Merge branch 'main' into restapi

# Conflicts:
#	src/main/java/org/jabref/logic/layout/format/MarkdownFormatter.java

.gitignore

@@ -10,6 +10,9 @@ src-gen/
 docs/book.pdf
 docs/_book/
 
+# Jekyll for docs/
+docs/Gemfile.lock
+
 # ignore the generated markdown file if the user forgets to delete it
 status.md
 

CHANGELOG.md

@@ -12,7 +12,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 ### Added
 
 - We added a field showing the BibTeX/biblatex source for added and deleted entries in the "External Changes Resolver" dialog. [#9509](https://github.com/JabRef/jabref/issues/9509)
-- We added a search history list in the search field's right click menu [#7906](https://github.com/JabRef/jabref/issues/7906)
+- We added a search history list in the search field's right click menu. [#7906](https://github.com/JabRef/jabref/issues/7906)
 - We added a full text fetcher for IACR eprints. [#9651](https://github.com/JabRef/jabref/pull/9651)
 - We added "Attach file from URL" to right-click context menu to download and store a file with the reference library. [#9646](https://github.com/JabRef/jabref/issues/9646)
 - We enabled updating an existing entry with data from InspireHEP. [#9351](https://github.com/JabRef/jabref/issues/9351)
@@ -24,34 +24,41 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 ### Changed
 
 - 'Get full text' now also checks the file url. [#568](https://github.com/koppor/jabref/issues/568)
-- `log.txt` now contains an entry if a BibTeX entry could not be parsed.
 - JabRef writes a new backup file only if there is a change. Before, JabRef created a backup upon start. [#9679](https://github.com/JabRef/jabref/pull/9679)
 - We modified the `Add Group` dialog to use the most recently selected group hierarchical context. [#9141](https://github.com/JabRef/jabref/issues/9141)
 - We refined the 'main directory not found' error message. [#9625](https://github.com/JabRef/jabref/pull/9625)
 - JabRef writes a new backup file only if there is a change. Before, JabRef created a backup upon start. [#9679](https://github.com/JabRef/jabref/pull/9679)
 - Backups of libraries are not stored per JabRef version, but collected together.
 - We streamlined the paths for logs and backups: The parent path fragement is always `logs` or `backups`.
+- `log.txt` now contains an entry if a BibTeX entry could not be parsed.
 - `log.txt` now contains debug messages. Debugging needs to be enabled explicitly. [#9678](https://github.com/JabRef/jabref/pull/9678)
 - `log.txt` does not contain entries for non-found files during PDF indexing. [#9678](https://github.com/JabRef/jabref/pull/9678)
 - We improved the Medline importer to correctly import ISO dates for `revised`. [#9536](https://github.com/JabRef/jabref/issues/9536)
-
+- To avoid cluttering of the directory, We always delete the `.sav` file upon successful write. [#9675](https://github.com/JabRef/jabref/pull/9675)
+- We improved the unlinking/deletion of multiple linked files of an entry using the <kbd>Delete</kbd> key. [#9473](https://github.com/JabRef/jabref/issues/9473)
 
