['--strip-debug','--compress', '2', '--no-header-files', '--no-man-pages']
+    options = ['--strip-debug', '--compress', '2', '--no-header-files', '--no-man-pages']
     launcher {
         name = 'JabRef'
     }

config/IntelliJ Code Style.xml

@@ -1,37 +1,38 @@
-<code_scheme name="JabRef">
-  <option name="CLASS_COUNT_TO_USE_IMPORT_ON_DEMAND" value="999" />
-  <option name="NAMES_COUNT_TO_USE_IMPORT_ON_DEMAND" value="999" />
-  <option name="PACKAGES_TO_USE_IMPORT_ON_DEMAND">
-    <value />
-  </option>
-  <option name="IMPORT_LAYOUT_TABLE">
-    <value>
-      <package name="java" withSubpackages="true" static="false" />
-      <emptyLine />
-      <package name="javax" withSubpackages="true" static="false" />
-      <emptyLine />
-      <package name="javafx" withSubpackages="true" static="false" />
-      <emptyLine />
-      <package name="org.jabref" withSubpackages="true" static="false" />
-      <emptyLine />
-      <package name="" withSubpackages="true" static="false" />
-      <emptyLine />
-      <package name="" withSubpackages="true" static="true" />
-    </value>
-  </option>
-  <option name="JD_P_AT_EMPTY_LINES" value="false" />
-  <option name="JD_KEEP_EMPTY_PARAMETER" value="false" />
-  <option name="JD_KEEP_EMPTY_EXCEPTION" value="false" />
-  <option name="JD_KEEP_EMPTY_RETURN" value="false" />
-  <option name="WRAP_COMMENTS" value="true" />
+<code_scheme name="JabRef" version="173">
+  <option name="RIGHT_MARGIN" value="0" />
+  <option name="SOFT_MARGINS" value="120" />
   <JavaCodeStyleSettings>
     <option name="DO_NOT_WRAP_AFTER_SINGLE_ANNOTATION" value="true" />
+    <option name="SPACE_INSIDE_ONE_LINE_ENUM_BRACES" value="true" />
+    <option name="CLASS_COUNT_TO_USE_IMPORT_ON_DEMAND" value="999" />
+    <option name="NAMES_COUNT_TO_USE_IMPORT_ON_DEMAND" value="999" />
+    <option name="PACKAGES_TO_USE_IMPORT_ON_DEMAND">
+      <value />
+    </option>
+    <option name="IMPORT_LAYOUT_TABLE">
+      <value>
+        <package name="java" withSubpackages="true" static="false" />
+        <emptyLine />
+        <package name="javax" withSubpackages="true" static="false" />
+        <emptyLine />
+        <package name="javafx" withSubpackages="true" static="false" />
+        <emptyLine />
+        <package name="org.jabref" withSubpackages="true" static="false" />
+        <emptyLine />
+        <package name="" withSubpackages="true" static="false" />
+        <emptyLine />
+        <package name="" withSubpackages="true" static="true" />
+      </value>
+    </option>
   </JavaCodeStyleSettings>
   <codeStyleSettings language="JAVA">
+    <option name="KEEP_CONTROL_STATEMENT_IN_ONE_LINE" value="false" />
     <option name="KEEP_BLANK_LINES_IN_DECLARATIONS" value="1" />
     <option name="KEEP_BLANK_LINES_IN_CODE" value="1" />
     <option name="KEEP_BLANK_LINES_BEFORE_RBRACE" value="0" />
     <option name="ALIGN_MULTILINE_CHAINED_METHODS" value="true" />
+    <option name="SPACE_BEFORE_ARRAY_INITIALIZER_LBRACE" value="true" />
+    <option name="WRAP_COMMENTS" value="true" />
     <arrangement>
       <rules>
         <section>
@@ -292,4 +293,4 @@
       </rules>
     </arrangement>
   </codeStyleSettings>
-</code_scheme>
+</code_scheme>