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

Author: BojiZhang

.gitattributes

@@ -5,8 +5,9 @@ gradlew text eol=lf
 # windows line endings at windows files
 *.bat text eol=crlf
 
-# ensure that line endings of *.bib, *.fxml, *.java, *.properties are normalized to LF
+# ensure that line endings of certain files are normalized to LF
 *.bib text eol=lf
+*.bak text eol=lf
 *.fxml text eol=lf
 *.java text eol=lf
 *.properties text eol=lf

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -13,6 +13,7 @@ body:
       label: JabRef version
       options:
         - "5.15 (latest release)"
+        - "6.0-alpha"
         - Latest development branch build (please note build date below)
         - Other (please describe below)
       description: The version as shown in the about dialog.

.github/ghprcomment.yml

@@ -4,6 +4,9 @@
     We use [Checkstyle](https://checkstyle.sourceforge.io/) to identify issues.
     Please carefully follow [the setup guide for the codestyle](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html).
     Afterwards, please [run checkstyle locally](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html#run-checkstyle) and fix the issues.
+
+    In case of issues with the import order, double check that you [activated Auto Import](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html#enable-proper-import-cleanup).
+    You can trigger fixing imports by pressing <kbd>Ctrl</kbd>+<kbd>Alt</kbd>+<kbd>O</kbd> to trigger [Optimize Imports](https://www.jetbrains.com/guide/tips/optimize-imports/).
 - jobName: OpenRewrite
   message: |
     Your code currently does not meet JabRef's code guidelines.

.github/workflows/assign-issue.yml

@@ -16,11 +16,11 @@ jobs:
     steps:
       - name: Assign the user or unassign stale assignments
         id: assign
-        uses: takanome-dev/assign-issue-action@beta
+        uses: takanome-dev/assign-issue-action@fix-rate-limit-err
         with:
           github_token: '${{ secrets.GITHUB_TOKEN }}'
           days_until_unassign: 90
-          maintainers: koppor, Siedlerchr, ThiloteE, calixtus, HoussemNasri
+          maintainers: 'koppor,Siedlerchr,ThiloteE,calixtus,HoussemNasri,subhramit,LinusDietz'
           assigned_comment: |
             👋 Hey @{{ handle }}, thank you for your interest in this issue! 🎉
 

.github/workflows/check-links.yml

@@ -32,7 +32,7 @@ jobs:
           restore-keys: cache-lychee-
       - name: Link Checker
         id: lychee
-        uses: lycheeverse/lychee-action@v2.1.0
+        uses: lycheeverse/lychee-action@v2.2.0
         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

@@ -69,12 +69,12 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v3.0.3
+        uses: gittools/actions/gitversion/setup@v3.1.11
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v3.0.3
+        uses: gittools/actions/gitversion/execute@v3.1.11
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:
@@ -245,7 +245,7 @@ jobs:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Download from GitHub workflow artifacts store (macOS)
         if: (steps.checksecrets.outputs.secretspresent == 'YES')
-        uses: actions/download-artifact@master
+        uses: actions/download-artifact@v4
         with:
           name: JabRef-macOS-arm-tbn
           path: build/distribution/

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

@@ -85,12 +85,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v3.0.3
+        uses: gittools/actions/gitversion/setup@v3.1.11
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v3.0.3
+        uses: gittools/actions/gitversion/execute@v3.1.11
 
