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* upstream/main: (30 commits)
  New translations JabRef_en.properties (German) (JabRef#9336)
  Fix Abbreviation for Escaped Ampersand (JabRef#9288)
  Fix font size preference not updating in preference dialog 8386 (JabRef#9287)
  New Crowdin updates (JabRef#9333)
  Refresh example styles
  Squashed 'buildres/csl/csl-styles/' changes from 4eee79a..13fd98e
  Bump unirest-java from 3.13.11 to 3.13.12 (JabRef#9330)
  Bump checkstyle from 10.3.4 to 10.4 (JabRef#9331)
  Bump gittools/actions from 0.9.14 to 0.9.15 (JabRef#9332)
  Group context menu presents relevant options depending on number of subgroups (JabRef#9286)
  Removed BibTeX file type and included HTML and Markdown types (JabRef#9318)
  Fix issue: Auto-linking files with safe character replacements JabRef#9267 (JabRef#9316)
  Fix for issue 8806: Button highlights doesn't respect rounded corners (JabRef#9320)
  New Crowdin updates (JabRef#9324)
  Update CHANGELOG.md
  Try to relocate listener binding (JabRef#9238)
  Changed the messages after importing unlinked local files to past passive tense. (JabRef#9308)
  Changed the color of found text from red to high contrast  (JabRef#9315)
  New Crowdin updates (JabRef#9317)
  Add skips for MacOS X build (JabRef#9305)
  ...
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Siedlerchr committed Nov 3, 2022
2 parents f00b843 + 1face3f commit f584ea3
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23 changes: 23 additions & 0 deletions .github/workflows/GreetingFirstTimeCodeContribution.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
name: GreetingFirstTimeCodeContribution

on:
issues:
types:
- labeled

jobs:
GreetingFirstTimeCodeContribution:
if: ${{ github.event.label.name == 'FirstTimeCodeContribution' }}
runs-on: ubuntu-latest
permissions:
issues: write
steps:
- name: GreetingFirstTimeCodeContribution
uses: peter-evans/create-or-update-comment@v2
with:
repo-token: ${{ secrets.GITHUB_TOKEN }}
issue-number: ${{ github.event.issue.number }}
body: |
As a general advice for newcomers: check out [Contributing](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md) for a start. Also, [guidelines for setting up a local workspace](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace) is worth having a look at.
Feel free to ask here at GitHub, if you have any issue related questions. If you have questions about how to setup your workspace use JabRef's [Gitter](https://gitter.im/JabRef/jabref) chat. Try to open a (draft) pull-request early on, so that people can see you are working on the issue and so that they can see the direction the pull request is heading towards. This way, you will likely receive valuable feedback.
4 changes: 2 additions & 2 deletions .github/workflows/automerge.yml
Original file line number Diff line number Diff line change
Expand Up @@ -16,12 +16,12 @@ jobs:
env:
GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
- name: Auto approve
uses: hmarr/auto-approve-action@v3.0.0
uses: hmarr/auto-approve-action@v3.1.0
if: steps.waitforstatuschecks.outputs.status == 'success'
with:
github-token: "${{ secrets.GITHUB_TOKEN }}"
- name: Merge pull requests
uses: pascalgn/[email protected].3
uses: pascalgn/[email protected].5
if: steps.waitforstatuschecks.outputs.status == 'success'
env:
MERGE_METHOD: "merge"
Expand Down
29 changes: 21 additions & 8 deletions .github/workflows/deployment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -51,45 +51,58 @@ jobs:
runs-on: ${{ matrix.os }}
name: Create installer and portable version for ${{ matrix.displayName }}
steps:
- name: Check secrets presence
id: checksecrets
shell: bash
run: |
if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
echo ::set-output name=secretspresent::false
else
echo ::set-output name=secretspresent::true
fi
env:
BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
- name: Fetch all history for all tags and branches
uses: actions/checkout@v3
with:
fetch-depth: 0
- name: Install GitVersion
uses: gittools/actions/gitversion/[email protected].14
uses: gittools/actions/gitversion/[email protected].15
with:
versionSpec: "5.x"
- name: Run GitVersion
id: gitversion
uses: gittools/actions/gitversion/[email protected].14
uses: gittools/actions/gitversion/[email protected].15
- name: Set up JDK
uses: actions/setup-java@v3
with:
java-version: 18
distribution: 'temurin'
cache: 'gradle'
- name: Setup OSX key chain on OSX
if: matrix.os == 'macos-latest'
if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
uses: apple-actions/import-codesign-certs@v1
with:
p12-file-base64: ${{ secrets.OSX_SIGNING_CERT }}
p12-password: ${{ secrets.OSX_CERT_PWD }}
keychain-password: jabref
- name: Setup OSX key chain on OSX for app id cert
if: matrix.os == 'macos-latest'
if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
uses: apple-actions/import-codesign-certs@v1
with:
p12-file-base64: ${{ secrets.OSX_SIGNING_CERT_APPLICATION }}
p12-password: ${{ secrets.OSX_CERT_PWD }}
create-keychain: false
keychain-password: jabref
- name: Build runtime image
if: (matrix.os != 'macos-latest') || steps.checksecrets.outputs.secretspresent
run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
- name: Build installer
if: (matrix.os != 'macos-latest') || steps.checksecrets.outputs.secretspresent
run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
shell: bash
- name: Resign app image for OSX and build dmg
if: matrix.os == 'macos-latest'
if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
shell: bash
run: |
codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: JabRef e.V. (6792V39SK3)" build/distribution/JabRef.app/Contents/runtime/Contents/MacOS/libjli.dylib
Expand All @@ -100,7 +113,7 @@ jobs:
jpackage --type pkg --dest build/distribution --name JabRef --mac-package-identifier JabRef --app-version "${{ 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 }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
productsign --sign "Developer ID Installer: JabRef e.V. (6792V39SK3)" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
- name: Notarize dmg and pkg installer
if: matrix.os == 'macos-latest' && startsWith(github.ref, 'refs/tags/')
if: (matrix.os == 'macos-latest') && startsWith(github.ref, 'refs/tags/') && steps.checksecrets.outputs.secretspresent
shell: bash
run: |
REQUEST_UUID_DMG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "6792V39SK3" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg" | grep RequestUUID | awk '{print $3}')
Expand Down Expand Up @@ -157,12 +170,12 @@ jobs:
- name: Fetch all history for all tags and branches
run: git fetch --prune --unshallow
- name: Install GitVersion
uses: gittools/actions/gitversion/[email protected].14
uses: gittools/actions/gitversion/[email protected].15
with:
versionSpec: '5.x'
- name: Run GitVersion
id: gitversion
uses: gittools/actions/gitversion/[email protected].14
uses: gittools/actions/gitversion/[email protected].15
- name: Get linux binaries
uses: actions/download-artifact@master
with:
Expand Down
19 changes: 0 additions & 19 deletions .github/workflows/greetings.yml

