Merge branch 'JabRef:main' into JabRef#3197-TeXworks

.github/workflows/add-to-projects.yml

@@ -15,28 +15,30 @@ jobs:
       - name: "good first issue"
         if: "${{ github.event.label.name == 'good first issue' }}"
         env:
-          GH_TOKEN: ${{ github.token }}
+          GH_TOKEN: ${{ secrets.GH_TOKEN_PROJECT_ITEM_ADD }}
         run: |
           ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
-          gh project item-add 5 --owner jabref --url $ISSUE_URL
+          gh project item-add 5 --owner JabRef --url $ISSUE_URL
       - name: needs-refinement
         if: github.event.label.name == 'needs-refinement'
         env:
-          GH_TOKEN: ${{ github.token }}
+          GH_TOKEN: ${{ secrets.GH_TOKEN_PROJECT_ITEM_ADD }}
         run: |
           ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
-          gh project item-add 15 --owner jabref --url $ISSUE_URL
+          gh project item-add 15 --owner JabRef --url $ISSUE_URL
       - name: "status: freeze"
         if: "${{ github.event.label.name == 'status: freeze' }}"
         env:
-          GH_TOKEN: ${{ github.token }}
+          GH_TOKEN: ${{ secrets.GH_TOKEN_PROJECT_ITEM_ADD }}
         run: |
           ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
-          gh project item-add 9 --owner jabref --url $ISSUE_URL
+          gh project item-add 9 --owner JabRef --url $ISSUE_URL
       - name: ui
         if: "${{ github.event.label.name == 'ui' }}"
         env:
-          GH_TOKEN: ${{ github.token }}
+          GH_DEBUG: api
+          GH_TOKEN: ${{ secrets.GH_TOKEN_PROJECT_ITEM_ADD }}
         run: |
           ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
-          gh project item-add 8 --owner jabref --url $ISSUE_URL
+          echo $ISSUE_URL
+          gh project item-add 8 --owner JabRef --url $ISSUE_URL

