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Merge pull request #9 from JabRef/main
update 20213.30
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‎.github/ISSUE_TEMPLATE/bug_report.md

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@@ -1,6 +1,9 @@
11
---
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name: Bug report
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about: Create a report to help us improve
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title: ''
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labels: ''
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assignees: ''
47

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---
69

‎.github/ISSUE_TEMPLATE/suggestion-for-improvement.md

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@@ -1,6 +1,9 @@
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---
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name: Suggestion for improvement
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about: Suggest an enhancement
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title: ''
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labels: ''
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assignees: ''
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58
---
69

‎.github/workflows/automerge.yml

+2-2
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@@ -5,7 +5,7 @@ jobs:
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automerge:
66
name: Automerge Dependabot
77
runs-on: ubuntu-latest
8-
if: github.actor == 'dependabot[bot]' || github.actor == 'dependabot-preview[bot]'
8+
if: github.actor == 'dependabot[bot]' || github.actor == 'dependabot-preview[bot]' || github.event.label.name == 'dependencies'
99
steps:
1010
- name: 'Wait for status checks'
1111
id: waitforstatuschecks
@@ -16,7 +16,7 @@ jobs:
1616
env:
1717
GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
1818
- name: Auto approve
19-
uses: hmarr/auto-approve-action@v2.0.0
19+
uses: hmarr/auto-approve-action@v2.1.0
2020
if: steps.waitforstatuschecks.outputs.status == 'success'
2121
with:
2222
github-token: "${{ secrets.GITHUB_TOKEN }}"

‎.github/workflows/deployment.yml

+23-22
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@ on:
44
workflow_dispatch:
55
push:
66
branches:
7-
- master
8-
- master-release
7+
- main
8+
- main-release
99
paths-ignore:
1010
- 'docs/**'
1111
- 'src/test/**'
@@ -104,27 +104,28 @@ jobs:
104104
codesign -s "Developer ID Application: Tobias Diez (W2PU6LW5U5)" --options runtime --entitlements buildres/mac/jabref.entitlements -vvvv --deep "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
105105
jpackage --type pkg --dest build/distribution --name JabRef --mac-package-identifier JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --app-image build/distribution/JabRef.app --verbose --type pkg --vendor JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
106106
productsign --sign "Developer ID Installer: Tobias Diez (W2PU6LW5U5)" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
107-
- name: Notarize dmg and pkg installer
108-
if: matrix.os == 'macos-latest' && github.ref == 'refs/heads/master'
109-
shell: bash
110-
run: |
111-
REQUEST_UUID_DMG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "W2PU6LW5U5" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg" | grep RequestUUID | awk '{print $3}')
112-
while xcrun altool --notarization-info "$REQUEST_UUID_DMG" -u ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} -p ${{ secrets.OSX_NOTARIZATION_APP_PWD }} | grep "Status: in progress" > /dev/null; do
113-
echo "Verification in progress..."
114-
sleep 30
115-
done
116-
xcrun stapler staple "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
117-
spctl -vvv --assess --type exec build/distribution/JabRef.app
118-
codesign -vvv --deep --strict "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
119-
codesign -dvv "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
120-
REQUEST_UUID_PKG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "W2PU6LW5U5" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg" | grep RequestUUID | awk '{print $3}')
121-
while xcrun altool --notarization-info "$REQUEST_UUID_PKG" -u ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} -p ${{ secrets.OSX_NOTARIZATION_APP_PWD }} | grep "Status: in progress" > /dev/null; do
122-
echo "Verification in progress..."
123-
sleep 30
124-
done
125-
xcrun stapler staple "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
126-
rm "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg"
127107
mv "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg"
108+
# DISABLED UNTIL WE HAVE A NEW APPLE DEVELOPER ACCOUNT
109+
# - name: Notarize dmg and pkg installer
110+
# if: matrix.os == 'macos-latest' && github.ref == 'refs/heads/main'
111+
# shell: bash
112+
# run: |
113+
# REQUEST_UUID_DMG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "W2PU6LW5U5" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg" | grep RequestUUID | awk '{print $3}')
114+
# while xcrun altool --notarization-info "$REQUEST_UUID_DMG" -u ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} -p ${{ secrets.OSX_NOTARIZATION_APP_PWD }} | grep "Status: in progress" > /dev/null; do
115+
# echo "Verification in progress..."
116+
# sleep 30
117+
# done
118+
# xcrun stapler staple "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
119+
# spctl -vvv --assess --type exec build/distribution/JabRef.app
120+
# codesign -vvv --deep --strict "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
121+
# codesign -dvv "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
122+
# REQUEST_UUID_PKG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "W2PU6LW5U5" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg" | grep RequestUUID | awk '{print $3}')
123+
# while xcrun altool --notarization-info "$REQUEST_UUID_PKG" -u ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} -p ${{ secrets.OSX_NOTARIZATION_APP_PWD }} | grep "Status: in progress" > /dev/null; do
124+
# echo "Verification in progress..."
125+
# sleep 30
126+
# done
127+
# xcrun stapler staple "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
128+
# rm "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg"
128129
- name: Package application image
129130
shell: bash
130131
run: ${{ matrix.archivePortable }}

