Merge remote-tracking branch 'origin/main' into fix-for-issue-8888

Author: Callum-Higginson

.github/workflows/binaries.yml

@@ -140,30 +140,35 @@ jobs:
             displayName: linux
             archivePortable: tar -c -C jabgui/build/packages/ubuntu-22.04 JabRef | pigz --rsyncable > jabgui/build/packages/ubuntu-22.04/JabRef-portable_linux.tar.gz && rm -R jabgui/build/packages/ubuntu-22.04/JabRef
             archivePortableJabKit: tar -c -C jabkit/build/packages/ubuntu-22.04 jabkit | pigz --rsyncable > jabkit/build/packages/ubuntu-22.04/jabkit-portable_linux.tar.gz && rm -R jabkit/build/packages/ubuntu-22.04/jabkit
+            archivePortableJabLS: tar -c -C jabls-cli/build/packages/ubuntu-22.04 jabls | pigz --rsyncable > jabls-cli/build/packages/ubuntu-22.04/jabls-portable_linux.tar.gz && rm -R jabls-cli/build/packages/ubuntu-22.04/jabls
             suffix: ''
             archForDebianRepack: '_amd64'
           - os: ubuntu-22.04-arm
             displayName: linux-arm
             archivePortable: tar -c -C jabgui/build/packages/ubuntu-22.04-arm JabRef | pigz --rsyncable > jabgui/build/packages/ubuntu-22.04-arm/JabRef-portable_linux_arm64.tar.gz && rm -R jabgui/build/packages/ubuntu-22.04-arm/JabRef
             archivePortableJabKit: tar -c -C jabkit/build/packages/ubuntu-22.04-arm jabkit | pigz --rsyncable > jabkit/build/packages/ubuntu-22.04-arm/jabkit-portable_linux_arm64.tar.gz && rm -R jabkit/build/packages/ubuntu-22.04-arm/jabkit
+            archivePortableJabLS: tar -c -C jabls-cli/build/packages/ubuntu-22.04-arm jabls | pigz --rsyncable > jabls-cli/build/packages/ubuntu-22.04-arm/jabls-cli-portable_linux_arm64.tar.gz && rm -R jabls-cli/build/packages/ubuntu-22.04-arm/jabls
             suffix: '_arm64'
             archForDebianRepack: '_arm64'
           - os: windows-latest
             displayName: windows
             archivePortable: 7z a -r jabgui/build/packages/windows-latest/JabRef-portable_windows.zip ./jabgui/build/packages/windows-latest/JabRef && rm -R jabgui/build/packages/windows-latest/JabRef
             archivePortableJabKit: 7z a -r jabkit/build/packages/windows-latest/jabkit-portable_windows.zip ./jabkit/build/packages/windows-latest/jabkit && rm -R jabkit/build/packages/windows-latest/jabkit
+            archivePortableJabLS: 7z a -r jabls-cli/build/packages/windows-latest/jabls-portable_windows.zip ./jabls-cli/build/packages/windows-latest/jabls && rm -R jabls-cli/build/packages/windows-latest/jabls
             suffix: ''
             archForDebianRepack: ''
           - os: macos-15-intel  # intel image
             displayName: macOS
             archivePortable: 7z a -r jabgui/build/packages/macos-15-intel/JabRef-portable_macos.zip ./jabgui/build/packages/macos-15-intel/JabRef.app && rm -R jabgui/build/packages/macos-15-intel/JabRef.app
             archivePortableJabKit: 7z a -r jabkit/build/packages/macos-15-intel/jabkit-portable_macos.zip ./jabkit/build/packages/macos-15-intel/jabkit.app && rm -R jabkit/build/packages/macos-15-intel/jabkit.app
+            archivePortableJabLS: 7z a -r jabls-cli/build/packages/macos-15-intel/jabls-portable_macos.zip ./jabls-cli/build/packages/macos-15-intel/jabls.app && rm -R jabls-cli/build/packages/macos-15-intel/jabls.app
             suffix: ''
             archForDebianRepack: ''
           - os: macos-15
             displayName: macOS-arm
             archivePortable: 7z a -r jabgui/build/packages/macos-15/JabRef-portable_macos-arm.zip ./jabgui/build/packages/macos-15/JabRef.app && rm -R jabgui/build/packages/macos-15/JabRef.app
             archivePortableJabKit: 7z a -r jabkit/build/packages/macos-15/jabkit-portable_macos-arm.zip ./jabkit/build/packages/macos-15/jabkit.app && rm -R jabkit/build/packages/macos-15/jabkit.app
+            archivePortableJabLS: 7z a -r jabls-cli/build/packages/macos-15/jabls-portable_macos-arm.zip ./jabls-cli/build/packages/macos-15/jabkit.app && rm -R jabls-cli/build/packages/macos-15/jabls.app
             suffix: '_arm64'
             archForDebianRepack: ''
     runs-on: ${{ matrix.os }}
@@ -265,6 +270,15 @@ jobs:
           set -e
           ${{ matrix.archivePortableJabKit }}
 
