Merge remote-tracking branch 'upstream/master' into testEA15Adopt

* upstream/master: (55 commits)
  Fix sort order in main table not stored (#6898)
  Window "Manage field names & content": make title consistent with menu (+ localization) (#6895)
  Complete rebranding of `bibtexkey` as `citationkey` (#6875)
  Dev-doc: ADR list (#6887)
  Bump lucene-queryparser from 8.6.1 to 8.6.2 (#6881)
  Bump fontbox from 2.0.20 to 2.0.21 (#6883)
  Bump org.beryx.jlink from 2.21.3 to 2.21.4 (#6882)
  Bump com.github.ben-manes.versions from 0.29.0 to 0.30.0 (#6884)
  Bump pdfbox from 2.0.20 to 2.0.21 (#6885)
  Bump mockito-core from 3.5.7 to 3.5.10 (#6886)
  lint changelog
  Dev Doc: Moving around ADR (end?) (#6873)
  Add MD031 to lint ignore list
  Add mlep's other email adress
  Fetch by ID: SAO/NASA Astrophysics Data System -> SAO/NASA ADS (#6876)
  Reimport -> Reload (#6874)
  GitBook: [master] 19 pages and 4 assets modified
  Add new author
  Delete .Rhistory
  Fix icon issue (#6858)
  ...

.github/workflows/tests.yml

@@ -257,7 +257,7 @@ jobs:
         uses: unsplash/comment-on-pr@master
         if: steps.authors_check.outputs.newauthor == 'true'
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GH_TOKEN_COMMENT_ON_PR }}
         with:
           msg: "${{ steps.authors_check.outputs.message }}"
           check_for_duplicate_msg: true

.mailmap

@@ -47,6 +47,7 @@ Frédéric Darboux <Frederic.Darboux@orleans.inra.fr>
 Frédéric Darboux <Frederic.Darboux@orleans.inra.fr> <fdar@users.sourceforge.net>
 Frédéric Darboux <Frederic.Darboux@orleans.inra.fr> <mlep@users.noreply.github.com>
 Frédéric Darboux <Frederic.Darboux@orleans.inra.fr> <mlep@github.com>
+Frédéric Darboux <frederic.darboux@inrae.fr>
 Florian Straßer <strassfn@studi.informatik.uni-stuttgart.de>
 Gregor Herrmann <gregoa@debian.org>
 Hakan Duran <ehakanduran@gmail.com> hakova <ehakanduran@gmail.com>

.markdownlint.yml

@@ -13,6 +13,9 @@ MD013: false
 MD026:
   punctuation: ".,;:!"
 
+# not supported by gitbook
+MD031: false
+
 MD033:
   # we have <a> tags with ids and superscript
   allowed_elements: ['a', 'sup']

AUTHORS

@@ -119,6 +119,7 @@ Ethan Harris
 Fabian Bauer
 Fabian Bieker
 Fabiani Giovanni
+Fabio Marcos
 Fabrice Dessaint
 Fancy Zhang
 Fedor Bezrukov
@@ -223,6 +224,7 @@ Lucas Beretti
 Luciana de Melo e Abud
 Lugduni Desrosiers
 Luis Romero
+m-mauersberger
 Mairieli Wessel
 Malik Atalla
 Malte Deiseroth

CHANGELOG.md

@@ -1,3 +1,4 @@
+
 # Changelog
 
 All notable changes to this project will be documented in this file.
@@ -13,15 +14,29 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 - We added a query parser and mapping layer to enable conversion of queries formulated in simplified lucene syntax by the user into api queries. [#6799](https://github.com/JabRef/jabref/pull/6799)
 - We added some basic functionality to customise the look of JabRef by importing a css theme file. [#5790](https://github.com/JabRef/jabref/issues/5790)
+- We added connection check function in network preference setting [#6560](https://github.com/JabRef/jabref/issues/6560)
 
