Merge branch 'main' into fix-for-issue-7730

.devcontainer/devcontainer.json

@@ -31,9 +31,9 @@
         // Install java.
         // See https://github.com/devcontainers/features/tree/main/src/java#options for details.
         "ghcr.io/devcontainers/features/java:1": {
-            "version": "21.0.1-librca",
+            "version": "23.0.1-tem",
             "installGradle": false,
-            "jdkDistro": "librca"
+            "jdkDistro": "Temurin"
         }
     }
 }

.git-blame-ignore-revs

@@ -0,0 +1,28 @@
+# Automatic code reformatting
+c5bcad738fe6e8dfcb62442a426c2778241515a1
+
+# net.sf.jabref -> org.jabref
+b2ad6eb279f5def38fa21be12cb5dd4545c1ba1a
+dd385f4ad6dc9251bfdb1c0b75ded402f680b32a
+a6e80311c6376c973b5860658f6e4ace7a3fd1f4
+648a4703e80ac0dbe1ff044f354bc0e332e4064d
+ac08c6a2c55e1600bf5072c0ea2e6aac920b915d
+ec863166cf4f38a1a6bcc80a607fd33299b815aa
+8c61577e4377746fc064db2a136bb68968cd4055
+0ef3228f0c1334ff203d4ea5e698e3ad88cb7089
+ce939b4ef19ca856e7ecac08275cf1ca764207b6
+7f1a8069d03737c202bcb7ce352b3755c6a36f5f
+dbd0cfbc8177ada414e89da038cd014657d48ed3
+bc7ea00c8cc3ec9ec8b1a799b0dd96513bc51404
+9a5cff44aa1e0d4b737296a30b97f7f384c8b885
+bf81b595a77f0f7f254872be6f05a063c44528d8
+277b40c9e79e0158d272de33e24fa7fc06af91bf
+662dd326d212ecfd336a00214e969145ec501c5a
+33f040cfbb16111ada117f858e98d606a6bee4fd
+29fe730f64eeb62ff9de10fcb460a63297e24be6
+
+# This commit should not exist
+185d7345946c29a2a4e2726c912be0c4db4810b9
+# Resulted in this problematic merge commits
+7e1645978b3028df5e65af19f0f819ddfd0f24aa
+a31f396765492ac12eaab228e33eb9d22487403b

.gitattributes

@@ -5,19 +5,10 @@ gradlew text eol=lf
 # windows line endings at windows files
 *.bat text eol=crlf
 
-# ensure that line endings of *.fxml, *.java, and *.properties are normalized
+# ensure that line endings of *.bib, *.fxml, *.java, *.properties are normalized to LF
+*.bib text eol=lf
 *.fxml text eol=lf
 *.java text eol=lf
 *.properties text eol=lf
 
-# .bib files have to be written using OS specific line endings to enable our tests working
-*.bib text !eol
-# Exception: The files used for the http server test - they should have linux line endings
-src/test/resources/org/jabref/http/server/*.bib text eol=lf
-
-# Citavi needs to be LF line ending
-# This overwrites the setting of "*.bib"
-Citavi*.bib eol=lf
-
-# disable after a release (otherwise, duplicate CHANGELOG.md entries will be generated)
-# CHANGELOG.md merge=union
+CHANGELOG.md merge=union

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -12,7 +12,7 @@ body:
     attributes:
       label: JabRef version
       options:
-        - "5.12 (latest release)"
+        - "5.15 (latest release)"
         - Latest development branch build (please note build date below)
         - Other (please describe below)
       description: The version as shown in the about dialog.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,10 +1,5 @@
-<!-- 
-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".
-"Closes" is a keyword GitHub uses to link PRs with issues; do not change it.
-Don't reference an issue in the PR title because GitHub does not support auto-linking there.
--->
+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".
 
 ### Mandatory checks
 
@@ -13,7 +8,8 @@ Don't reference an issue in the PR title because GitHub does not support auto-li
 - [x] done; [ ] not done / not applicable
 -->
 
-- [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if 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)

.github/dependabot.yml

@@ -25,3 +25,7 @@ updates:
       interval: weekly
     labels:
       - "dependencies"
+  - package-ecosystem: "gitsubmodule"
+    directory: "/"
+    schedule:
+      interval: weekly

.github/ghprcomment.yml

@@ -0,0 +1,40 @@
+- jobName: Checkstyle
+  message: |
+    Your code currently does not meet [JabRef's code guidelines](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html).
+    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.
+    We use [OpenRewrite](https://docs.openrewrite.org/) to ensure "modern" Java coding practices.
+    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: |
+    While the PR was in progress, a new version of JabRef has been released.
+    You have to merge `upstream/main` and move your entry in `CHANGELOG.md` up to the section `## [Unreleased]`.
+- jobName: 'Unit tests'
+  message: |
+    JUnit tests are failing. 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.