 
 ### Fixed
 
-- We fixed an issue where the browser import would add ' characters before the BibTeX entry on Linux [#9588](https://github.com/JabRef/jabref/issues/9588)
-- We fixed an issue where searching for a specific term with the DOAB fetcher lead to an exception [#9571](https://github.com/JabRef/jabref/issues/9571)
-- We fixed an issue where the "Import" -> "Library to import to" did not show the correct library name if two opened libraries had the same suffix [#9567](https://github.com/JabRef/jabref/issues/9567)
-- We fixed an issue where the rpm-Version of JabRef could not be properly uninstalled and reinstalled [#9558](https://github.com/JabRef/jabref/issues/9558), [#9603](https://github.com/JabRef/jabref/issues/9603)
-- We fixed an issue where the command line export using `--exportMatches` flag does not create an output bib file [#9581](https://github.com/JabRef/jabref/issues/9581)
-- We fixed an issue where custom field in the custom entry types could not be set to mulitline [#9609](https://github.com/JabRef/jabref/issues/9609)
-- We fixed an issue where the Office XML exporter did not resolve BibTeX-Strings when exporting entries [forum#3741](https://discourse.jabref.org/t/exporting-bibtex-constant-strings-to-ms-office-2007-xml/3741)
+- We fixed an issue where the browser import would add ' characters before the BibTeX entry on Linux. [#9588](https://github.com/JabRef/jabref/issues/9588)
+- We fixed an issue where searching for a specific term with the DOAB fetcher lead to an exception. [#9571](https://github.com/JabRef/jabref/issues/9571)
+- We fixed an issue where the "Import" -> "Library to import to" did not show the correct library name if two opened libraries had the same suffix. [#9567](https://github.com/JabRef/jabref/issues/9567)
+- We fixed an issue where the rpm-Version of JabRef could not be properly uninstalled and reinstalled. [#9558](https://github.com/JabRef/jabref/issues/9558), [#9603](https://github.com/JabRef/jabref/issues/9603)
+- We fixed an issue where the command line export using `--exportMatches` flag does not create an output bib file. [#9581](https://github.com/JabRef/jabref/issues/9581)
+- We fixed an issue where custom field in the custom entry types could not be set to mulitline. [#9609](https://github.com/JabRef/jabref/issues/9609)
+- We fixed an issue where the Office XML exporter did not resolve BibTeX-Strings when exporting entries. [forum#3741](https://discourse.jabref.org/t/exporting-bibtex-constant-strings-to-ms-office-2007-xml/3741)
+- We fixed an issue where the Merge Entries Toolbar configuration was not saved after hitting 'Merge Entries' button. [#9091](https://github.com/JabRef/jabref/issues/9091)
+- We fixed an issue where the password is saved locally if user wants to use proxy with authentication. [#8055](https://github.com/JabRef/jabref/issues/8055)
 - JabRef is now more relaxed when parsing field content: In case a field content ended with `\`, the combination `\}` was treated as plain `}`. [#9668](https://github.com/JabRef/jabref/issues/9668)
+- We resolved an issue that cut off the number of group entries when it exceedet four digits. [#8797](https://github.com/JabRef/jabref/issues/8797)
+- We fixed an issue where the Global Search UI preview is still white in dark theme. [#9362](https://github.com/JabRef/jabref/issues/9362)
+- We fixed the double paste issue when <kbd>Cmd</kbd> + <kbd>v</kbd> is pressed on 'New entry from plaintext' dialog. [#9367](https://github.com/JabRef/jabref/issues/9367)
 
 
 ### Removed
 
-- We removed the support of BibTeXML.[#9540](https://github.com/JabRef/jabref/issues/9540)
+- We removed the support of BibTeXML. [#9540](https://github.com/JabRef/jabref/issues/9540)
+- We removed support for Markdown syntax for strikethrough and task lists in comment fields. [#9726](https://github.com/JabRef/jabref/pull/9726)
 
 
 

README.md

@@ -35,7 +35,7 @@ It supports you in every step of your research work.
 
 - Native BibTeX and Biblatex support
 - Cite-as-you-write functionality for external applications such as Emacs, Kile, LyX, Texmaker, TeXstudio, Vim and WinEdt.
-- Format references in one of the many thousand built-in citation styles or create your style
+- Format references using one of thousands of built-in citation styles or create your own style
 - Support for Word and LibreOffice/OpenOffice for inserting and formatting citations
 
 ### Share

build.gradle

@@ -99,7 +99,7 @@ dependencyLocking {
 }
 
 javafx {
- version = "19"
+ version = "20"
  modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
 }
 
@@ -130,14 +130,14 @@ dependencies {
 
  implementation 'commons-cli:commons-cli:1.5.0'
 
- implementation 'org.libreoffice:unoloader:7.5.0'
- implementation 'org.libreoffice:libreoffice:7.5.0'
+ implementation 'org.libreoffice:unoloader:7.5.1'
+ implementation 'org.libreoffice:libreoffice:7.5.1'
 
  implementation 'io.github.java-diff-utils:java-diff-utils:4.12'
  implementation 'info.debatty:java-string-similarity:2.0.0'
 
