Merge remote-tracking branch 'upstream/main' into fix-for-issue-8189

* upstream/main: (111 commits)
  Fix link and remove obsolete FAQ
  Rename 'Close' to 'Cancel' in the External Changes Resolver dialog (JabRef#9130)
  Tiny rephrasing
  Linked files with an absolute path can be opened again (JabRef#9129)
  Oberservable Preferences M (CleanupPreferences) (JabRef#9126)
  fix broken link
  Fix broken link
  Fix old JabRef linked files containing the file directory as element in the filename (JabRef#9046)
  PDFs are not stored next to .bib file if file directory is configured (JabRef#9113)
  Remove double stateManager.activeDatabaseProperty() (JabRef#9127)
  Don't show the info button when the authors field content is identical (JabRef#9128)
  "study.yml" is static now (JabRef#9125)
  fix l10n
  Compile fix
  Fix parsing of JabRef v5.7 study.yml files (JabRef#9124)
  Fix integrity check  for tilde accents in author names (JabRef#9097)
  Rework the Define study parameters dialog (JabRef#9123)
  Fix parsing of save actions (JabRef#9122)
  Fix exception that occurs when saving name formatters (JabRef#9121)
  Refine code for BibEntry#replaceDownloadedFile (JabRef#9118)
  ...

.gitattributes

@@ -13,5 +13,9 @@ gradlew text eol=lf
 # .bib files have to be written using OS specific line endings to enable our tests working
 *.bib text !eol
 
-# disable after a release
-CHANGELOG.md merge=union
+# Citavi needs to be LF line ending
+# This overwrites the setting of "*.bib"
+Citavi*.bib eol=lf
+
+# disable after a release (otherwise, duplicate CHANGELOG.md entries will be generated)
+# CHANGELOG.md merge=union

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -12,7 +12,7 @@ body:
     attributes:
       label: JabRef version
       options:
-        - "5.6 (latest release)"
+        - "5.7 (latest release)"
         - "3.8.2"
         - Latest development branch build (please note build date below)
         - Other (please describe below)

.github/workflows/automerge.yml

@@ -16,7 +16,7 @@ jobs:
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Auto approve
-        uses: hmarr/auto-approve-action@v2.2.1
+        uses: hmarr/auto-approve-action@v2.4.0
         if: steps.waitforstatuschecks.outputs.status == 'success'
         with:
           github-token: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/cleanup_pr.yml

@@ -27,7 +27,7 @@ jobs:
           echo "##[set-output name=branch;]$(echo ${{ github.event.pull_request.head.ref }})"
       - name: Delete folder on builds.jabref.org
         if: ${{ steps.checksecrets.outputs.secretspresent }}
-        uses: appleboy/ssh-action@v0.1.4
+        uses: appleboy/ssh-action@v0.1.5
         with:
           script: rm -rf /var/www/builds.jabref.org/www/${{ steps.extract_branch.outputs.branch }} || true
           host: build-upload.jabref.org