 ### Changed
 
+- We restructured the 'File' tab and extracted some parts into the 'Linked files' tab [#6779](https://github.com/JabRef/jabref/pull/6779)
 - JabRef now offers journal lists from <https://abbrv.jabref.org>. JabRef the lists which use a dot inside the abbreviations. [#5749](https://github.com/JabRef/jabref/pull/5749)
+- We removed two useless preferences in the groups preferences dialog. [#6836](https://github.com/JabRef/jabref/pull/6836)
+- Synchronization of SpecialFields to keywords is now disabled by default. [#6621](https://github.com/JabRef/jabref/issues/6621)
+- JabRef no longer opens the entry editor with the first entry on startup [#6855](https://github.com/JabRef/jabref/issues/6855)
+- We completed the rebranding of `bibtexkey` as `citationkey` which was started in JabRef 5.1.
+- JabRef no longer opens the entry editor with the first entry on startup [#6855](https://github.com/JabRef/jabref/issues/6855)
+- Fetch by ID: (long) "SAO/NASA Astrophysics Data System" replaced by (short) "SAO/NASA ADS" [#6876](https://github.com/JabRef/jabref/pull/6876)
+- We changed the title of the window  "Manage field names and content":  to have the same title as the corresponding menu item  [#6895](https://github.com/JabRef/jabref/pull/6895)
 
 ### Fixed
 
-### Removed
+- We fixed an issue changing the icon link_variation_off that is not meaningful. [#6834][https://github.com/JabRef/jabref/issues/6834]
+- We fixed an issue where the `.sav` file was not deleted upon exiting JabRef. [#6109](https://github.com/JabRef/jabref/issues/6109)
+- We fixed a linked identifier icon inconsistency. [#6705](https://github.com/JabRef/jabref/issues/6705)
+- We fixed the wrong behavior that font size changes are not reflected in dialogs. [#6039](https://github.com/JabRef/jabref/issues/6039)
+- We fixed an issue where the sort order of the entry table was reset after a restart of JabRef [#6898](https://github.com/JabRef/jabref/pull/6898)
 
+### Removed
 
 ## [5.1] – 2020-08-30
 

build.gradle

@@ -13,10 +13,10 @@ plugins {
     id 'application'
     id "com.simonharrer.modernizer" version '2.1.0-1'
     id 'me.champeau.gradle.jmh' version '0.5.1'
-    id 'com.github.ben-manes.versions' version '0.29.0'
+    id 'com.github.ben-manes.versions' version '0.30.0'
     id 'org.javamodularity.moduleplugin' version '1.7.0'
     id 'org.openjfx.javafxplugin' version '0.0.9'
-    id 'org.beryx.jlink' version '2.21.3'
+    id 'org.beryx.jlink' version '2.21.4'
 
     // nicer test outputs during running and completion
     // Homepage: https://github.com/radarsh/gradle-test-logger-plugin
@@ -46,7 +46,7 @@ java {
 }
 
 application {
-    mainClassName = "$moduleName/org.jabref.JabRefLauncher"
+    mainClassName = "$moduleName/org.jabref.gui.JabRefLauncher"
 }
 
 // TODO: Ugly workaround to temporarily ignore build errors to dependencies of latex2unicode
@@ -105,8 +105,8 @@ dependencies {
     // Include all jar-files in the 'lib' folder as dependencies
     implementation fileTree(dir: 'lib', includes: ['*.jar'])
 
-    implementation 'org.apache.pdfbox:pdfbox:2.0.20'
-    implementation 'org.apache.pdfbox:fontbox:2.0.20'
+    implementation 'org.apache.pdfbox:pdfbox:2.0.21'
+    implementation 'org.apache.pdfbox:fontbox:2.0.21'
     implementation 'org.apache.pdfbox:xmpbox:2.0.20'
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.8'
@@ -137,7 +137,7 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.8-1'
     implementation 'org.antlr:antlr4-runtime:4.8-1'
 
-    implementation (group: 'org.apache.lucene', name: 'lucene-queryparser', version: '8.6.1') {
+    implementation (group: 'org.apache.lucene', name: 'lucene-queryparser', version: '8.6.2') {
         exclude group: 'org.apache.lucene', module: 'lucene-sandbox'
     }
 
@@ -207,9 +207,10 @@ dependencies {
     testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.14'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
-    testImplementation 'org.mockito:mockito-core:3.5.7'
+    testImplementation 'org.mockito:mockito-core:3.5.10'
     testImplementation 'org.xmlunit:xmlunit-core:2.7.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.7.0'
+    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.14.1'
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.14.1'
     testImplementation "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"
     testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
@@ -442,6 +443,11 @@ test {
         excludeTags 'DatabaseTest', 'FetcherTest', 'GUITest'
     }
 