       # JDK
       - name: 'Set up JDK ${{ matrix.jdk }}'

.github/workflows/deployment.yml

@@ -37,10 +37,10 @@ jobs:
   build:
     strategy:
       fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-13]
+      matrix: # if you change the os version rename all other occurrences
+        os: [ubuntu-22.04, windows-latest, macos-13]
         include:
-          - os: ubuntu-latest
+          - os: ubuntu-22.04
             displayName: linux
             archivePortable: tar -c -C build/distribution JabRef | pigz --rsyncable > build/distribution/JabRef-portable_linux.tar.gz && rm -R build/distribution/JabRef
           - os: windows-latest
@@ -75,18 +75,18 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install pigz and cache (linux)
-        if: (matrix.os == 'ubuntu-latest')
+        if: (matrix.os == 'ubuntu-22.04')
         uses: awalsh128/cache-apt-pkgs-action@latest
         with:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v3.0.3
+        uses: gittools/actions/gitversion/setup@v3.1.11
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v3.0.3
+        uses: gittools/actions/gitversion/execute@v3.1.11
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:
@@ -212,7 +212,7 @@ jobs:
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "${{ steps.gitversion.outputs.AssemblySemVer }}","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}"}
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "portable","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-portable"}
       - name: Repack deb file for Debian
-        if: (matrix.os == 'ubuntu-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        if: (matrix.os == 'ubuntu-22.04') && (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: |
           cd build/distribution
@@ -247,7 +247,7 @@ jobs:
         # macOS: Negated condition of "Upload to GitHub workflow artifacts store (macOS)"
         #        Reason: We either upload the non-notarized files - or notarize the files later (and upload these later)
         # needs to be on one line; multi line does not work
-        if: ${{ (!startsWith(github.ref, 'refs/heads/gh-readonly-queue')) && (steps.checksecrets.outputs.secretspresent == 'YES') && ((matrix.os == 'ubuntu-latest') || ((matrix.os == 'macos-13') && !((startsWith(github.ref, 'refs/tags/') || inputs.notarization == true)))) }}
+        if: ${{ (!startsWith(github.ref, 'refs/heads/gh-readonly-queue')) && (steps.checksecrets.outputs.secretspresent == 'YES') && ((matrix.os == 'ubuntu-22.04') || ((matrix.os == 'macos-13') && !((startsWith(github.ref, 'refs/tags/') || inputs.notarization == true)))) }}
         shell: bash
         run: |
           rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' build/distribution/ [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
@@ -268,7 +268,7 @@ jobs:
           compression-level: 0 # no compression
   announce:
     name: Comment on pull request
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     needs: [build]
     if: ${{ github.event_name == 'pull_request' }}
     steps:
@@ -314,7 +314,7 @@ jobs:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Download from GitHub workflow artifacts store (macOS)
         if: (steps.checksecrets.outputs.secretspresent == 'YES')
-        uses: actions/download-artifact@master
+        uses: actions/download-artifact@v4
         with:
           name: JabRef-macOS-tbn
           path: build/distribution/

.github/workflows/gource.yml

@@ -26,7 +26,7 @@ jobs:
       - name: 'Development history of current build'
         uses: BoundfoxStudios/action-gource@v2
         with:
-          gource_title: 'JabRef v5.16 (in development) | more information at contribute.jabref.org'
+          gource_title: 'JabRef v6.0 (in development) | more information at contribute.jabref.org'
           logo_url: 'https://www.jabref.org/img/JabRef-icon-256.png'
           avatars_auto_fetch: true
           # 5s * 365 / 4 = 7.5min
@@ -36,7 +36,7 @@ jobs:
       - name: 'Store video'
         run: |
           mkdir gource-videos
-          mv ./gource/gource.mp4 ./gource-videos/jabref-v5.16-dev.mp4
+          mv ./gource/gource.mp4 ./gource-videos/jabref-v6.0-dev.mp4
       - name: 'Development history of last release'
         uses: BoundfoxStudios/action-gource@v2
         with:

.github/workflows/tests.yml

@@ -109,7 +109,7 @@ jobs:
           submodules: 'false'
           show-progress: 'false'
       - name: markdownlint-cli2-action
-        uses: DavidAnson/markdownlint-cli2-action@v18
+        uses: DavidAnson/markdownlint-cli2-action@v19
         with:
           globs: |
             *.md

.vscode/settings.json

@@ -2,5 +2,5 @@
     "java.configuration.updateBuildConfiguration": "interactive",
     "java.format.settings.url": "/config/VSCode Code Style.xml",
     "java.checkstyle.configuration": "${workspaceFolder}/config/checkstyle/checkstyle_reviewdog.xml",
-    "java.checkstyle.version": "10.3.4"
+    "java.checkstyle.version": "10.21.0"
 }

