Merge branch 'main' into koppor-patch-1

.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/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

@@ -69,12 +69,12 @@ 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:

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

@@ -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

@@ -81,12 +81,12 @@ 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
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

.github/workflows/tests.yml

@@ -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
@@ -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 }}

.moderne/moderne.yml

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

CHANGELOG.md

@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- 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)
@@ -41,9 +42,12 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - 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
 
@@ -75,6 +79,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - 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
 
@@ -111,11 +117,13 @@ 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)
 
 ### 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  

build.gradle

@@ -29,7 +29,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.27.0'
+    id 'org.openrewrite.rewrite' version '6.27.2'
 
     id "org.itsallcode.openfasttrace" version "3.0.1"
 }
@@ -54,13 +54,14 @@ java {
 
     toolchain {
         // If this is updated, also update
-        // - .gitpod.Dockerfile
+        // - build.gradle -> jacoco -> toolVersion (because JaCoCo does not support newest JDK out of the box. Check versions at https://www.jacoco.org/jacoco/trunk/doc/changes.html)
         // - .devcontainer/devcontainer.json#L34 and
+        // - .gitpod.Dockerfile
+        // - .moderne/moderne.yml
         // - .github/workflows/deployment*.yml
         // - .github/workflows/tests*.yml
         // - .github/workflows/update-gradle-wrapper.yml
         // - docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.md
-        // - build.gradle -> jacoco -> toolVersion (because JaCoCo does not support newest JDK out of the box. Check versions at https://www.jacoco.org/jacoco/trunk/doc/changes.html)
         languageVersion = JavaLanguageVersion.of(23)
         // See https://docs.gradle.org/current/javadoc/org/gradle/jvm/toolchain/JvmVendorSpec.html for a full list
         // vendor = JvmVendorSpec.AMAZON
@@ -255,7 +256,7 @@ dependencies {
         exclude group: 'tech.units'
     }
     // Required by gemsfx
-    implementation 'tech.units:indriya:2.2'
+    implementation 'tech.units:indriya:2.2.1'
     // Required by gemsfx and langchain4j
     implementation ('com.squareup.retrofit2:retrofit:2.11.0') {
         exclude group: 'com.squareup.okhttp3'
@@ -265,7 +266,7 @@ dependencies {
 
     // region HTTP clients
     implementation 'org.jsoup:jsoup:1.18.1'
-    implementation 'com.konghq:unirest-java-core:4.4.4'
+    implementation 'com.konghq:unirest-java-core:4.4.5'
     implementation 'com.konghq:unirest-modules-gson:4.4.5'
     implementation 'org.apache.httpcomponents.client5:httpclient5:5.4'
     // endregion
@@ -278,7 +279,7 @@ dependencies {
     // route all requests to java.util.logging to SLF4J (which in turn routes to tinylog)
     implementation 'org.slf4j:jul-to-slf4j:2.0.16'
     // route all requests to log4j to SLF4J
-    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.24.1'
+    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.24.2'
 
     implementation('de.undercouch:citeproc-java:3.1.0') {
         exclude group: 'org.antlr'
@@ -334,23 +335,23 @@ dependencies {
     implementation 'org.yaml:snakeyaml:2.3'
 
     // region AI
-    implementation 'dev.langchain4j:langchain4j:0.35.0'
+    implementation 'dev.langchain4j:langchain4j:0.36.0'
     // Even though we use jvm-openai for LLM connection, we still need this package for tokenization.
-    implementation('dev.langchain4j:langchain4j-open-ai:0.35.0') {
+    implementation('dev.langchain4j:langchain4j-open-ai:0.36.2') {
         exclude group: 'com.squareup.okhttp3'
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
         exclude group: 'org.jetbrains.kotlin'
     }
-    implementation('dev.langchain4j:langchain4j-mistral-ai:0.35.0') {
+    implementation('dev.langchain4j:langchain4j-mistral-ai:0.36.2') {
         exclude group: 'com.squareup.okhttp3'
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
         exclude group: 'org.jetbrains.kotlin'
     }
-    implementation('dev.langchain4j:langchain4j-google-ai-gemini:0.35.0') {
+    implementation('dev.langchain4j:langchain4j-google-ai-gemini:0.36.0') {
         exclude group: 'com.squareup.okhttp3'
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
     }
-    implementation('dev.langchain4j:langchain4j-hugging-face:0.35.0') {
+    implementation('dev.langchain4j:langchain4j-hugging-face:0.36.0') {
         exclude group: 'com.squareup.okhttp3'
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
         exclude group: 'org.jetbrains.kotlin'
@@ -367,20 +368,20 @@ dependencies {
         exclude group: 'org.jetbrains.kotlin', module: 'kotlin-stdlib-jdk8'
     }
     // GemxFX also (transitively) depends on kotlin
-    implementation 'org.jetbrains.kotlin:kotlin-stdlib-jdk8:2.0.21'
+    implementation 'org.jetbrains.kotlin:kotlin-stdlib-jdk8:2.1.0'
     // endregion
 
-    implementation 'commons-io:commons-io:2.17.0'
+    implementation 'commons-io:commons-io:2.18.0'
 
     // Even if "compileOnly" is used, IntelliJ always adds to module-info.java. To avoid issues during committing, we use "implementation" instead of "compileOnly"
     implementation 'io.github.adr:e-adr:2.0.0-SNAPSHOT'
 
