Merge branch 'main' into use-garbage-collector-ZGC

JabRef · Feb 13, 2025 · bd46e05 · bd46e05
2 parents 71df28d + 1a9af9a
commit bd46e05
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diff --git a/.devcontainer/devcontainer.json b/.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"
         }
     }
 }
diff --git a/.gitattributes b/.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

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.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.

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.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)

diff --git a/.github/ghprcomment.yml b/.github/ghprcomment.yml
@@ -2,12 +2,11 @@
   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.
-    The tool reviewdog already placed comments on GitHub to indicate the places. See the tab "Files" in you PR.
     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.
 
-
-    You can check review dog's comments at the tab "Files changed" of your pull request.
+    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.
@@ -34,3 +33,8 @@
   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.
diff --git a/.github/workflows/add-greeting-to-issue.yml b/.github/workflows/add-greeting-to-issue.yml
diff --git a/.github/workflows/add-to-projects.yml b/.github/workflows/add-to-projects.yml
diff --git a/.github/workflows/assign-issue.yml b/.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@fix-rate-limit-err
+        with:
+          github_token: '${{ secrets.GITHUB_TOKEN }}'
+          days_until_unassign: 90
+          maintainers: 'koppor,Siedlerchr,ThiloteE,calixtus,HoussemNasri,subhramit,LinusDietz'
+          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: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
+          project-url: "https://github.com/orgs/JabRef/projects/5"
+          target-labels: "📍 Assigned"
+          target-column: "Assigned"
+          ignored-columns: ""
+          default-column: "Free to take"
+          skip-if-not-in-project: true
diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -10,13 +10,13 @@ jobs:
     runs-on: ubuntu-latest
     # Run only if PR is inside JabRef's main repository and created by dependabot or by an update workflow
     if: >
-      (github.repository == 'JabRef/jabref') && 
+      (github.repository == 'JabRef/jabref') &&
       (github.event.pull_request.head.repo.full_name == 'JabRef/jabref') &&
       (
         (github.actor == 'dependabot[bot]') ||
         (
-          startsWith(github.event.pull_request.title, '[Bot] ') || 
-          startsWith(github.event.pull_request.title, 'Bump ') || 
+          startsWith(github.event.pull_request.title, '[Bot] ') ||
+          startsWith(github.event.pull_request.title, 'Bump ') ||
           startsWith(github.event.pull_request.title, 'New Crowdin updates') ||
           startsWith(github.event.pull_request.title, 'Update Gradle Wrapper from')
         )
@@ -26,9 +26,9 @@ jobs:
         run: gh pr review --approve "$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}}
diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml
@@ -18,6 +18,7 @@ concurrency:
 
 jobs:
   lychee:
+    if: github.repository_owner == 'JabRef'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -31,7 +32,7 @@ jobs:
           restore-keys: cache-lychee-
       - name: Link Checker
         id: lychee
-        uses: lycheeverse/lychee-action@v1.10.0
+        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'
diff --git a/.github/workflows/cleanup-pr.yml b/.github/workflows/cleanup-pr.yml
@@ -6,6 +6,7 @@ on:
 
 jobs:
   cleanup:
+    if: github.repository_owner == 'JabRef'
     runs-on: ubuntu-latest
     steps:
       - name: Cancel deployment run
@@ -28,7 +29,7 @@ jobs:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Delete folder on builds.jabref.org
         if: steps.checksecrets.outputs.secretspresent == 'YES'
-        uses: appleboy/ssh-action@v1.0.3
+        uses: appleboy/ssh-action@v1.2.0
         with:
           script: rm -rf /var/www/builds.jabref.org/www/pull/${{ github.event.pull_request.number }} || true
           host: build-upload.jabref.org
@@ -37,8 +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
diff --git a/.github/workflows/deployment-arm64.yml b/.github/workflows/deployment-arm64.yml
@@ -34,6 +34,7 @@ concurrency:
 
 jobs:
   build:
+    if: github.repository_owner == 'JabRef'
     strategy:
       fail-fast: false
       matrix:
@@ -68,16 +69,16 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v3.0.0
+        uses: gittools/actions/gitversion/setup@v3.1.11
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v3.0.0
+        uses: gittools/actions/gitversion/execute@v3.1.11
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:
-          java-version: 21.0.2
+          java-version: 23.0.1
           distribution: 'temurin'
       - name: Clean up keychain
         run: |
@@ -209,7 +210,7 @@ jobs:
         if: ${{ (!startsWith(github.ref, 'refs/heads/gh-readonly-queue')) && (steps.checksecrets.outputs.secretspresent == 'YES') && ((matrix.os == 'ubuntu-latest') || ((matrix.os == 'macos-14') && !((startsWith(github.ref, 'refs/tags/') || inputs.notarization == true)))) }}
         shell: bash
         run: |
-          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' build/distribution/ [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
+          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ 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
       - name: Upload to GitHub workflow artifacts store (macOS)
         if: (matrix.os == 'macos-14') && (steps.checksecrets.outputs.secretspresent == 'YES') && (startsWith(github.ref, 'refs/tags/') || inputs.notarization == true)
         uses: actions/upload-artifact@v4
@@ -248,7 +249,7 @@ 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/

diff --git a/.github/workflows/deployment-jdk-ea.yml b/.github/workflows/deployment-jdk-ea.yml
@@ -32,11 +32,12 @@ concurrency:
 
 jobs:
   build:
+    if: github.repository_owner == 'JabRef'
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest, buildjet-8vcpu-ubuntu-2204-arm]
-        jdk: [22]
+        jdk: [23]
         javafx: [24]
         include:
           - os: ubuntu-latest
@@ -84,12 +85,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v3.0.0
+        uses: gittools/actions/gitversion/setup@v3.1.11
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v3.0.0
+        uses: gittools/actions/gitversion/execute@v3.1.11
 
       # JDK
       - name: 'Set up JDK ${{ matrix.jdk }}'
@@ -266,7 +267,7 @@ jobs:
         shell: cmd
         # for rsync installed by chocolatey, we need the ssh.exe delivered with that installation
         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/jdk-ea && rsync" -e 'C:\ProgramData\chocolatey\lib\rsync\tools\bin\ssh.exe -p 9922 -i sshkey -o StrictHostKeyChecking=no' build/distribution/ [email protected]:/var/www/builds.jabref.org/www/jdk-ea/
+          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/jdk-ea && rsync" -e 'C:\ProgramData\chocolatey\lib\rsync\tools\bin\ssh.exe -p 9922 -i sshkey -o StrictHostKeyChecking=no' build/distribution/ [email protected]:/var/www/builds.jabref.org/www/jdk-ea/ || true
       - name: Upload to builds.jabref.org (linux, macOS)
         if: (matrix.os != 'windows-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (github.ref == 'refs/heads/main')
         shell: bash