.github/workflows/deployment-jdk-ea.yml

@@ -30,28 +30,38 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  setup-matrix:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.javafx_versions.outputs.matrix }}
+    steps:
+      - id: javafx_versions
+        run: |
+          curl -s "https://search.maven.org/solrsearch/select?q=g:org.openjfx+AND+a:javafx&rows=5&core=gav" > /tmp/versions.json
+          jq '[.response.docs[] | select(.v | test(".*-ea\\+.*")) | select(.v | test("^17") | not) | {version: .v}] | group_by(.version | capture("^(?<major>\\d+).*").major) | map(max_by(.version))' < /tmp/versions.json > /tmp/versions-latest.json
+          versions_json=$(jq -r '[.[].version]' /tmp/versions-latest.json | jq -r tostring)
+          include_json=$(jq -n '[
+            {"os": "ubuntu-latest", "displayName": "linux", "archivePortable": "tar -c -C build/distribution JabRef | pigz --rsyncable > build/distribution/JabRef-portable_linux.tar.gz && rm -R build/distribution/JabRef"},
+            {"os": "buildjet-4vcpu-ubuntu-2204-arm", "displayName": "linux-arm", "archivePortable": "tar -c -C build/distribution JabRef | pigz --rsyncable > build/distribution/JabRef-portable_linux-arm64.tar.gz && rm -R build/distribution/JabRef"},
+            {"os": "windows-latest", "displayName": "windows", "archivePortable": "7z a -r build/distribution/JabRef-portable_windows.zip ./build/distribution/JabRef && rm -R build/distribution/JabRef"},
+            {"os": "macos-latest", "displayName": "macOS", "archivePortable": "brew install pigz && tar -c -C build/distribution JabRef.app | pigz --rsyncable > build/distribution/JabRef-portable_macos.tar.gz && rm -R build/distribution/JabRef.app"}
+          ]')
+          matrix=$(jq -n \
+            --argjson versionsContent "$versions_json" \
+            --argjson includeContent "$include_json" \
+            '{"os": ["ubuntu-latest", "windows-latest", "macos-latest", "buildjet-4vcpu-ubuntu-2204-arm"], "jdk": [22, 23], "javafx": $versionsContent, "include": $includeContent}')
+          echo matrix=$matrix >> $GITHUB_OUTPUT
   build:
+    needs: setup-matrix
     strategy:
       fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        jdk: [22, 23]
-        include:
-          - os: ubuntu-latest
-            displayName: linux
-            archivePortable: tar -c -C build/distribution JabRef | pigz --rsyncable > build/distribution/JabRef-portable_linux.tar.gz && rm -R build/distribution/JabRef
-          - os: windows-latest
-            displayName: windows
-            archivePortable: 7z a -r build/distribution/JabRef-portable_windows.zip ./build/distribution/JabRef && rm -R build/distribution/JabRef
-          - os: macos-latest
-            displayName: macOS
-            archivePortable: brew install pigz && tar -c -C build/distribution JabRef.app | pigz --rsyncable > build/distribution/JabRef-portable_macos.tar.gz && rm -R build/distribution/JabRef.app
+      matrix: ${{fromJson(needs.setup-matrix.outputs.matrix)}}
     runs-on: ${{ matrix.os }}
     outputs:
       major: ${{ steps.gitversion.outputs.Major }}
       minor: ${{ steps.gitversion.outputs.Minor }}
       branchname: ${{ steps.gitversion.outputs.branchName }}
-    name: "JDK ${{ matrix.jdk }}: ${{ matrix.displayName }} installer and portable version"
+    name: "JDK ${{ matrix.jdk }}: ${{ matrix.displayName }} JavaFX ${{ matrix.javafx }}"
     steps:
       - name: Check secrets presence
         id: checksecrets
@@ -71,8 +81,9 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install pigz and cache (linux)
-        if: (matrix.os == 'ubuntu-latest')
-        uses: awalsh128/cache-apt-pkgs-action@latest
+        if: (matrix.os == 'ubuntu-latest') || (matrix.os == 'buildjet-4vcpu-ubuntu-2204-arm')
+        # 1.3.1 works, 1.4.1 does not (https://github.com/awalsh128/cache-apt-pkgs-action/issues/126)
+        uses: koppor/cache-apt-pkgs-action@add-arm64-support
         with:
           packages: pigz
           version: 1.0
@@ -100,6 +111,12 @@ jobs:
         if: (matrix.os == 'macos-latest')
         shell: bash
         run: sed -i'.bak' 's/JavaLanguageVersion.of(.*)/JavaLanguageVersion.of(${{ matrix.jdk }})/' build.gradle
+      - name: 'Set JavaFX (linux, Windows)'
+        if: (matrix.os != 'macos-latest')
+        run: sed -i '/javafx {/{n;s/version = ".*"/version = "${{ matrix.javafx }}"/}' build.gradle
+      - name: 'Set JavaFX (macOS)'
+        if: (matrix.os == 'macos-latest')
+        run: sed -i '.bak' -e '/javafx {/{n' -e 's/version = ".*"/version = "${{ matrix.javafx }}"/;}' build.gradle
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:
@@ -141,7 +158,7 @@ jobs:
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "${{ steps.gitversion.outputs.AssemblySemVer }}","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}"}
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "portable","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-portable"}
       - name: Repack deb file for Debian
-        if: (matrix.os == 'ubuntu-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        if: (matrix.os == 'ubuntu-latest')
         shell: bash
         run: |
           cd build/distribution
@@ -157,7 +174,7 @@ jobs:
           for file in build/distribution/*.*; do
             base=${file%.*}
             ext=${file##*.}
-            mv "$file" "${base}-jdk${{ matrix.jdk }}.${ext}"
+            mv "$file" "${base}-jdk${{ matrix.jdk }}-javafx${{ matrix.javafx }}.${ext}"
           done
       - name: Setup rsync (macOS)
         if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))