.github/workflows/assign-issue.yml

@@ -0,0 +1,57 @@
+name: Assign Issue
+
+on:
+  schedule:
+    - cron: 4 12 * * *
+  issue_comment:
+    types: [created]
+  workflow_dispatch:
+
+jobs:
+  assign:
+    if: github.repository_owner == 'JabRef'
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+      - name: Assign the user or unassign stale assignments
+        id: assign
+        uses: takanome-dev/assign-issue-action@beta
+        with:
+          github_token: '${{ secrets.GITHUB_TOKEN }}'
+          days_until_unassign: 90
+          maintainers: koppor, Siedlerchr, ThiloteE, calixtus, HoussemNasri
+          assigned_comment: |
+            👋 Hey @{{ handle }}, thank you for your interest in this issue! 🎉
+
+            We're excited to have you on board. Start by exploring our [Contributing](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md) guidelines, and don't forget to check out our [workspace setup guidelines](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace) to get started smoothly.
+
+            In case you encounter failing tests during development, please check our [developer FAQs](https://devdocs.jabref.org/code-howtos/faq.html)!
+
+            Having any questions or issues? Feel free to ask here on GitHub. Need help setting up your local workspace? Join the conversation on [JabRef's Gitter chat](https://gitter.im/JabRef/jabref). And don't hesitate to open a (draft) pull request early on to show the direction it is heading towards. This way, you will receive valuable feedback.
+
+            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.
+      - name: Move Issue to "Assigned" Column in "Candidates for University Projects"
+        if: steps.assign.outputs.assigned == 'yes'
+        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 "Assigned" Column in "Good First Issues"
+        if: steps.assign.outputs.assigned == 'yes'
+        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/automerge.yml

@@ -10,24 +10,25 @@ jobs:
     runs-on: ubuntu-latest
     # Run only if PR is inside JabRef's main repository and created by dependabot or by an update workflow
     if: >
-      (github.repository == 'JabRef/jabref') && 
+      (github.repository == 'JabRef/jabref') &&
       (github.event.pull_request.head.repo.full_name == 'JabRef/jabref') &&
       (
         (github.actor == 'dependabot[bot]') ||
         (
-          startsWith(github.event.pull_request.title, '[Bot] ') || 
-          startsWith(github.event.pull_request.title, 'Bump ') || 
-          startsWith(github.event.pull_request.title, 'New Crowdin updates')
+          startsWith(github.event.pull_request.title, '[Bot] ') ||
+          startsWith(github.event.pull_request.title, 'Bump ') ||
+          startsWith(github.event.pull_request.title, 'New Crowdin updates') ||
+          startsWith(github.event.pull_request.title, 'Update Gradle Wrapper from')
         )
       )
     steps:
       - name: Approve PR
         run: gh pr review --approve "$PR_URL"
         env:
           PR_URL: ${{github.event.pull_request.html_url}}
-          GITHUB_TOKEN: ${{secrets.GH_TOKEN_JABREF_MACHINE_PR_APPROVE}}
+          GH_TOKEN: ${{secrets.GH_TOKEN_JABREF_MACHINE_PR_APPROVE}}
       - name: Merge PR
         run: gh pr merge --auto --squash "$PR_URL"
         env:
           PR_URL: ${{github.event.pull_request.html_url}}
-          GITHUB_TOKEN: ${{secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER}}
+          GH_TOKEN: ${{secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER}}

.github/workflows/check-links.yml

@@ -4,6 +4,8 @@ on:
   push:
     paths:
       - '.github/workflows/check-links.yml'
+      - '.lycheeignore'
+      - 'lychee.toml'
       - '**/*.md'
   schedule:
     # Run on the first of each month at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07)
@@ -16,20 +18,21 @@ concurrency:
 
 jobs:
   lychee:
+    if: github.repository_owner == 'JabRef'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
         with:
           show-progress: 'false'
       - name: Restore lychee cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: .lycheecache
           key: cache-lychee-${{ github.sha }}
           restore-keys: cache-lychee-
       - name: Link Checker
         id: lychee
-        uses: lycheeverse/lychee-action@v1.8.0
+        uses: lycheeverse/lychee-action@v2.1.0
         with:
           fail: true
-          args: --max-concurrency 1 --cache --no-progress --exclude-all-private './**/*.md'
+          args: --accept '200,201,202,203,204,403,429,500' --max-concurrency 1 --cache --no-progress --exclude-all-private './**/*.md'

.github/workflows/cleanup-pr.yml

@@ -6,10 +6,11 @@ on:
 
 jobs:
   cleanup:
+    if: github.repository_owner == 'JabRef'
     runs-on: ubuntu-latest
     steps:
       - name: Cancel deployment run
-        uses: styfle/[email protected].0
+        uses: styfle/[email protected].1
         with:
           ignore_sha: true
           workflow_id: 9813 # workflow "Deployment"
@@ -19,14 +20,16 @@ jobs:
         run: |
           if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
             echo "secretspresent=NO" >> $GITHUB_OUTPUT
+            echo "❌ Secret BUILDJABREFPRIVATEKEY not present"
           else
             echo "secretspresent=YES" >> $GITHUB_OUTPUT
+            echo "✔️ Secret BUILDJABREFPRIVATEKEY present"
           fi
         env:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Delete folder on builds.jabref.org
         if: steps.checksecrets.outputs.secretspresent == 'YES'
-        uses: appleboy/ssh-action@v1.0.2
+        uses: appleboy/ssh-action@v1.2.0
         with:
           script: rm -rf /var/www/builds.jabref.org/www/pull/${{ github.event.pull_request.number }} || true
           host: build-upload.jabref.org
@@ -35,8 +38,8 @@ jobs:
           key: ${{ secrets.buildJabRefPrivateKey }}
       - name: Update PR comment
         if: steps.checksecrets.outputs.secretspresent == 'YES'
-        uses: thollander/actions-comment-pull-request@v2
+        uses: thollander/actions-comment-pull-request@v3
         with:
-          comment_tag: download-link
+          comment-tag: download-link
           message: The build for this PR is no longer available. Please visit <https://builds.jabref.org/main/> for the latest build.
           mode: upsert