Merge branch 'main' of https://github.com/JabRef/jabref into fix-for-issue-JabRef#12272

Author: oops-shlok

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,6 +1,6 @@
-YOU HAVE TO MODIFIY THIS TEXT TO FIT YOUR PR. OTHERWISE YOUR PR WILL BE CLOSED WITHOUT FURTHER COMMENT.
+YOU HAVE TO MODIFY THIS TEXT TO FIT YOUR PR. OTHERWISE, YOUR PR WILL BE CLOSED WITHOUT FURTHER COMMENT.
 Describe the changes you have made here: what, why, ...
-Link the issue that will be closed, e.g., "Closes #333". If your PR closes a koppor issue, link it using its URL, e.g., "Closes https://github.com/koppor/jabref/issues/47".
+Link the issue that will be closed. Example: "Closes #333".
 
 ### Mandatory checks
 

.github/workflows/assign-issue.yml

@@ -16,7 +16,7 @@ jobs:
     steps:
       - name: Assign the user or unassign stale assignments
         id: assign
-        uses: takanome-dev/assign-issue-action@fix-rate-limit-err
+        uses: takanome-dev/assign-issue-action@beta
         with:
           github_token: '${{ secrets.GITHUB_TOKEN }}'
           days_until_unassign: 45

.github/workflows/cleanup-pr.yml

@@ -29,7 +29,7 @@ jobs:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Delete folder on builds.jabref.org
         if: steps.checksecrets.outputs.secretspresent == 'YES'
-        uses: appleboy/[email protected].0
+        uses: appleboy/[email protected].1
         with:
           script: rm -rf /var/www/builds.jabref.org/www/pull/${{ github.event.pull_request.number }} || true
           host: build-upload.jabref.org

.github/workflows/on-labeled-issue.yml renamed to .github/workflows/on-issue-labeled.yml

@@ -14,23 +14,23 @@ jobs:
     permissions:
       issues: write
     steps:
-      - name: Move Issue to "Free to take" Column in "Candidates for University Projects"
+      - name: Move Issue to "Assigned" Column in "Candidates for University Projects"
         uses: m7kvqbe1/github-action-move-issues@feat/skip-if-not-in-project-flag
         with:
           github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
           project-url: "https://github.com/orgs/JabRef/projects/3"
           target-labels: "📍 Assigned"
-          target-column: "Free to take"
+          target-column: "Assigned"
           ignored-columns: ""
           default-column: "Free to take"
           skip-if-not-in-project: true
-      - name: Move Issue to "Free to take" Column in "Good First Issues"
+      - name: Move Issue to "Assigned" Column in "Good First Issues"
         uses: m7kvqbe1/github-action-move-issues@feat/skip-if-not-in-project-flag
         with:
           github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
           project-url: "https://github.com/orgs/JabRef/projects/5"
           target-labels: "📍 Assigned"
-          target-column: "Free to take"
+          target-column: "Assigned"
           ignored-columns: ""
           default-column: "Free to take"
           skip-if-not-in-project: true
@@ -110,15 +110,3 @@ jobs:
         run: |
           ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
           gh project item-add 9 --owner JabRef --url $ISSUE_URL
-  ui:
-    if: "${{ github.event.label.name == 'ui' && github.repository_owner == 'JabRef' }}"
-    runs-on: ubuntu-latest
-    steps:
-      - name: ui
-        env:
-          GH_DEBUG: api
-          GH_TOKEN: ${{ secrets.GH_TOKEN_PROJECT_ITEM_ADD }}
-        run: |
-          ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
-          echo $ISSUE_URL
-          gh project item-add 8 --owner JabRef --url $ISSUE_URL