CHANGELOG.md

@@ -11,11 +11,61 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Added
 
+- In case a backup is found, the filename of the backup is shown.
+- On startup, JabRef notifies the user if there were parsing errors during opening.
+- We integrated a new three-way merge UI for merging entries in the Entries Merger Dialog, the Duplicate Resolver Dialog, the Entry Importer Dialog, and the External Changes Resolver Dialog. [#8945](https://github.com/JabRef/jabref/pull/8945)
+- We added the ability to merge groups, keywords, comments and files when merging entries. [#9022](https://github.com/JabRef/jabref/pull/9022)
+- We added a warning message next to the authors field in the merge dialog to warn users when the authors are the same but formatted differently. [#8745](https://github.com/JabRef/jabref/issues/8745)
+
+### Changed
+
+- We improved the Citavi Importer to also import so called Knowledge-items into the field `comment` of the corresponding entry [#9025](https://github.com/JabRef/jabref/issues/9025)
+- We removed wrapping of string constants when writing to a `.bib` file.
+- We call backup files `.bak` and temporary writing files now `.sav`.
+- JabRef keeps 10 older versions of a `.bib` file in the [user data dir](https://github.com/harawata/appdirs#supported-directories) (instead of a single `.sav` (now: `.bak`) file in the directory of the `.bib` file)
+- We changed the button label from "Return to JabRef" to "Return to library" to better indicate the purpose of the action.
+- We removed "last-search-date" from the SLR feature, because the last-search-date can be deducted from the git logs. [#9116](https://github.com/JabRef/jabref/pull/9116)
+- A user can now add arbitrary data into `study.yml`. JabRef just ignores this data. [#9124](https://github.com/JabRef/jabref/pull/9124)
+- We reworked the External Changes Resolver dialog. [#9021](https://github.com/JabRef/jabref/pull/9021)
+- The fallback directory of the file folder now is the general file directory. In case there was a directory configured for a library and this directory was not found, JabRef placed the PDF next to the .bib file and not into the general file directory.
+- The global default directory for storing PDFs is now the subdirectory "JabRef" in the user's home.
+- We reworked the Define study parameters dialog. [#9123](https://github.com/JabRef/jabref/pull/9123)
+
+### Fixed
+
+- We fixed an issue where author names with tilde accents (for example ñ) were marked as "Names are not in the standard BibTex format" [#8071](https://github.com/JabRef/jabref/issues/8071)
+- We fixed an issue where the possibility to generate a subdatabase from an aux file was writing empty files when called from the commandline [#9115](https://github.com/JabRef/jabref/issues/9115), [forum#3516](https://discourse.jabref.org/t/export-subdatabase-from-aux-file-on-macos-command-line/3516)
+- We fixed the display of issue, number, eid and pages fields in the entry preview. [#8607](https://github.com/JabRef/jabref/pull/8607), [#8372](https://github.com/JabRef/jabref/issues/8372), [Koppor#514](https://github.com/koppor/jabref/issues/514), [forum#2390](https://discourse.jabref.org/t/unable-to-edit-my-bibtex-file-that-i-used-before-vers-5-1/2390), [forum#3462](https://discourse.jabref.org/t/jabref-5-6-need-help-with-export-from-jabref-to-microsoft-word-entry-preview-of-apa-7-not-rendering-correctly/3462)
+- We fixed the page ranges checker to detect article numbers in the pages field (used at [Check Integrity](https://docs.jabref.org/finding-sorting-and-cleaning-entries/checkintegrity)). [#8607](https://github.com/JabRef/jabref/pull/8607)
+- The [HtmlToLaTeXFormatter](https://docs.jabref.org/finding-sorting-and-cleaning-entries/saveactions#html-to-latex) keeps single `<` characters.
+- 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 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)
+- We fixed an issue where title case didn't capitalize words after en-dash characters. [#9068](https://github.com/JabRef/jabref/pull/9068)
+- We fixed an issue where JabRef would not exit when a connection to a LibreOffice document was established previously and the document is still open. [#9075](https://github.com/JabRef/jabref/issues/9075)
+
+### Removed
+
+
+
+
+
+
+
+## [5.7] - 2022-08-05
+
+### Added
+
 - We added a fetcher for [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/). [8539](https://github.com/JabRef/jabref/issues/8539)
 - We added support for multiple messages in the snackbar. [#7340](https://github.com/JabRef/jabref/issues/7340)
 - We added an extra option in the 'Find Unlinked Files' dialog view to ignore unnecessary files like Thumbs.db, DS_Store, etc. [koppor#373](https://github.com/koppor/jabref/issues/373)
 - JabRef now writes log files. Linux: `$home/.cache/jabref/logs/version`, Windows: `%APPDATA%\..\Local\harawata\jabref\version\logs`, Mac: `Users/.../Library/Logs/jabref/version`
 - We added an importer for Citavi backup files, support ".ctv5bak" and ".ctv6bak" file formats. [#8322](https://github.com/JabRef/jabref/issues/8322)
+- We added a feature to drag selected entries and drop them to other opened inactive library tabs [koppor521](https://github.com/koppor/jabref/issues/521).
+- We added support for the [biblatex-apa](https://github.com/plk/biblatex-apa) legal entry types `Legislation`, `Legadminmaterial`, `Jurisdiction`, `Constitution` and `Legal` [#8931](https://github.com/JabRef/jabref/issues/8931)
 
