Merge branch 'main' into fix-for-issue-348

.github/workflows/check-links.yml

@@ -11,7 +11,7 @@ on:
   workflow_dispatch:
 
 concurrency:
-  group: "${{ github.workflow }}-${{ github.head_ref }}"
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
   cancel-in-progress: true
 
 jobs:

.github/workflows/deployment-arm64.yml

@@ -22,7 +22,7 @@ env:
   JAVA_OPTS: -Xmx4g
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
   cancel-in-progress: true
 
 jobs:
@@ -63,7 +63,6 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
       - name: Clean up keychain
         run: |
          security delete-keychain signing_temp.keychain ${{runner.temp}}/keychain/notarization.keychain || true
@@ -85,6 +84,8 @@ jobs:
           mkdir ${{runner.temp}}/keychain
           security create-keychain -p jabref ${{runner.temp}}/keychain/notarization.keychain
           security set-keychain-settings ${{runner.temp}}/keychain/notarization.keychain
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Prepare merged jars and modules dir (macOS)
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" prepareModulesDir
       - name: Build dmg (macOS)

.github/workflows/deployment.yml

@@ -31,7 +31,7 @@ env:
   JDK21: ""
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
   cancel-in-progress: true
 
 jobs:
@@ -94,7 +94,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Prepare merged jars and modules dir (macOS)
         if: (matrix.os == 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'NO')
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" prepareModulesDir

.github/workflows/refresh-journal-lists.yml

@@ -32,7 +32,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Check whether journal-list.mv can be generated (the "real" generation is done inside JabRef's build process)
         run: |
           ./gradlew generateJournalListMV

.github/workflows/tests-fetchers.yml

@@ -29,7 +29,7 @@ env:
   BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey_FOR_TESTS}}
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
   cancel-in-progress: true
 
 permissions:
@@ -50,7 +50,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run fetcher tests
         run: ./gradlew fetcherTest
         env:

.github/workflows/tests.yml

@@ -18,7 +18,7 @@ env:
   JAVA_OPTS: -Xmx4g
 
 concurrency:
-  group: tests-${{ github.head_ref }}
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
   cancel-in-progress: true
 
 permissions:
@@ -39,14 +39,15 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
       - name: Run checkstyle reporter
         uses: nikitasavinov/checkstyle-action@master
         with:
           reporter: github-pr-review
           github_token: ${{ secrets.GITHUB_TOKEN }}
           checkstyle_config: 'config/checkstyle/checkstyle_reviewdog.xml'
           checkstyle_version: '10.3'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run checkstyle using gradle
         run: ./gradlew checkstyleMain checkstyleTest checkstyleJmh
   openrewrite:
@@ -63,7 +64,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run OpenRewrite
         run: |
           ./gradlew rewriteDryRun
@@ -81,7 +83,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run modernizer
         run: |
           # enable failing of this task if modernizer complains
@@ -97,7 +100,7 @@ jobs:
           submodules: 'false'
           show-progress: 'false'
       - name: markdownlint-cli2-action
-        uses: DavidAnson/markdownlint-cli2-action@v13
+        uses: DavidAnson/markdownlint-cli2-action@v14
         with:
           globs: |
             *.md
@@ -162,7 +165,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run tests
         run: xvfb-run --auto-servernum ./gradlew check -x checkstyleJmh -x checkstyleMain -x checkstyleTest -x modernizer
         env:
@@ -197,7 +201,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run tests on PostgreSQL
         run: ./gradlew databaseTest --rerun-tasks
         env:
@@ -234,7 +239,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run GUI tests
         run: xvfb-run --auto-servernum ./gradlew guiTest
         env:
@@ -278,7 +284,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Update test coverage metrics
         if: (github.ref == 'refs/heads/main') && (steps.checksecrets.outputs.secretspresent == 'YES')
         run: xvfb-run --auto-servernum ./gradlew jacocoTestReport

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

@@ -8,9 +8,14 @@ on:
 jobs:
   update-gradle-wrapper:
     runs-on: ubuntu-latest
-
+   
     steps:
       - uses: actions/checkout@v4
+      - name: Setup JDK
+        uses: actions/setup-java@v3
+        with:
+          java-version: 21.0.1
+          distribution: 'liberica'
 
       - name: Update Gradle Wrapper
         uses: gradle-update/update-gradle-wrapper-action@v1

CHANGELOG.md

@@ -17,6 +17,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added the option to use System Preference for Light/Dark Theme [#8729](https://github.com/JabRef/jabref/issues/8729).
 - We added [scholar.archive.org](https://scholar.archive.org/) as a new fetcher. [#10498](https://github.com/JabRef/jabref/issues/10498)
 - We integrated predatory journal checking as part of the Integrity Checker based on the [check-bib-for-predatory](https://github.com/CfKu/check-bib-for-predatory). [koppor#348](https://github.com/koppor/jabref/issues/348)
+- We added a 'More options' section in the main table right click menu opening the preferences dialog. [#9432](https://github.com/JabRef/jabref/issues/9432)
 