.github/workflows/on-issue-unlabeled.yml

@@ -0,0 +1,35 @@
+name: On unlabeled issue
+
+on:
+  issues:
+     types:
+       - unlabeled
+
+jobs:
+  ensure_column:
+    name: "📍 Assigned or FirstTimeCodeContribution"
+    if: ${{ (github.event.label.name == '📍 Assigned' || github.event.label.name == 'FirstTimeCodeContribution') && github.repository_owner == 'JabRef' }}
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+      - name: Move Issue to "Free to take" Column in "Candidates for University Projects"
+        uses: m7kvqbe1/github-action-move-issues@feat/skip-if-not-in-project-flag
+        with:
+          github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
+          project-url: "https://github.com/orgs/JabRef/projects/3"
+          target-labels: "📍 Assigned"
+          target-column: "Assigned"
+          ignored-columns: ""
+          default-column: "Free to take"
+          skip-if-not-in-project: true
+      - name: Move Issue to "Free to take" Column in "Good First Issues"
+        uses: m7kvqbe1/github-action-move-issues@feat/skip-if-not-in-project-flag
+        with:
+          github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
+          project-url: "https://github.com/orgs/JabRef/projects/5"
+          target-labels: "📍 Assigned"
+          target-column: "Assigned"
+          ignored-columns: ""
+          default-column: "Free to take"
+          skip-if-not-in-project: true

.github/workflows/on-labeled-pr.yml renamed to .github/workflows/on-pr-labeled.yml

@@ -8,7 +8,10 @@ on:
 jobs:
   automerge:
     name: Auto Merge
-    if: "${{ github.event.label.name == 'automerge' && github.repository_owner == 'JabRef' }}"
+    if: >
+      github.event.label.name == 'automerge' &&
+      github.repository == 'JabRef/jabref' &&
+      github.event.pull_request.head.repo.full_name == 'JabRef/jabref'
     runs-on: ubuntu-latest
     steps:
       - name: Approve PR

.github/workflows/on-unlabeled-issue.yml

@@ -54,7 +54,7 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
       - name: jbang
         if: ${{ steps.read-pr_number.outputs.pr_number != '' && steps.isCrossRepository.outputs.isCrossRepository == 'true' }}
-        uses: jbangdev/jbang-action@v0.119.0
+        uses: jbangdev/jbang-action@v0.124.0
         with:
           script: ghprcomment@koppor/ghprcomment
           scriptargs: "-r JabRef/jabref -p ${{ steps.read-pr_number.outputs.pr_number }} -w ${{ github.event.workflow_run.id }}"

.github/workflows/pr-comment.yml

@@ -7,6 +7,8 @@ on:
     paths:
       - 'src/main/java/org/jabref/logic/importer/fetcher/**'
       - 'src/test/java/org/jabref/logic/importer/fetcher/**'
+      - 'src/main/java/org/jabref/logic/importer/fileformat/PdfMergeMetadataImporter.java'
+      - 'src/test/java/org/jabref/logic/importer/fileformat/PdfMergeMetadataImporterTest.java'
       - 'src/main/java/org/jabref/logic/crawler/**'
       - 'src/test/java/org/jabref/logic/crawler/**'
       - '.github/workflows/tests-fetchers.yml'
@@ -15,6 +17,10 @@ on:
     paths:
       - 'src/main/java/org/jabref/logic/importer/fetcher/**'
       - 'src/test/java/org/jabref/logic/importer/fetcher/**'
+      - 'src/main/java/org/jabref/logic/importer/fileformat/PdfMergeMetadataImporter.java'
+      - 'src/test/java/org/jabref/logic/importer/fileformat/PdfMergeMetadataImporterTest.java'
+      - 'src/main/java/org/jabref/logic/crawler/**'
+      - 'src/test/java/org/jabref/logic/crawler/**'
       - '.github/workflows/tests-fetchers.yml'
       - 'build.gradle'
   schedule:

.github/workflows/product-map.yml

@@ -151,11 +151,20 @@ jobs:
           submodules: 'false'
           show-progress: 'false'
           fetch-depth: 0
-      - name: Install clparse
+      - name: Cache clparse jar
+        id: cache-clparse
+        uses: actions/cache@v4
+        with:
+          path: /tmp/clparse
+          key: clparse-0.9.1
+      - name: unzip
+        if: steps.cache-clparse.outputs.cache-hit != 'true'
         run: |
+          cd /tmp
           curl -LO https://github.com/marcaddeo/clparse/releases/download/0.9.1/clparse-0.9.1-x86_64-unknown-linux-musl.tar.gz
           tar xzvf clparse-0.9.1-x86_64-unknown-linux-musl.tar.gz
-          sudo mv clparse /usr/local/bin/clparse
+      - name: Install clparse
+        run: sudo mv /tmp/clparse /usr/local/bin/clparse
       - name: Check CHANGELOG.md diff
         run: |
           diff \

