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Merge remote-tracking branch 'upstream/master' into testEA15Adopt
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* 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)
  ...
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Siedlerchr committed Sep 12, 2020
2 parents a42ccdd + 1d2ecff commit 784c025
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2 changes: 1 addition & 1 deletion .github/workflows/tests.yml
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Expand Up @@ -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
6 changes: 3 additions & 3 deletions .idea/runConfigurations/JabRef_Main.xml

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1 change: 1 addition & 0 deletions .mailmap
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Expand Up @@ -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>
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3 changes: 3 additions & 0 deletions .markdownlint.yml
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Expand Up @@ -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']
2 changes: 2 additions & 0 deletions AUTHORS
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Expand Up @@ -119,6 +119,7 @@ Ethan Harris
Fabian Bauer
Fabian Bieker
Fabiani Giovanni
Fabio Marcos
Fabrice Dessaint
Fancy Zhang
Fedor Bezrukov
Expand Down Expand Up @@ -223,6 +224,7 @@ Lucas Beretti
Luciana de Melo e Abud
Lugduni Desrosiers
Luis Romero
m-mauersberger
Mairieli Wessel
Malik Atalla
Malte Deiseroth
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17 changes: 16 additions & 1 deletion CHANGELOG.md
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@@ -1,3 +1,4 @@

# Changelog

All notable changes to this project will be documented in this file.
Expand All @@ -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

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20 changes: 13 additions & 7 deletions build.gradle
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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'
Expand Down Expand Up @@ -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'
}

Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"
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2 changes: 1 addition & 1 deletion buildres/linux/JabRef.desktop
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Expand Up @@ -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
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20 changes: 4 additions & 16 deletions docs/README.md
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@@ -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

Expand Down Expand Up @@ -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

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1 change: 1 addition & 0 deletions docs/SUMMARY.md
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Expand Up @@ -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)
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25 changes: 23 additions & 2 deletions docs/adr.md
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@@ -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.

2 changes: 1 addition & 1 deletion docs/adr/0003-use-gradle-as-build-tool.md
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Expand Up @@ -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/)
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