- antlr4 'org.antlr:antlr4:4.9.3'
- implementation 'org.antlr:antlr4-runtime:4.9.3'
+ antlr4 'org.antlr:antlr4:4.12.0'
+ implementation 'org.antlr:antlr4-runtime:4.12.0'
 
  implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.5.0.202303070854-r'
 
@@ -170,15 +170,15 @@ dependencies {
  implementation 'com.jfoenix:jfoenix:9.0.10'
  implementation 'org.controlsfx:controlsfx:11.1.2'
 
- implementation 'org.jsoup:jsoup:1.15.3'
+ implementation 'org.jsoup:jsoup:1.15.4'
  implementation 'com.konghq:unirest-java:3.14.2'
 
  implementation 'org.slf4j:slf4j-api:2.0.7'
  implementation "org.tinylog:tinylog-api:2.6.1"
  implementation "org.tinylog:slf4j-tinylog:2.6.1"
- implementation "org.tinylog:tinylog-impl:2.6.0"
+ implementation "org.tinylog:tinylog-impl:2.6.1"
 
- implementation 'de.undercouch:citeproc-java:3.0.0-alpha.6'
+ implementation 'de.undercouch:citeproc-java:3.0.0-beta.2'
 
  // Data mapping
  implementation 'jakarta.xml.bind:jakarta.xml.bind-api:4.0.0'
@@ -228,7 +228,7 @@ dependencies {
  testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
  testImplementation "org.hamcrest:hamcrest-library:2.2"
 
- checkstyle 'com.puppycrawl.tools:checkstyle:10.8.1'
+ checkstyle 'com.puppycrawl.tools:checkstyle:10.9.3'
  // 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'

buildres/csl/csl-locales/Gemfile.lock

@@ -62,20 +62,20 @@ GEM
  ruby-progressbar (~> 1.4)
  git_diff (0.4.3)
  hashdiff (0.3.7)
- mini_portile2 (2.8.0)
+ mini_portile2 (2.8.1)
  multipart-post (2.1.1)
  namae (1.1.1)
- nokogiri (1.13.4)
+ nokogiri (1.13.10)
  mini_portile2 (~> 2.8.0)
  racc (~> 1.4)
- nokogiri (1.13.4-x64-mingw32)
+ nokogiri (1.13.10-x64-mingw32)
  racc (~> 1.4)
  octokit (4.21.0)
  faraday (>= 0.9)
  sawyer (~> 0.8.0, >= 0.5.3)
  ostruct (0.5.2)
  public_suffix (4.0.6)
- racc (1.6.0)
+ racc (1.6.2)
  rake (13.0.6)
  reverse_markdown (2.1.1)
  nokogiri

buildres/csl/csl-locales/composer.json

@@ -0,0 +1,19 @@
+{
+ "name": "citation-style-language/locales",
+ "description": "Citation Style Language (CSL) Locales",
+ "type": "library",
+ "license": "CC-BY-SA-3.0",
+ "homepage": "http://citationstyles.org/",
+ "authors": [
+ {
+ "name": "Citation Style Language (CSL) Team",
+ "homepage": "http://citationstyles.org/about/#Credits"
+ }
+ ],
+ "extra": {
+ "branch-alias": {
+ "dev-master": "1.0.x-dev"
+ }
+ },
+ "require": {}
+}

buildres/csl/csl-locales/locales-eu.xml

@@ -4,14 +4,17 @@
  <translator>
  <name>Amaraun</name>
  </translator>
+ <translator>
+ <name>Miren BZ</name>
+ </translator>
  <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
  <updated>2012-07-04T23:31:02+00:00</updated>
  </info>
  <style-options punctuation-in-quote="false"/>
  <date form="text">
  <date-part name="year" suffix="(e)ko "/>
  <date-part name="month" suffix="aren "/>
- <date-part name="day" suffix="a"/>
+ <date-part name="day" suffix="(e)an"/>
  </date>
  <date form="numeric">
  <date-part name="year" suffix="/"/>
@@ -64,7 +67,7 @@
  <term name="edition" form="short">arg.</term>
  <term name="et-al">et al.</term>
  <term name="forthcoming">bidean</term>
- <term name="from">-(e)tik</term>
+ <term name="from">hemendik: </term>
  <term name="ibid">ibíd.</term>
  <term name="in">in</term>
  <term name="in press">moldiztegian</term>
@@ -84,7 +87,7 @@
  </term>
  <term name="retrieved">berreskuratua</term>
  <term name="scale">scale</term>
- <term name="version">version</term>
+ <term name="version">bertsioa</term>
 