.github/workflows/tests-fetchers.yml

@@ -11,10 +11,13 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added a feature to rename the subgroup, with the keybinding (<kbd>F2</kbd>) for quick access. [#11896](https://github.com/JabRef/jabref/issues/11896)
 - We added a new functionality that displays a drop-down list of matching suggestions when typing a citation key pattern. [#12502](https://github.com/JabRef/jabref/issues/12502)
 - We added a new CLI that supports txt, csv, and console-based output for consistency in BibTeX entries. [#11984](https://github.com/JabRef/jabref/issues/11984)
 - We added a new dialog for bibliography consistency check. [#11950](https://github.com/JabRef/jabref/issues/11950)
 - We added a feature for copying entries to libraries, available via the context menu, with an option to include cross-references. [#12374](https://github.com/JabRef/jabref/pull/12374)
+- We added a new "Copy citation (text)" button in the context menu of the preview. [#12551](https://github.com/JabRef/jabref/issues/12551)
+- We added a new "Export to clipboard" button in the context menu of the preview. [#12551](https://github.com/JabRef/jabref/issues/12551)
 - We added an integrity check if a URL appears in a title. [#12354](https://github.com/JabRef/jabref/issues/12354)
 
 ### Changed
@@ -29,9 +32,13 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - For the Citation key generator patterns, we reverted how `[authorsAlpha]` would behave to the original pattern and renamed the LNI-based pattern introduced in V6.0-alpha to `[authorsAlphaLNI]`. [#12499](https://github.com/JabRef/jabref/pull/12499)
 - We keep the list of recent files if one files could not be found. [#12517](https://github.com/JabRef/jabref/pull/12517)
 - During the import process, the labels indicating individual paragraphs within an abstract returned by PubMed/Medline XML are preserved. [#12527](https://github.com/JabRef/jabref/issues/12527)
+- We changed the "Copy Preview" button to "Copy citation (html) in the context menu of the preview. [#12551](https://github.com/JabRef/jabref/issues/12551)
+- Pressing Tab in empty text fields of the entry editor now moves the focus to the next field instead of inserting a tab character. [#11938](https://github.com/JabRef/jabref/issues/11938)
+- The embedded PostgresSQL server for the search now supports Linux and macOS ARM based distributions natively [#12607](https://github.com/JabRef/jabref/pull/12607)
 
 ### Fixed
 
+- We fixed an issue where the F4 shortcut key did not work without opening the right-click context menu. [#6101](https://github.com/JabRef/jabref/pull/6101)
 - We fixed an issue where the file renaming dialog was not resizable and its size was too small for long file names. [#12518](https://github.com/JabRef/jabref/pull/12518)
 - We fixed an issue where the name of the untitled database was shown as a blank space in the right-click context menu's "Copy to" option. [#12459](https://github.com/JabRef/jabref/pull/12459)
 - We fixed an issue where the F3 shortcut key did not work without opening the right-click context menu. [#12417](https://github.com/JabRef/jabref/pull/12417)
@@ -47,6 +54,10 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where CSL style citations with citation keys having special characters (such as hyphens or colons) would not be recognized as valid by JabRef. [forum#5431](https://discourse.jabref.org/t/error-when-connecting-to-libreoffice/5431)
 - We fixed an issue where the `[authorsAlpha]` pattern in Citation key generator would not behave as per the user documentation. [#12312](https://github.com/JabRef/jabref/issues/12312)
 - We fixed an issue where import at "Search for unlinked local files" would re-add already imported files. [#12274](https://github.com/JabRef/jabref/issues/12274)
+- We fixed an issue where month values 21–24 (ISO 8601-2019 season codes) in Biblatex date fields were not recognized as seasons during parsing. [#12437](https://github.com/JabRef/jabref/issues/12437)
+- We fixed an issue where migration of "Search groups" would fail with an exception when the search query is invalid. [#12555](https://github.com/JabRef/jabref/issues/12555)
+- We fixed an issue where not all linked files from BibDesk in the field `bdsk-file-...` were parsed. [#12555](https://github.com/JabRef/jabref/issues/12555)
+
 
 ### Removed
 

.github/workflows/tests.yml

@@ -206,7 +206,7 @@ dependencies {
 
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '7.1.0.202411261347-r'
 
-    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.18.2'
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.18.3'
     implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.18.2'
 
     implementation 'com.fasterxml:aalto-xml:1.3.3'
@@ -271,7 +271,7 @@ dependencies {
     implementation 'org.apache.httpcomponents.client5:httpclient5:5.4.2'
     // endregion
 
