Merge remote-tracking branch 'origin/main' into gsoc-ocr-tess4j-initial-implementation

Author: koppor

.dockerignore

@@ -1,22 +1,27 @@
+.git
 .gitignore
 .dockerignore
 
 Dockerfile
 Dockerfile.*
 .github/
 
+.devcontainer/
+
+*/bin
+*/build
+*/out
+
+docs/
+
+gg.cmd
+gradlew.bat
+
 # no generated files in version control
 src/main/gen/
 src/main/generated/
 src-gen/
 
-src/main/resources/csl-styles
-src/main/resources/csl-locales
-buildres/abbrv.jabref.org
-
-jablib/src/main/resources/csl-styles
-jablib/src/main/resources/csl-locales
-
 .lycheecache
 
 .kotlin

.github/dependabot.yml

@@ -4,6 +4,7 @@ updates:
     directories:
       - "/build-logic"   # versions of 3rd party gradle plugins
       - "/versions"      # versions of 3rd party dependencies of all JabRef modules
+      - "/"              # plugins
     schedule:
       interval: weekly
     labels:

.github/workflows/automerge.yml

@@ -14,8 +14,8 @@ jobs:
         id: shouldrun
         shell: bash
         run: |
-          actor="${{ github.actor }}"
-          title="${{ github.event.pull_request.title }}"
+          actor='${{ github.actor }}'
+          title='${{ github.event.pull_request.title }}'
 
           if [[ "$actor" == "renovate-bot" ]]; then
             echo "✅ from renote-bot"

.github/workflows/dockerimages.yml

@@ -3,6 +3,7 @@ name: Docker Images
 on:
   pull_request:
     paths:
+      - '.dockerignore'
       - '.github/workflows/dockerimages.yml'
       - 'Dockerfile.*'
   push:
@@ -51,6 +52,19 @@ jobs:
         uses: docker/setup-qemu-action@v3
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
+      - name: Fetch all history for all tags and branches
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: 'true'
+          show-progress: 'false'
+      - name: Install GitVersion
+        uses: gittools/actions/gitversion/setup@v3.2.1
+        with:
+          versionSpec: "5.x"
+      - name: Run GitVersion
+        id: gitversion
+        uses: gittools/actions/gitversion/execute@v3.2.1
       - name: Build and push
         uses: docker/build-push-action@v6
         with:
@@ -63,3 +77,6 @@ jobs:
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
           file: Dockerfile.${{ matrix.component }}
+          build-args: |
+            VERSION=${{ steps.gitversion.outputs.AssemblySemVer }}
+            VERSION_INFO=${{ steps.gitversion.outputs.InformationalVersion }}

.github/workflows/tests.yml

@@ -66,9 +66,24 @@ jobs:
           distribution: 'zulu'
       - name: Setup Gradle
         uses: gradle/actions/setup-gradle@v4
+      - name: Generate JBang cache key
+        id: cache-key
+        shell: bash
+        run: |
+          echo "cache_key=jbang-$(date +%F)" >> $GITHUB_OUTPUT
+      - name: Use cache
+        uses: actions/cache@v4
+        with:
+          lookup-only: true
+          path: ~/.jbang
+          key: ${{ steps.cache-key.outputs.cache_key }}
+          restore-keys:
+            jbang-
+      - name: Setup JBang
+        uses: jbangdev/setup-jbang@main
       - name: Run OpenRewrite
         run: |
-          ./gradlew rewriteDryRun
+          ./gradlew --no-configuration-cache :rewriteDryRun
 
   modernizer:
     name: Modernizer
@@ -135,7 +150,7 @@ jobs:
       - name: Lint CHANGELOG.md
         run: |
           # run heylogs verification
-          jbang com.github.nbbrd.heylogs:heylogs-cli:0.9.3:bin check CHANGELOG.md > heylogs.txt || true
+          jbang com.github.nbbrd.heylogs:heylogs-cli:0.10.0:bin check CHANGELOG.md > heylogs.txt || true
 
           # improve output
           sed -i 's/all-h2-contain-a-version/all-h2-contain-a-version (ignored)/' heylogs.txt
@@ -465,7 +480,8 @@ jobs:
 
   checklist-checked:
     if: >
-      github.event_name == 'pull_request' && !(
+      (github.repository_owner != 'JabRef') &&
+      (github.event_name == 'pull_request') && !(
         (github.actor == 'dependabot[bot]') ||
         (
           startsWith(github.event.pull_request.title, '[Bot] ') ||