 ### Changed
 
@@ -41,6 +91,9 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Fixed
 
+- We fixed an issue where linked fails containing parts of the main file directory could not be opened. [#8991](https://github.com/JabRef/jabref/issues/8991)
+- Linked files with an absolute path can be opened again. [#8991](https://github.com/JabRef/jabref/issues/8991)
+- We fixed an issue where the user could not rate an entry in the main table when an entry was not yet ranked. [#5842](https://github.com/JabRef/jabref/issues/5842)
 - We fixed an issue that caused JabRef to sometimes open multiple instances when "Remote Operation" is enabled. [#8653](https://github.com/JabRef/jabref/issues/8653)
 - We fixed an issue where linked files with the filetype "application/pdf" in an entry were not shown with the correct PDF-Icon in the main table [8930](https://github.com/JabRef/jabref/issues/8930)
 - We fixed an issue where "open folder" for linked files did not open the folder and did not select the file unter certain Linux desktop environments [#8679](https://github.com/JabRef/jabref/issues/8679), [#8849](https://github.com/JabRef/jabref/issues/8849)
@@ -58,20 +111,15 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed a bug where switching between themes will cause an error/exception. [#8939](https://github.com/JabRef/jabref/pull/8939)
 - We fixed a bug where files that were deleted in the source bibtex file were kept in the index. [#8962](https://github.com/JabRef/jabref/pull/8962)
 - We fixed "Error while sending to JabRef" when the browser extension interacts with JabRef. [JabRef-Browser-Extension#479](https://github.com/JabRef/JabRef-Browser-Extension/issues/479)
+- We fixed a bug where updating group view mode (intersection or union) requires re-selecting groups to take effect. [#6998](https://github.com/JabRef/jabref/issues/6998)
+- We fixed a bug that prevented external group metadata changes from being merged. [#8873](https://github.com/JabRef/jabref/issues/8873)
+- We fixed the shared database opening dialog to remember autosave folder and tick. [#7516](https://github.com/JabRef/jabref/issues/7516)
+- We fixed an issue where name formatter could not be saved. [#9120](https://github.com/JabRef/jabref/issues/9120)
 
 ### Removed
 
 - We removed the social media buttons for our Twitter and Facebook pages. [#8774](https://github.com/JabRef/jabref/issues/8774)
 
-
-
-
-
-
-
-
-
-
 ## [5.6] - 2022-04-25
 
 ### Added
@@ -842,7 +890,8 @@ The changelog of JabRef 4.x is available at the [v4.3.1 tag](https://github.com/
 The changelog of JabRef 3.x is available at the [v3.8.2 tag](https://github.com/JabRef/jabref/blob/v3.8.2/CHANGELOG.md).
 The changelog of JabRef 2.11 and all previous versions is available as [text file in the v2.11.1 tag](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG).
 
-[Unreleased]: https://github.com/JabRef/jabref/compare/v5.6...HEAD
+[Unreleased]: https://github.com/JabRef/jabref/compare/v5.7...HEAD
+[5.7]: https://github.com/JabRef/jabref/compare/v5.6...v5.7
 [5.6]: https://github.com/JabRef/jabref/compare/v5.5...v5.6
 [5.5]: https://github.com/JabRef/jabref/compare/v5.4...v5.5
 [5.4]: https://github.com/JabRef/jabref/compare/v5.3...v5.4

CONTRIBUTING.md

@@ -3,8 +3,9 @@
 When contributing to this repository, please first discuss the change you wish to make via issue,
 email, or any other method with the owners of this repository before making a change.
 