-    implementation 'org.slf4j:slf4j-api:2.0.16'
+    implementation 'org.slf4j:slf4j-api:2.0.17'
     implementation 'org.tinylog:tinylog-api:2.7.0'
     implementation 'org.tinylog:slf4j-tinylog:2.7.0'
     implementation 'org.tinylog:tinylog-impl:2.7.0'
@@ -332,7 +332,7 @@ dependencies {
     implementation 'com.github.vatbub:mslinks:1.0.6.2'
 
     // YAML formatting
-    implementation 'org.yaml:snakeyaml:2.3'
+    implementation 'org.yaml:snakeyaml:2.4'
 
     // region AI
     implementation 'dev.langchain4j:langchain4j:0.36.2'
@@ -377,13 +377,15 @@ dependencies {
     implementation 'io.github.adr:e-adr:2.0.0-SNAPSHOT'
 
     implementation 'io.zonky.test:embedded-postgres:2.1.0'
-    implementation enforcedPlatform('io.zonky.test.postgres:embedded-postgres-binaries-bom:17.2.0')
+    implementation enforcedPlatform('io.zonky.test.postgres:embedded-postgres-binaries-bom:17.4.0')
+    implementation 'io.zonky.test.postgres:embedded-postgres-binaries-darwin-arm64v8'
+    implementation 'io.zonky.test.postgres:embedded-postgres-binaries-linux-arm64v8'
 
     testImplementation 'io.github.classgraph:classgraph:4.8.179'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.11.4'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.11.4'
 
-    testImplementation 'org.mockito:mockito-core:5.15.2'
+    testImplementation 'org.mockito:mockito-core:5.16.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.10.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.10.0'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.4.0'
@@ -396,7 +398,7 @@ dependencies {
     // recommended by https://github.com/wiremock/wiremock/issues/2149#issuecomment-1835775954
     testImplementation 'org.wiremock:wiremock-standalone:3.10.0'
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.21.2'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.21.3'
     // 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'

CHANGELOG.md

@@ -40,6 +40,14 @@
         <property name="fileExtensions" value="groovy,java" />
     </module>
 
+    <!-- Prevent multiple closing curly braces in the same line -->
+    <module name="RegexpSingleline">
+        <property name="id" value="NoMultipleClosingBracesAtEndOfLine"/>
+        <property name="message" value="Multiple closing curly braces in the same line are not allowed" />
+        <property name="format" value="\}\s*\}\s*$" />
+        <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 -->

build.gradle

@@ -40,6 +40,14 @@
         <property name="fileExtensions" value="groovy,java" />
     </module>
 
+    <!-- Prevent multiple closing curly braces in the same line -->
+    <module name="RegexpSingleline">
+        <property name="id" value="NoMultipleClosingBracesAtEndOfLine"/>
+        <property name="message" value="Multiple closing curly braces in the same line are not allowed" />
+        <property name="format" value="\}\s*\}\s*$" />
+        <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 -->

buildres/abbrv.jabref.org

@@ -9,4 +9,6 @@
     <suppress checks="[a-zA-Z0-9]*" files="[\\/]src-gen[\\/]" />
     <!-- We ignore this file because it's a modification of the original java code https://github.com/openjdk/jfx/blob/jfx15/modules/javafx.controls/src/main/java/javafx/scene/control/skin/TitledPaneSkin.java -->
     <suppress checks="[a-zA-Z0-9]*" files="CustomTitledPaneSkin.java" />
+    <!-- Following contain examples or comments with "}}" that are necessary -->
+    <suppress id="NoMultipleClosingBracesAtEndOfLine" files="(BibtexParserTest|StringUtil).java" />
 </suppressions>

config/checkstyle/checkstyle.xml

@@ -87,6 +87,7 @@ Code: `Localization.lang("Imported %0 entries", "Imported %0 entry.", "Imported
 
 ## More Information
 
+- [Pluralization: A Guide to Localizing Plurals](https://phrase.com/blog/posts/pluralization/)
 - [Language Plural Rules](https://www.unicode.org/cldr/charts/43/supplemental/language_plural_rules.html)
 - [Unicode CLDR Project's Plural Rules](https://cldr.unicode.org/index/cldr-spec/plural-rules)
 - [Implementation in Mozilla Firefox](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Intl/PluralRules)