This file was deleted.

6 changes: 2 additions & 4 deletions .github/workflows/tests-fetchers.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,8 @@ on:
- 'build.gradle'
pull_request:
paths:
- 'src/main/java/org/jabref/logic/**'
- 'src/test/java/org/jabref/logic/**'
- 'src/main/java/org/jabref/model/**'
- 'src/test/java/org/jabref/model/**'
- 'src/main/java/org/jabref/logic/importer/fetcher/**'
- 'src/test/java/org/jabref/logic/importer/fetcher/**'
- '.github/workflows/tests-fetchers.yml'
- 'build.gradle'
schedule:
Expand Down
11 changes: 11 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,13 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- We fixed an issue where a message about changed metadata would occur on saving although nothing changed. [#9159](https://github.com/JabRef/jabref/issues/9159)
- When adding or editing a subgroup it is placed w.r.t. to alphabetical ordering rather than at the end. [koppor#577](https://github.com/koppor/jabref/issues/577)
- We modified the Directory of Open Access Books (DOAB) fetcher so that it will now also fetch the ISBN when possible. [#8708](https://github.com/JabRef/jabref/issues/8708)
- Groups context menu now shows appropriate options depending on number of subgroups. [koppor#579](https://github.com/koppor/jabref/issues/579)
- We changed the color of found text from red to high-contrast colors (background: yellow; font color: purple). [koppor#552](https://github.com/koppor/jabref/issues/552)
- We modified the "Delete file" dialog and add the full file path to the dialog text. The file path in the title was changed to file name only. [koppor#534](https://github.com/koppor/jabref/issues/534)
- Download from URL now automatically fills with URL from clipboard. [koppor#535](https://github.com/koppor/jabref/issues/535)
- We added HTML and Markdown files to Find Unlinked Files and removed BibTeX.[koppor#547](https://github.com/koppor/jabref/issues/547)
- We changed the messages after importing unlinked local files to past tense. [koppor#548](https://github.com/koppor/jabref/issues/548)
- We fixed an issue where the wrong icon for a successful import of a bib entry was shown [#9308](https://github.com/JabRef/jabref/pull/9308)

### Fixed

Expand All @@ -59,6 +66,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- We fixed a performance regression when opening large libraries [#9041](https://github.com/JabRef/jabref/issues/9041)
- We fixed a bug where spaces are trimmed when highlighting differences in the Entries merge dialog. [koppor#371](https://github.com/koppor/jabref/issues/371)
- We fixed some visual glitches with the linked files editor field in the entry editor and increased its height. [#8823](https://github.com/JabRef/jabref/issues/8823)
- We fixed some visual inconsistencies (round corners of highlighted buttons). [#8806](https://github.com/JabRef/jabref/issues/8806)
- We fixed several bugs regarding the manual and the autosave of library files that sometimes lead to exceptions or data loss. [#9067](https://github.com/JabRef/jabref/pull/9067), [#8448](https://github.com/JabRef/jabref/issues/8484), [#8746](https://github.com/JabRef/jabref/issues/8746), [#6684](https://github.com/JabRef/jabref/issues/6684), [#6644](https://github.com/JabRef/jabref/issues/6644), [#6102](https://github.com/JabRef/jabref/issues/6102), [#6002](https://github.com/JabRef/jabref/issues/6000)
- We fixed an issue where applied save actions on saving the library file would lead to the dialog "The library has been modified by another program" popping up [#4877](https://github.com/JabRef/jabref/issues/4877)
- We fixed issues with save actions not correctly loaded when opening the library. [#9122](https://github.com/JabRef/jabref/pull/9122)
Expand All @@ -73,6 +81,9 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- We fixed an issue where hitting enter on the search field within the preferences dialog closed the dialog. [koppor#630](https://github.com/koppor/jabref/issues/630)
- We fixed a typo within a connection error message. [koppor#625](https://github.com/koppor/jabref/issues/625)
- We fixed an issue where the 'close dialog' key binding was not closing the Preferences dialog. [#8888](https://github.com/jabref/jabref/issues/8888)
- We fixed an issue where journal abbreviations would not abbreviate journal titles with escaped ampersands (\\&). [#8948](https://github.com/JabRef/jabref/issues/8948)
- We fixed an issue where font size preferences did not apply correctly to preference dialog window and the menu bar. [#8386](https://github.com/JabRef/jabref/issues/8386) and [#9279](https://github.com/JabRef/jabref/issues/9279)
- We fixed an issue when using an unsafe character in the citation key, the auto-linking feature fails to link files. [#9267](https://github.com/JabRef/jabref/issues/9267)

### Removed

Expand Down
16 changes: 8 additions & 8 deletions build.gradle
Original file line number Diff line number Diff line change
Expand Up @@ -115,11 +115,11 @@ dependencies {
implementation 'org.apache.pdfbox:fontbox:3.0.0-RC1'
implementation 'org.apache.pdfbox:xmpbox:3.0.0-RC1'

implementation 'org.apache.lucene:lucene-core:9.4.0'
implementation 'org.apache.lucene:lucene-queryparser:9.4.0'
implementation 'org.apache.lucene:lucene-queries:9.4.0'
implementation 'org.apache.lucene:lucene-analysis-common:9.4.0'
implementation 'org.apache.lucene:lucene-highlighter:9.4.0'
implementation 'org.apache.lucene:lucene-core:9.4.1'
implementation 'org.apache.lucene:lucene-queryparser:9.4.1'
implementation 'org.apache.lucene:lucene-queries:9.4.1'
implementation 'org.apache.lucene:lucene-analysis-common:9.4.1'
implementation 'org.apache.lucene:lucene-highlighter:9.4.1'

implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.9.0'
implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.12.0'
Expand Down Expand Up @@ -176,7 +176,7 @@ dependencies {
implementation 'org.controlsfx:controlsfx:11.1.2'

implementation 'org.jsoup:jsoup:1.15.3'
implementation 'com.konghq:unirest-java:3.13.11'
implementation 'com.konghq:unirest-java:3.13.12'

implementation 'org.slf4j:slf4j-api:2.0.3'
implementation "org.tinylog:tinylog-api:2.5.0"
Expand Down Expand Up @@ -208,7 +208,7 @@ dependencies {
testImplementation 'org.junit.jupiter:junit-jupiter:5.9.1'
testImplementation 'org.junit.platform:junit-platform-launcher:1.9.1'

testImplementation 'org.mockito:mockito-core:4.8.0'
testImplementation 'org.mockito:mockito-core:4.8.1'
testImplementation 'org.xmlunit:xmlunit-core:2.9.0'
testImplementation 'org.xmlunit:xmlunit-matchers:2.9.0'
testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.0.0'
Expand All @@ -217,7 +217,7 @@ dependencies {
testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
testImplementation "org.hamcrest:hamcrest-library:2.2"

