Merge branch 'main' into branch-1

.devcontainer/devcontainer.json

@@ -31,7 +31,7 @@
         // Install java.
         // See https://github.com/devcontainers/features/tree/main/src/java#options for details.
         "ghcr.io/devcontainers/features/java:1": {
-            "version": "21.0.2-tem",
+            "version": "23.0.1-tem",
             "installGradle": false,
             "jdkDistro": "Temurin"
         }

.github/workflows/assign-issue.yml

@@ -19,7 +19,7 @@ jobs:
         uses: takanome-dev/assign-issue-action@beta
         with:
           github_token: '${{ secrets.GITHUB_TOKEN }}'
-          days_until_unassign: 30
+          days_until_unassign: 90
           maintainers: koppor, Siedlerchr, ThiloteE, calixtus, HoussemNasri
           assigned_comment: |
             👋 Hey @{{ handle }}, thank you for your interest in this issue! 🎉

.github/workflows/check-links.yml

@@ -32,7 +32,7 @@ jobs:
           restore-keys: cache-lychee-
       - name: Link Checker
         id: lychee
-        uses: lycheeverse/lychee-action@v2.0.2
+        uses: lycheeverse/lychee-action@v2.1.0
         with:
           fail: true
           args: --accept '200,201,202,203,204,403,429,500' --max-concurrency 1 --cache --no-progress --exclude-all-private './**/*.md'

.github/workflows/cleanup-pr.yml

@@ -29,7 +29,7 @@ jobs:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Delete folder on builds.jabref.org
         if: steps.checksecrets.outputs.secretspresent == 'YES'
-        uses: appleboy/ssh-action@v1.1.0
+        uses: appleboy/ssh-action@v1.2.0
         with:
           script: rm -rf /var/www/builds.jabref.org/www/pull/${{ github.event.pull_request.number }} || true
           host: build-upload.jabref.org

.github/workflows/deployment-arm64.yml

@@ -69,16 +69,16 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].0
+        uses: gittools/actions/gitversion/[email protected].3
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].0
+        uses: gittools/actions/gitversion/[email protected].3
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:
-          java-version: 21.0.5
+          java-version: 23.0.1
           distribution: 'temurin'
       - name: Clean up keychain
         run: |

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

@@ -37,7 +37,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest, buildjet-8vcpu-ubuntu-2204-arm]
-        jdk: [21]
+        jdk: [23]
         javafx: [24]
         include:
           - os: ubuntu-latest
@@ -85,12 +85,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].0
+        uses: gittools/actions/gitversion/[email protected].3
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].0
+        uses: gittools/actions/gitversion/[email protected].3
 
       # JDK
       - name: 'Set up JDK ${{ matrix.jdk }}'

.github/workflows/deployment.yml

@@ -81,16 +81,16 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].0
+        uses: gittools/actions/gitversion/[email protected].3
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].0
+        uses: gittools/actions/gitversion/[email protected].3
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:
-          java-version: 21.0.5
+          java-version: 23.0.1
           distribution: 'temurin'
       - name: Setup Gradle
         uses: gradle/actions/setup-gradle@v4

.github/workflows/tests-fetchers.yml

@@ -48,7 +48,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          java-version: 21.0.5
+          java-version: 23.0.1
           distribution: 'temurin'
       - name: Setup Gradle
         uses: gradle/actions/setup-gradle@v4

