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Merge remote-tracking branch 'upstream/master' into addInfoPlist
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# 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
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Siedlerchr committed Apr 26, 2020
2 parents 1a01b70 + d7a57b8 commit e692f4b
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2 changes: 1 addition & 1 deletion .github/outdatedDependencies.md
Original file line number Diff line number Diff line change
@@ -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title: Outdated dependencies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[There are outdated dependencies!](https://github.com/JabRef/jabref/actions?query=is%3Afailure+workflow%3A%22Check+dependencies%22)
23 changes: 1 addition & 22 deletions .github/workflows/deployment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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 }}
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18 changes: 18 additions & 0 deletions .github/workflows/stale.yml
Original file line number Diff line number Diff line change
@@ -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'
2 changes: 1 addition & 1 deletion .github/workflows/tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
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1 change: 1 addition & 0 deletions .idea/runConfigurations/JabRef_Main.xml

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13 changes: 11 additions & 2 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

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4 changes: 2 additions & 2 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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`.
Expand Down
28 changes: 16 additions & 12 deletions build.gradle
Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand Down Expand Up @@ -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'
Expand All @@ -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"
}
Expand All @@ -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'
Expand Down Expand Up @@ -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'
Expand Down Expand Up @@ -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"
Expand All @@ -662,6 +664,7 @@ jlink {
'--icon', "${projectDir}/src/main/resources/icons/JabRef-icon-64.png",
]
installerOptions = [
'--verbose',
'--vendor', 'JabRef',
'--app-version', "${project.version}",
// '--temp', "$buildDir/installer",
Expand All @@ -681,10 +684,11 @@ jlink {
'--resource-dir', "${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"
]
}
}
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65 changes: 60 additions & 5 deletions config/checkstyle/checkstyle.xml
Original file line number Diff line number Diff line change
Expand Up @@ -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">
Expand All @@ -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"/>
Expand All @@ -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"
Expand All @@ -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>
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