-    implementation 'io.zonky.test:embedded-postgres:2.0.7'
-    implementation enforcedPlatform('io.zonky.test.postgres:embedded-postgres-binaries-bom:17.0.0')
+    implementation 'io.zonky.test:embedded-postgres:2.1.0'
+    implementation enforcedPlatform('io.zonky.test.postgres:embedded-postgres-binaries-bom:17.2.0')
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.177'
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.11.0'
-    testImplementation 'org.junit.platform:junit-platform-launcher:1.10.3'
+    testImplementation 'io.github.classgraph:classgraph:4.8.179'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.11.3'
+    testImplementation 'org.junit.platform:junit-platform-launcher:1.11.3'
 
     testImplementation 'org.mockito:mockito-core:5.14.2'
     testImplementation 'org.xmlunit:xmlunit-core:2.10.0'
@@ -393,14 +394,14 @@ dependencies {
     testImplementation "com.github.javaparser:javaparser-symbol-solver-core:3.26.2"
 
     // recommended by https://github.com/wiremock/wiremock/issues/2149#issuecomment-1835775954
-    testImplementation 'org.wiremock:wiremock-standalone:3.3.1'
+    testImplementation 'org.wiremock:wiremock-standalone:3.9.2'
 
     checkstyle 'com.puppycrawl.tools:checkstyle:10.20.1'
     // 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'
 
-    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.19.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.22.0"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")

config/IntelliJ Code Style.xml

@@ -293,4 +293,4 @@
       </rules>
     </arrangement>
   </codeStyleSettings>
-</code_scheme>
+</code_scheme>

config/checkstyle/checkstyle.xml

@@ -33,6 +33,13 @@
         <property name="fileExtensions" value="groovy,java" />
     </module>
 
+    <!-- Prevent newline after catch opening parenthesis -->
+    <module name="RegexpMultiline">
+        <property name="message" value="No newline allowed after catch opening parenthesis" />
+        <property name="format" value="catch\s*\(\s*[\r]?\n" />
+        <property name="fileExtensions" value="groovy,java" />
+    </module>
+
     <!-- Checks for size violations: https://checkstyle.sourceforge.io/config_sizes.html -->
 
     <!-- LineLength not in place as PreviewerViewer and RelatedArticlesTab have line length with more than 500 charachters -->

config/checkstyle/checkstyle_reviewdog.xml

@@ -33,6 +33,13 @@
         <property name="fileExtensions" value="groovy,java" />
     </module>
 
+    <!-- Prevent newline after catch opening parenthesis -->
+    <module name="RegexpMultiline">
+        <property name="message" value="No newline allowed after catch opening parenthesis" />
+        <property name="format" value="catch\s*\(\s*[\r]?\n" />
+        <property name="fileExtensions" value="groovy,java" />
+    </module>
+
     <!-- Checks for size violations: https://checkstyle.sourceforge.io/config_sizes.html -->
 
     <!-- LineLength not in place as PreviewerViewer and RelatedArticlesTab have line length with more than 500 charachters -->

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

@@ -54,6 +54,7 @@ ${CanonicalBibEntry.getCanonicalRepresentation($entry)}
 * Good, because it has simple syntax, and it is designed for simple template workflows.
 * Good, because it has a stable syntax ([source](https://stackoverflow.com/a/1984458/10037342)).
 * Bad, because it is in maintenance mode.
+* Bad, because [removed from Spring 5.0.1](https://www.baeldung.com/spring-template-engines#other-template-engines)
 
 ### Apache FreeMarker
 
@@ -107,4 +108,7 @@ Here are the papers you are analyzing:
 
 As stated in [the template discussion issue](https://github.com/koppor/jabref/issues/392), we should choose a template engine, and then slowly migrate previous code and templates to the chosen engine.
 
+Other template engines are discussed at <https://www.baeldung.com/spring-template-engines>, especially [`#other-template-engines`](https://www.baeldung.com/spring-template-engines#other-template-engines).
+We did not find any other engine there worth switching to.
+
 <!-- markdownlint-disable-file MD004 -->

gradle/wrapper/gradle-wrapper.properties

@@ -1,7 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionSha256Sum=31c55713e40233a8303827ceb42ca48a47267a0ad4bab9177123121e71524c26
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.10.2-bin.zip
+distributionSha256Sum=f397b287023acdba1e9f6fc5ea72d22dd63669d59ed4a289a29b1a76eee151c6
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.11.1-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

rewrite.yml

@@ -209,7 +209,8 @@ recipeList:
   - org.openrewrite.java.testing.junit5.RemoveDuplicateTestTemplates
   - org.openrewrite.java.testing.junit5.RemoveTryCatchFailBlocks
   - org.openrewrite.java.testing.junit5.LifecycleNonPrivate
-  - org.openrewrite.java.testing.junit5.StaticImports
+  # Does not work on some JDK releases. See https://github.com/openrewrite/rewrite-logging-frameworks/issues/177.
+  # - org.openrewrite.java.testing.junit5.StaticImports
 
   # Logging
   - org.openrewrite.java.logging.slf4j.Slf4jBestPractices

src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -99,7 +99,7 @@ public ArgumentProcessor(String[] args,
     }
 
     /**
-     * Will open a file (like {@link #importFile(String)}, but will also request JabRef to focus on this database.
+     * Will open a file (like {@link #importFile(String)}, but will also request JabRef to focus on this library.
      *
      * @return ParserResult with setToOpenTab(true)
      */