.github/workflows/tests.yml

@@ -37,7 +37,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          java-version: 21.0.5
+          java-version: 23.0.1
           distribution: 'temurin'
       - name: Run checkstyle reporter
         uses: dbelyaev/action-checkstyle@master
@@ -65,7 +65,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          java-version: 21.0.5
+          java-version: 23.0.1
           distribution: 'temurin'
       - name: Setup Gradle
         uses: gradle/actions/setup-gradle@v4
@@ -87,7 +87,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          java-version: 21.0.5
+          java-version: 23.0.1
           distribution: 'temurin'
       - name: Setup Gradle
         uses: gradle/actions/setup-gradle@v4
@@ -109,7 +109,7 @@ jobs:
           submodules: 'false'
           show-progress: 'false'
       - name: markdownlint-cli2-action
-        uses: DavidAnson/markdownlint-cli2-action@v17
+        uses: DavidAnson/markdownlint-cli2-action@v18
         with:
           globs: |
             *.md
@@ -175,7 +175,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          java-version: 21.0.5
+          java-version: 23.0.1
           distribution: 'temurin'
       - name: Setup Gradle
         uses: gradle/actions/setup-gradle@v4
@@ -218,7 +218,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          java-version: 21.0.5
+          java-version: 23.0.1
           distribution: 'temurin'
       - name: Setup Gradle
         uses: gradle/actions/setup-gradle@v4
@@ -259,7 +259,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          java-version: 21.0.5
+          java-version: 23.0.1
           distribution: 'temurin'
       - name: Setup Gradle
         uses: gradle/actions/setup-gradle@v4
@@ -309,7 +309,7 @@ jobs:
         if: github.ref == 'refs/heads/main'
         uses: actions/setup-java@v4
         with:
-          java-version: 21.0.5
+          java-version: 23.0.1
           distribution: 'temurin'
       - name: Setup Gradle
         uses: gradle/actions/setup-gradle@v4
@@ -322,7 +322,7 @@ jobs:
           CI: "true"
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
           DBMS: "postgresql"
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         if: (github.ref == 'refs/heads/main') && (steps.checksecrets.outputs.secretspresent == 'YES')
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -342,7 +342,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          java-version: 21.0.5
+          java-version: 23.0.1
           distribution: 'temurin'
       - name: Setup Gradle
         uses: gradle/actions/setup-gradle@v4

.github/workflows/update-gradle-wrapper.yml

@@ -15,7 +15,7 @@ jobs:
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:
-          java-version: 21.0.5
+          java-version: 23.0.1
           distribution: 'temurin'
 
       - name: Update Gradle Wrapper

.gitpod.Dockerfile

@@ -5,4 +5,4 @@ FROM gitpod/workspace-full
 # All available versions can be listed using sdk ls java
 # More information about SDKMAN available at https://github.com/sdkman/sdkman-cli#sdkman-cli
 RUN bash -c ". /home/gitpod/.sdkman/bin/sdkman-init.sh \
-             && sdk install java 21-open"
+             && sdk install java 23-open"

.moderne/moderne.yml

@@ -0,0 +1,3 @@
+specs: specs.moderne.ai/v1/cli
+java:
+  selectedJdk: '23'