+    moduleOptions {
+        // TODO: Remove this as soon as archunit is modularized
+        runOnClasspath = true
+    }
+
     testLogging {
         // set options for log level LIFECYCLE
         // for debugging tests: add "STANDARD_OUT", "STANDARD_ERROR"

buildres/linux/JabRef.desktop

@@ -9,4 +9,4 @@ Type=Application
 DESKTOP_MIMES
 Categories=DEPLOY_BUNDLE_CATEGORY
 Keywords=bibtex;biblatex;latex;bibliography
-StartupWMClass=org.jabref.JabRefMain
+StartupWMClass=org.jabref.gui.JabRefMain

docs/README.md

@@ -1,6 +1,6 @@
 # Overview on Developing
 
-This page presents all development informatation around JabRef.
+This page presents all development information around JabRef.
 
 ## Starting point for newcomers
 
@@ -37,23 +37,11 @@ Without jlink, it is not possible to generate a fat jar any more. During develop
 
 Diagram showing aspects of groups: [Groups.uml](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/Groups.uml).
 
-## Decision Records
+## Architectural Decision Records
 
-This log lists the decisions for JabRef.
+[Architectural decisions for JabRef](adr.md) are recorded.
 
-* [ADR-0000](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0000-use-markdown-architectural-decision-records.md) - Use Markdown Architectural Decision Records
-* [ADR-0001](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0001-use-crowdin-for-translations.md) - Use Crowdin for translations
-* [ADR-0002](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0002-use-slf4j-for-logging.md) - Use slf4j together with log4j2 for logging
-* [ADR-0003](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0003-use-gradle-as-build-tool.md) - Use Gradle as build tool
-* [ADR-0004](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0004-use-mariadb-connector.md) - Use MariaDB Connector
-* [ADR-0005](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0005-fully-support-utf8-only-for-latex-files.md) - Fully Support UTF-8 Only For LaTeX Files
-* [ADR-0006](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0006-only-translated-strings-in-language-file.md) - Only translated strings in language file
-* [ADR-0007](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0007-human-readable-changelog.md) - Provide a human-readable changelog
-* [ADR-0008](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0008-use-public-final-instead-of-getters.md) - Use public final instead of getters to offer access to immutable variables
-* [ADR-0009](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0009-use-plain-junit5-for-testing.md) - Use Plain JUnit5 for advanced test assertions
-* [ADR-0010](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0010-use-h2-as-internal-database.md) - Use H2 as Internal SQL Database
-
-For new ADRs, please use [template.md](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/template.md) as basis. More information on MADR is available at [https://adr.github.io/madr/](https://adr.github.io/madr/). General information about architectural decision records is available at [https://adr.github.io/](https://adr.github.io/).
+For new ADRs, please use [template.md](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/template.md) as basis. More information on MADR is available at [https://adr.github.io/madr/](https://adr.github.io/madr/). General information about architectural decision records is available at [https://adr.github.io/](https://adr.github.io/). Add them to the [list of architectural decision records](adr.md).
 
 ## FAQ
 

docs/SUMMARY.md

@@ -13,6 +13,7 @@
   * [Code Quality](advanced-reading/code-quality.md)
   * [Recommendations for UI design](advanced-reading/ui-recommendations.md)
   * [Custom SVG icons](advanced-reading/custom-svg-icons.md)
+  * [Working on fetchers](advanced-reading/fetchers.md)
   * [Creating a binary and debug it](advanced-reading/jpackage.md)
 * [JabRef and Software Engineering](teaching.md)
 * [Readings on Coding](readings-on-coding/README.md)

docs/adr.md

@@ -1,6 +1,27 @@
 # Architectural Decisions
 
-This directory contains the architectural decisions for JabRef.
+Architectural decisions for JabRef:
 