CHANGELOG.md

@@ -11,6 +11,33 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- 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)
+
+### 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)
+
+### Fixed
+
+- 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)
+- We fixed an issue where a bib file with UFF-8 charset was wrongly loaded with a different charset [forum#5369](https://discourse.jabref.org/t/jabref-5-15-opens-bib-files-with-shift-jis-encoding-instead-of-utf-8/5369/)
+- We fixed an issue where new entries were inserted in the middle of the table instead of at the end. [#12371](https://github.com/JabRef/jabref/pull/12371)
+- We fixed an issue where removing the sort from the table did not restore the original order. [#12371](https://github.com/JabRef/jabref/pull/12371)
+- We fixed an issue where JabRef icon merges with dark background [#7771](https://github.com/JabRef/jabref/issues/7771)
+- We fixed an issue where an entry's group was no longer highlighted on selection [#12413](https://github.com/JabRef/jabref/issues/12413)
+- We fixed an issue where BibTeX Strings were not included in the backup file [#12462](https://github.com/JabRef/jabref/issues/12462)
+
+### Removed
+
+- "Web of Science" [journal abbreviation list](https://docs.jabref.org/advanced/journalabbreviations) was removed. [abbrv.jabref.org#176](https://github.com/JabRef/abbrv.jabref.org/issues/176)
+
+## [6.0-alpha] – 2024-12-23
+
+### 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)
@@ -83,6 +110,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - 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)
+- We changed the icon for macOS to be more consistent with Apple's Guidelines [#8443](https://github.com/JabRef/jabref/issues/8443)
 
 ### Fixed
 
@@ -127,19 +155,15 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - 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)
 - We fixed an issue with the ui not scaling when changing the font size [#11219](https://github.com/JabRef/jabref/issues/11219)
+- We fixed an issue where a custom application for external file types would not be saved [#112311](https://github.com/JabRef/jabref/issues/12311)
+- We fixed an issue where a file that no longer exists could not be deleted from an entry using keyboard shortcut [#9731](https://github.com/JabRef/jabref/issues/9731)
 
 ### Removed
 
 - We removed the description of search strings. [#11542](https://github.com/JabRef/jabref/pull/11542)
 - We removed support for importing using the SilverPlatterImporter (`Record INSPEC`). [#11576](https://github.com/JabRef/jabref/pull/11576)
 - We removed support for automatically generating file links using the CLI (`--automaticallySetFileLinks`).
 
-
-
-
-
-
-
 ## [5.15] – 2024-07-10
 
 ### Added
@@ -1486,7 +1510,8 @@ The changelog of JabRef 4.x is available at the [v4.3.1 tag](https://github.com/
 The changelog of JabRef 3.x is available at the [v3.8.2 tag](https://github.com/JabRef/jabref/blob/v3.8.2/CHANGELOG.md).
 The changelog of JabRef 2.11 and all previous versions is available as [text file in the v2.11.1 tag](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG).
 
-[Unreleased]: https://github.com/JabRef/jabref/compare/v5.15...HEAD
+[Unreleased]: https://github.com/JabRef/jabref/compare/v6.0-alpha...HEAD
+[6.0-alpha]: https://github.com/JabRef/jabref/compare/v5.15...v6.0-alpha
 [5.15]: https://github.com/JabRef/jabref/compare/v5.14...v5.15
 [5.14]: https://github.com/JabRef/jabref/compare/v5.13...v5.14
 [5.13]: https://github.com/JabRef/jabref/compare/v5.12...v5.13

GitVersion.yml

@@ -5,5 +5,5 @@ mode: ContinuousDeployment
 branches:
   main:
     regex: ^main
-    tag: ''
-    pre-release-weight: 0  # 0 after stable release, 15000 before alpha release, 30000 before beta release, 50000 before stable release
+    tag: 'alpha'
+    pre-release-weight: 15000 # 0 after stable release, 15000 before alpha release, 30000 before beta release, 50000 before stable release