-Support on code contribution is available at <https://devdocs.jabref.org/contributing>.
-General overview on contributing is available at <https://contribute.jabref.org>.
+Support on **code contribution** is available at <https://devdocs.jabref.org/contributing>.
+
+General overview about contributing for programmers and non-programmers is available at <https://contribute.jabref.org>.
 
 ## Pull Request Process
 

build.gradle

@@ -10,7 +10,7 @@ plugins {
 
     id 'me.champeau.gradle.jmh' version '0.5.3'
 
-    id 'org.javamodularity.moduleplugin' version '1.8.11'
+    id 'org.javamodularity.moduleplugin' version '1.8.12'
 
     id 'org.openjfx.javafxplugin' version '0.0.13'
 
@@ -85,7 +85,6 @@ repositories {
 }
 
 configurations {
-    antlr3
     antlr4
     // TODO: Remove the following workaround for split error messages such as
     // error: module java.xml.bind reads package javax.annotation from both jsr305 and java.annotation
@@ -100,7 +99,7 @@ dependencyLocking {
 }
 
 javafx {
-    version = "18.0.1"
+    version = "18.0.2"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
 }
 
@@ -116,11 +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:9.2.0'
-    implementation 'org.apache.lucene:lucene-queryparser:9.2.0'
-    implementation 'org.apache.lucene:lucene-queries:9.2.0'
-    implementation 'org.apache.lucene:lucene-analysis-common:9.2.0'
-    implementation 'org.apache.lucene:lucene-highlighter:9.2.0'
+    implementation 'org.apache.lucene:lucene-core:9.3.0'
+    implementation 'org.apache.lucene:lucene-queryparser:9.3.0'
+    implementation 'org.apache.lucene:lucene-queries:9.3.0'
+    implementation 'org.apache.lucene:lucene-analysis-common:9.3.0'
+    implementation 'org.apache.lucene:lucene-highlighter:9.3.0'
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.9.0'
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.12.0'
@@ -129,19 +128,16 @@ dependencies {
     implementation group: 'org.apache.tika', name: 'tika-core', version: '2.4.1'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    implementation 'org.bouncycastle:bcprov-jdk18on:1.71'
+    implementation 'org.bouncycastle:bcprov-jdk18on:1.71.1'
 
     implementation 'commons-cli:commons-cli:1.5.0'
 
-    implementation 'org.libreoffice:libreoffice:7.3.4'
-    implementation 'org.libreoffice:unoloader:7.3.4'
+    implementation 'org.libreoffice:libreoffice:7.4.0'
+    implementation 'org.libreoffice:unoloader:7.4.0'
 
-    implementation 'io.github.java-diff-utils:java-diff-utils:4.11'
+    implementation 'io.github.java-diff-utils:java-diff-utils:4.12'
     implementation 'info.debatty:java-string-similarity:2.0.0'
 
-    antlr3 'org.antlr:antlr:3.5.3'
-    implementation 'org.antlr:antlr-runtime:3.5.3'
-
     antlr4 'org.antlr:antlr4:4.9.3'
     implementation 'org.antlr:antlr4-runtime:4.9.3'
 
@@ -152,7 +148,7 @@ dependencies {
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.6'
 
-    implementation 'org.postgresql:postgresql:42.4.0'
+    implementation 'org.postgresql:postgresql:42.5.0'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
@@ -178,13 +174,13 @@ dependencies {
     implementation 'com.jfoenix:jfoenix:9.0.10'
     implementation 'org.controlsfx:controlsfx:11.1.1'
 
-    implementation 'org.jsoup:jsoup:1.15.1'
-    implementation 'com.konghq:unirest-java:3.13.10'
+    implementation 'org.jsoup:jsoup:1.15.3'
+    implementation 'com.konghq:unirest-java:3.13.11'
 