+      - name: Build JabLS-CLI
+        shell: bash
+        run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" :jabls-cli:jpackage
+      - name: Package JabLS-CLI application image
+        shell: bash
+        run: |
+          set -e
+          ${{ matrix.archivePortableJabLS }}
+
       # region Upload to builds.jabref.org / GitHub artifacts store
       - name: Setup SSH key
         if: (needs.conditions.outputs.upload-to-builds-jabref-org == 'true')
@@ -304,9 +318,13 @@ jobs:
       - name: Upload jabkkit to builds.jabref.org (Windows)
         if: ${{ (steps.diskspace.outputs.available == 'true') && (matrix.os == 'windows-latest') }}
         shell: cmd
-        # for rsync installed by chocolatey, we need the ssh.exe delivered with that installation
         run: |
           rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'C:\ProgramData\chocolatey\lib\rsync\tools\bin\ssh.exe -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabkit/build/packages/${{ matrix.os }}/ [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
+      - name: Upload jabls-cli to builds.jabref.org (Windows)
+        if: ${{ (steps.diskspace.outputs.available == 'true') && (matrix.os == 'windows-latest') }}
+        shell: cmd
+        run: |
+          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'C:\ProgramData\chocolatey\lib\rsync\tools\bin\ssh.exe -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabls-cli/build/packages/${{ matrix.os }}/ [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
       - name: Upload jabgui to builds.jabref.org (linux, macOS)
         if: ${{ (steps.diskspace.outputs.available == 'true') && (startsWith(matrix.os, 'macos') || startsWith(matrix.os, 'ubuntu')) }}
         shell: bash
@@ -317,6 +335,11 @@ jobs:
         shell: bash
         run: |
           rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabkit/build/packages/${{ matrix.os }}/ [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
+      - name: Upload jabls-cli to builds.jabref.org (linux, macOS)
+        if: ${{ (steps.diskspace.outputs.available == 'true') && (startsWith(matrix.os, 'macos') || startsWith(matrix.os, 'ubuntu')) }}
+        shell: bash
+        run: |
+          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabls-cli/build/packages/${{ matrix.os }}/ [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
       - name: Upload to GitHub workflow artifacts store (macOS)
         if: ${{ (startsWith(matrix.os, 'macos')) && (needs.conditions.outputs.should-notarize == 'true') }}
         uses: actions/upload-artifact@v4

.jbang/JabKitLauncher.java

@@ -34,7 +34,7 @@
 //DEPS org.jabref:jablib:6.0-SNAPSHOT
 // https://jitpack.io/#jabref/jabref/main-SNAPSHOT
 // DEPS com.github.jabref:jabref:main-SNAPSHOT
-
+//DEPS io.github.darvil82:terminal-text-formatter:2.2.0
 //DEPS info.picocli:picocli:4.7.7
 
 import org.jabref.JabKit;

.jbang/JabLsLauncher.java

@@ -36,6 +36,7 @@
 // https://jitpack.io/#jabref/jabref/main-SNAPSHOT
 // DEPS com.github.jabref:jabref:main-SNAPSHOT
 