‎.github/workflows/gource.yml

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@@ -0,0 +1,55 @@
1+
name: Gource
2+
3+
on:
4+
push:
5+
branches:
6+
- gource
7+
schedule:
8+
- cron: '15 3 1 1,4,7,10 *'
9+
10+
jobs:
11+
action:
12+
runs-on: ubuntu-latest
13+
steps:
14+
- name: 'Checkout'
15+
uses: actions/checkout@v2
16+
with:
17+
fetch-depth: 0
18+
- name: Determine dates
19+
id: dates
20+
run: |
21+
echo ::set-output name=start_date::`date -d "$(date +%Y-%m-01) -3 months" +%Y-%m-%d`
22+
echo ::set-output name=stop_date::`date -d "$(date +%Y-%m-01) -1 day" +%Y-%m-%d`
23+
echo ::set-output name=quarter::`date -d "$(date +%Y-%m-01) -1 day" +%Y`-Q$(( ((`date -d "$(date +%Y-%m-01) -1 day" +%m`)-1)/3+1 ))
24+
- name: 'Development history of last quarter'
25+
uses: nbprojekt/gource-action@v1
26+
with:
27+
gource_title: 'JabRef | more information at contribute.jabref.org'
28+
logo_url: 'https://www.jabref.org/img/JabRef-icon-256.png'
29+
# 5s * 365 / 4 = 7.5min
30+
gource_seconds_per_day: 5
31+
gource_start_date: ${{ steps.dates.outputs.start_date }}
32+
gource_stop_date: ${{ steps.dates.outputs.stop_date }}
33+
gource_file_filter: csl$
34+
- name: 'Store video'
35+
run: |
36+
mkdir gource-videos
37+
mv ./gource/gource.mp4 ./gource-videos/jabref-${{ steps.dates.outputs.quarter }}.mp4
38+
- name: 'Complete development history'
39+
uses: nbprojekt/gource-action@v1
40+
with:
41+
gource_title: 'JabRef | more information at contribute.jabref.org'
42+
logo_url: 'https://www.jabref.org/img/JabRef-icon-256.png'
43+
# 0.01 leads to a 45 second video for the complete history until end of 2020
44+
# 0.1 leads to a 8 minute video
45+
gource_seconds_per_day: 0.1
46+
gource_file_filter: csl$
47+
- name: 'Store video'
48+
run: |
49+
mv gource/gource.mp4 gource-videos/jabref-complete.mp4
50+
- name: 'Upload gource video'
51+
uses: actions/upload-artifact@v2
52+
with:
53+
name: Gource
54+
path: ./gource-videos/
55+
retention-days: 80

‎.github/workflows/refresh-csl-subtrees.yml

+2-2
Original file line numberDiff line numberDiff line change
@@ -15,11 +15,11 @@ jobs:
1515
- name: Checkout source
1616
uses: actions/checkout@v2
1717
with:
18-
ref: master
18+
ref: main
1919
fetch-depth: 0
2020
- name: Initialize git
2121
run: |
22-
git checkout master
22+
git checkout main
2323
git config --local core.editor /usr/bin/cat
2424
git config user.name "github actions"
2525
git config user.email "[email protected]"

‎.github/workflows/refresh-journal-lists.yml

+1-1
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@ jobs:
1212
- name: Fetch all history for all tags and branches
1313
uses: actions/checkout@v2
1414
with:
15-
ref: master
15+
ref: main
1616
persist-credentials: false
1717
fetch-depth: 0
1818
- name: Set up JDK

‎.github/workflows/tests-fetchers.yml

+1-1
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@ name: Fetcher Tests
33
on:
44
push:
55
branches:
6-
- master
6+
- main
77
paths:
88
- 'src/main/java/org/jabref/logic/importer/fetcher/**'
99
- 'src/test/java/org/jabref/logic/importer/fetcher/**'

‎.github/workflows/update-gradle-wrapper.yml

+18
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@@ -0,0 +1,18 @@
1+
name: Update Gradle Wrapper
2+
3+
on:
4+
schedule:
5+
- cron: "0 5 * * 1"
6+
7+
jobs:
8+
update-gradle-wrapper:
9+
runs-on: ubuntu-latest
10+
11+
steps:
12+
- uses: actions/checkout@v2
13+
14+
- name: Update Gradle Wrapper
15+
uses: gradle-update/update-gradle-wrapper-action@v1
16+
with:
17+
labels: dependencies
18+
repo-token: ${{ secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER }}