CHANGELOG.md

@@ -16,11 +16,14 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a fetcher for [ISIDORE](https://isidore.science/), simply paste in the link into the text field or the last 6 digits in the link that identify that paper. [#10423](https://github.com/JabRef/jabref/issues/10423)
 - When importing entries form the "Citation relations" tab, the field [cites](https://docs.jabref.org/advanced/entryeditor/entrylinks) is now filled according to the relationship between the entries. [#10572](https://github.com/JabRef/jabref/pull/10752)
 - We added a new group icon column to the main table showing the icons of the entry's groups. [#10801](https://github.com/JabRef/jabref/pull/10801)
+- When deleting an entry, the files linked to the entry are now optionally deleted as well. [#10509](https://github.com/JabRef/jabref/issues/10509)
+- We added support to move the file to the system trash (instead of deleting it). [#10591](https://github.com/JabRef/jabref/pull/10591)
 - We added ability to jump to an entry in the command line using `-j CITATIONKEY`. [koppor#540](https://github.com/koppor/jabref/issues/540)
 - We added a new boolean to the style files for Openoffice/Libreoffice integration to switch between ZERO_WIDTH_SPACE (default) and no space. [#10843](https://github.com/JabRef/jabref/pull/10843)
 - When pasting HTML into the abstract or a comment field, the hypertext is automatically converted to Markdown. [#10558](https://github.com/JabRef/jabref/issues/10558)
 - We added the possibility to redownload files that had been present but are no longer in the specified location. [#10848](https://github.com/JabRef/jabref/issues/10848)
 - We added the citation key pattern `[camelN]`. Equivalent to the first N words of the `[camel]` pattern.
+- We added ability to export in CFF (Citation File Format) [#10661](https://github.com/JabRef/jabref/issues/10661).
 
 ### Changed
 
@@ -31,6 +34,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We changed the arrangement of the lists in the "Citation relations" tab. `Cites` are now on the left and `Cited by` on the right [#10572](https://github.com/JabRef/jabref/pull/10752)
 - Sub libraries based on `aux` file can now also be generated if some citations are not found library. [#10775](https://github.com/JabRef/jabref/pull/10775)
 - We rearranged the tab order in the entry editor and renamed the "Scite Tab" to "Citation information". [#10821](https://github.com/JabRef/jabref/issues/10821)
+- We changed the duplicate handling in the Import entries dialog. Potential duplicate entries are marked with an icon and importing will now trigger the merge dialog [#10914](https://github.com/JabRef/jabref/pull/10914)
 - We made the command "Push to TexShop" more robust to allow cite commands with a character before the first slash. [forum#2699](https://discourse.jabref.org/t/push-to-texshop-mac/2699/17?u=siedlerchr)
 - We only show the notification "Saving library..." if the library contains more than 2000 entries. [#9803](https://github.com/JabRef/jabref/issues/9803)
 - We enhanced the dialog for adding new fields in the content selector with a selection box containing a list of standard fields. [#10912](https://github.com/JabRef/jabref/pull/10912)
@@ -42,10 +46,12 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the preview panel showing the wrong entry (an entry that is not selected in the entry table). [#9172](https://github.com/JabRef/jabref/issues/9172)
 - We fixed an issue where HTML-reserved characters like '&' and '<', in addition to HTML entities like '&amp;' were not rendered correctly in entry preview. [#10677](https://github.com/JabRef/jabref/issues/10677)
 - The last page of a PDF is now indexed by the full text search. [#10193](https://github.com/JabRef/jabref/issues/10193)
+- The default owner of an entry can be changed again. [#10924](https://github.com/JabRef/jabref/issues/10924)
 - We fixed an issue where the duplicate check did not take umlauts or other LaTeX-encoded characters into account. [#10744](https://github.com/JabRef/jabref/pull/10744)
 - We fixed the colors of the icon on hover for unset special fields. [#10431](https://github.com/JabRef/jabref/issues/10431)
 - We fixed an issue where the CrossRef field did not work if autocompletion was disabled [#8145](https://github.com/JabRef/jabref/issues/8145)
 - We fixed an issue where exporting`@electronic` and `@online` entry types to the Office XMl would duplicate the field `title`  [#10807](https://github.com/JabRef/jabref/issues/10807)
+- We fixed an issue where the `CommentsTab` was not properly formatted when the `defaultOwner` contained capital or special letters. [#10870](https://github.com/JabRef/jabref/issues/10870)
 
