Merge branch 'main' into restore-auto-rename-feature-2

Author: wtfjjking

.gitattributes

@@ -13,3 +13,4 @@ gradlew text eol=lf
 *.properties text eol=lf
 
 CHANGELOG.md merge=union
+src/main/resources/l10n/JabRef_en.properties merge=union

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,21 +1,27 @@
-<!-- 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, ...
+<!-- YOU HAVE TO MODIFY THE TEXT BELOW TO FIT YOUR PR. OTHERWISE, YOUR PR WILL BE CLOSED WITHOUT FURTHER COMMENT. -->
 
 <!-- LINK THE ISSUE WITH THE "Closes" KEYWORD -->
-<!-- Example: Closes (link) OR Closes #xyz -->
+<!-- Example: Closes (link) OR Closes #12345 -->
+
+Closes _____
+Describe the changes you have made here: what, where, why, ...
+If your work is not yet complete, please open a draft pull request. In that case, outline your intended next steps. Do you need feedback? Will you continue in parallel? ...
 
 ### Mandatory checks
 
 <!--
-- Go through the list below. Please don't remove any items.
-- [x] done; [ ] not done / not applicable
+Go throgh the checklist below. It is mandatory, even for a draft pull request.
+
+Keep ALL the items. Mark them as follows: 
+[x] done 
+[ ] not done 
+[/] not applicable
 -->
 
 - [x] I own the copyright of the code submitted and I licence it under the [MIT license](https://github.com/JabRef/jabref/blob/main/LICENSE)
 - [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if change is visible to the user)
 - [ ] Tests created for changes (if applicable)
 - [ ] Manually tested changed features in running JabRef (always required)
-- [ ] Screenshots added in PR description (for UI changes)
+- [ ] Screenshots added in PR description (if change is visible to the user)
 - [ ] [Checked developer's documentation](https://devdocs.jabref.org/): Is the information available and up to date? If not, I outlined it in this pull request.
 - [ ] [Checked documentation](https://docs.jabref.org/): Is the information available and up to date? If not, I created an issue at <https://github.com/JabRef/user-documentation/issues> or, even better, I submitted a pull request to the documentation repository.

.github/ghprcomment.yml

@@ -5,6 +5,7 @@
     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
@@ -14,20 +15,23 @@
     The issues found can be **automatically fixed**.
     Please execute the gradle task *`rewriteRun`*, check the results, commit, and push.
 
+
     You can check the detailed error output by navigating to your pull request, selecting the tab "Checks", section "Tests" (on the left), subsection "OpenRewrite".
 - jobName: Modernizer
   message: >
     Your code currently does not meet JabRef's code guidelines.
     We use [Gradle Modernizer Plugin](https://github.com/andygoossens/gradle-modernizer-plugin#gradle-modernizer-plugin) to ensure "modern" Java coding practices.
     Please fix the detected errors, commit, and push.
 
+
     You can check the detailed error output by navigating to your pull request, selecting the tab "Checks", section "Tests" (on the left), subsection "Modernizer".
 - jobName: Markdown
   message: >
     You modified Markdown (`*.md`) files and did not meet JabRef's rules for consistently formatted Markdown files.
     To ensure consistent styling, we have [markdown-lint](https://github.com/DavidAnson/markdownlint) in place.
     [Markdown lint's rules](https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md#rules) help to keep our Markdown files consistent within this repository and consistent with the Markdown files outside here.
 
+
     You can check the detailed error output by navigating to your pull request, selecting the tab "Checks", section "Tests" (on the left), subsection "Markdown".
 - jobName: CHANGELOG.md
   message: |
@@ -39,17 +43,16 @@
     In the area "Some checks were not successful", locate "Tests / Unit tests (pull_request)" and click on "Details".
     This brings you to the test output.
 
+
     You can then run these tests in IntelliJ to reproduce the failing tests locally.
     We offer a quick test running howto in the section [Final build system checks](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.html#final-build-system-checks) in our setup guide.
 - jobName: no-force-push
   message: >
     Do not force-push!
-    Force push is off limits and very bad style when working together on a project.
-    ([Mainly because it is not supported well by GitHub istself.](https://github.com/orgs/community/discussions/3478))
-    Commits will be lost, comments on commits will loose their context.
-    This makes it harder to review.
-    In the end, all commits will be [squashed](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/incorporating-changes-from-a-pull-request/about-pull-request-merges#squash-and-merge-your-commits) either way before being merged into the `main`` branch.
-- jobName: move_issue
+    Force pushing is a very bad practice when working together on a project (mainly because it is [not supported well by GitHub itself](https://github.com/orgs/community/discussions/3478)).
+    Commits are lost and comments on commits lose their context, thus making it harder to review changes.
+    At the end, all commits will be [squashed](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/incorporating-changes-from-a-pull-request/about-pull-request-merges#squash-and-merge-your-commits) anyway before being merged into the `main` branch.
+- jobName: 'Mark issue as in progress'
   message: |
     Your pull request needs to link an issue.
 