CHANGELOG.md

@@ -11,11 +11,12 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
-- Implemented BackupManagerGit to handle automatic backups of .bib files using Git, ensuring centralized, version-controlled backup management. [#2961] (https://github.com/JabRef/jabref/issues/2961#event-14646591632)
-- Added automatic copying of .bib files to a jabref/backups directory every 19 seconds with comprehensive commit history. [#2961]
-- Added support for unique file naming using UUIDs to prevent overwriting files with identical names in the backup directory. [#2961]
-- Introduced UI functionality (only during opening) for saving, restoring, reviewing and discarding changes with accurate commit details retrieval. [#2961]
-- Enabled a "Restore" button to recover specific backup versions. [#2961]
+- Implemented BackupManagerGit to handle automatic backups of .bib files using Git, ensuring centralized, version-controlled backup management. [#2961](https://github.com/JabRef/jabref/issues/2961)
+- Added automatic copying of .bib files to a jabref/backups directory every 19 seconds with comprehensive commit history. [#2961](https://github.com/JabRef/jabref/issues/2961)
+- Added support for unique file naming using UUIDs to prevent overwriting files with identical names in the backup directory. [#2961](https://github.com/JabRef/jabref/issues/2961)
+- Introduced UI functionality (only during opening) for saving, restoring, reviewing and discarding changes with accurate commit details retrieval. [#2961](https://github.com/JabRef/jabref/issues/2961)
+- Enabled a "Restore" button to recover specific backup versions. [#2961](https://github.com/JabRef/jabref/issues/2961)
+- We added a Markdown export layout. [#12220](https://github.com/JabRef/jabref/pull/12220)
 - We added a "view as BibTeX" option before importing an entry from the citation relation tab. [#11826](https://github.com/JabRef/jabref/issues/11826)
 - We added support finding LaTeX-encoded special characters based on plain Unicode and vice versa. [#11542](https://github.com/JabRef/jabref/pull/11542)
 - When a search hits a file, the file icon of that entry is changed accordingly. [#11542](https://github.com/JabRef/jabref/pull/11542)
@@ -42,17 +43,21 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a different background color to the search bar to indicate when the search syntax is wrong. [#11658](https://github.com/JabRef/jabref/pull/11658)
 - We added a setting which always adds the literal "Cited on pages" text before each JStyle citation. [#11691](https://github.com/JabRef/jabref/pull/11732)
 - We added a new plain citation parser that uses LLMs. [#11825](https://github.com/JabRef/jabref/issues/11825)
+- We added support for `langid` field for biblatex libraries. [#10868](https://github.com/JabRef/jabref/issues/10868)
 - We added support for modifier keys when dropping a file on an entry in the main table. [#12001](https://github.com/JabRef/jabref/pull/12001)
 - We added an importer for SSRN URLs. [#12021](https://github.com/JabRef/jabref/pull/12021)
 - We added a compare button to the duplicates in the citation relations tab to open the "Possible duplicate entries" window. [#11192](https://github.com/JabRef/jabref/issues/11192)
 - We added automatic browser extension install on Windows for Chrome and Edge. [#6076](https://github.com/JabRef/jabref/issues/6076)
+- We added support to automatically open a `.bib` file in the current/parent folder if no other library is opened. [koppor#377](https://github.com/koppor/jabref/issues/377)
 - We added a search bar for filtering keyboard shortcuts. [#11686](https://github.com/JabRef/jabref/issues/11686)
+- We added new modifiers `camel_case`, `camel_case_n`, `short_title`, and `very_short_title` for the [citation key generator](https://docs.jabref.org/setup/citationkeypatterns). [#11367](https://github.com/JabRef/jabref/issues/11367)
 - By double clicking on a local citation in the Citation Relations Tab you can now jump the linked entry. [#11955](https://github.com/JabRef/jabref/pull/11955)
 - We use the menu icon for background tasks as a progress indicator to visualise an import's progress when dragging and dropping several PDF files into the main table. [#12072](https://github.com/JabRef/jabref/pull/12072)
+- The PDF content importer now supports importing title from upto the second page of the PDF. [#12139](https://github.com/JabRef/jabref/issues/12139)
 
 ### Changed
 
-- Refactored backup-related components to integrate with the new BackupManagerGit, replacing the older BackupManager logic. [#2961]
+- Refactored backup-related components to integrate with the new BackupManagerGit, replacing the older BackupManager logic. [#2961](https://github.com/JabRef/jabref/issues/2961)
 - A search in "any" fields ignores the [groups](https://docs.jabref.org/finding-sorting-and-cleaning-entries/groups). [#7996](https://github.com/JabRef/jabref/issues/7996)
 - When a communication error with an [online service](https://docs.jabref.org/collect/import-using-online-bibliographic-database) occurs, JabRef displays the HTTP error. [#11223](https://github.com/JabRef/jabref/issues/11223)
 - The Pubmed/Medline Plain importer now imports the PMID field as well [#11488](https://github.com/JabRef/jabref/issues/11488)
@@ -79,7 +84,10 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - When importing a file using "Find Unlinked Files", when one or more file directories are available, the file path will be relativized where possible [koppor#549](https://github.com/koppor/jabref/issues/549)
 - We added minimum window sizing for windows dedicated to creating new entries [#11944](https://github.com/JabRef/jabref/issues/11944)
 - We changed the name of the library-based file directory from 'General File Directory' to 'Library-specific File Directory' per issue. [#571](https://github.com/koppor/jabref/issues/571)
+- We changed the defualt [unwanted charachters](https://docs.jabref.org/setup/citationkeypatterns#removing-unwanted-characters) in the citation key generator and allow a dash (`-`) and colon (`:`) being part of a citation key. [#12144](https://github.com/JabRef/jabref/pull/12144)
 - The CitationKey column is now a default shown column for the entry table. [#10510](https://github.com/JabRef/jabref/issues/10510)
+- We disabled the actions "Open Terminal here" and "Reveal in file explorer" for unsaved libraries. [#11920](https://github.com/JabRef/jabref/issues/11920)
+- JabRef now opens the corresponding directory in the library properties when "Browse" is clicked. [#12223](https://github.com/JabRef/jabref/pull/12223)
 