 ### Changed
 

CITATION.cff

@@ -0,0 +1,58 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: JabRef
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Oliver
+    family-names: Kopp
+    orcid: 'https://orcid.org/0000-0001-6962-4290'
+  - given-names: Tobias
+    family-names: Diez
+    orcid: 'https://orcid.org/0000-0002-1407-7696'
+  - given-names: Christoph
+    family-names: Schwentker
+  - given-names: Carl Christian
+    family-names: Snethlage
+  - given-names: Jonatan
+    family-names: Asketorp
+  - given-names: Benedikt
+    family-names: Tutzer
+  - given-names: Thilo
+    family-names: Ertel
+  - given-names: Houssem
+    family-names: Nasri
+repository-code: 'https://github.com/jabref/jabref/'
+url: 'https://www.jabref.org'
+abstract: >-
+  JabRef is an open-source, cross-platform citation and
+  reference management tool.
+keywords:
+  - reference manager
+  - bibtex
+  - biblatex
+license: MIT
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Kopp"
+    given-names: "Oliver"
+    orcid: "https://orcid.org/0000-0001-6962-4290"
+  - family-names: "Snethlage"
+    given-names: "Carl Christian"
+  - family-names: "Schwentker"
+    given-names: "Christoph"
+  doi: "10.47397/tb/44-3/tb138kopp-jabref"
+  journal: "TUGboat"
+  month: 11
+  start: 441
+  end: 447
+  title: "JabRef: BibTeX-based literature management software"
+  issue: 138
+  volume: 44
+  number: 3
+  year: 2023

build.gradle

@@ -124,11 +124,11 @@ dependencies {
     implementation 'org.apache.lucene:lucene-highlighter:9.8.0'
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.10.0'
-    implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.13.0'
+    implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.14.0'
     implementation 'com.h2database:h2-mvstore:2.2.224'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    implementation 'org.bouncycastle:bcprov-jdk18on:1.76'
+    implementation 'org.bouncycastle:bcprov-jdk18on:1.77'
 
     implementation 'commons-cli:commons-cli:1.6.0'
 
@@ -253,7 +253,7 @@ dependencies {
     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:2.5.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.5.1"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")
@@ -277,7 +277,8 @@ processResources {
                 "astrophysicsDataSystemAPIKey": System.getenv('AstrophysicsDataSystemAPIKey') ? System.getenv('AstrophysicsDataSystemAPIKey') : '',
                 "ieeeAPIKey": System.getenv('IEEEAPIKey') ? System.getenv('IEEEAPIKey') : '',
                 "scienceDirectApiKey": System.getenv('SCIENCEDIRECTAPIKEY') ? System.getenv('SCIENCEDIRECTAPIKEY') : '',
-                "biodiversityHeritageApiKey": System.getenv('BiodiversityHeritageApiKey') ? System.getenv('BiodiversityHeritageApiKey') : ''
+                "biodiversityHeritageApiKey": System.getenv('BiodiversityHeritageApiKey') ? System.getenv('BiodiversityHeritageApiKey') : '',
+                "semanticScholarApiKey": System.getenv('SemanticScholarApiKey') ? System.getenv("SemanticScholarApiKey") : ''
         )
         filteringCharset = 'UTF-8'
     }

docs/code-howtos/fetchers.md

@@ -5,15 +5,16 @@ parent: Code Howtos
 
 Fetchers are the implementation of the [search using online services](https://docs.jabref.org/collect/import-using-online-bibliographic-database). Some fetchers require API keys to get them working. To get the fetchers running in a JabRef development setup, the keys need to be placed in the respective environment variable. The following table lists the respective fetchers, where to get the key from and the environment variable where the key has to be placed.
 