@@ -81,3 +84,16 @@
     - ✅ `Fixes https://github.com/JabRef/jabref/issues/xyz` links pull-request to issue. Merging the PR will close the issue.
     - ✅ `Fixes https://github.com/Koppor/jabref/issues/xyz` links pull-request to issue. Merging the PR will close the issue.
     - ❌ `Fixes [#xyz](https://github.com/JabRef/jabref/issues/xyz)` links pull-request to issue. Merging the PR will **NOT** close the issue.
+- jobName: 'Conflicts with target branch'
+  message: >
+    Your pull request conflicts with the target branch.
+
+
+    Please [merge `upstream/main`](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork#syncing-a-fork-branch-from-the-command-line) with your code.
+    For a step-by-step guide to resolve merge conflicts, see <https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/addressing-merge-conflicts/resolving-a-merge-conflict-using-the-command-line>.
+- jobName: 'Submodules not modified'
+  message: >
+    Your pull request modified git submodules.
+
+
+    Please follow our [FAQ on submodules](https://devdocs.jabref.org/code-howtos/faq.html#submodules) to fix.

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

@@ -16,7 +16,7 @@ jobs:
         uses: takanome-dev/assign-issue-action@edge
         with:
           github_token: '${{ secrets.GITHUB_TOKEN }}'
-          days_until_unassign: 45
+          days_until_unassign: 14
           maintainers: 'koppor,Siedlerchr,ThiloteE,calixtus,HoussemNasri,subhramit,LinusDietz'
           assigned_comment: |
             👋 Hey @{{ handle }}, thank you for your interest in this issue! 🎉
@@ -29,7 +29,7 @@ jobs:
 
             Happy coding! 🚀
 
-            ⏳ 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.
+            ⏳ Please note, you will be automatically unassigned if there is not a (draft) pull request within **{{ total_days }} days** (by **{{ unassigned_date }}**).
           assignment_suggestion_comment: >
             👋 Hey @{{ handle }}, looks like you’re eager to work on this issue—great! 🎉
             It also looks like you skipped reading our [CONTRIBUTING.md](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md), which explains exactly how to participate. No worries, it happens to the best of us.

.github/workflows/on-pr-closed.yml

@@ -56,6 +56,10 @@ jobs:
         run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --remove-label "📍 Assigned"
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Remove pinned label
+        run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --remove-label "📌 Pinned"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - name: Remove FirstTimeCodeContribution label
         run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --remove-label "FirstTimeCodeContribution"
         env:

.github/workflows/on-pr-opened.yml

@@ -45,6 +45,36 @@ jobs:
           default-column: "In Progress"
           issue-number: ${{ steps.get_issue_number.outputs.ticketNumber }}
           skip-if-not-in-project: true
+      - uses: actions/checkout@v4
+        with:
+          show-progress: 'false'
+      - name: Assign PR creator to issue
+        # "gh issue edit" cannot be used - workaround found at https://github.com/cli/cli/issues/9620#issuecomment-2703135049
+        run: gh api -X PATCH /repos/JabRef/jabref/issues/${{ steps.get_issue_number.outputs.ticketNumber }} -f assignee=${{ github.event.pull_request.user.login }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Add label "📌 Pinned"
+        run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --add-label "📌 Pinned"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  conflicts_with_target:
+    name: Conflicts with target branch
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          show-progress: 'false'
+      - name: Check PR mergeability
+        id: check_mergeable
+        run: |
+          MERGEABLE=$(gh pr view --json mergeable ${{ github.event.number }} --template '{{.mergeable}}')
+          if [ "$MERGEABLE" == "CONFLICTING" ]; then
+            echo "❌ Merge conflicts"
+            exit 1
+          fi
+          echo "✅ No merge conflicts"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   upload-pr-number:
     runs-on: ubuntu-latest
     steps:

.github/workflows/pr-comment.yml

@@ -7,7 +7,7 @@ name: Comment on PR
 
 on:
   workflow_run:
-    workflows: ["Tests", "Mark issue as in progress"]
+    workflows: ["Tests", "On PR opened"]
     types:
       - completed
 

.github/workflows/tests.yml

@@ -136,6 +136,7 @@ jobs:
           grep -q "1 problem" heylogs.txt || exit 1
 
   changelog-unreleased-only:
+    if: github.event_name == 'pull_request'
     name: CHANGELOG.md - only unreleased touched
     runs-on: ubuntu-latest
     steps:
@@ -367,13 +368,13 @@ jobs:
         uses: olivernybroe/[email protected]
 
   no-force-push:
+    if: github.event_name == 'pull_request'
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
-
       - name: Check force push
         id: force_push_check
         run: |
@@ -389,7 +390,31 @@ jobs:
             exit 1
           fi
 