-    implementation 'org.slf4j:slf4j-api:2.0.0-alpha7'
-    implementation "org.tinylog:tinylog-api:2.4.1"
-    implementation "org.tinylog:slf4j-tinylog:2.4.1"
-    implementation "org.tinylog:tinylog-impl:2.4.1"
+    implementation 'org.slf4j:slf4j-api:2.0.0'
+    implementation "org.tinylog:tinylog-api:2.5.0"
+    implementation "org.tinylog:slf4j-tinylog:2.5.0"
+    implementation "org.tinylog:tinylog-impl:2.5.0"
 
     implementation 'de.undercouch:citeproc-java:3.0.0-alpha.6'
 
@@ -208,10 +204,10 @@ dependencies {
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 
     testImplementation 'io.github.classgraph:classgraph:4.8.149'
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
-    testImplementation 'org.junit.platform:junit-platform-launcher:1.8.2'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.9.0'
+    testImplementation 'org.junit.platform:junit-platform-launcher:1.9.0'
 
-    testImplementation 'org.mockito:mockito-core:4.6.1'
+    testImplementation 'org.mockito:mockito-core:4.7.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.0'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.23.1'
@@ -220,7 +216,7 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.3.1'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.3.3'
     // 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'
@@ -273,14 +269,14 @@ task generateSource(dependsOn: ["generateBstGrammarSource",
 }
 
 tasks.register("generateBstGrammarSource", JavaExec) {
-    main = "org.antlr.Tool"
-    classpath = configurations.antlr3
+    main = "org.antlr.v4.Tool"
+    classpath = configurations.antlr4
     group = "JabRef"
-    description = 'Generates BstLexer.java and BstParser.java from the Bst.g grammar file using antlr3.'
+    description = 'Generates BstLexer.java and BstParser.java from the Bst.g grammar file using antlr4.'
 
-    inputs.dir('src/main/antlr3/org/jabref/bst/')
+    inputs.dir('src/main/antlr4/org/jabref/bst/')
     outputs.dir("src-gen/main/java/org/jabref/logic/bst/")
-    args = ["-o", "src-gen/main/java/org/jabref/logic/bst/" , "$projectDir/src/main/antlr3/org/jabref/bst/Bst.g" ]
+    args = ["-o", "src-gen/main/java/org/jabref/logic/bst/", "-visitor", "-no-listener", "-package", "org.jabref.logic.bst", "$projectDir/src/main/antlr4/org/jabref/bst/Bst.g4"]
 }
 
 tasks.register("generateSearchGrammarSource", JavaExec) {

buildSrc/build.gradle

@@ -8,7 +8,7 @@ repositories {
 dependencies {
     implementation 'com.h2database:h2-mvstore:2.1.214'
     implementation 'org.apache.commons:commons-csv:1.9.0'
-    implementation 'org.slf4j:slf4j-api:2.0.0-alpha7'
+    implementation 'org.slf4j:slf4j-api:2.0.0'
 }
 
 sourceSets{

buildres/csl/csl-locales/.github/workflows/merge.yaml

@@ -136,14 +136,14 @@ jobs:
 
     - name: Bump version and push tag
       id: tag_version
-      uses: mathieudutour/github-tag-action@v5.6
+      uses: mathieudutour/github-tag-action@v6.0
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         default_bump: patch
       if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
 
     - name: Create a GitHub release
-      uses: softprops/action-gh-release@v0.1.14
+      uses: softprops/action-gh-release@v1
       env:
         github_token: ${{ secrets.GITHUB_TOKEN }}
       with:

buildres/csl/csl-styles/.github/workflows/merge.yaml

@@ -136,14 +136,14 @@ jobs:
 
     - name: Bump version and push tag
       id: tag_version
-      uses: mathieudutour/github-tag-action@v5.6
+      uses: mathieudutour/github-tag-action@v6.0
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         default_bump: patch
       if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
 
     - name: Create a GitHub release
-      uses: softprops/action-gh-release@v0.1.14
+      uses: softprops/action-gh-release@v1
       env:
         github_token: ${{ secrets.GITHUB_TOKEN }}
       with: