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

Author: BojiZhang

.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
@@ -34,7 +34,7 @@ jobs:
 
             ⏳ Please note, you will be automatically unassigned if the issue isn't closed within **{{ total_days }} days** (by **{{ unassigned_date }}**). A maintainer can also add the "**{{ pin_label }}**"" label to prevent automatic unassignment.
       - name: Move Issue to "Assigned" Column in "Candidates for University Projects"
-        uses: koppor/github-action-move-issues@work-for-labeled
+        uses: m7kvqbe1/github-action-move-issues@feat/skip-if-not-in-project-flag
         # Action currently works for issues only - pre-condition: https://github.com/takanome-dev/assign-issue-action/issues/269 fixed
         if: github.event_name == 'issue_comment'
         with:
@@ -46,7 +46,7 @@ jobs:
           default-column: "Free to take"
           skip-if-not-in-project: true
       - name: Move Issue to "Assigned" Column in "Good First Issues"
-        uses: koppor/github-action-move-issues@work-for-labeled
+        uses: m7kvqbe1/github-action-move-issues@feat/skip-if-not-in-project-flag
         if: github.event_name == 'issue_comment'
         with:
           github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}

.github/workflows/cleanup-pr.yml

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

.github/workflows/on-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

@@ -22,11 +22,10 @@ jobs:
           FILES=$(git diff --name-only ${{ github.event.before }} ${{ github.sha }} -- '*.java' | sed 's|^|\"|' | sed 's|$|\"|' | paste -sd "," -)
           if [ -z "$FILES" ]; then FILES="\"dummy.java\""; fi
           echo "expected_files=(${FILES})" >> $GITHUB_ENV
+          echo "Files: ${FILES}"
 
       - name: ProductMap Map Generation
-        uses: product-map/[email protected]
-        # disabled because of https://github.com/product-map/product-map-action/issues/7
-        if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.fork == false
+        uses: product-map/product-map-action@main
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           expected_files: ${{ env.expected_files }}

.github/workflows/product-map.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/tests-fetchers.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.yml

@@ -11,26 +11,40 @@ 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)
 - We added batch fetching of bibliographic data for multiple entries in the "Lookup" menu. [#12275](https://github.com/JabRef/jabref/issues/12275)
+- We added a feature for enabling drag-and-drop of files into groups  [#12540](https://github.com/JabRef/jabref/issues/12540)
+- We added support for reordering keywords via drag and drop, automatic alphabetical ordering, and improved pasting and editing functionalities in the keyword editor. [#10984](https://github.com/JabRef/jabref/issues/10984)
 
 ### Changed
 
 - We moved the "Generate a new key for imported entries" option from the "Web search" tab to the "Citation key generator" tab in preferences. [#12436](https://github.com/JabRef/jabref/pull/12436)
 - We improved the offline parsing of BibTeX data from PDF-documents. [#12278](https://github.com/JabRef/jabref/issues/12278)
 - The tab bar is now hidden when only one library is open. [#9971](https://github.com/JabRef/jabref/issues/9971)
+- We renamed "Rename file to a given name" to "Rename files to configured filename format pattern" in the entry editor. [#12587](https://github.com/JabRef/jabref/pull/12587)
+- We renamed "Move DOIs from note and URL field to DOI field and remove http prefix" to "Move DOIs from 'note' field and 'URL' field to 'DOI' field and remove http prefix" in the Cleanup entries. [#12587](https://github.com/JabRef/jabref/pull/12587)
+- We renamed "Move preprint information from 'URL' and 'journal' field to the 'eprint' field" to "Move preprint information from 'URL' field and 'journal' field to the 'eprint' field" in the Cleanup entries. [#12587](https://github.com/JabRef/jabref/pull/12587)
+- We renamed "Move URL in note field to url field" to "Move URL in 'note' field to 'URL' field" in the Cleanup entries. [#12587](https://github.com/JabRef/jabref/pull/12587)
+- We renamed "Rename PDFs to given filename format pattern" to "Rename files to configured filename format pattern" in the Cleanup entries. [#12587](https://github.com/JabRef/jabref/pull/12587)
+- We renamed "Rename only PDFs having a relative path" to "Only rename files that have a relative path" in the Cleanup entries. [#12587](https://github.com/JabRef/jabref/pull/12587)
+- We renamed "Filename format pattern: " to "Filename format pattern (from preferences)" in the Cleanup entries. [#12587](https://github.com/JabRef/jabref/pull/12587)
 - When working with CSL styles in LibreOffice, citing with a new style now updates all other citations in the document to have the currently selected style. [#12472](https://github.com/JabRef/jabref/pull/12472)
 - We improved the user comments field visibility so that it remains displayed if it contains text. Additionally, users can now easily toggle the field on or off via buttons unless disabled in preferences. [#11021](https://github.com/JabRef/jabref/issues/11021)
 - The LibreOffice integration for CSL styles is now more performant. [#12472](https://github.com/JabRef/jabref/pull/12472)
 - The "automatically sync bibliography when citing" feature of the LibreOffice integration is now disabled by default (can be enabled in settings). [#12472](https://github.com/JabRef/jabref/pull/12472)
 - 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
 
@@ -50,8 +64,11 @@ 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)
+- We fixed an issue where JabRef displayed an incorrect deletion notification when canceling entry deletion [#12645](https://github.com/JabRef/jabref/issues/12645)
+
 
 ### Removed
 

CHANGELOG.md

@@ -5,8 +5,11 @@ General overview about contributing for non-programmers is available at <https:/
 We welcome contributions to JabRef and encourage you to follow the GitHub workflow specified below.
 If you are not familiar with this type of workflow, take a look at GitHub's excellent overview on the [GitHub flow](https://docs.github.com/en/get-started/using-github/github-flow) and the explanation of [Feature Branch Workflow](https://atlassian.com/git/tutorials/comparing-workflows#feature-branch-workflow) for the idea behind this kind of development.
 
+**JabRef regards its contributors as [software engineers, not just programmers](https://www.phoenix.edu/blog/programmer-vs-software-engineer-key-differences.html)**.
+As one consequence, for non-basic issues, you will have to work on the requirements side, too.
+
 Before you start, get the JabRef code on your local machine.
-Detailed instructions about this step can be found in our [guidelines for setting up a local workspace](getting-into-the-code/guidelines-for-setting-up-a-local-workspace/).
+Detailed instructions about this step can be found in our [guidelines for setting up a local workspace](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/).
 
 ## Table of Contents
 
@@ -27,11 +30,27 @@ Some are simpler, while others are more complex. Our primary aim is to guide you
 
 ### I am a student and I want to start with something easy
 
-We collect good issues to start with at our [list of good first issues](https://github.com/orgs/JabRef/projects/5/views/1).
+We collect good issues to start with at our [list of unassigned good first issues](https://github.com/JabRef/jabref/issues?q=sort%3Aupdated-desc%20is%3Aissue%20is%3Aopen%20label%3A%22good%20first%20issue%22%20no%3Aassignee).
 
 ### I am a student and I want to choose from a curated list of university projects
 
-Take a look at [JabRef's candidates for university projects](https://github.com/orgs/JabRef/projects/3). There, a list of possible projects to work on during a teaching period is offered.
+Apart from "good first issues", we also offer collections of curated issues to work on.
+We categorize them into "small", "medium", and "large".
+All of them are intended to
+a) bring you closer to a larger code base with a dedicated issue and
+b) be clear in their description of work.
+Sometimes, you may need to refine the requirements:
+We see contributors as software engineers and [not just programmers](https://www.phoenix.edu/blog/programmer-vs-software-engineer-key-differences.html).
+Thus, requirement engineering inherently comes up as a part of the process.
+
+Take a look at [JabRef's candidates for university projects](https://github.com/orgs/JabRef/projects/3).
+Here, you will get a table of curated issues.
+The table offers filtering for small, medium, and large projects.
+You can check the main focus (UI, logic, or both), the issue understanding effort, the implementation effort, and testing effort.
+The "issue understanding effort" is an indication of how much time you will need to understand the issue before you can do any coding. It may depend on how easy it is to reproduce the issue, how much background knowledge is needed, etc.
+The "implementation effort" is based on our experience of JabRef development.
+Note that there may be issues with a high effort in understanding, but low implementation effort.
+The challenge of these issues is to understand **where** in the code base something needs to be modified.
 
 ### I am a lecturer
 

CONTRIBUTING.md

@@ -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'