.jbang/JabSrvLauncher.java

@@ -9,23 +9,30 @@
 //FILES tinylog.properties=../jabsrv-cli/src/main/resources/tinylog.properties
 
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/dto/BibEntryDTO.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/dto/cayw/SimpleJson.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/dto/GlobalExceptionMapper.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/dto/GsonFactory.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/JabrefMediaType.java
-//SOURCES ../jabsrv/src/main/java/org/jabref/http/JabRefResourceLocator.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/CAYWResource.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/CAYWQueryParams.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/gui/CAYWEntry.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/gui/SearchDialog.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/gui/SearchField.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/gui/SearchResultContainer.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/gui/SelectedItemsContainer.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/format/BibLatexFormatter.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/format/CAYWFormatter.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/format/FormatterService.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/format/SimpleJsonFormatter.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/CORSFilter.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/LibrariesResource.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/LibraryResource.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/PreferencesFactory.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/RootResource.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/Server.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/services/ContextsToServe.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/services/FilesToServe.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/server/services/ServerUtils.java
 
 // REPOS mavencentral,snapshots=https://central.sonatype.com/repository/maven-snapshots/
 //REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,s01oss=https://s01.oss.sonatype.org/content/repositories/snapshots/,oss=https://oss.sonatype.org/content/repositories,jitpack=https://jitpack.io,oss2=https://oss.sonatype.org/content/groups/public,ossrh=https://oss.sonatype.org/content/repositories/snapshots

.jbang/README.md

@@ -0,0 +1,53 @@
+# JBang scripts for JabRef
+
+This directory contains JBang scripts for JabRef.
+[JBang](https://www.jbang.dev/) allows for running Java applications without having a JDK installed (before).
+
+Three use cases:
+
+- Try out any pull request with minimal installation. See [our blog entry](https://blog.jabref.org/2025/05/31/run-pr/) for details.
+- Run JabKit - JabRef's CLI tool.
+- Run JabSrv - JabRef's HTTP server.
+
+## Running JabKit without installation
+
+By using [gg.cmd](https://github.com/eirikb/gg#ggcmd) you can "just run" JabKit with minimal setup:
+
+1. Download `gg.cmd` from: <https://github.com/eirikb/gg#ggcmd>. `gg.cmd` is a "binary" running on macOS, Linux, and Windows. No need for different binaries on different operating systems.
+2. Run `gg.cmd`. This will download and use JBang as wrapper around running JabKit:
+
+    - Linux/macOS: Run `sh ./gg.cmd jbang jabkit@jabref --help`.
+    - Windows: Run `gg.cmd jbang jabkit@jabref --help`.
+
+You can also put `gg.cmd` on your `PATH` and make it executable.
+Then you enable `alias jabkit='gg.cmd jbang jabkit@jabref`.
+
+## Running JabKit with JBang
+
+If you have JBang installed, just run
+
+```terminal
+jbang jabkit@jabref --help
+```
+
+You can also install `jabkit` permanently in your `PATH`:
+
+1. [Install JBang](https://www.jbang.dev/download/). E.g., by `brew install jbangdev/tap/jbang` or `choco install jbang`
+2. Make `jabkit` available on the command line: `jbang app install jabkit@jabref`
+3. Run `jabkit --help`
+
+[JBang takes care about updating JabKit automatically](https://github.com/orgs/jbangdev/discussions/1636#discussioncomment-6150992).
+
+## Running JabSrv
+
+If you have JBang installed, just run following command
+
+```terminal
+jbang jabsrv@jabref --help
+```
+
+With `gg.cmd`:
+
+```terminal
+sh ./gg.cmd jbang jabsrv@jabref --help
+```

.vscode/ltex.dictionary.en-US.txt

@@ -1,9 +1,10 @@
 Checkstyle
 CouchDB
 JabDrive
+JabKit
 JabRef
+JabSrv
+JBang
 OpenFastTrace
 OpenRewrite
 Temurin
-
-JabKit