-| Service                                                                                                                                              | Key Source                                                                                                     | Environment Variable           | Rate Limit                       |
-|:-----------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------|--------------------------------|----------------------------------|
-| [IEEEXplore](https://docs.jabref.org/collect/import-using-online-bibliographic-database#ieeexplore)                                                  | [IEEE Xplore API portal](https://developer.ieee.org)                                                           | `IEEEAPIKey`                   | 200 calls/day                    |
-| [MathSciNet](http://www.ams.org/mathscinet)                                                                                                          | (none)                                                                                                         | (none)                         | Depending on the current network |
-| [SAO/NASA Astrophysics Data System](https://docs.jabref.org/collect/import-using-online-bibliographic-database#sao-nasa-astrophysics-data-system)    | [ADS UI](https://ui.adsabs.harvard.edu/user/settings/token)                                                    | `AstrophysicsDataSystemAPIKey` | 5000 calls/day                   |
-| [ScienceDirect](https://www.sciencedirect.com)                                                                                                       |                                                                                                                | `ScienceDirectApiKey`          |                                  |
-| [Springer Nature](https://docs.jabref.org/collect/import-using-online-bibliographic-database#springer)                                               | [Springer Nature API Portal](https://dev.springernature.com)                                                   | `SpringerNatureAPIKey`         | 5000 calls/day                   |
-| [Zentralblatt Math](https://www.zbmath.org)                                                                                                          | (none)                                                                                                         | (none)                         | Depending on the current network |
-| [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/)                                                                                | [Biodiversitylibrary](https://about.biodiversitylibrary.org/tools-and-services/developer-and-data-tools/#APIs) | `BiodiversityHeritageApiKey`   |  -                               |
+| Service                                                                                                                                           | Key Source                                                                                                     | Environment Variable           | Rate Limit                       |
+|:--------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------|--------------------------------|----------------------------------|
+| [IEEEXplore](https://docs.jabref.org/collect/import-using-online-bibliographic-database#ieeexplore)                                               | [IEEE Xplore API portal](https://developer.ieee.org)                                                           | `IEEEAPIKey`                   | 200 calls/day                    |
+| [MathSciNet](http://www.ams.org/mathscinet)                                                                                                       | (none)                                                                                                         | (none)                         | Depending on the current network |
+| [SAO/NASA Astrophysics Data System](https://docs.jabref.org/collect/import-using-online-bibliographic-database#sao-nasa-astrophysics-data-system) | [ADS UI](https://ui.adsabs.harvard.edu/user/settings/token)                                                    | `AstrophysicsDataSystemAPIKey` | 5000 calls/day                   |
+| [ScienceDirect](https://www.sciencedirect.com)                                                                                                    |                                                                                                                | `ScienceDirectApiKey`          |                                  |
+| [SemanticScholar](https://www.semanticscholar.org/)                                                                                               | <https://www.semanticscholar.org/product/api#api-key-form>                                                     | `SemanticScholarApiKey`        |                                  |
+| [Springer Nature](https://docs.jabref.org/collect/import-using-online-bibliographic-database#springer)                                            | [Springer Nature API Portal](https://dev.springernature.com)                                                   | `SpringerNatureAPIKey`         | 5000 calls/day                   |
+| [Zentralblatt Math](https://www.zbmath.org)                                                                                                       | (none)                                                                                                         | (none)                         | Depending on the current network |
+| [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/)                                                                             | [Biodiversitylibrary](https://about.biodiversitylibrary.org/tools-and-services/developer-and-data-tools/#APIs) | `BiodiversityHeritageApiKey`   | -                                |
 
 "Depending on the current network" means that it depends on whether your request is routed through a network having paid access. For instance, some universities have subscriptions to MathSciNet.
 
@@ -72,7 +73,7 @@ springerNatureAPIKey=${springerNatureAPIKey}
 In `build.gradle`, these variables are filled:
 
 ```groovy
-"springerNatureAPIKey": System.getenv('SpringerNatureAPIKey')
+"springerNatureAPIKey" : System.getenv('SpringerNatureAPIKey')
 ```
 
 The `BuildInfo` class reads from that file.

gradle/wrapper/gradle-wrapper.properties

@@ -1,7 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionSha256Sum=3e1af3ae886920c3ac87f7a91f816c0c7c436f276a6eefdb3da152100fef72ae
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
+distributionSha256Sum=9d926787066a081739e8200858338b4a69e837c3a821a33aca9db09dd4a41026
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

src/main/java/org/jabref/gui/MainMenu.java

@@ -157,7 +157,7 @@ private void createMenu() {
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.SHOW_PREFS, new ShowPreferencesAction(frame, taskExecutor)),
+                factory.createMenuItem(StandardActions.SHOW_PREFS, new ShowPreferencesAction(frame)),
 
                 new SeparatorMenuItem(),
 

src/main/java/org/jabref/gui/actions/StandardActions.java

@@ -1,5 +1,6 @@
 package org.jabref.gui.actions;
 
+import java.util.Objects;
 import java.util.Optional;
 
 import org.jabref.gui.icon.IconTheme;
@@ -194,7 +195,7 @@ public enum StandardActions implements Action {
     GROUP_ENTRIES_ADD(Localization.lang("Add selected entries to this group")),
     GROUP_ENTRIES_REMOVE(Localization.lang("Remove selected entries from this group"));
 
-    private final String text;
+    private String text;
     private final String description;
     private final Optional<JabRefIcon> icon;
     private final Optional<KeyBinding> keyBinding;
@@ -271,4 +272,9 @@ public String getText() {
     public String getDescription() {
         return description;
     }
+
+    public Action withText(String text) {
+        this.text = Objects.requireNonNull(text);
+        return this;
+    }
 }