‎CHANGELOG.md

+9
Original file line numberDiff line numberDiff line change
@@ -19,6 +19,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
1919
- We added keybindings for setting and clearing the read status. [#7264](https://github.com/JabRef/jabref/issues/7264)
2020
- We added two new fields to track the creation and most recent modification date and time for each entry. [koppor#130](https://github.com/koppor/jabref/issues/130)
2121
- We added a feature that allows the user to copy highlighted text in the preview window. [#6962](https://github.com/JabRef/jabref/issues/6962)
22+
- We added a feature that allows you to create new BibEntry via paste arxivId [#2292](https://github.com/JabRef/jabref/issues/2292)
2223

2324
### Changed
2425

@@ -35,6 +36,10 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
3536

3637
### Fixed
3738

39+
- We fixed an issue where the table column sort order was not properly stored and resulted in unsorted eports [#7524](https://github.com/JabRef/jabref/issues/7524)
40+
- We fixed an issue where the value of the field `school` or `institution` would be printed twice in the HTML Export [forum#2634](https://discourse.jabref.org/t/problem-with-exporting-techreport-phdthesis-mastersthesis-to-html/2634)
41+
- We fixed an issue preventing to connect to a shared database. [#7570](https://github.com/JabRef/jabref/pull/7570)
42+
- We fixed an issue preventing files from being dragged & dropped into an empty library. [#6851](https://github.com/JabRef/jabref/issues/6851)
3843
- We fixed an issue where double-click onto PDF in file list under the 'General' tab section should just open the file. [#7465](https://github.com/JabRef/jabref/issues/7465)
3944
- We fixed an issue where the dark theme did not extend to a group's custom color picker. [#7481](https://github.com/JabRef/jabref/issues/7481)
4045
- We fixed an issue where choosing the fields on which autocompletion should not work in "Entry editor" preferences had no effect. [#7320](https://github.com/JabRef/jabref/issues/7320)
@@ -54,6 +59,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
5459
- We fixed an issue where the password for a shared SQL database was only remembered if it was the same as the username [#6869](https://github.com/JabRef/jabref/issues/6869)
5560
- We fixed an issue where some custom exports did not use the new authors formatter and therefore did not export authors correctly [#7356](https://github.com/JabRef/jabref/issues/7356)
5661
- We fixed an issue where alt+keyboard shortcuts do not work [#6994](https://github.com/JabRef/jabref/issues/6994)
62+
- We fixed an issue about the file link editor did not allow to change the file name according to the default pattern after changing an entry. [#7525](https://github.com/JabRef/jabref/issues/7525)
5763
- We fixed an issue where the file path is invisible in dark theme. [#7382](https://github.com/JabRef/jabref/issues/7382)
5864
- We fixed an issue where the secondary sorting is not working for some special fields. [#7015](https://github.com/JabRef/jabref/issues/7015)
5965
- We fixed an issue where changing the font size makes the font size field too small. [#7085](https://github.com/JabRef/jabref/issues/7085)
@@ -64,7 +70,10 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
6470
- We fixed an issue where drag and drop of bib files for opening resulted in uncaught exceptions [#7464](https://github.com/JabRef/jabref/issues/7464)
6571
- We fixed an issue where columns shrink in width when we try to enlarge JabRef window. [#6818](https://github.com/JabRef/jabref/issues/6818)
6672
- We fixed an issue where Content selector does not seem to work for custom fields. [#6819](https://github.com/JabRef/jabref/issues/6819)
73+
- We fixed an issue where font size of the preferences dialog does not update with the rest of the GUI. [#7416](https://github.com/JabRef/jabref/issues/7416)
6774
- We fixed an issue in which a linked online file consisting of a web page was saved as an invalid pdf file upon being downloaded. The user is now notified when downloading a linked file results in an HTML file. [#7452](https://github.com/JabRef/jabref/issues/7452)
75+
- We fixed an issue where opening BibTex file (doubleclick) from Folder with spaces not working. [#6487](https://github.com/JabRef/jabref/issues/6487)
76+
- We fixed an issue with saving large `.bib` files [#7265](https://github.com/JabRef/jabref/issues/7265)
6877

6978
### Removed
7079

‎GitVersion.yml

+2-2
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@ assembly-informational-format: '{major}.{minor}{PreReleaseTagWithDash}--{CommitD
33
mode: ContinuousDeployment
44