+//DEPS io.github.darvil82:terminal-text-formatter:2.2.0
 //DEPS info.picocli:picocli:4.7.7
 //DEPS org.jspecify:jspecify:1.0.0
 

.jbang/JabSrvLauncher.java

@@ -58,6 +58,7 @@
 // https://jitpack.io/#jabref/jabref/main-SNAPSHOT
 // DEPS com.github.jabref:jabref:main-SNAPSHOT
 
+//DEPS io.github.darvil82:terminal-text-formatter:2.2.0
 //DEPS info.picocli:picocli:4.7.7
 //DEPS org.jspecify:jspecify:1.0.0
 
@@ -86,7 +87,7 @@
 //DEPS com.google.guava:guava:33.5.0-jre
 //DEPS org.jabref:afterburner.fx:2.0.0
 //DEPS net.harawata:appdirs:1.5.0
-//DEPS de.undercouch:citeproc-java:3.3.0
+//DEPS de.undercouch:citeproc-java:3.4.0
 
 /// This class is required for [jbang](https://www.jbang.dev/)
 public class JabSrvLauncher {

CHANGELOG.md

@@ -49,6 +49,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Changed
 
+- We moved all sorting options into a dedicated “Sort” sub-menu in the Groups menu. ([#14017](https://github.com/JabRef/jabref/issues/14017))
 - We merged `Citation information` and `Citation relations` into a singular tab. [#13618](https://github.com/JabRef/jabref/issues/13618)
 - We changed `ISSNCleanup` into `NormalizeIssn` a `ISSN` formatter. [#13748](https://github.com/JabRef/jabref/issues/13748)
 - We changed Citation Relations tab and gave tab panes more descriptive titles and tooltips. [#13619](https://github.com/JabRef/jabref/issues/13619)
@@ -102,6 +103,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We improved the event viewer for debugging [#13783](https://github.com/JabRef/jabref/pull/13783).
 - We improved "REDACTED" replacement of API key value in web fetcher search URL [#13796](https://github.com/JabRef/jabref/issues/13796)
 - When the pin "Keep dialog always on top" in the global search dialog is selected, the search window stays open when double-clicking on an entry. [#13840](https://github.com/JabRef/jabref/issues/13840)
+- We improved the UI of regex replacement in the citation key generator tab. [#13939](https://github.com/JabRef/jabref/pull/13939)
 - We improved the way we check for matching curly braces in BibTeX fields and made error messages easier to understand. [#12605](https://github.com/JabRef/jabref/issues/12605)
 
 ### Fixed

build-logic/src/main/kotlin/org.jabref.gradle.base.dependency-rules.gradle.kts

@@ -219,6 +219,11 @@ extraJavaModuleInfo {
         overrideModuleName()
         exportAllPackages()
     }
+
+    module("io.github.darvil82:utils", "utils"){
+        patchRealModule()
+        exportAllPackages()
+    }
     module("io.github.adr:e-adr", "io.github.adr") {
         patchRealModule()
         exportAllPackages()

docs/code-howtos/testing.md

@@ -27,6 +27,28 @@ Imagine you want to test the method `format(String value)` in the class `BracesF
 * _Bug fixing:_ write a test case covering the bug and then fix it, leaving the test as a security that the bug will never reappear.
 * Do not catch exceptions in tests, instead use the `assertThrows(Exception.class, () -> doSomethingThrowsEx())` feature of [junit-jupiter](https://junit.org/junit5/docs/current/user-guide/) to the test method.
 
+### Use `@ParamterizedTests`
+
+If possible, use `@ParamterizedTests`.
+Read more at <https://mikemybytes.com/2021/10/19/parameterize-like-a-pro-with-junit-5-csvsource/>.
+
+Example for a nicely formatted `@CsvSource`
+
+```java
+@ParameterizedTest
+@CsvSource(delimiterString = "->", textBlock = """
+    # underscore removed
+    junit_jupiter -> JunitJupiter
+    # camel case kept
+    fooBar        -> FooBar
+    CsvSource     -> CsvSource
+""")
+void convertsToUpperCamelCase(String input, String expected) {
+    String converted = caseConverter.toUpperCamelCase(input);
+    Assertions.assertEquals(expected, converted);
+}
+```
+
 ## Coverage
 