checkstyle 'com.puppycrawl.tools:checkstyle:10.3.4'
checkstyle 'com.puppycrawl.tools:checkstyle:10.4'
// xjc needs the runtime as well for the ant task, otherwise it fails
xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'
Expand Down
4 changes: 2 additions & 2 deletions buildres/csl/csl-styles/Gemfile.lock
Original file line number Diff line number Diff line change
Expand Up @@ -65,10 +65,10 @@ GEM
mini_portile2 (2.8.0)
multipart-post (2.1.1)
namae (1.1.1)
nokogiri (1.13.6)
nokogiri (1.13.9)
mini_portile2 (~> 2.8.0)
racc (~> 1.4)
nokogiri (1.13.6-x64-mingw32)
nokogiri (1.13.9-x64-mingw32)
racc (~> 1.4)
octokit (4.21.0)
faraday (>= 0.9)
Expand Down
139 changes: 139 additions & 0 deletions buildres/csl/csl-styles/arcadia-science.csl
Original file line number Diff line number Diff line change
@@ -0,0 +1,139 @@
<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="never" default-locale="en-US">
<!-- This style was edited with the Visual CSL Editor (https://editor.citationstyles.org/visualEditor/) -->
<info>
<title>Arcadia Science</title>
<id>http://www.zotero.org/styles/arcadia-science</id>
<link rel="self" href="http://www.zotero.org/styles/arcadia-science"/>
<link rel="template" href="http://www.zotero.org/styles/elife"/>
<link rel="documentation" href="https://research.arcadiascience.com/pub/perspective-publishing-round-one"/>
<author>
<name>Feridun Mert Celebi</name>
<email>[email protected]</email>
</author>
<author>
<name>Megan Hochstrasser</name>
<email>[email protected] </email>
</author>
<category citation-format="author-date"/>
<summary>Arcadia's CSL style is a simplified version of the eLife CSL style that can be found on https://github.com/citation-style-language/styles/blob/master/elife.csl and https://citationstyles.org/</summary>
<updated>2022-06-27T17:41:25+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
<macro name="author">
<names variable="author">
<name delimiter-precedes-last="always" initialize-with="" name-as-sort-order="all" sort-separator=" "/>
<label prefix=", "/>
<substitute>
<names variable="editor"/>
<names variable="translator"/>
<text macro="title"/>
</substitute>
</names>
</macro>
<macro name="author-short">
<names variable="author">
<name form="short" and="text" delimiter=", " initialize-with=". "/>
<substitute>
<names variable="editor"/>
<names variable="translator"/>
<choose>
<if type="bill book graphic legal_case legislation motion_picture report song" match="any">
<text variable="title" form="short" font-style="italic"/>
</if>
<else>
<text variable="title" form="short" quotes="true"/>
</else>
</choose>
</substitute>
</names>
</macro>
<macro name="access">
<choose>
<if variable="DOI">
<text variable="DOI" prefix="https://doi.org/"/>
</if>
<else-if variable="URL">
<text variable="URL"/>
</else-if>
</choose>
</macro>
<macro name="title">
<choose>
<if type="report thesis" match="any">
<text variable="title"/>
<group prefix=" (" suffix=")" delimiter=" ">
<text variable="genre"/>
<text variable="number" prefix="No. "/>
</group>
</if>
<else-if type="bill book graphic legal_case legislation motion_picture report song speech" match="any">
<text variable="title"/>
<text macro="edition" prefix=", "/>
</else-if>
<else-if type="webpage">
<text variable="title"/>
</else-if>
<else>
<text variable="title"/>
</else>
</choose>
</macro>
<macro name="issued">
<choose>
<if variable="issued">
<date variable="issued">
<date-part name="year"/>
</date>
</if>
<else>
<text term="no date" form="short"/>
</else>
</choose>
</macro>
<macro name="edition">
<group delimiter=" ">
<choose>
<if is-numeric="edition">
<number variable="edition" form="ordinal"/>
</if>
<else>
<text variable="edition" suffix="."/>
</else>
</choose>
<text value="ed"/>
</group>
</macro>
<citation et-al-min="3" et-al-use-first="1" disambiguate-add-givenname="true" disambiguate-add-year-suffix="true" collapse="year" cite-group-delimiter=", ">
<sort>
<key macro="author"/>
<key macro="issued" sort="descending"/>
</sort>
<layout prefix="(" suffix=")" delimiter="; ">
<group delimiter=", ">
<text macro="author-short"/>
<text macro="issued"/>
<group delimiter=" ">
<label variable="locator" form="short"/>
<text variable="locator"/>
</group>
</group>
</layout>
</citation>
<bibliography hanging-indent="true" entry-spacing="0" line-spacing="1">
<sort>
<key macro="author"/>
<key macro="issued" sort="descending"/>
</sort>
<layout>
<group>
<text macro="author" suffix="."/>
<text macro="issued" strip-periods="false" prefix=" (" suffix=")"/>
<group prefix=". ">
<text macro="title"/>
</group>
</group>
<text macro="access" prefix=". "/>
</layout>
</bibliography>
</style>
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