55
branches:
6-
master:
7-
regex: ^master
6+
main:
7+
regex: ^main
88
tag: ''
99
pre-release-weight: 0 # 0 after stable release, 15000 before alpha release, 30000 before beta release, 50000 before stable release

‎build.gradle

+11-10
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ plugins {
1414
id 'com.github.ben-manes.versions' version '0.38.0'
1515
id 'org.javamodularity.moduleplugin' version '1.7.0'
1616
id 'org.openjfx.javafxplugin' version '0.0.9'
17-
id 'org.beryx.jlink' version '2.23.3'
17+
id 'org.beryx.jlink' version '2.23.5'
1818
// nicer test outputs during running and completion
1919
// Homepage: https://github.com/radarsh/gradle-test-logger-plugin
2020
id 'com.adarshr.test-logger' version '2.1.1'
@@ -101,14 +101,14 @@ dependencies {
101101
// Include all jar-files in the 'lib' folder as dependencies
102102
implementation fileTree(dir: 'lib', includes: ['*.jar'])
103103

104-
implementation 'org.apache.pdfbox:pdfbox:2.0.22'
105-
implementation 'org.apache.pdfbox:fontbox:2.0.22'
106-
implementation 'org.apache.pdfbox:xmpbox:2.0.22'
104+
implementation 'org.apache.pdfbox:pdfbox:2.0.23'
105+
implementation 'org.apache.pdfbox:fontbox:2.0.23'
106+
implementation 'org.apache.pdfbox:xmpbox:2.0.23'
107107

108108
implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.8'
109109
implementation 'com.h2database:h2-mvstore:1.4.200'
110110

111-
implementation group: 'org.apache.tika', name: 'tika-core', version: '1.25'
111+
implementation group: 'org.apache.tika', name: 'tika-core', version: '1.26'
112112

113113
// required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
114114
implementation 'org.bouncycastle:bcprov-jdk15on:1.68'
@@ -131,7 +131,7 @@ dependencies {
131131
exclude group: 'org.apache.lucene', module: 'lucene-sandbox'
132132
}
133133

134-
implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '5.10.0.202012080955-r'
134+
implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '5.11.0.202103091610-r'
135135

136136
implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.12.2'
137137
implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.12.2'
@@ -145,7 +145,7 @@ dependencies {
145145
exclude module: 'oraclepki'
146146
}
147147

148-
implementation ('com.google.guava:guava:30.1-jre') {
148+
implementation ('com.google.guava:guava:30.1.1-jre') {
149149
// TODO: Remove this as soon as https://github.com/google/guava/issues/2960 is fixed
150150
exclude module: "jsr305"
151151
}
@@ -159,7 +159,7 @@ dependencies {
159159
implementation 'de.saxsys:mvvmfx:1.8.0'
160160
implementation 'com.tobiasdiez:easybind:2.1.0'
161161
implementation 'org.fxmisc.flowless:flowless:0.6.3'
162-
implementation 'org.fxmisc.richtext:richtextfx:0.10.4'
162+
implementation 'org.fxmisc.richtext:richtextfx:0.10.6'
163163
implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
164164
implementation 'com.jfoenix:jfoenix:9.0.10'
165165
implementation 'org.controlsfx:controlsfx:11.1.0'
@@ -196,7 +196,7 @@ dependencies {
196196
implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.62.2'
197197
implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.62.2'
198198

199-
testImplementation 'io.github.classgraph:classgraph:4.8.102'
199+
testImplementation 'io.github.classgraph:classgraph:4.8.104'
200200
testImplementation 'org.junit.jupiter:junit-jupiter:5.7.1'
201201
testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.7.1'
202202
testImplementation 'org.junit.platform:junit-platform-launcher:1.7.1'
@@ -213,7 +213,7 @@ dependencies {
213213
testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
214214
testImplementation "org.hamcrest:hamcrest-library:2.2"
215215

216-
checkstyle 'com.puppycrawl.tools:checkstyle:8.41'
216+
checkstyle 'com.puppycrawl.tools:checkstyle:8.41.1'
217217
xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.3'
218218
}
219219

@@ -601,6 +601,7 @@ jlink {
601601
uses 'com.airhacks.afterburner.injection.PresenterFactory'
602602
uses 'org.apache.logging.log4j.spi.Provider'
603603
uses 'org.mariadb.jdbc.credential.CredentialPlugin'
604+
uses 'org.mariadb.jdbc.authentication.AuthenticationPlugin'
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uses 'org.mariadb.jdbc.tls.TlsSocketPlugin'
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uses 'org.mariadb.jdbc.LocalInfileInterceptor'
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uses 'org.eclipse.jgit.transport.SshSessionFactory';

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