  <!-- LONG ITEM TYPE FORMS -->
  <term name="article">preprint</term>
@@ -170,7 +173,7 @@
  <term name="ordinal">.</term>
 
  <!-- LONG ORDINALS -->
- <term name="long-ordinal-01">lehengo</term>
+ <term name="long-ordinal-01">lehenengo</term>
  <term name="long-ordinal-02">bigarren</term>
  <term name="long-ordinal-03">hirugarren</term>
  <term name="long-ordinal-04">laugarren</term>
@@ -291,8 +294,8 @@
  <multiple>bertsoak</multiple>
  </term>
  <term name="volume">
- <single>luburikia</single>
- <multiple>luburukiak</multiple>
+ <single>liburukia</single>
+ <multiple>liburukiak</multiple>
  </term>
 
  <!-- SHORT LOCATOR FORMS -->
@@ -565,23 +568,23 @@
  <term name="editortranslator" form="verb-short">-(e)k arg. eta itzul.</term>
 
  <!-- LONG MONTH FORMS -->
- <term name="month-01">urtarrilak</term>
- <term name="month-02">otsailak</term>
- <term name="month-03">martxoak</term>
- <term name="month-04">apirilak</term>
- <term name="month-05">maiatzak</term>
- <term name="month-06">ekainak</term>
- <term name="month-07">uztailak</term>
- <term name="month-08">abuztuak</term>
- <term name="month-09">irailak</term>
- <term name="month-10">urriak</term>
- <term name="month-11">azaroak</term>
- <term name="month-12">abenduak</term>
+ <term name="month-01">urtarrila</term>
+ <term name="month-02">otsaila</term>
+ <term name="month-03">martxoa</term>
+ <term name="month-04">apirila</term>
+ <term name="month-05">maiatza</term>
+ <term name="month-06">ekaina</term>
+ <term name="month-07">uztaila</term>
+ <term name="month-08">abuztua</term>
+ <term name="month-09">iraila</term>
+ <term name="month-10">urria</term>
+ <term name="month-11">azaroa</term>
+ <term name="month-12">abendua</term>
 
  <!-- SHORT MONTH FORMS -->
  <term name="month-01" form="short">urt.</term>
  <term name="month-02" form="short">ots.</term>
- <term name="month-03" form="short">martx.</term>
+ <term name="month-03" form="short">mar.</term>
  <term name="month-04" form="short">apr.</term>
  <term name="month-05" form="short">mai.</term>
  <term name="month-06" form="short">eka.</term>

buildres/csl/csl-locales/locales-nb-NO.xml

@@ -307,7 +307,7 @@
  <term name="opus" form="short">op.</term>
  <term name="page" form="short">
  <single>s.</single>
- <multiple>ss.</multiple>
+ <multiple>s.</multiple>
  </term>
  <term name="number-of-pages" form="short">
  <single>s.</single>

buildres/csl/csl-locales/locales-nl-NL.xml

@@ -162,7 +162,7 @@
  <term name="close-quote">’</term>
  <term name="open-inner-quote">“</term>
  <term name="close-inner-quote">”</term>
- <term name="page-range-delimiter">–</term>
+ <term name="page-range-delimiter">-</term>
  <term name="colon">:</term>
  <term name="comma">,</term>
  <term name="semicolon">;</term>
@@ -614,7 +614,7 @@
  <!-- SEASONS -->
  <term name="season-01">lente</term>
  <term name="season-02">zomer</term>
- <term name="season-03">herst</term>
+ <term name="season-03">herfst</term>
  <term name="season-04">winter</term>
  </terms>
 </locale>

buildres/csl/csl-locales/locales-nn-NO.xml

@@ -307,7 +307,7 @@
  <term name="opus" form="short">op.</term>
  <term name="page" form="short">
  <single>s.</single>
- <multiple>ss.</multiple>
+ <multiple>s.</multiple>
  </term>
  <term name="number-of-pages" form="short">
  <single>s.</single>