Merge branch 'main' into fix-for-issue-#372

.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

@@ -2,7 +2,7 @@ name: Assign Issue
 
 on:
   schedule:
-    - cron: 0 0 * * *
+    - cron: 4 12 * * *
   issue_comment:
     types: [created]
   workflow_dispatch:

.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/deployment-arm64.yml

@@ -78,7 +78,7 @@ jobs:
       - 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

.github/workflows/deployment.yml

@@ -90,7 +90,7 @@ jobs:
       - 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
@@ -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
@@ -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"

CHANGELOG.md

@@ -41,6 +41,7 @@ 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)
 - 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)
 - Added batch fetching of bibliographic data for multiple entries in the "Lookup" menu. [koppor#372](https://github.com/koppor/jabref/issues/372)
@@ -74,6 +75,7 @@ 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)
 
 ### Fixed
@@ -112,7 +114,9 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - 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 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)
 
 ### Removed

build.gradle

@@ -6,7 +6,7 @@ import org.jabref.build.xjc.XjcTask
 plugins {
     id 'application'
 
-    id 'com.github.andygoossens.modernizer' version '1.9.3'
+    id 'com.github.andygoossens.modernizer' version '1.10.0'
 
     id 'me.champeau.jmh' version '0.7.2'
 
@@ -15,7 +15,7 @@ plugins {
 
     id 'org.openjfx.javafxplugin' version '0.1.0'
 
-    id 'org.beryx.jlink' version '3.0.1'
+    id 'org.beryx.jlink' version '3.1.0-rc-1'
 
     // nicer test outputs during running and completion
     // Homepage: https://github.com/radarsh/gradle-test-logger-plugin
@@ -29,7 +29,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.25.1'
+    id 'org.openrewrite.rewrite' version '6.27.0'
 
     id "org.itsallcode.openfasttrace" version "3.0.1"
 }
@@ -45,8 +45,8 @@ group = "org.jabref"
 version = project.findProperty('projVersion') ?: '100.0.0'
 
 java {
-    sourceCompatibility = JavaVersion.VERSION_21
-    targetCompatibility = JavaVersion.VERSION_21
+    sourceCompatibility = JavaVersion.VERSION_23
+    targetCompatibility = JavaVersion.VERSION_23
 
     // Workaround needed for Eclipse, probably because of https://github.com/gradle/gradle/issues/16922
     // Should be removed as soon as Gradle 7.0.1 is released ( https://github.com/gradle/gradle/issues/16922#issuecomment-828217060 )
@@ -60,7 +60,8 @@ java {
         // - .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
-        languageVersion = JavaLanguageVersion.of(21)
+        // - 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
     }
@@ -129,6 +130,7 @@ sourceSets {
 repositories {
     mavenCentral()
     maven { url 'https://s01.oss.sonatype.org/content/repositories/snapshots/' }
+    maven { url 'https://oss.sonatype.org/content/repositories/snapshots' }
     maven { url 'https://jitpack.io' }
     maven { url 'https://oss.sonatype.org/content/groups/public' }
 
@@ -150,7 +152,7 @@ javafx {
 }
 
 jacoco {
-    toolVersion = "0.8.10"
+    toolVersion = "0.8.13-SNAPSHOT"
 }
 
 dependencies {
@@ -183,7 +185,7 @@ dependencies {
     implementation 'com.h2database:h2-mvstore:2.3.232'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    implementation 'org.bouncycastle:bcprov-jdk18on:1.78.1'
+    implementation 'org.bouncycastle:bcprov-jdk18on:1.79'
 
     implementation 'commons-cli:commons-cli:1.9.0'
 
@@ -203,8 +205,8 @@ dependencies {
 
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '7.0.0.202409031743-r'
 
-    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.18.0'
-    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.18.0'
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.18.1'
+    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.18.1'
 
     implementation 'com.fasterxml:aalto-xml:1.3.3'
 
@@ -241,7 +243,7 @@ dependencies {
     }
     implementation 'org.fxmisc.flowless:flowless:0.7.3'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.3'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.63.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.64.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude module: 'commons-lang3'
         exclude group: 'org.apache.commons.validator'
@@ -264,7 +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-modules-gson:4.4.4'
+    implementation 'com.konghq:unirest-modules-gson:4.4.5'
     implementation 'org.apache.httpcomponents.client5:httpclient5:5.4'
     // endregion
 
@@ -315,7 +317,7 @@ dependencies {
     // HTTP server
     // implementation 'org.glassfish.jersey.containers:jersey-container-netty-http:3.1.1'
     implementation 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.9'
-    testImplementation 'org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:3.1.8'
+    testImplementation 'org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:3.1.9'
     // Allow objects "magically" to be mapped to JSON using GSON
     // implementation 'org.glassfish.jersey.media:jersey-media-json-gson:3.1.1'
 
@@ -354,7 +356,7 @@ dependencies {
         exclude group: 'org.jetbrains.kotlin'
     }
 
-    implementation 'org.apache.velocity:velocity-engine-core:2.3'
+    implementation 'org.apache.velocity:velocity-engine-core:2.4.1'
     implementation platform('ai.djl:bom:0.30.0')
     implementation 'ai.djl:api'
     implementation 'ai.djl.huggingface:tokenizers'
@@ -365,7 +367,7 @@ dependencies {
         exclude group: 'org.jetbrains.kotlin', module: 'kotlin-stdlib-jdk8'
     }
     // GemxFX also (transitively) depends on kotlin
-    implementation 'org.jetbrains.kotlin:kotlin-stdlib-jdk8:2.0.20'
+    implementation 'org.jetbrains.kotlin:kotlin-stdlib-jdk8:2.0.21'
     // endregion
 
     implementation 'commons-io:commons-io:2.17.0'
@@ -393,7 +395,7 @@ dependencies {
     // recommended by https://github.com/wiremock/wiremock/issues/2149#issuecomment-1835775954
     testImplementation 'org.wiremock:wiremock-standalone:3.3.1'
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.18.2'
+    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'

docs/code-howtos/localization.md

@@ -45,8 +45,9 @@ To write a localized string in FXML file, prepend it with `%`, like in this code
 ## General hints
 
 * Use the String you want to localize directly, do not use members or local variables: `Localization.lang("Translate me");` instead of `Localization.lang(someVariable)` (possibly in the form `someVariable = Localization.lang("Translate me")`
-* Use `%x`-variables where appropriate: `Localization.lang("Exported %0 entries.", number)` instead of `Localization.lang("Exported ") + number + Localization.lang(" entries.");`
+* Use `%x`-variables where appropriate: `Localization.lang("Exported %0 entry(s).", number)` instead of `Localization.lang("Exported ") + number + Localization.lang(" entry(s).");`
 * Use a full stop/period (".") to end full sentences
+* For pluralization, use a combined form. E.g., `Localization.lang("checked %0 entry(s)")`.
 
 ## Checking for correctness
 

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 -->