 ### Removed
 

build.gradle

@@ -5,7 +5,7 @@ import org.jabref.build.xjc.XjcTask
 plugins {
     id 'application'
 
-    id 'com.github.andygoossens.modernizer' version '1.9.0'
+    id 'com.github.andygoossens.modernizer' version '1.9.2'
 
     id 'me.champeau.jmh' version '0.7.2'
 
@@ -119,11 +119,12 @@ dependencies {
         exclude group: 'org.junit.jupiter'
     }
 
-    implementation 'org.apache.lucene:lucene-core:9.9.2'
-    implementation 'org.apache.lucene:lucene-queryparser:9.9.2'
-    implementation 'org.apache.lucene:lucene-queries:9.9.1'
-    implementation 'org.apache.lucene:lucene-analysis-common:9.9.2'
-    implementation 'org.apache.lucene:lucene-highlighter:9.9.2'
+    def luceneVersion = "9.10.0"
+    implementation "org.apache.lucene:lucene-core:$luceneVersion"
+    implementation "org.apache.lucene:lucene-queryparser:$luceneVersion"
+    implementation "org.apache.lucene:lucene-queries:$luceneVersion"
+    implementation "org.apache.lucene:lucene-analysis-common:$luceneVersion"
+    implementation "org.apache.lucene:lucene-highlighter:$luceneVersion"
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.10.0'
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.14.0'
@@ -176,7 +177,7 @@ dependencies {
     implementation('com.tobiasdiez:easybind:2.2.1-SNAPSHOT')
     implementation 'org.fxmisc.flowless:flowless:0.7.2'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.2'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '1.97.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.0.3') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude group: 'org.apache.logging.log4j'
     }
@@ -195,7 +196,7 @@ dependencies {
     // route all requests to java.util.logging to SLF4J (which in turn routes to tinylog)
     implementation 'org.slf4j:jul-to-slf4j:2.0.9'
     // route all requests to log4j to SLF4J
-    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.22.1'
+    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.23.0'
 
     implementation('de.undercouch:citeproc-java:3.0.0-beta.2') {
         exclude group: 'org.antlr'
@@ -560,7 +561,7 @@ tasks.register('deleteInstallerTemp', Delete) {
 jpackage.dependsOn deleteInstallerTemp
 jlinkZip.dependsOn jpackage
 jlink {
-    addOptions('--strip-debug', '--compress', '2', '--no-header-files', '--no-man-pages')
+    addOptions('--strip-debug', '--compress', 'zip-6', '--no-header-files', '--no-man-pages')
     launcher {
         name = 'JabRef'
     }
@@ -577,7 +578,8 @@ jlink {
 
     // TODO: Remove the following correction to the merged module
     // The module descriptor automatically generated by the plugin for the merged module contained some invalid entries.
-    // Execute ./gradlew suggestMergedModuleInfo and include the suggested directives here.
+    // This is based on ./gradlew suggestMergedModuleInfo, sort, strip ";"", comment non-used modules, and include the suggested directives here.
+    //   However, we need to fine-tune this manually (non-alphabetic order)
     mergedModule {
         requires 'java.compiler'
         requires 'java.datatransfer'
@@ -600,6 +602,7 @@ jlink {
         requires 'jdk.security.jgss'
         requires 'jdk.xml.dom'
         requires 'com.google.gson'
+        requires 'org.jsoup'
         requires 'org.slf4j'
         requires 'jakarta.xml.bind'
         requires 'org.apache.commons.lang3'

docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.md

@@ -139,7 +139,8 @@ Press "OK".
 ## Disable too advanced code folding
 
 Go to **File > Settings... > Editor > General > Code Folding**.
-At "Java", disable "General > File header", "General > Imports", and "Java > One-line methods".
+At section "General", disable "File header" and "Imports".
+At section "Java", disable "One-line methods".
 
 {% figure caption:"Code foldings disabled" %}
 ![Code foldings disabled](guidelines-settings-intellij-code-foldings.png)