 ### Fixed
 
@@ -116,10 +124,14 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the "Do not ask again" checkbox was not working, when asking for permission to use Grobid [koppor#556](https://github.com/koppor/jabref/issues/566).
 - We fixed an issue where we display warning message for moving attached open files. [#10121](https://github.com/JabRef/jabref/issues/10121)
 - We fixed an issue where it was not possible to select selecting content of other user's comments.[#11106](https://github.com/JabRef/jabref/issues/11106)
+- We fixed an issue when handling URLs containing a pipe (`|`) character. [#11876](https://github.com/JabRef/jabref/issues/11876)
 - We fixed an issue where web search preferences "Custom API key" table modifications not discarded. [#11925](https://github.com/JabRef/jabref/issues/11925)
 - We fixed an issue when opening attached files in [extra file columns](https://docs.jabref.org/finding-sorting-and-cleaning-entries/filelinks#adding-additional-columns-to-entry-table-for-file-types). [#12005](https://github.com/JabRef/jabref/issues/12005)
 - We fixed an issue where trying to open a library from a failed mounted directory on Mac would cause an error. [#10548](https://github.com/JabRef/jabref/issues/10548)
+- We fixed an issue when the preview was out of sync. [#9172](https://github.com/JabRef/jabref/issues/9172)
 - We fixed an issue where identifier paste couldn't work with Unicode REPLACEMENT CHARACTER. [#11986](https://github.com/JabRef/jabref/issues/11986)
+- We fixed an issue when click on entry at "Check Integrity" wasn't properly focusing the entry and field. [#11997](https://github.com/JabRef/jabref/issues/11997)
+- We fixed an issue with the ui not scaling when changing the font size [#11219](https://github.com/JabRef/jabref/issues/11219)
 
 ### Removed
 

README.md

@@ -95,6 +95,33 @@ We will discuss improvements with you and agree to merge them once the [develope
 Please also remember to discuss bigger changes early with the core developers to ensure properly spend time and work.
 Some fundamental design decisions can be found within our list of [Architectural Decision Records](https://devdocs.jabref.org/decisions/).
 
+## Research and Education
+
+JabRef welcomes research applied to it.
+The current list of papers where JabRef helped to enhance science is maintained at <https://github.com/JabRef/jabref/wiki/JabRef-in-the-Media>.
+
+The JabRef team also fosters to use JabRef in Software Engineering training.
+We offer guidelines for this at <https://devdocs.jabref.org/teaching.html>.
+
+When citing JabRef, please use following citation:
+
+```bibtex
+@Article{jabref,
+  author  = {Oliver Kopp and Carl Christian Snethlage and Christoph Schwentker},
+  title   = {JabRef: BibTeX-based literature management software},
+  journal = {TUGboat},
+  volume  = {44},
+  number  = {3},
+  pages   = {441--447},
+  doi     = {10.47397/tb/44-3/tb138kopp-jabref},
+  issn    = {0896-3207},
+  issue   = {138},
+  year    = {2023},
+}
+```
+
+DOI (also includes [full text](https://tug.org/TUGboat/tb44-3/tb138kopp-jabref.pdf)): [10.47397/tb/44-3/tb138kopp-jabref](https://doi.org/10.47397/tb/44-3/tb138kopp-jabref).
+
 ## Sponsoring
 
 JabRef development is powered by YourKit Java Profiler