-For new ADRs, please use [template.md](https://github.com/JabRef/jabref/tree/98e9fc3ddc7b59ca35101c7f37b183ca2e69d8a0/docs/adr/template.md) as basis. More information on the used format is available at [https://adr.github.io/madr/](https://adr.github.io/madr/). General information about architectural decision records is available at [https://adr.github.io/](https://adr.github.io/).
+* [ADR-0000](https://github.com/JabRef/jabref/tree/docs/adr/0000-use-markdown-architectural-decision-records.md) - Use Markdown Architectural Decision Records
+* [ADR-0001](https://github.com/JabRef/jabref/tree/docs/adr/0001-use-crowdin-for-translations.md) - Use Crowdin for translations
+* [ADR-0002](https://github.com/JabRef/jabref/tree/docs/adr/0002-use-slf4j-for-logging.md) - Use slf4j together with log4j2 for logging
+* [ADR-0003](https://github.com/JabRef/jabref/tree/docs/adr/0003-use-gradle-as-build-tool.md) - Use Gradle as build tool
+* [ADR-0004](https://github.com/JabRef/jabref/tree/docs/adr/0004-use-mariadb-connector.md) - Use MariaDB Connector
+* [ADR-0005](https://github.com/JabRef/jabref/tree/docs/adr/0005-fully-support-utf8-only-for-latex-files.md) - Fully Support UTF-8 Only For LaTeX Files
+* [ADR-0006](https://github.com/JabRef/jabref/tree/docs/adr/0006-only-translated-strings-in-language-file.md) - Only translated strings in language file
+* [ADR-0007](https://github.com/JabRef/jabref/tree/docs/adr/0007-human-readable-changelog.md) - Provide a human-readable changelog
+* [ADR-0008](https://github.com/JabRef/jabref/tree/docs/adr/0008-use-public-final-instead-of-getters.md) - Use public final instead of getters to offer access to immutable variables
+* [ADR-0009](https://github.com/JabRef/jabref/tree/docs/adr/0009-use-plain-junit5-for-testing.md) - Use Plain JUnit5 for advanced test assertions
+* [ADR-0010](https://github.com/JabRef/jabref/tree/docs/adr/0010-use-h2-as-internal-database.md) - Use H2 as Internal SQL Database
+* [ADR-0011](https://github.com/JabRef/jabref/tree/docs/adr/0011-test-external-links-in-documentation.md) - Test external links in documentation
+* [ADR-0012](https://github.com/JabRef/jabref/tree/docs/adr/0012-handle-different-bibEntry-formats-of-fetchers.md) - Handle different bibentry formats of fetchers by adding a layer
+* [ADR-0013](https://github.com/JabRef/jabref/tree/docs/adr/0013-add-native-support-biblatex-software.md) - Add Native Support for BibLatex-Sotware
+fix checkstyle in adr
+* [ADR-0014](https://github.com/JabRef/jabref/tree/docs/adr/0014-separate-URL-creation-to-enable-proper-logging.md) - Separate URL creation to enable proper logging
+* [ADR-0015](https://github.com/JabRef/jabref/tree/docs/adr/0015-support-an-abstract-query-syntax-for-query-conversion.md) - Query syntax design
+* [ADR-0016](https://github.com/JabRef/jabref/tree/docs/adr/0016-mutable-preferences-objects.md) - Mutable preferences objects
+* [ADR-0017](https://github.com/JabRef/jabref/tree/docs/adr/0017-allow-model-access-logic.md) - Allow org.jabref.model to access org.jabref.logic
+
+
+For new ADRs, please use [template.md](https://github.com/JabRef/jabref/tree/98e9fc3ddc7b59ca35101c7f37b183ca2e69d8a0/docs/adr/template.md) as basis. More information on the used format is available at [https://adr.github.io/madr/](https://adr.github.io/madr/). General information about architectural decision records is available at [https://adr.github.io/](https://adr.github.io/). Then add them to the above list.
 

docs/adr/0003-use-gradle-as-build-tool.md

@@ -38,7 +38,7 @@ Chosen option: "Gradle", because it is lean and fits our development style.
 * Good, because [it offers custom dependency scopes](https://gradle.org/maven-vs-gradle/)
 * Good, because [it has good community support](https://linuxhint.com/ant-vs-maven-vs-gradle/)
 * Good, because [its performance can be 100 times more than maven's performance](https://gradle.org/gradle-vs-maven-performance/).
-* Bad, because [not that many plugins are available/maintained yet](https://blog.philipphauer.de/moving-back-from-gradle-to-maven/)
+* Bad, because [not that many plugins are available/maintained yet](https://phauer.com/2018/moving-back-from-gradle-to-maven/)
 * Bad, because [it lacks a wide variety of application server integrations](http://pages.zeroturnaround.com/rs/zeroturnaround/images/java-build-tools-part-2.pdf)
 * Bad, because [it has a medium popularity](http://pages.zeroturnaround.com/rs/zeroturnaround/images/java-build-tools-part-2.pdf)
 * Bad, because [it allows custom build scripts which need to be debugged](https://www.softwareyoga.com/10-reasons-why-we-chose-maven-over-gradle/)