+  unmodified_submodules:
+    name: Submodules not modified
+    if: github.actor != 'dependabot[bot]' && github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+          show-progress: 'false'
+      - name: Check for submodule modifications
+        id: check_submodule
+        run: |
+          git fetch origin ${{ github.base_ref }}
+
+          # enable diffing of submodules
+          sed -i "s/ all/ untracked/" .gitmodules
+
+          if ! git diff --submodule=log origin/${{ github.base_ref }} HEAD | grep -vzq "Submodule src"; then
+            echo "❌ Submodule modifications detected"
+            exit 1
+          fi
+          echo "✅ No submodule modifications"
+
   other_than_main:
+    if: github.event_name == 'pull_request'
     name: Source branch is other than "main"
     runs-on: ubuntu-latest
     steps:

.github/workflows/unassign-issues.yml

@@ -19,7 +19,7 @@ jobs:
         uses: takanome-dev/assign-issue-action@edge
         with:
           github_token: '${{ secrets.GITHUB_TOKEN }}'
-          days_until_unassign: 45
+          days_until_unassign: 14
   move_unassigned_issues:
     needs: unassign_issues
     if: ${{ needs.unassign_issues.outputs.unassigned_issues != '[]' }}

CHANGELOG.md

@@ -12,7 +12,11 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 ### Added
 
 
+
 - We added automatic file renaming functionality: when entry data is changed, associated filenames are updated automatically without requiring manual clicks on the "Generate" button. [#12604](https://github.com/JabRef/jabref/pull/12604)
+
+- We added <kbd>F5</kbd> as a shortcut key for fetching data and <kbd>Alt+F</kbd> as a shortcut for looking up data using DOI. [#11802](https://github.com/JabRef/jabref/issues/11802)
+
 - 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)
@@ -23,6 +27,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added an integrity check if a URL appears in a title. [#12354](https://github.com/JabRef/jabref/issues/12354)
 - 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)
+- We added a new functionality where author names having multiple spaces in-between will be considered as separate user block as it does for " and ". [#12701](https://github.com/JabRef/jabref/issues/12701)
 
 ### Changed
 
@@ -52,6 +57,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We improved the Check Integrity dialog entry interaction so that a single click focuses on the corresponding entry and a double-click both focuses on the entry and closes the dialog. [#12245](https://github.com/JabRef/jabref/issues/12245)
 - We improved journal abbreviation lookup with fuzzy matching to handle minor input errors and variations. [#12467](https://github.com/JabRef/jabref/issues/12467)
 - We changed the phrase "Cleanup entries" to "Clean up entries". [#12703](https://github.com/JabRef/jabref/issues/12703)
+- A tooltip now appears after 300ms (instead of 2s). [#12649](https://github.com/JabRef/jabref/issues/12649)
+- We improved search in preferences and keybindings. [#12647](https://github.com/JabRef/jabref/issues/12647)
 
 ### Fixed
 
@@ -74,8 +81,11 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - 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 user-defined keyword separator does not apply to Merge Groups. [#12535](https://github.com/JabRef/jabref/issues/12535)
+- We fixed an issue where duplicate items cannot be removed correctly when merging groups or keywords. [#12585](https://github.com/JabRef/jabref/issues/12585)
 - We fixed an issue where JabRef displayed an incorrect deletion notification when canceling entry deletion [#12645](https://github.com/JabRef/jabref/issues/12645)
-
+- We fixed an issue where JabRef displayed an incorrect deletion notification when canceling entry deletion. [#12645](https://github.com/JabRef/jabref/issues/12645)
+- We fixed an issue where an exception would occur when running abbreviate journals for multiple entries. [#12634](https://github.com/JabRef/jabref/issues/12634)
 
 ### Removed
 
@@ -611,7 +621,6 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We now have more "dots" in the offered journal abbreviations. [#9504](https://github.com/JabRef/jabref/pull/9504)
 - We now disable the button "Full text search" in the Searchbar by default [#9527](https://github.com/JabRef/jabref/pull/9527)
 
-
 ### Fixed
 
 - The tab "deprecated fields" is shown in biblatex-mode only. [#7757](https://github.com/JabRef/jabref/issues/7757)
@@ -1576,4 +1585,5 @@ The changelog of JabRef 2.11 and all previous versions is available as [text fil
 [5.0]: https://github.com/JabRef/jabref/compare/v5.0-beta...v5.0
 [5.0-beta]: https://github.com/JabRef/jabref/compare/v5.0-alpha...v5.0-beta
 [5.0-alpha]: https://github.com/JabRef/jabref/compare/v4.3...v5.0-alpha
-<!-- markdownlint-disable-file MD012 MD024 MD033 MD053 -->
+
+<!-- markdownlint-disable-file MD024 MD033 MD053 -->