 IntelliJ has build in test coverage reports. Choose "Run with coverage".

docs/decisions/0039-use-apache-velocity-as-template-engine.md

@@ -29,6 +29,7 @@ Implementation decision drivers:
 * Thymeleaf
 * Handlebars (Mustache)
 * Jinja
+* Pebble
 
 ## Decision Outcome
 

jabgui/src/main/java/org/jabref/gui/actions/StandardActions.java

@@ -182,7 +182,6 @@ public enum StandardActions implements Action {
 
     HELP(Localization.lang("Online help"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
     HELP_GROUPS(Localization.lang("Open Help page"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
-    HELP_KEY_PATTERNS(Localization.lang("Help on key patterns"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
     HELP_REGEX_SEARCH(Localization.lang("Help on regular expression search"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
     HELP_NAME_FORMATTER(Localization.lang("Help on Name Formatting"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
     HELP_SPECIAL_FIELDS(Localization.lang("Help on special fields"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),

jabgui/src/main/java/org/jabref/gui/groups/GroupTreeView.java

@@ -614,10 +614,15 @@ private ContextMenu createContextMenuForGroup(GroupNodeViewModel group) {
                 factory.createMenuItem(StandardActions.GROUP_SUBGROUP_ADD, new ContextAction(StandardActions.GROUP_SUBGROUP_ADD, group)),
                 factory.createMenuItem(StandardActions.GROUP_SUBGROUP_RENAME, new ContextAction(StandardActions.GROUP_SUBGROUP_RENAME, group)),
                 factory.createMenuItem(StandardActions.GROUP_SUBGROUP_REMOVE, new ContextAction(StandardActions.GROUP_SUBGROUP_REMOVE, group)),
-                factory.createMenuItem(StandardActions.GROUP_SUBGROUP_SORT, new ContextAction(StandardActions.GROUP_SUBGROUP_SORT, group)),
-                factory.createMenuItem(StandardActions.GROUP_SUBGROUP_SORT_REVERSE, new ContextAction(StandardActions.GROUP_SUBGROUP_SORT_REVERSE, group)),
-                factory.createMenuItem(StandardActions.GROUP_SUBGROUP_SORT_ENTRIES, new ContextAction(StandardActions.GROUP_SUBGROUP_SORT_ENTRIES, group)),
-                factory.createMenuItem(StandardActions.GROUP_SUBGROUP_SORT_ENTRIES_REVERSE, new ContextAction(StandardActions.GROUP_SUBGROUP_SORT_ENTRIES_REVERSE, group)),
+                new Menu(Localization.lang("Sort"), null,
+                        factory.createMenuItem(StandardActions.GROUP_SUBGROUP_SORT,
+                                new GroupTreeView.ContextAction(StandardActions.GROUP_SUBGROUP_SORT, group)),
+                        factory.createMenuItem(StandardActions.GROUP_SUBGROUP_SORT_REVERSE,
+                                new GroupTreeView.ContextAction(StandardActions.GROUP_SUBGROUP_SORT_REVERSE, group)),
+                        factory.createMenuItem(StandardActions.GROUP_SUBGROUP_SORT_ENTRIES,
+                                new GroupTreeView.ContextAction(StandardActions.GROUP_SUBGROUP_SORT_ENTRIES, group)),
+                        factory.createMenuItem(StandardActions.GROUP_SUBGROUP_SORT_ENTRIES_REVERSE,
+                                new GroupTreeView.ContextAction(StandardActions.GROUP_SUBGROUP_SORT_ENTRIES_REVERSE, group))),
                 new SeparatorMenuItem(),
                 factory.createMenuItem(StandardActions.GROUP_ENTRIES_ADD, new ContextAction(StandardActions.GROUP_ENTRIES_ADD, group)),
                 factory.createMenuItem(StandardActions.GROUP_ENTRIES_REMOVE, new ContextAction(StandardActions.GROUP_ENTRIES_REMOVE, group))