CHANGELOG.md

@@ -13,6 +13,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 - We introduced a settings parameter to manage citations' relations local storage time-to-live with a default value set to 30 days. [#11189](https://github.com/JabRef/jabref/issues/11189)
 - We distribute arm64 images for Linux. [#10842](https://github.com/JabRef/jabref/issues/10842)
+- When adding an entry to a library, a warning is displayed if said entry already exists in an active library. [#13261](https://github.com/JabRef/jabref/issues/13261)
 - We added the field `monthfiled` to the default list of fields to resolve BibTeX-Strings for [#13375](https://github.com/JabRef/jabref/issues/13375)
 - We added a new ID based fetcher for [EuropePMC](https://europepmc.org/). [#13389](https://github.com/JabRef/jabref/pull/13389)
 - We added an initial [cite as you write](https://retorque.re/zotero-better-bibtex/citing/cayw/) endpoint. [#13187](https://github.com/JabRef/jabref/issues/13187)  
@@ -36,15 +37,14 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added an "Open example library" button to Welcome Tab. [#13014](https://github.com/JabRef/jabref/issues/13014)
 - We added automatic detection and selection of the identifier type (e.g., DOI, ISBN, arXiv) based on clipboard content when opening the "New Entry" dialog [#13111](https://github.com/JabRef/jabref/pull/13111)
 - We added support for import of a Refer/BibIX file format. [#13069](https://github.com/JabRef/jabref/issues/13069)
+- We added markdown rendering and copy capabilities to AI chat responses. [#12234](https://github.com/JabRef/jabref/issues/12234)
 - We added a new `jabkit` command `pseudonymize` to pseudonymize the library. [#13109](https://github.com/JabRef/jabref/issues/13109)
 - We added functionality to focus running instance when trying to start a second instance. [#13129](https://github.com/JabRef/jabref/issues/13129)
 - We added a highlighted diff regarding changes to the Group Tree Structure of a bib file, made outside JabRef. [#11221](https://github.com/JabRef/jabref/issues/11221)
 - We added a new setting in the 'Entry Editor' preferences to hide the 'File Annotations' tab when no annotations are available. [#13143](https://github.com/JabRef/jabref/issues/13143)
 - We added support for multi-file import across different formats. [#13269](https://github.com/JabRef/jabref/issues/13269)
+- We improved the detection of DOIs on the first page of a PDF. [#13487](https://github.com/JabRef/jabref/pull/13487)
 - We added support for dark title bar on Windows. [#11457](https://github.com/JabRef/jabref/issues/11457)
-
-### Changed
-
 - We moved some functionality from the graphical application `jabref` with new command verbs `generate-citation-keys`, `check-consistency`, `fetch`, `search`, `convert`, `generate-bib-from-aux`, `preferences` and `pdf` to the new toolkit. [#13012](https://github.com/JabRef/jabref/pull/13012) [#110](https://github.com/JabRef/jabref/issues/110)
 - We merged the 'New Entry', 'Import by ID', and 'New Entry from Plain Text' tools into a single 'Create New Entry' tool. [#8808](https://github.com/JabRef/jabref/issues/8808)
 - We renamed the "Body Text" CSL bibliography header format name to "Text body" as per internal LibreOffice conventions. [#13074](https://github.com/JabRef/jabref/pull/13074)

Dockerfile.jabkit

@@ -1,16 +1,21 @@
 FROM gradle:jdk24-noble AS build
 
-WORKDIR /app
+LABEL org.opencontainers.image.title="jabkit"
+LABEL org.opencontainers.image.description="JabRef's CLI tool"
 
-COPY . .
+ARG VERSION="100.0.0"
+ARG VERSION_INFO="100.0.0"
+ARG TAG_BUILD="false"
+
+WORKDIR /build
 
-RUN gradle --no-daemon :jabkit:jpackage
+COPY . .
 
-RUN find jabkit/build/distribution
+RUN gradle --no-daemon -PprojVersion="${VERSION}" -PprojVersionInfo="${VERSION_INFO}" -Ptagbuild="${TAG_BUILD}" :jabkit:jpackage
 
 RUN mkdir /dist
 
-RUN mv jabkit/build/distribution/jabkit /dist
+RUN mv jabkit/build/packages/*/* /dist
 
 # jpackage needs glibc; alpine does not work
 FROM debian:bookworm-slim AS runtime